Last update:
Tue Jun 25 08:09:22 MDT 2024
J. L. Boldrini and
R. C. Bassanezi and
A. C. Moretti and
F. J. Von Zuben and
W. A. C. Godoy and
C. J. Von Zuben and
S. F. dos Reis RETRACTED: Non-local Interactions and
the Dynamics of Dispersal in Immature
Insects . . . . . . . . . . . . . . . . 523--531
Arancha Casal and
Cenk Sumen and
Timothy E. Reddy and
Mark S. Alber and
Peter P. Lee Agent-based modeling of the context
dependency in T cell recognition . . . . 376--391
Jinzhi Lei Stochasticity in single gene expression
with both intrinsic noise and
fluctuation in kinetic parameters . . . 485--492
C. J. Evans and
R. M. Phillips and
P. F. Jones and
P. M. Loadman and
B. D. Sleeman and
C. J. Twelves and
S. W. Smye A mathematical model of doxorubicin
penetration through multicellular layers 598--608
Zhongxing Mai and
Haiyan Liu Boolean network-based analysis of the
apoptosis network: Irreversible
apoptosis and stable surviving . . . . . 760--769
Liene Daukste and
Britta Basse and
Bruce C. Baguley and
David J. N. Wall Using a stem cell and progeny model to
illustrate the relationship between cell
cycle times of in vivo human tumour cell
tissue populations, in vitro primary
cultures and the cell lines derived from
them . . . . . . . . . . . . . . . . . . 563--571
Ha Youn Lee and
Elena E. Giorgi and
Brandon F. Keele and
Brian Gaschen and
Gayathri S. Athreya and
Jesus F. Salazar-Gonzalez and
Kimmy T. Pham and
Paul A. Goepfert and
J. Michael Kilby and
Michael S. Saag and
Eric L. Delwart and
Michael P. Busch and
Beatrice H. Hahn and
George M. Shaw and
Bette T. Korber and
Tanmoy Bhattacharya and
Alan S. Perelson Modeling sequence evolution in acute
HIV-1 infection . . . . . . . . . . . . 341--360
Alison J. Marks and
Deenan Pillay and
Angela R. McLean The effect of intrinsic stochasticity on
transmitted HIV drug resistance patterns 1--13
J. V. Ross Computationally exact methods for
stochastic periodic dynamics:
Spatiotemporal dispersal and temporally
forced transmission . . . . . . . . . . 14--22
Valentina Rossetti and
Bettina E. Schirrmeister and
Marco V. Bernasconi and
Homayoun C. Bagheri The evolutionary path to terminal
differentiation and division of labor in
cyanobacteria . . . . . . . . . . . . . 23--34
L. Preziosi and
D. Ambrosi and
C. Verdier An elasto-visco-plastic model of cell
aggregates . . . . . . . . . . . . . . . 35--47
Ryosuke Omori and
Ben Adams and
Akira Sasaki Coexistence conditions for strains of
influenza with immune cross-reaction . . 48--57
Brian Cox A multi-scale, discrete-cell simulation
of organogenesis: Application to the
effects of strain stimulus on collective
cell behavior during ameloblast
migration . . . . . . . . . . . . . . . 58--72
Oscar Moran Model of the cAMP activation of chloride
transport by CFTR channel and the
mechanism of potentiators . . . . . . . 73--79
Ross Cressman CSS, NIS and dynamic stability for
two-species behavioral models with
continuous trait spaces . . . . . . . . 80--89
Dominique Pontier and
David Fouchet and
Joël Bried Can cat predation help competitors
coexist in seabird communities? . . . . 90--96
Ronette Gehring and
Phillip Schumm and
Mina Youssef and
Caterina Scoglio A network-based approach for resistance
transmission in bacterial populations 97--106
Joel C. Miller and
Bahman Davoudi and
Rafael Meza and
Anja C. Slim and
Babak Pourbohloul Epidemics with general generation
interval distributions . . . . . . . . . 107--115
Ariane Verdy and
Priyanga Amarasekare Alternative stable states in communities
with intraguild predation . . . . . . . 116--128
Kenneth Kragh Jensen Light-dependent orientation responses in
animals can be explained by a model of
compass cue integration . . . . . . . . 129--141
Alessandro Bertuzzi and
Antonio Fasano and
Alberto Gandolfi and
Carmela Sinisgalli Necrotic core in EMT6/Ro tumour
spheroids: Is it caused by an ATP
deficit? . . . . . . . . . . . . . . . . 142--150
Elodie Briefer and
Tomasz S. Osiejuk and
Fanny Rybak and
Thierry Aubin Are bird song complexity and song
sharing shaped by habitat structure? An
information theory and statistical
approach . . . . . . . . . . . . . . . . 151--164
Robert M. French The Red Tooth Hypothesis: a
computational model of predator--prey
relations, protean escape behavior and
sexual reproduction . . . . . . . . . . 165--176
Anuj Mubayi and
Carlos Castillo-Chavez and
Gerardo Chowell and
Christopher Kribs-Zaleta and
Niyamat Ali Siddiqui and
Narendra Kumar and
Pradeep Das Transmission dynamics and underreporting
of Kala-azar in the Indian state of
Bihar . . . . . . . . . . . . . . . . . 177--185
Tobias Galla Independence and interdependence in the
nest-site choice by honeybee swarms:
Agent-based models, analytical
approaches and pattern formation . . . . 186--196
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--196 (7 January 2010) . . . . . ??
Brett A. Boghigian and
Kyongbum Lee and
Blaine A. Pfeifer Computational analysis of phenotypic
space in heterologous polyketide
biosynthesis --- Applications to
\bionameEscherichia coli,
\bionameBacillus subtilis, and
\bionameSaccharomyces cerevisiae . . . . 197--207
Tong Wang and
Tian Xia and
Xiao-ming Hu Geometry preserving projections
algorithm for predicting membrane
protein types . . . . . . . . . . . . . 208--213
Tijana Boji\'c and
Aleksandra Vuckovic and
Aleksandar Kalauzi Modeling EEG fractal dimension changes
in wake and drowsy states in humans ---
a preliminary study . . . . . . . . . . 214--222
Takashi Uehara and
Yoh Iwasa Global mutations and local mutations
have very different effects on
evolution, illustrated by mixed
strategies of asymmetric binary games 223--231
Sorinel Adrian Oprisan Existence and stability criteria for
phase-locked modes in ring neural
networks based on the spike time
resetting curve method . . . . . . . . . 232--244
Yosi E. Maruvka and
Nadav M. Shnerb and
David A. Kessler Universal features of surname
distribution in a subsample of a growing
population . . . . . . . . . . . . . . . 245--256
A. Golubev Exponentially modified Gaussian (EMG)
relevance to distributions related to
cell proliferation and differentiation 257--266
C. A. Chung and
Tze-Hung Lin and
Shih-Di Chen and
Hsing-I Huang Hybrid cellular automaton modeling of
nutrient modulated cell growth in tissue
engineering constructs . . . . . . . . . 267--278
Éva Kisdi Costly dispersal can destabilize the
homogeneous equilibrium of a
metapopulation . . . . . . . . . . . . . 279--283
Sandeep K. Kushwaha and
Madhvi Shakya Protein interaction network analysis ---
Approach for potential drug target
identification in \bionameMycobacterium
tuberculosis . . . . . . . . . . . . . . 284--294
Mark A. Hallen and
Anita T. Layton Expanding the scope of quantitative FRAP
analysis . . . . . . . . . . . . . . . . 295--305
Peter Pivonka and
Jan Zimak and
David W. Smith and
Bruce S. Gardiner and
Colin R. Dunstan and
Natalie A. Sims and
T. John Martin and
Gregory R. Mundy Theoretical investigation of the role of
the RANK-RANKL-OPG system in bone
remodeling . . . . . . . . . . . . . . . 306--316
Yongchao Dou and
Xiaoqi Zheng and
Jun Wang Several appropriate background
distributions for entropy-based protein
sequence conservation measures . . . . . 317--322
S. Azaele and
R. Muneepeerakul and
A. Rinaldo and
I. Rodriguez-Iturbe Inferring plant ecosystem organization
from species occurrences . . . . . . . . 323--329
Lan Zou and
Weinian Zhang and
Shigui Ruan Modeling the transmission dynamics and
control of hepatitis B virus in China 330--338
Andy Gardner Sex-biased dispersal of adults mediates
the evolution of altruism among
juveniles . . . . . . . . . . . . . . . 339--345
A. Yu. Morozov and
E. G. Arashkevich Towards a correct description of
zooplankton feeding in models: Taking
into account food-mediated
unsynchronized vertical migration . . . 346--360
Ehab R. El-Haroun and
Dominique P. Bureau and
John P. Cant A mechanistic model of nutritional
control of protein synthesis in animal
tissues . . . . . . . . . . . . . . . . 361--369
Dawei Hong and
Shushuang Man Signal propagation in small-world
biological networks with weak noise . . 370--380
Jinzhi Lei Corrigendum to: ``Stochasticity in
single gene expression with both
intrinsic noise and fluctuation in
kinetic parameters'' [J. Theor. Biol.
\bf 256 (2009) 485--492] . . . . . . . . 381--381
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 197--382 (21 January 2010) . . . . ??
Yi Fang and
Junmei Jing Geometry, thermodynamics, and protein 383--390
Peter D. Taylor and
A. Grafen Relatedness with different interaction
configurations . . . . . . . . . . . . . 391--397
Garrett M. Dancik and
Douglas E. Jones and
Karin S. Dorman Parameter estimation and sensitivity
analysis in an agent-based model of
Leishmania major infection . . . . . . . 398--412
J. G. Sumner and
M. A. Charleston Phylogenetic estimation with partial
likelihood tensors . . . . . . . . . . . 413--424
D. C. Walker and
N. T. Georgopoulos and
J. Southgate Anti-social cells: Predicting the
influence of E-cadherin loss on the
growth of epithelial cell populations 425--440
Katharine F. Preedy and
Piet\`a G. Schofield and
Sijia Liu and
Anastasios Matzavinos and
Mark A. J. Chaplain and
Stephen F. Hubbard Modelling contact spread of infection in
host-parasitoid systems: Vertical
transmission of pathogens can cause
chaos . . . . . . . . . . . . . . . . . 441--451
Nick D. L. Owens and
Jon Timmis and
Andrew Greensted and
Andy Tyrrell Elucidation of T cell signalling models 452--470
Phillip Schumm and
Caterina M. Scoglio and
Deon van der Merwe A network model of successive
partitioning-limited solute diffusion
through the stratum corneum . . . . . . 471--477
Bilge Uz and
Erdem Arslan and
Ian J. Laurenzi Maximum likelihood estimation of the
kinetics of receptor-mediated adhesion 478--487
Sourav Rakshit and
G. K. Ananthasuresh A novel approach for large-scale
polypeptide folding based on elastic
networks using continuous optimization 488--497
Yue Chan and
Richard G. Haverkamp and
James M. Hill Force-extension formula for the
worm-like chain model from a variational
principle . . . . . . . . . . . . . . . 498--504
Éric J. M. Delhez and
Eric Deleersnijder Residence time and exposure time of
sinking phytoplankton in the euphotic
layer . . . . . . . . . . . . . . . . . 505--516
Kenneth W. Crane and
James P. Grover Coexistence of mixotrophs, autotrophs,
and heterotrophs in planktonic microbial
communities . . . . . . . . . . . . . . 517--527
Jian Zu and
Masayasu Mimura and
Joe Yuichiro Wakano The evolution of phenotypic traits in a
predator--prey system subject to Allee
effect . . . . . . . . . . . . . . . . . 528--543
T. Bastogne and
A. Samson and
P. Vallois and
S. Wantz-Mézi\`eres and
S. Pinel and
D. Bechet and
M. Barberi-Heyob Phenomenological modeling of tumor
diameter growth based on a mixed effects
model . . . . . . . . . . . . . . . . . 544--552
Lara Barazzuol and
Neil G. Burnet and
Raj Jena and
Bleddyn Jones and
Sarah J. Jefferies and
Norman F. Kirkby A mathematical model of brain tumour
response to radiotherapy and
chemotherapy considering radiobiological
aspects . . . . . . . . . . . . . . . . 553--565
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 383--566 (7 February 2010) . . . . ??
Michael B. Bonsall The impact of non-lethal synergists on
the population and evolutionary dynamics
of host-pathogen interactions . . . . . 567--575
Yijun Zuo and
Guolian Kang A mixed two-stage method for detecting
interactions in genomewide association
studies . . . . . . . . . . . . . . . . 576--583
C. A. Klausmeier Successional state dynamics: a novel
approach to modeling nonequilibrium
foodweb dynamics . . . . . . . . . . . . 584--595
Daniel D. Wiegmann and
Steven M. Seubert and
Gordon A. Wade Mate choice and optimal search behavior:
Fitness returns under the fixed sample
and sequential search strategies . . . . 596--600
Ariosto S. Silva and
Robert A. Gatenby and
Robert J. Gillies and
Jose Andres Yunes A quantitative theoretical model for the
development of malignancy in ductal
carcinoma in situ . . . . . . . . . . . 601--613
Sylvie Lorthois and
Francis Cassot Fractal analysis of vascular networks:
Insights from morphogenesis . . . . . . 614--633
Samantha L. Winter and
John H. Challis The expression of the skeletal muscle
force-length relationship in vivo: a
simulation study . . . . . . . . . . . . 634--643
Tingting Gao and
Zhixia Yang and
Yong Wang and
Ling Jing Identifying translation initiation sites
in prokaryotes using support vector
machine . . . . . . . . . . . . . . . . 644--649
Franck Jabot A stochastic dispersal-limited
trait-based model of community dynamics 650--661
Kevin R. Abbott Background evolution in camouflage
systems: a
predator--prey/pollinator-flower game 662--678
Hannah L. Callender and
Mary Ann Horn and
Dianne L. DeCamp and
Paul C. Sternweis and
H. Alex Brown Modeling species-specific diacylglycerol
dynamics in the RAW 264.7 macrophage . . 679--690
Albert L. Kwansa and
Joseph W. Freeman Elastic energy storage in an
unmineralized collagen type I molecular
model with explicit solvation and water
infiltration . . . . . . . . . . . . . . 691--697
Luis P. Villarreal and
Guenther Witzany Viruses are essential agents within the
roots and stem of the tree of life . . . 698--710
Xue Zhong and
Jaros\law E. Kro$\cdot$l and
Eva M. Top and
Stephen M. Krone Accounting for mating pair formation in
plasmid population dynamics . . . . . . 711--719
Karina García-Martínez and
Kalet León Modeling the role of IL-2 in the
interplay between CD4+ helper and
regulatory T cells: Assessing general
dynamical properties . . . . . . . . . . 720--732
Hector Tejero and
Arturo Marín and
Francisco Montero Effect of lethality on the extinction
and on the error threshold of
quasispecies . . . . . . . . . . . . . . 733--741
Lianping Yang and
Xiangde Zhang and
Tianming Wang The Burrows--Wheeler similarity
distribution between biological
sequences based on Burrows--Wheeler
transform . . . . . . . . . . . . . . . 742--749
Chen Huang and
Ruijie Zhang and
Zhiqiang Chen and
Yongshuai Jiang and
Zhenwei Shang and
Peng Sun and
Xuehong Zhang and
Xia Li Predict potential drug targets from the
ion channel proteins based on SVM . . . 750--756
Martial L. Ndeffo Mbah and
Christopher A. Gilligan Optimization of control strategies for
epidemics in heterogeneous populations
with symmetric and asymmetric
transmission . . . . . . . . . . . . . . 757--763
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 567--764 (21 February 2010) . . . ??
Sheng-Feng Shen and
H. Kern Reeve Reproductive skew theory unified: The
general bordered tug-of-war model . . . 1--12
Satoshi Uchida and
Karl Sigmund The competition of assessment rules for
indirect reciprocity . . . . . . . . . . 13--19
Lihai Zhang and
Bruce S. Gardiner and
David W. Smith and
Peter Pivonka and
Alan J. Grodzinsky On the role of diffusible binding
partners in modulating the transport and
concentration of proteins in tissues . . 20--29
Hiroshi Haeno and
Franziska Michor The evolution of tumor metastases during
clonal expansion . . . . . . . . . . . . 30--44
James R. Edwards and
William G. Gibson A model for Ca$^{2+}$ waves in networks
of glial cells incorporating both
intercellular and extracellular
communication pathways . . . . . . . . . 45--58
Patricia Román-Román and
Desirée Romero and
Francisco Torres-Ruiz A diffusion process to model generalized
von Bertalanffy growth patterns: Fitting
to real data . . . . . . . . . . . . . . 59--69
Bernd Lütkenhöner and
Wolfgang Stoll and
Türker Basel Modeling the vestibular evoked myogenic
potential . . . . . . . . . . . . . . . 70--78
María Luz Cárdenas and
Juan-Carlos Letelier and
Claudio Gutierrez and
Athel Cornish-Bowden and
Jorge Soto-Andrade Closure to efficient causation,
computability and artificial life . . . 79--92
Andrew L. Nevai and
Kevin M. Passino and
Parthasarathy Srinivasan Stability of choice in the honey bee
nest-site selection process . . . . . . 93--107
Elizabeth S. Allman and
Mark T. Holder and
John A. Rhodes Estimating trees from filtered data:
Identifiability of models for
morphological phylogenetics . . . . . . 108--119
Alexei B. Ryabov and
Lars Rudolf and
Bernd Blasius Vertical distribution and composition of
phytoplankton under the influence of an
upper mixed layer . . . . . . . . . . . 120--133
K. R. Philipsen and
L. E. Christiansen and
H. Hasman and
H. Madsen Modelling conjugation with stochastic
differential equations . . . . . . . . . 134--142
James Whitacre and
Axel Bender Degeneracy: a design principle for
achieving robustness and evolvability 143--153
G. Quiroz and
R. Femat Theoretical blood glucose control in
hyper- and hypoglycemic and exercise
scenarios by means of an $ H_\infty $
algorithm . . . . . . . . . . . . . . . 154--160
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--160 (7 March 2010) . . . . . . ??
Ryo Hironaga and
Norio Yamamura Effects of extinction on food web
structures on an evolutionary time scale 161--168
Christinah Chiyaka and
Zindoga Mukandavire and
Prasenjit Das and
Farai Nyabadza and
Senelani D. Hove-Musekwa and
Henry Mwambi Theoretical analysis of mixed
\bionamePlasmodium malariae and
\bionamePlasmodium falciparum infections
with partial cross-immunity . . . . . . 169--178
Jasmine Foo and
Franziska Michor Evolution of resistance to anti-cancer
therapy during general dosing schedules 179--188
A. Koseska and
E. Ullner and
E. Volkov and
J. Kurths and
J. García-Ojalvo Cooperative differentiation through
clustering in multicellular populations 189--202
Maryam Esmaeili and
Hassan Mohabatkar and
Sasan Mohsenzadeh Using the concept of Chou's pseudo amino
acid composition for risk type
prediction of human papillomaviruses . . 203--209
Koichi Saeki and
Yoh Iwasa Optimal number of regulatory T cells . . 210--218
C. Y. Cyrus Chu A two-sex life history model of handicap
signaling . . . . . . . . . . . . . . . 219--226
Zhao-Hui Qi and
Xiao-Qin Qi and
Chen-Chen Liu New method for global alignment of 2 DNA
sequences by the tree data structure . . 227--236
John Vandermeer and
Aaron King Consequential classes of resources:
Subtle global bifurcation with dramatic
ecological consequences in a simple
population model . . . . . . . . . . . . 237--241
Robert J. Vickerstaff and
Allen Cheung Which coordinate system for modelling
path integration? . . . . . . . . . . . 242--261
Weini Huang and
Arne Traulsen Fixation probabilities of random mutants
under frequency dependent selection . . 262--268
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 161--268 (21 March 2010) . . . . . ??
Kevin J. Flynn and
H. Christopher Greenwell and
Robert W. Lovitt and
Robin J. Shields Selection for fitness at the individual
or population levels: Modelling effects
of genetic modifications in microalgae
on productivity and environmental safety 269--280
Berkin Malkoç and
Duygu Balcan and
Ayse Erzan Information content based model for the
topological properties of the gene
regulatory network of
\bionameEscherichia coli . . . . . . . . 281--294
Efrath Barta and
Arieh Drugan Glucose transport from mother to fetus
--- a theoretical study . . . . . . . . 295--302
Fabien Crauste and
Ivan Demin and
Olivier Gandrillon and
Vitaly Volpert Mathematical study of feedback control
roles and relevance in stress
erythropoiesis . . . . . . . . . . . . . 303--316
Michael L. Manapat and
Irene A. Chen and
Martin A. Nowak The basic reproductive ratio of life . . 317--327
M. Tugrul and
A. Kabakçio\uglu Anomalies in the transcriptional
regulatory network of the Yeast
\bionameSaccharomyces cerevisiae . . . . 328--336
Edward N. Trifonov Base pair stacking in nucleosome DNA and
bendability sequence pattern . . . . . . 337--339
Areli Hernández-Valdez and
Moisés Santillán and
Eduardo S. Zeron Cycling expression and cooperative
operator interaction in the trp operon
of \bionameEscherichia coli . . . . . . 340--352
Peter Olofsson and
Alison A. Bertuch Modeling growth and telomere dynamics in
\bionameSaccharomyces cerevisiae . . . . 353--359
Ning Zhang and
Guangyou Duan and
Shan Gao and
Jishou Ruan and
Tao Zhang Prediction of the parallel/antiparallel
orientation of beta-strands using amino
acid pairing preferences and support
vector machines . . . . . . . . . . . . 360--368
R. A. Sergeev and
R. E. Batorsky and
I. M. Rouzine Model with two types of CTL regulation
and experiments on CTL dynamics . . . . 369--384
R. A. Sergeev and
R. E. Batorsky and
J. M. Coffin and
I. M. Rouzine Interpreting the effect of vaccination
on steady state infection in animals
challenged with Simian immunodeficiency
virus . . . . . . . . . . . . . . . . . 385--392
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 269--392 (7 April 2010) . . . . . ??
Kerri-Ann Norton and
Michael Wininger and
Gyan Bhanot and
Shridar Ganesan and
Nicola Barnard and
Troy Shinbrot A 2D mechanistic model of breast ductal
carcinoma in situ (DCIS) morphology and
progression . . . . . . . . . . . . . . 393--406
Michael Günther and
Syn Schmitt A macroscopic ansatz to deduce the Hill
relation . . . . . . . . . . . . . . . . 407--418
A. Voß-Böhme and
A. Deutsch The cellular basis of cell sorting
kinetics . . . . . . . . . . . . . . . . 419--436
Iva Dostálková and
Marek Spinka When to go with the crowd: Modelling
synchronization of all-or-nothing
activity transitions in grouped animals 437--448
Masashi Tachikawa A mathematical model for
period-memorizing behavior in
\bionamePhysarum plasmodium . . . . . . 449--454
Blerta Shtylla and
James P. Keener A mechanomolecular model for the
movement of chromosomes during mitosis
driven by a minimal kinetochore bicyclic
cascade . . . . . . . . . . . . . . . . 455--470
Kun Qu and
Anastasia M. Yesnik and
Peter J. Ortoleva Alternative splicing regulatory network
reconstruction from exon array data . . 471--480
J. P. Keener A molecular ruler mechanism for length
control of extended protein structures
in bacteria . . . . . . . . . . . . . . 481--489
H. James Cleaves II The origin of the biologically coded
amino acids . . . . . . . . . . . . . . 490--498
Yandi Dharmadi and
Ramon Gonzalez Elementary network reconstruction: a
framework for the analysis of regulatory
networks in biological systems . . . . . 499--509
Anna Ochab-Marcinek Extrinsic noise passing through a
Michaelis--Menten reaction: a universal
response of a genetic switch . . . . . . 510--520
A. Kebir and
S. Ben Miled and
M. L. Hbid and
R. Bravo de la Parra Effects of density dependent sex
allocation on the dynamics of a
simultaneous hermaphroditic population:
Modelling and analysis . . . . . . . . . 521--529
Natalia L. Komarova and
Dominik Wodarz ODE models for oncolytic virus dynamics 530--543
William Hoppitt and
Neeltje J. Boogert and
Kevin N. Laland Detecting social transmission in
networks . . . . . . . . . . . . . . . . 544--555
Ernesto Estrada Generalized walks-based centrality
measures for complex biological networks 556--565
Hedia Fgaier and
Hermann J. Eberl A competition model between Pseudomonas
fluorescens and pathogens via iron
chelation . . . . . . . . . . . . . . . 566--578
Mark Broom and
Andrew D. Higginson and
Graeme D. Ruxton Optimal investment across different
aspects of anti-predator defences . . . 579--586
Jihua Wu and
Edward Susko Rate-variation need not defeat
phylogenetic inference through pairwise
sequence comparisons . . . . . . . . . . 587--589
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 393--590 (21 April 2010) . . . . . ??
Mauro Mobilia Oscillatory dynamics in
rock-paper-scissors games with mutations 1--10
Pierre Samozino and
Jean-Beno\^\it Morin and
Frédérique Hintzy and
Alain Belli Jumping ability: a theoretical
integrative approach . . . . . . . . . . 11--18
Zhaojin Xu and
Zhen Wang and
Lianzhong Zhang Bounded rationality in volunteering
public goods games . . . . . . . . . . . 19--23
Jiang-Nan Yang Cooperation and the evolution of
anisogamy . . . . . . . . . . . . . . . 24--36
Alexey A. Fedorov and
Vladimir E. Kurochkin and
Alexandr I. Martynov and
Ram V. Petrov Theoretical and experimental
investigation of immunoprecipitation
pattern formation in gel medium . . . . 37--44
Vasile Lavric and
David W. Graham Birth, growth and death as structuring
operators in bacterial population
dynamics . . . . . . . . . . . . . . . . 45--54
Rachid Ait-Haddou and
Yoshihisa Kurachi and
Taishin Nomura On calcium-buffer dynamics within the
excess buffer regime . . . . . . . . . . 55--65
Martin Kroon On the correlation between continuum
mechanics entities and cell activity in
biological soft tissues: Assessment of
three possible criteria for
cell-controlled fibre reorientation in
collagen gels and collagenous tissues 66--76
Fuzhong Nian and
Xingyuan Wang Efficient immunization strategies on
complex networks . . . . . . . . . . . . 77--83
Masakazu Akiyama and
Atsushi Tero and
Ryo Kobayashi A mathematical model of cleavage . . . . 84--94
Gui-Quan Sun and
Quan-Xing Liu and
Zhen Jin and
Amit Chakraborty and
Bai-Lian Li Influence of infection rate and
migration on extinction of disease in
spatial epidemics . . . . . . . . . . . 95--103
Natalia L. Komarova and
Simon A. Levin Eavesdropping and language dynamics . . 104--118
Jiapu Zhang Studies on the structural stability of
rabbit prion probed by molecular
dynamics simulations of its wild-type
and mutants . . . . . . . . . . . . . . 119--122
L. Barberis and
C. A. Condat and
A. S. Gliozzi and
P. P. Delsanto Concurrent growth of phenotypic
features: a phenomenological
universalities approach . . . . . . . . 123--129
Yan Xu and
Xiao-Bo Wang and
Jun Ding and
Ling-Yun Wu and
Nai-Yang Deng Lysine acetylation sites prediction
using an ensemble of support vector
machine classifiers . . . . . . . . . . 130--135
Hisashi Ohtsuki Stochastic evolutionary dynamics of
bimatrix games . . . . . . . . . . . . . 136--142
Shimpei Koike and
Mayuko Nakamaru and
Masahiro Tsujimoto Evolution of cooperation in rotating
indivisible goods game . . . . . . . . . 143--153
B. Dubey and
T. G. Zhao and
M. Jonsson and
H. Rahmanov A solution to the
accelerated-predator-satiety
Lotka--Volterra predator--prey problem
using Boubaker polynomial expansion
scheme . . . . . . . . . . . . . . . . . 154--160
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--160 (7 May 2010) . . . . . . . ??
Angela Reynolds and
G. Bard Ermentrout and
Gilles Clermont A mathematical model of pulmonary gas
exchange under inflammatory stress . . . 161--173
Nam-phuong Nguyen and
Chris Myers and
Hiroyuki Kuwahara and
Chris Winstead and
James Keener Design and analysis of a robust genetic
Muller C-element . . . . . . . . . . . . 174--187
Masanori Takezawa and
Michael E. Price Revisiting ``The Evolution of
Reciprocity in Sizable Groups'':
Continuous reciprocity in the repeated
$n$-person prisoner's dilemma . . . . . 188--196
Yossi Ben-Zion and
Yahel Cohen and
Nadav M. Shnerb Modeling epidemics dynamics on
heterogeneous networks . . . . . . . . . 197--204
Alexandros Bousios and
David Waxman and
Stephen R. Pearce Absence of close-facing
retrotransposons: a comparison of
molecular data and theory . . . . . . . 205--210
Babatunde A. Ogunnaike and
Claudio A. Gelmi and
Jeremy S. Edwards A probabilistic framework for microarray
data analysis: Fundamental probability
models and statistical inference . . . . 211--222
Tetsuya Akita and
Hiroyuki Matsuda Why do sex ratio dimorphisms exist in
\bionameQuercus masting? Evolution of
imperfect synchronous reproduction in
Monoecious trees . . . . . . . . . . . . 223--236
Alberto d'Onofrio and
Piero Manfredi Vaccine demand driven by vaccine side
effects: Dynamic implications for SIR
diseases . . . . . . . . . . . . . . . . 237--252
Alberto d'Onofrio and
Alberto Gandolfi Chemotherapy of vascularised tumours:
Role of vessel density and the effect of
vascular ``pruning'' . . . . . . . . . . 253--265
Mark Broom and
Mary L. Crowe and
Meghan R. Fitzgerald and
Jan Rychtár The stochastic modelling of
kleptoparasitism using a Markov process 266--272
Miranda I. Teboh-Ewungkem and
Thomas Yuster A within-vector mathematical model of
\bionamePlasmodium falciparum and
implications of incomplete fertilization
on optimal gametocyte sex ratio . . . . 273--286
Markus Scholz and
Arnd Gross and
Markus Loeffler A biomathematical model of human
thrombopoiesis under chemotherapy . . . 287--300
A. Németh and
K. Takács The paradox of cooperation benefits . . 301--311
S. Hummert and
C. Hummert and
A. Schröter and
B. Hube and
S. Schuster Game theoretical modelling of survival
strategies of \bionameCandida albicans
inside macrophages . . . . . . . . . . . 312--318
Jia-wei Luo and
Ting Wang Motif discovery using an immune genetic
algorithm . . . . . . . . . . . . . . . 319--325
Hong-Bin Shen and
Kuo-Chen Chou Gneg-mPLoc: a top-down strategy to
enhance the quality of predicting
subcellular localization of
Gram-negative bacterial proteins . . . . 326--333
Katja Rateitschak and
Olaf Wolkenhauer Thresholds in transient dynamics of
signal transduction pathways . . . . . . 334--346
E. Van Derlinden and
K. Bernaerts and
J. F. Van Impe Simultaneous versus sequential optimal
experiment design for the identification
of multi-parameter microbial growth
kinetics as a function of temperature 347--355
Alexei Vazquez Optimal cytoplasmatic density and flux
balance model under macromolecular
crowding effects . . . . . . . . . . . . 356--359
Federico Vazquez and
Cristóbal López and
Justin M. Calabrese and
Miguel A. Muñoz Dynamical phase coexistence: a simple
solution to the ``savanna problem'' . . 360--366
Gang Zhao Phase organization of circadian
oscillators in extended gate and
oscillator models . . . . . . . . . . . 367--376
Eduardo S. Zeron and
Moisés Santillán Distributions for
negative-feedback-regulated stochastic
gene expression: Dimension reduction and
numerical solution of the chemical
master equation . . . . . . . . . . . . 377--385
Hui-Shen Shen Buckling and postbuckling of radially
loaded microtubules by nonlocal shear
deformable shell model . . . . . . . . . 386--394
David M. Drew and
Geoffrey M. Downes and
Michael Battaglia CAMBIUM, a process-based model of daily
xylem development in Eucalyptus . . . . 395--406
B. D. Fulcher and
A. J. K. Phillips and
P. A. Robinson Quantitative physiologically based
modeling of subjective fatigue during
sleep deprivation . . . . . . . . . . . 407--419
Guy Dimonte A cell kinetics model for prostate
cancer and its application to clinical
data and individual patients . . . . . . 420--442
C. Wellard and
J. Markham and
E. D. Hawkins and
P. D. Hodgkin The effect of correlations on the
population dynamics of lymphocytes . . . 443--449
Alejandro Rosas Evolutionary game theory meets social
science: Is there a unifying rule for
human cooperation? . . . . . . . . . . . 450--456
Mariusz Pietruszka Exact analytic solutions for a global
equation of plant cell growth . . . . . 457--466
Jingxin Nie and
Lei Guo and
Gang Li and
Carlos Faraco and
L. Stephen Miller and
Tianming Liu A computational model of cerebral cortex
folding . . . . . . . . . . . . . . . . 467--478
Erik G. Noonburg and
Roger M. Nisbet and
Tin Klanjscek Effects of life history variation on
vertical transfer of toxicants in marine
mammals . . . . . . . . . . . . . . . . 479--489
Natsuki Tanaka and
Garegin A. Papoian Reverse-engineering of biochemical
reaction networks from spatio-temporal
correlations of fluorescence
fluctuations . . . . . . . . . . . . . . 490--500
S. Funk and
E. Gilad and
V. A. A. Jansen Endemic disease, awareness, and local
behavioural response . . . . . . . . . . 501--509
Ido Filin Target size and optimal life history
when individual growth and energy budget
are stochastic . . . . . . . . . . . . . 510--516
Yoshito Hirata and
Nicholas Bruchovsky and
Kazuyuki Aihara Development of a mathematical model that
predicts the outcome of hormone therapy
for prostate cancer . . . . . . . . . . 517--527
Ryan T. Roper and
Maria Pia Saccomani and
Paolo Vicini Cellular signaling identifiability
analysis: a case study . . . . . . . . . 528--537
Imraan Faruque and
J. Sean Humbert Dipteran insect flight dynamics. Part 1.
Longitudinal motion about hover . . . . 538--552
Tharindi Hapuarachchi and
Chang Sub Park and
Stephen Payne Quantification of the effects of
vasomotion on mass transport to tissue
from axisymmetric blood vessels . . . . 553--559
Beatriz Carely Luna Olivera and
Edgardo Ugalde and
Agustino Martínez-Antonio Regulatory dynamics of standard
two-component systems in bacteria . . . 560--569
Dimitri Perrin and
Heather J. Ruskin and
Tohru Niwa Cell type-dependent, infection-induced,
aberrant DNA methylation in gastric
cancer . . . . . . . . . . . . . . . . . 570--577
Minghao Wang and
Xiaofeng Song and
Ping Han and
Wei Li and
Bin Jiang New syntax to describe local continuous
structure-sequence information for
recognizing new pre-miRNAs . . . . . . . 578--584
Natalya Kurochkina Helix-helix interactions and their
impact on protein motifs and assemblies 585--592
Roland Kaunas and
Zuyi Huang and
Juergen Hahn A kinematic model coupling stress fiber
dynamics with JNK activation in response
to matrix stretching . . . . . . . . . . 593--603
Even Tjòrve How to resolve the SLOSS debate: Lessons
from species-diversity models . . . . . 604--612
Ahmed Ahmed and
Gabriel Frey and
Christian J. Michel Essential molecular functions associated
with the circular code evolution . . . . 613--622
Sanyi Tang and
Guangyao Tang and
Robert A. Cheke Optimum timing for integrated pest
management: Modelling rates of pesticide
application and natural enemy releases 623--638
Richard F. Burton Evolutionary determinants of the
concentrations of inorganic ions in body
fluids . . . . . . . . . . . . . . . . . 639--640
Allen Cheung The fourth moment of the radial
displacement of a discrete
correlated/persistent random walk . . . 641--644
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 161--644 (21 May 2010) . . . . . . ??
Joanna Pressley and
Erika M. C. D'Agata and
Glenn F. Webb The effect of co-colonization with
community-acquired and hospital-acquired
methicillin-resistant
\bionameStaphylococcus aureus strains on
competitive exclusion . . . . . . . . . 645--656
Scott A. Sands and
Bradley A. Edwards and
Vanessa J. Kelly and
Malcolm R. Davidson and
Malcolm H. Wilkinson and
Philip J. Berger A model investigation of the impact of
ventilation-perfusion mismatch on
oxygenation during apnea in preterm
infants . . . . . . . . . . . . . . . . 657--662
Yohsuke Murase and
Takashi Shimada and
Nobuyasu Ito and
Per Arne Rikvold Random walk in genome space: a key
ingredient of intermittent dynamics of
community assembly on evolutionary time
scales . . . . . . . . . . . . . . . . . 663--672
Allyson G. Hindle and
Markus Horning Energetics of breath-hold hunting:
Modeling the effects of aging on
foraging success in the Weddell seal . . 673--682
R. M. T. Fleming and
I. Thiele and
G. Provan and
H. P. Nasheuer Integrated stoichiometric, thermodynamic
and kinetic modelling of steady state
metabolism . . . . . . . . . . . . . . . 683--692
Thibaut Jombart and
Sandrine Pavoine and
Sébastien Devillard and
Dominique Pontier Putting phylogeny into the analysis of
biological traits: a methodological
approach . . . . . . . . . . . . . . . . 693--701
Alexey V. Melkikh and
Vladimir D. Seleznev and
Oksana I. Chesnokova Analytical model of ion transport and
conversion of light energy in
chloroplasts . . . . . . . . . . . . . . 702--710
Fernando Castro-Chavez The rules of variation: Amino acid
exchange according to the rotating
circular genetic code . . . . . . . . . 711--721
Andrea Veglio The shade avoidance syndrome: a
non-Markovian stochastic growth model 722--728
Romulus Breban and
John M. Drake and
Pejman Rohani A general multi-strain model with
environmental transmission: Invasion
conditions for the disease-free and
endemic states . . . . . . . . . . . . . 729--736
Marcus Salomonsson Group selection: The quest for social
preferences . . . . . . . . . . . . . . 737--746
Xiaohai Li and
Jizhong Xiao Swarming in homogeneous environments: a
social interaction based framework . . . 747--759
Jiang Zhang and
Liangpeng Guo Scaling behaviors of weighted food webs
as energy transportation networks . . . 760--770
Bo Li and
Bin Shao and
Chenlu Yu and
Qi Ouyang and
Hongli Wang A mathematical model for cell size
control in fission yeast . . . . . . . . 771--781
Kazuhiro Takemoto and
Masanori Arita Nested structure acquired through simple
evolutionary process . . . . . . . . . . 782--786
Viola Pavlová and
Lud\uek Berec and
David S. Boukal Caught between two Allee effects:
Trade-off between reproduction and
predation risk . . . . . . . . . . . . . 787--798
Hervé Seligmann Positive correlations between molecular
and morphological rates of evolution . . 799--807
Eric de Silva and
J. Krishnan and
Russell Betney and
Ian Stansfield A mathematical modelling framework for
elucidating the role of feedback control
in translation termination . . . . . . . 808--821
S. M. Minhaz Ud-Dean Structural explanation for the effect of
humidity on persistence of airborne
virus: Seasonality of influenza . . . . 822--829
João Carlos de Oliveira Guerra and
Pedro Licinio The role played by exons in genomic DNA
sequence correlations . . . . . . . . . 830--837
Amy L. Bauer and
Trachette L. Jackson and
Yi Jiang and
Thimo Rohlf Receptor cross-talk in angiogenesis:
Mapping environmental cues to cell
phenotype using a stochastic, Boolean
signaling network model . . . . . . . . 838--846
Rui Dilão and
Daniele Muraro mRNA diffusion explains protein
gradients in \bionameDrosophila early
development . . . . . . . . . . . . . . 847--853
José Santos and
Ángel Monteagudo Study of the genetic code adaptability
by means of a genetic algorithm . . . . 854--865
Christopher P. Brooks and
Haimeng Zhang A null model of community disassembly
effects on vector-borne disease risk . . 866--873
Da Zhou and
Bin Wu and
Hao Ge Evolutionary stability and
quasi-stationary strategy in stochastic
evolutionary game dynamics . . . . . . . 874--881
Sefi Givli Towards multi-scale modeling of muscle
fibers with sarcomere non-uniformities 882--892
M. Raghib and
S. A. Levin and
I. G. Kevrekidis Multiscale analysis of collective motion
and decision-making in swarms: An
advection-diffusion equation with memory
approach . . . . . . . . . . . . . . . . 893--913
Kouroush Sadegh Zadeh and
Hubert J. Montas A class of exact solutions for
biomacromolecule diffusion-reaction in
live cells . . . . . . . . . . . . . . . 914--933
Meng Liu and
Ke Wang Persistence and extinction of a
stochastic single-specie model under
regime switching in a polluted
environment . . . . . . . . . . . . . . 934--944
Elke K. Markert and
Nils Baas and
Arnold J. Levine and
Alexei Vazquez Higher order Boolean networks as models
of cell state dynamics . . . . . . . . . 945--951
J. Zanghellini and
F. Wodlei and
H. H. von Grünberg Phospholipid demixing and the birth of a
lipid droplet . . . . . . . . . . . . . 952--961
Hugo A. van den Berg and
Zoe A. Duncombe Eradication-resolution dynamics with
stochastic flare-ups . . . . . . . . . . 962--970
Yara-Elena Sánchez-Corrales and
Elena R. Álvarez-Buylla and
Luis Mendoza The \bionameArabidopsis thaliana flower
organ specification gene regulatory
network determines a robust
differentiation process . . . . . . . . 971--983
S. Roy Caplan and
Gloria S. Tannenbaum and
Rose M. Johnstone An enzymatic model of the growth
hormone-releasing hormone oscillator
incorporating neuronal synchronization 984--989
Sarah L. Noble and
Eric Sherer and
Robert E. Hannemann and
Doraiswami Ramkrishna and
Terry Vik and
Ann E. Rundell Using adaptive model predictive control
to customize maintenance therapy
chemotherapeutic dosing for childhood
acute lymphoblastic leukemia . . . . . . 990--1002
G. A. Parker and
S. Immler and
S. Pitnick and
T. R. Birkhead Sperm competition games: Sperm size
(mass) and number under raffle and
displacement, and the evolution of $ P_2
$ . . . . . . . . . . . . . . . . . . . 1003--1023
Loris Nanni and
Jian-Yu Shi and
Sheryl Brahnam and
Alessandra Lumini Protein classification using texture
descriptors extracted from the protein
backbone image . . . . . . . . . . . . . 1024--1032
Peter A. Abrams and
Simon R. Fung Prey persistence and abundance in
systems with intraguild predation and
type-2 functional responses . . . . . . 1033--1042
Stephen J. Montgomery-Smith and
Francis J. Schmidt Statistical methods for estimating
complexity from competition experiments
between two populations . . . . . . . . 1043--1046
Travis Ingram and
Mike Steel Modelling the unpredictability of future
biodiversity in ecological networks . . 1047--1056
Kevin J. Painter and
Nicola J. Armstrong and
Jonathan A. Sherratt The impact of adhesion on cellular
invasion processes in cancer and
development . . . . . . . . . . . . . . 1057--1067
Jeremy D. Scheff and
Steve E. Calvano and
Stephen F. Lowry and
Ioannis P. Androulakis Modeling the influence of circadian
rhythms on the acute inflammatory
response . . . . . . . . . . . . . . . . 1068--1076
Elan Gin and
Elly M. Tanaka and
Lutz Brusch A model for cyst lumen expansion and
size regulation via fluid secretion . . 1077--1088
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 645--1088 (7 June 2010) . . . . . ??
Christian Cibert and
Jérémy Toscano and
Vincent Pensée and
Guy Bonnet Bending of the ``9+2'' axoneme analyzed
by the finite element method . . . . . . 1089--1101
A. Jamie Wood Strategy selection under predation;
evolutionary analysis of the emergence
of cohesive aggregations . . . . . . . . 1102--1110
Luping Zhang and
Gang Zhao Superiority of single covalent
modification in specificity: From
deterministic to stochastic viewpoint 1111--1119
D. Waxman and
L. Loewe A stochastic model for a single click of
Muller's ratchet . . . . . . . . . . . . 1120--1132
Krasimira Tsaneva-Atanasova and
Hinke M. Osinga and
Thorsten Rieß and
Arthur Sherman Full system bifurcation analysis of
endocrine bursting models . . . . . . . 1133--1146
Osvaldo Chara and
Diego E. Pafundo and
Pablo J. Schwarzbaum Negative feedback of extracellular ADP
on ATP release in goldfish hepatocytes:
a theoretical study . . . . . . . . . . 1147--1158
Lili Xi and
Shuyan Li and
Huanxiang Liu and
Jiazhong Li and
Beilei Lei and
Xiaojun Yao Global and local prediction of protein
folding rates based on sequence
autocorrelation information . . . . . . 1159--1168
Dominique Chu and
David J. Barnes Modeling fimbriae mediated parasite-host
interactions . . . . . . . . . . . . . . 1169--1176
Djomangan A. Ouattara and
Wassim Abou-Jaoudé and
Marcelle Kaufman From structure to dynamics: Frequency
tuning in the p53-Mdm2 network. II:
Differential and stochastic approaches 1177--1189
Zhao Lu and
Ynte H. Schukken and
Rebecca L. Smith and
Yrjo T. Grohn Stochastic simulations of a multi-group
compartmental model for Johne's disease
on US dairy herds with test-based
culling intervention . . . . . . . . . . 1190--1201
Daniel Ashlock and
Elizabeth L. Clare and
Taika E. von Königslöw and
Wendy Ashlock Evolution and instability in ring
species complexes: An in silico approach
to the study of speciation . . . . . . . 1202--1213
Britta Göbel and
Dirk Langemann and
Kerstin M. Oltmanns and
Matthias Chung Compact energy metabolism model: Brain
controlled energy supply . . . . . . . . 1214--1224
Katherine Wendelsdorf and
Josep Bassaganya-Riera and
Raquel Hontecillas and
Stephen Eubank Model of colonic inflammation: Immune
modulatory mechanisms in inflammatory
bowel disease . . . . . . . . . . . . . 1225--1239
Matthijs van Veelen and
Julián García and
Leticia Avilés It takes grouping and cooperation to get
sociality . . . . . . . . . . . . . . . 1240--1253
Hermann B. Frieboes and
Fang Jin and
Yao-Li Chuang and
Steven M. Wise and
John S. Lowengrub and
Vittorio Cristini Three-dimensional multispecies nonlinear
tumor growth-II: Tumor invasion and
angiogenesis . . . . . . . . . . . . . . 1254--1278
László Zsolt Szabó and
János Vincze and
László Csernoch and
Péter Szentesi Improved spark and ember detection using
stationary wavelet transforms . . . . . 1279--1292
István Scheuring Egalitarian motive in punishing
defectors . . . . . . . . . . . . . . . 1293--1295
Pierrick Blanchard and
Sébastien Devillard On the evolutionary consequences of a
Trivers--Willard effect in humans:
Further analysis of Dr S. Kanazawa's
paper on `beautiful parents' . . . . . . 1296--1298
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1089--1298 (21 June 2010) . . . . ??
P. E. Vincent and
S. J. Sherwin and
P. D. Weinberg The effect of the endothelial glycocalyx
layer on concentration polarisation of
low density lipoprotein in arteries . . 1--17
Ana I. Borthagaray and
Miguel A. Fuentes and
Pablo A. Marquet Vegetation pattern formation in a
fog-dependent ecosystem . . . . . . . . 18--26
Sonja J. Prohaska and
Peter F. Stadler and
David C. Krakauer Innovation in gene regulation: The case
of chromatin computation . . . . . . . . 27--44
Andrew Yu. Morozov Emergence of Holling type III
zooplankton functional response:
Bringing together field evidence and
mathematical modelling . . . . . . . . . 45--54
Ardashir Kharabian An efficient computational method for
screening functional SNPs in plants . . 55--62
Markku Larjavaara Maintenance cost, toppling risk and size
of trees in a self-thinning stand . . . 63--67
Chiaki Oka and
Chae Young Cha and
Akinori Noma Characterization of the cardiac Na$^+$
/K$^+$ pump by development of a
comprehensive and mechanistic model . . 68--77
Petr Keil and
Tomás Herben and
James Rosindell and
David Storch Predictions of Taylor's power law,
density dependence and pink noise from a
neutrally modeled time series . . . . . 78--86
Huseyin Coskun and
Taryn L. S. Summerfield and
Douglas A. Kniss and
Avner Friedman Mathematical modeling of preadipocyte
fate determination . . . . . . . . . . . 87--94
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--94 (7 July 2010) . . . . . . . ??
Christian Cibert and
Andrei Ludu Is the curvature of the flagellum
involved in the apparent cooperativity
of the dynein arms along the ``9+2''
axoneme? . . . . . . . . . . . . . . . . 95--103
Pierre A. Fortier Detecting and estimating rectification
of gap junction conductance based on
simulations of dual-cell recordings from
a pair and a network of coupled cells 104--114
Nikolai I. Kononenko and
Nataliya M. Berezetskaya Modeling the spontaneous activity in
suprachiasmatic nucleus neurons: Role of
cation single channels . . . . . . . . . 115--125
J. Balakrishnan and
B. Ashok The role of Hopf bifurcation dynamics in
sensory processes . . . . . . . . . . . 126--135
Sunmi Lee and
Gerardo Chowell and
Carlos Castillo-Chávez Optimal control for pandemic influenza:
The role of limited antiviral treatment
and isolation . . . . . . . . . . . . . 136--150
Donald M. Henderson and
Darren Naish Predicting the buoyancy, equilibrium and
potential swimming ability of giraffes
by computational analysis . . . . . . . 151--159
James O. Lloyd-Smith Modeling density dependence in
heterogeneous landscapes: Dispersal as a
case study . . . . . . . . . . . . . . . 160--166
Utkarsh Dang and
Chris T. Bauch A population biological approach to the
collective dynamics of countries
undergoing demographic transition . . . 167--176
Ping Yan Impulsive SUI epidemic model for
HIV/AIDS with chronological age and
infection age . . . . . . . . . . . . . 177--184
R. Serra and
M. Villani and
A. Barbieri and
S. A. Kauffman and
A. Colacci On the dynamics of random Boolean
networks subject to noise: Attractors,
ergodic sets and cell types . . . . . . 185--193
Shiyuan Wang and
Fengchun Tian and
Yu Qiu and
Xiao Liu Bilateral similarity function: a novel
and universal method for similarity
analysis of biological sequences . . . . 194--201
Thomas Siegmund and
Matthew R. Allen and
David B. Burr Can deterministic mechanical size
effects contribute to fracture and
microdamage accumulation in trabecular
bone? . . . . . . . . . . . . . . . . . 202--210
Yukari Suzuki-Ohno and
Maki N. Inoue and
Kazunori Ohno Applying geographic profiling used in
the field of criminology for predicting
the nest locations of bumble bees . . . 211--217
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 95--218 (21 July 2010) . . . . . . ??
Yao Li and
Changxing Ma and
Zhong Wang and
Gang Chen and
Kwangmi Ahn and
Philip Lazarus and
Rongling Wu A disequilibrium model for detecting
genetic mutations for cancer . . . . . . 218--224
C. J. Rhodes and
A. P. Martin The influence of viral infection on a
plankton ecosystem undergoing nutrient
enrichment . . . . . . . . . . . . . . . 225--237
Philip H. Crowley and
Kyung Hwan Baik Variable valuations and voluntarism
under group selection: An evolutionary
public goods game . . . . . . . . . . . 238--244
Padmesh Anjukandi and
Gerald G. Pereira and
Martin A. K. Williams Langevin dynamics simulations reveal
biologically relevant folds arising from
the incorporation of a torsional
potential . . . . . . . . . . . . . . . 245--249
Maurício Vieira Kritz and
Marcelo Trindade dos Santos and
Sebastián Urrutia and
Jean-Marc Schwartz Organising metabolic networks: Cycles in
flux distributions . . . . . . . . . . . 250--260
Dirk Koschützki and
Björn H. Junker and
Jörg Schwender and
Falk Schreiber Structural analysis of metabolic
networks based on flux centrality . . . 261--269
N. J. Warren and
M. H. Tawhai and
E. J. Crampin The effect of intracellular calcium
oscillations on fluid secretion in
airway epithelium . . . . . . . . . . . 270--277
Josep Sardanyés and
Santiago F. Elena Error threshold in RNA quasispecies
models with complementation . . . . . . 278--286
Guoli Ji and
Xiaohui Wu and
Yingjia Shen and
Jiangyin Huang and
Qingshun Quinn Li A classification-based prediction model
of messenger RNA polyadenylation sites 287--296
Akio Iwagami and
Naoki Masuda Upstream reciprocity in heterogeneous
networks . . . . . . . . . . . . . . . . 297--305
Imraan Faruque and
J. Sean Humbert Dipteran insect flight dynamics. Part 2:
Lateral-directional motion about hover 306--313
Cheng-Liang Chen and
Hong-Wen Tsai and
Sio-Si Wong Modeling the physiological
glucose-insulin dynamic system on
diabetics . . . . . . . . . . . . . . . 314--322
Wei Huang and
Jianmin Zhang and
Yurong Wang and
Dan Huang A simple method to analyze the
similarity of biological sequences based
on the fuzzy theory . . . . . . . . . . 323--328
C. Turner and
M. Kohandel Investigating the link between
epithelial-mesenchymal transition and
the cancer stem cell phenotype: a
mathematical approach . . . . . . . . . 329--335
Giulio Caravagna and
Alberto d'Onofrio and
Paolo Milazzo and
Roberto Barbuti Tumour suppression by immune system
through stochastic oscillations . . . . 336--345
Marcelo Alves Pereira and
Alexandre Souto Martinez Pavlovian Prisoner's Dilemma ---
Analytical results, the quasi-regular
phase and spatio-temporal patterns . . . 346--358
Nessy Tania and
James P. Keener Calsequestrin mediates changes in
spontaneous calcium release profiles . . 359--376
Frédéric Fabre and
Joël Chadoeuf and
Caroline Costa and
Hervé Lecoq and
Cécile Desbiez Asymmetrical over-infection as a process
of plant virus emergence . . . . . . . . 377--388
Manas K. Roy and
Paromita Banerjee and
Tapas K. Sengupta and
Sushanta Dattagupta Glucose induced fractal colony pattern
of \bionameBacillus thuringiensis . . . 389--395
Emily R. Stirk and
Grant Lythe and
Hugo A. van den Berg and
Carmen Molina-París Stochastic competitive exclusion in the
maintenance of the na\"\ive T cell
repertoire . . . . . . . . . . . . . . . 396--410
Aina Astudillo Fernandez and
Anne-Catherine Mailleux and
Fabrice Saffre and
Bertrand Krafft and
Jean Louis Deneubourg Effect of retentive markers on the
dynamics of settlement: The case of
arthropod silk . . . . . . . . . . . . . 411--421
Benito Hernández-Bermejo Renormalization group approach to
power-law modeling of complex metabolic
networks . . . . . . . . . . . . . . . . 422--432
Serdar Göktepe and
Oscar John Abilez and
Kevin Kit Parker and
Ellen Kuhl A multiscale model for eccentric and
concentric cardiac growth through
sarcomerogenesis . . . . . . . . . . . . 433--442
Gaël Bougaran and
Olivier Bernard and
Antoine Sciandra Modeling continuous cultures of
microalgae colimited by nitrogen and
phosphorus . . . . . . . . . . . . . . . 443--454
Andrzej Mizera and
Barbara Gambin Stochastic modelling of the eukaryotic
heat shock response . . . . . . . . . . 455--466
Raluca Eftimie and
Jonathan L. Bramson and
David J. D. Earn Modeling anti-tumor Th1 and Th2 immunity
in the rejection of melanoma . . . . . . 467--480
Martin Zumsande and
Thilo Gross Bifurcations and chaos in the MAPK
signaling cascade . . . . . . . . . . . 481--491
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 218--492 (7 August 2010) . . . . . ??
Yulia M. Serebrennikova and
Janus Patel and
Wilbur K. Milhous and
Luis H. García-Rubio Quantitative analysis of morphological
alterations in \bionamePlasmodium
falciparum infected red blood cells
through theoretical interpretation of
spectral measurements . . . . . . . . . 493--500
K. M. Pepin and
I. Volkov and
J. R. Banavar and
C. O. Wilke and
B. T. Grenfell Phenotypic differences in viral immune
escape explained by linking within-host
dynamics to host-population immunity . . 501--510
Nadia Marchettini and
Emilio Del Giudice and
Vladimir Voeikov and
Enzo Tiezzi Water: a medium where dissipative
structures are produced by a coherent
dynamics . . . . . . . . . . . . . . . . 511--516
Sz. Horvát and
A. Derzsi and
Z. Néda and
A. Balog A spatially explicit model for tropical
tree diversity patterns . . . . . . . . 517--523
P. M. Drysdale and
J. P. Huber and
P. A. Robinson and
K. M. Aquino Spatiotemporal BOLD dynamics from a
poroelastic hemodynamic model . . . . . 524--534
Andreas Dress and
Vincent Moulton and
Mike Steel and
Taoyang Wu Species, clusters and the `Tree of
life': a graph-theoretic perspective . . 535--542
A. Fasano and
M. A. Herrero and
J. M. López and
E. Medina On the dynamics of the growth plate in
primary ossification . . . . . . . . . . 543--553
Brian R. Ginn The implications of gene heterozygosity
for protein folding and protein turnover 554--564
Shi Jian-Cheng Signal transduction and amplification in
a circadian oscillator: Interaction
between two colored noises . . . . . . . 565--571
Jianhua Pang and
Jing-an Cui and
Xueyong Zhou Dynamical behavior of a hepatitis B
virus transmission model with
vaccination . . . . . . . . . . . . . . 572--578
Om Prakash and
Shakti Mehrotra and
Aneesh Krishna and
Bhartendu N. Mishra A neural network approach for the
prediction of in vitro culture
parameters for maximum biomass yields in
hairy root cultures . . . . . . . . . . 579--585
Simeone Marino and
Amy Myers and
JoAnne L. Flynn and
Denise E. Kirschner TNF and IL-10 are major factors in
modulation of the phagocytic cell
environment in lung and lymph node in
tuberculosis: a next-generation
two-compartmental model . . . . . . . . 586--598
J. Flores and
E. Corvera Poiré and
J. A. del Río and
M. López de Haro A plausible explanation for heart rates
in mammals . . . . . . . . . . . . . . . 599--603
Wes Maciejewski An analysis of the orientation of an
orb-web spider . . . . . . . . . . . . . 604--608
Simone Pigolotti and
Massimo Cencini Coexistence and invasibility in a
two-species competition model with
habitat-preference . . . . . . . . . . . 609--617
Shuyan Ding and
Qi Dai and
Hongmei Liu and
Tianming Wang A simple feature representation vector
for phylogenetic analysis of DNA
sequences . . . . . . . . . . . . . . . 618--623
David G. Rand and
Joseph J. Armao IV and
Mayuko Nakamaru and
Hisashi Ohtsuki Anti-social punishment can prevent the
co-evolution of punishment and
cooperation . . . . . . . . . . . . . . 624--632
Paul L. Hooper and
Hillard S. Kaplan and
James L. Boone A theory of leadership in human
cooperative groups . . . . . . . . . . . 633--646
D. Maxin and
L. Berec A two-sex demographic model with
single-dependent divorce rate . . . . . 647--656
Lambertus A. Peletier and
Neil Benson and
Piet H. van der Graaf Impact of protein binding on receptor
occupancy: a two-compartment model . . . 657--671
Jason N. Bazil and
Gregery T. Buzzard and
Ann E. Rundell A bioenergetic model of the
mitochondrial population undergoing
permeability transition . . . . . . . . 672--690
Xiufen Zou and
Xueshuang Xiang and
Yan Chen and
Tao Peng and
Xuelian Luo and
Zishu Pan Understanding inhibition of viral
proteins on type I IFN signaling
pathways with modeling and optimization 691--703
Samira Khalili and
James M. Monaco and
Antonios Armaou Development of a stochastic model for
the efficacy of NRTIs using known
mechanisms of action . . . . . . . . . . 704--717
Shahab Sheikh-Bahaei and
Jacquelyn J. Maher and
C. Anthony Hunt Computational experiments reveal
plausible mechanisms for changing
patterns of hepatic zonation of
xenobiotic clearance and hepatotoxicity 718--733
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 493--734 (21 August 2010) . . . . ??
Loris Nanni and
Sheryl Brahnam and
Alessandra Lumini High performance set of PseAAC and
sequence based descriptors for protein
classification . . . . . . . . . . . . . 1--10
Simona Ginsburg and
Eva Jablonka The evolution of associative learning: a
factor in the Cambrian explosion . . . . 11--20
Milan Randi\'c and
Marjana Novic and
Marjan Vracko and
Dejan Plavsi\'c Study of proteome maps using partial
ordering . . . . . . . . . . . . . . . . 21--28
Xinzhu Meng and
Zhenqing Li The dynamics of plant disease models
with continuous and impulsive cultural
control strategies . . . . . . . . . . . 29--40
Michail Stamatakis and
Kyriacos Zygourakis A mathematical and computational
approach for integrating the major
sources of cell population heterogeneity 41--61
P. R. Shorten and
A. J. Peterson and
A. R. O'Connell and
J. L. Juengel and
K. P. McNatty and
T. K. Soboleva A mathematical model of pregnancy
recognition in mammals . . . . . . . . . 62--69
Filippo Posta and
Tom Chou A mathematical model of intercellular
signaling during epithelial wound
healing . . . . . . . . . . . . . . . . 70--78
Atsushi Yamauchi and
Arndt Telschow and
Yutaka Kobayashi Evolution of cytoplasmic sex ratio
distorters: Effect of paternal
transmission . . . . . . . . . . . . . . 79--87
Vladislav Victorovich Khrustalev and
Eugene Victorovich Barkovsky The level of cytosine is usually much
higher than the level of guanine in
two-fold degenerated sites from third
codon positions of genes from Simplex-
and Varicelloviruses with G+C higher
than 50% . . . . . . . . . . . . . . . . 88--98
Melissa Reneaux and
Manoj Gopalakrishnan Theoretical results for chemotactic
response and drift of \bionameE. coli in
a weak attractant gradient . . . . . . . 99--106
Karen Magnuson-Ford and
Arne Mooers and
Sébastien Rioux Paquette and
Mike Steel Comparing strategies to preserve
evolutionary diversity . . . . . . . . . 107--116
Olaf Till and
Tobias Siebert and
Reinhard Blickhan A mechanism accounting for independence
on starting length of tension increase
in ramp stretches of active skeletal
muscle at short half-sarcomere lengths 117--123
G. S. Stamatakos and
E. A. Kolokotroni and
D. D. Dionysiou and
E. Ch. Georgiadi and
C. Desmedt An advanced discrete state-discrete
event multiscale simulation model of the
response of a solid tumor to
chemotherapy: Mimicking a clinical study 124--139
Aiman Alam-Nazki and
J. Krishnan A mathematical modelling framework for
understanding chemorepulsive signal
transduction in \bionameDictyostelium 140--153
Byul Nim Kim and
Luis F. Gordillo and
Yongkuk Kim A model for the transmission dynamics of
\bionameOrientia tsutsugamushi among its
natural reservoirs . . . . . . . . . . . 154--161
Justin N. Marleau and
Frédéric Guichard and
François Mallard and
Michel Loreau Nutrient flows between ecosystems can
destabilize simple food chains . . . . . 162--174
Helen Greenwood Hansma Possible origin of life between mica
sheets . . . . . . . . . . . . . . . . . 175--188
Rafael Muñoz-Tamayo and
Béatrice Laroche and
Éric Walter and
Joël Doré and
Marion Leclerc Mathematical modelling of carbohydrate
degradation by human colonic microbiota 189--201
Eyal Nitzany and
Ilan Hammel and
Isaac Meilijson Quantal basis of vesicle growth and
information content, a unified approach 202--209
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--210 (7 September 2010) . . . . ??
Ludek Berec and
Jan Eisner and
Vlastimil K\vrivan Adaptive foraging does not always lead
to more complex food webs . . . . . . . 211--218
T. Preece and
Y. Mao The evolution of gynodioecy on a lattice 219--225
Priyadarshi Majumdar and
Sudipto Roy A theoretical interpretation of
length-biomass allometry of
predominantly bidimensional seaweeds . . 226--230
Jie Yang and
Jia-Huang Li and
Jin Wang and
Chen-Yu Zhang Molecular modeling of BAD complex
resided in a mitochondrion integrating
glycolysis and apoptosis . . . . . . . . 231--241
Lin Hua and
Dong-guo Li and
Hui Lin and
Lin Li and
Xia Li and
Zhi-cheng Liu The correlation of gene expression and
co-regulated gene patterns in
characteristic KEGG pathways . . . . . . 242--249
Abdelouahed Tounsi and
Houari Heireche and
Hachemi Benhassaini and
Miloud Missouri Vibration and length-dependent flexural
rigidity of protein microtubules using
higher order shear deformation theory 250--255
Doanh Nguyen Ngoc and
Rafael Bravo de la Parra and
Miguel A. Zavala and
Pierre Auger Competition and species coexistence in a
metapopulation model: Can fast
asymmetric migration reverse the outcome
of competition in a homogeneous
environment? . . . . . . . . . . . . . . 256--263
J. R. Artalejo and
M. J. Lopez-Herrero Quasi-stationary and ratio of
expectations distributions: a
comparative study . . . . . . . . . . . 264--274
Mohammad Reza Rahbar and
Iraj Rasooli and
Seyed Latif Mousavi Gargari and
Jafar Amani and
Yaser Fattahian In silico analysis of antibody
triggering biofilm associated protein in
\bionameAcinetobacter baumannii . . . . 275--290
Yanrong Ren and
Xiaolin Chen and
Xiaobo Li and
Han Lai and
Qiang Wang and
Peng Zhou and
Guoping Chen Quantitative prediction of the thermal
motion and intrinsic disorder of protein
cofactors in crystalline state: a case
study on halide anions . . . . . . . . . 291--298
Kyeongah Nah and
Yongkuk Kim and
Jung Min Lee The dilution effect of the domestic
animal population on the transmission of
\bionameP. vivax malaria . . . . . . . . 299--306
Irina Baltcheva and
Laura Codarri and
Giuseppe Pantaleo and
Jean-Yves Le Boudec Lifelong dynamics of human CD4 + CD25 +
regulatory T cells: Insights from in
vivo data and mathematical modeling . . 307--322
Atsushi Mochizuki and
Daisuke Saito Analyzing steady states of dynamics of
bio-molecules from the structure of
regulatory networks . . . . . . . . . . 323--335
Amke Caliebe and
Arne Jochens and
Michael Krawczak and
Uwe Rösler A Markov chain description of the
stepwise mutation model: Local and
global behaviour of the allele process 336--342
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 211--342 (21 September 2010) . . . ??
Vijayanarasimha H. Pakka and
Adam Prügel-Bennett and
Srinandan Dasmahapatra Correlated fluctuations carry signatures
of gene regulatory network dynamics . . 343--357
Feng Fu and
Martin A. Nowak and
Christoph Hauert Invasion and expansion of cooperators in
lattice populations: Prisoner's dilemma
vs. snowdrift games . . . . . . . . . . 358--366
Satoki Sakai With whom is the gene in conflict in
offspring production?: Synthesis of the
theories of intragenomic and
parent-offspring conflict . . . . . . . 367--373
Xu-Qing Li and
Ping Fan A duplex DNA model with regular
inter-base-pair hydrogen bonds . . . . . 374--379
Joanna Jedrzejewska-Szmek and
JarosLaw Zygierewicz Depressing synapse as a detector of
frequency change . . . . . . . . . . . . 380--390
Michaelangelo Tabone and
Bard Ermentrout and
Brent Doiron Balancing organization and flexibility
in foraging dynamics . . . . . . . . . . 391--400
Aristotelis Kittas Evolution of the rate of biological
aging using a phenotype based
computational model . . . . . . . . . . 401--407
Stephen A. Gaeta and
Trine Krogh-Madsen and
David J. Christini Feedback-control induced pattern
formation in cardiac myocytes: a
mathematical modeling study . . . . . . 408--418
Elise Filotas and
Martin Grant and
Lael Parrott and
Per Arne Rikvold Positive interactions and the emergence
of community structure in
metacommunities . . . . . . . . . . . . 419--429
Miguel A. Rodríguez-Gironés and
Guadalupe Corcobado and
Jordi Moya-Laraño Silk elasticity as a potential
constraint on spider body size . . . . . 430--435
Dominik M. Wittmann and
Carsten Marr and
Fabian J. Theis Biologically meaningful update rules
increase the critical connectivity of
generalized Kauffman networks . . . . . 436--448
K. E. Atkins and
J. M. J. Travis Local adaptation and the evolution of
species' ranges under climate change . . 449--457
Céline Hauzy and
Mathias Gauduchon and
Florence D. Hulot and
Michel Loreau Density-dependent dispersal and relative
dispersal affect the stability of
predator--prey metacommunities . . . . . 458--469
Peder A. Tyvand and
Steinar Thorvaldsen Wright--Fisher model of social insects
with haploid males and diploid females 470--478
Ivan Couée and
Françoise Bringel Expanding importance of mRNA expression
in understanding stress and stress
responses . . . . . . . . . . . . . . . 479--482
Jiang Zhang and
Liangpeng Guo Corrigendum to ``Scaling behaviors of
weighted food webs as energy
transportation networks'' [J. Theor.
Biol. \bf 264 (2010) 760--770] . . . . . 483--483
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 343--484 (7 October 2010) . . . . ??
Tuyen Quang Le and
Doyoung Byun and
Saputra and
Jin Hwan Ko and
Hoon Choel Park and
Minjun Kim Numerical investigation of the
aerodynamic characteristics of a
hovering Coleopteran insect . . . . . . 485--495
Mrinmay Kumar Mallik A hypothesis and theoretical model
speculating the possible role of therapy
mediated neoplastic cell loss in
promoting the process of glioblastoma
relapse . . . . . . . . . . . . . . . . 496--503
Justin T. Mark and
Brian B. Marion and
Donald D. Hoffman Natural selection and veridical
perceptions . . . . . . . . . . . . . . 504--515
Alireza S. Sarvestani Compliance of bio-adhesive substrates
controls the kinetics of
membrane-substrate association . . . . . 516--521
Tadeusz P\latkowski Cooperation in two-person evolutionary
games with complex personality profiles 522--528
Michael Doebeli and
Iaroslav Ispolatov Continuously stable strategies as
evolutionary branching points . . . . . 529--535
Ed Reznik and
Daniel Segr\`e On the stability of metabolic cycles . . 536--549
Farida N. Enikeeva and
Konstantin V. Severinov and
Mikhail S. Gelfand Restriction-modification systems and
bacteriophage invasion: Who wins? . . . 550--559
Majid Masso and
Iosif I. Vaisman Knowledge-based computational
mutagenesis for predicting the disease
potential of human non-synonymous single
nucleotide polymorphisms . . . . . . . . 560--568
Massimo Di Giulio Biological evidence against the
panspermia theory . . . . . . . . . . . 569--572
P. Nouvellet and
J. P. Bacon and
D. Waxman Testing the level of ant activity
associated with quorum sensing: An
empirical approach leading to the
establishment and test of a null-model 573--583
Christopher C. Strelioff and
Richard E. Lenski and
Charles Ofria Evolutionary dynamics, epistatic
interactions, and biological information 584--594
Akiko Satake Diversity of plant life cycles is
generated by dynamic epigenetic
regulation in response to vernalization 595--605
Martin Hinsch and
Jan Komdeur Defence, intrusion and the evolutionary
stability of territoriality . . . . . . 606--613
Antonio Z. Politi and
Graham M. Donovan and
Merryn H. Tawhai and
Michael J. Sanderson and
Anne-Marie Lauzon and
Jason H. T. Bates and
James Sneyd A multiscale, spatially distributed
model of asthmatic airway
hyper-responsiveness . . . . . . . . . . 614--624
Laurence Palk and
James Sneyd and
Trevor J. Shuttleworth and
David I. Yule and
Edmund J. Crampin A dynamic model of saliva secretion . . 625--640
Assieh Saadatpour and
István Albert and
Réka Albert Attractor analysis of asynchronous
Boolean models of signal transduction
networks . . . . . . . . . . . . . . . . 641--656
Sanjeeva Balasuriya Invasions with density-dependent
ecological parameters . . . . . . . . . 657--666
Dorota Bieli\'nska-Wa\cz and
Shankar Subramaniam Classification studies based on a
spectral representation of DNA . . . . . 667--674
David M. Ramsey A large population parental care game:
Polymorphisms and feedback between
patterns of care and the operational sex
ratio . . . . . . . . . . . . . . . . . 675--690
David-Elie Levy and
Avraham Seifert Parameter study of simplified dragonfly
airfoil geometry at Reynolds number of
6000 . . . . . . . . . . . . . . . . . . 691--702
Jie Feng and
Yong Hu and
Ping Wan and
Aibing Zhang and
Weizhong Zhao New method for comparing DNA primary
sequences based on a discrimination
measure . . . . . . . . . . . . . . . . 703--707
Matthew D. Johnston and
Philip K. Maini and
S. Jonathan Chapman and
Carina M. Edwards and
Walter F. Bodmer On the proportion of cancer stem cells
in a tumour . . . . . . . . . . . . . . 708--711
Taichiro Kobayashi and
Kenshi Terajima and
Motohiro Nozumi and
Michihiro Igarashi and
Kouhei Akazawa A stochastic model of neuronal growth
cone guidance regulated by multiple
sensors . . . . . . . . . . . . . . . . 712--722
Jordan Ang and
Sangram Bagh and
Brian P. Ingalls and
David R. McMillen Considerations for using integral
feedback control to construct a
perfectly adapting synthetic gene
network . . . . . . . . . . . . . . . . 723--738
Peter Nonacs Bordered tug-of-war models are neither
general nor predictive of reproductive
skew . . . . . . . . . . . . . . . . . . 739--741
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 485--742 (21 October 2010) . . . . ??
Lezheng Yu and
Yanzhi Guo and
Yizhou Li and
Gongbing Li and
Menglong Li and
Jiesi Luo and
Wenjia Xiong and
Wenli Qin SecretP: Identifying bacterial secreted
proteins by fusing new features into
Chou's pseudo-amino acid composition . . 1--6
Zoran Nikoloski and
Patrick May and
Joachim Selbig Algebraic connectivity may explain the
evolution of gene regulatory networks 7--14
Ricky O'Brien and
Nev Fowkes and
Andrew P. Bassom Models for gibberellic acid transport
and enzyme production and transport in
the aleurone layer of barley . . . . . . 15--21
Christoph Hauert Replicator dynamics of reward and
reputation in public goods games . . . . 22--28
Zhi-Cheng Wu and
Xuan Xiao and
Kuo-Chen Chou 2D-MH: a web-server for generating
graphic representation of protein
sequences based on the physicochemical
properties of their constituent amino
acids . . . . . . . . . . . . . . . . . 29--34
Benjamin R. Morin and
Liana Medina-Rios and
Erika T. Camacho and
Carlos Castillo-Chavez Static behavioral effects on gonorrhea
transmission dynamics in a MSM
population . . . . . . . . . . . . . . . 35--40
Jianlei Zhang and
Chunyan Zhang and
Tianguang Chu Cooperation enhanced by the `survival of
the fittest' rule in prisoner's dilemma
games on complex networks . . . . . . . 41--47
Sam F. Greenbury and
Iain G. Johnston and
Matthew A. Smith and
Jonathan P. K. Doye and
Ard A. Louis The effect of scale-free topology on the
robustness and evolvability of genetic
regulatory networks . . . . . . . . . . 48--61
Philipp M. Altrock and
Arne Traulsen and
R. Guy Reeves and
Floyd A. Reed Using underdominance to bi-stably
transform local populations . . . . . . 62--75
Segismundo S. Izquierdo and
Luis R. Izquierdo and
Fernando Vega-Redondo The option to leave: Conditional
dissociation in the evolution of
cooperation . . . . . . . . . . . . . . 76--84
Andrew J. Black and
Alan J. McKane Stochastic amplification in an epidemic
model with seasonal forcing . . . . . . 85--94
D. N. Georgiou and
T. E. Karakasidis and
Juan J. Nieto and
A. Torres A study of entropy/clarity of genetic
sequences using metric spaces and fuzzy
sets . . . . . . . . . . . . . . . . . . 95--105
J. E. F. Green and
S. L. Waters and
J. P. Whiteley and
L. Edelstein-Keshet and
K. M. Shakesheff and
H. M. Byrne Non-local models for the formation of
hepatocyte-stellate cell aggregates . . 106--120
Kenta Suzuki and
Takashi Ikegami Allometry and catastrophic regime shifts
in food chains . . . . . . . . . . . . . 121--128
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--128 (7 November 2010) . . . . . ??
Wei Zhu and
Jingyu Hou and
Yi-Ping Phoebe Chen Semantic and layered protein function
prediction from PPI networks . . . . . . 129--136
Shawn A. Means and
James Sneyd Spatio-temporal calcium dynamics in
pacemaking units of the interstitial
cells of Cajal . . . . . . . . . . . . . 137--152
Yuuya Tachiki and
Yoh Iwasa and
Akiko Satake Pollinator coupling can induce
synchronized flowering in different
plant species . . . . . . . . . . . . . 153--163
J. Zahiri and
G. Mahdevar and
A. Nowzari-dalini and
H. Ahrabian and
M. Sadeghi A novel efficient dynamic programming
algorithm for haplotype block
partitioning . . . . . . . . . . . . . . 164--170
Isaac Salazar-Ciudad A two level mutation-selection model of
cultural evolution and diversity . . . . 171--185
Dorota Mackiewicz and
Marta Zawierta and
Wojciech Waga and
StanisLaw Cebrat Genome analyses and modelling the
relationships between coding density,
recombination rate and chromosome length 186--192
Ricard V. Solé and
Joan Saldaña and
Jose M. Montoya and
Douglas H. Erwin Simple model of recovery dynamics after
mass extinction . . . . . . . . . . . . 193--200
Kazuhiro Bessho and
Yoh Iwasa Optimal seasonal schedules and the
relative dominance of heteromorphic and
isomorphic life cycles in macroalgae . . 201--212
Jun Ohkubo and
Kazushi Yoshida and
Yuichi Iino and
Naoki Masuda Long-tail behavior in locomotion of
\bionameCaenorhabditis elegans . . . . . 213--222
Yohei Ito and
Kenko Uchida Formulas for intrinsic noise evaluation
in oscillatory genetic networks . . . . 223--234
Francesco Accatino and
Carlo De Michele and
Renata Vezzoli and
Davide Donzelli and
Robert J. Scholes Tree-grass co-existence in savanna:
Interactions of rain and fire . . . . . 235--242
Sunny E. Townsend and
Daniel T. Haydon and
Louise Matthews On the generality of
stability-complexity relationships in
Lotka--Volterra ecosystems . . . . . . . 243--251
Davide Giacché and
Takuji Ishikawa Hydrodynamic interaction of two unsteady
model microorganisms . . . . . . . . . . 252--263
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 129--264 (21 November 2010) . . . ??
Naoto Kato and
Koji Kotani and
Seiya Ueno and
Hiroyuki Matsuda Optimal risk management of human
alveolar echinococcosis with vermifuge 265--271
Tian Liu and
Cangzhi Jia A high-accuracy protein structural class
prediction algorithm using predicted
secondary structural information . . . . 272--275
Samit Bhattacharyya and
C. T. Bauch A game dynamic model for delayer
strategies in vaccinating behaviour for
pediatric infectious diseases . . . . . 276--282
Meng Liu and
Ke Wang Persistence and extinction of a
stochastic single-specie model under
regime switching in a polluted
environment II . . . . . . . . . . . . . 283--291
Nikolai W. F. Bode and
Daniel W. Franks and
A. Jamie Wood Making noise: Emergent stochasticity in
collective motion . . . . . . . . . . . 292--299
Clément de Loubens and
Albert Magnin and
Eric Verin and
Marion Doyennette and
Ioan Cristian Tréléa and
Isabelle Souchon A lubrication analysis of pharyngeal
peristalsis: Application to flavour
release . . . . . . . . . . . . . . . . 300--311
Xuanmin Guang and
Yanzhi Guo and
Jiamin Xiao and
Xia Wang and
Jing Sun and
Wenjia Xiong and
Menglong Li Predicting the state of cysteines based
on sequence information . . . . . . . . 312--318
Thomas J. Lee and
Michael P. Speed The effect of metapopulation dynamics on
the survival and spread of a novel,
conspicuous prey . . . . . . . . . . . . 319--329
J. Guedj and
A. U. Neumann Understanding hepatitis C viral dynamics
with direct-acting antiviral agents due
to the interplay between intracellular
replication and cellular infection
dynamics . . . . . . . . . . . . . . . . 330--340
A. Golubev Random discrete competing events vs.
dynamic bistable switches in cell
proliferation in differentiation . . . . 341--354
Wei-chung Liu and
Hsuan-Wien Chen and
Ferenc Jordán and
Wen-Hsieh Lin and
Chester Wai-Jen Liu Quantifying the interaction structure
and the topological importance of
species in food webs: a signed digraph
approach . . . . . . . . . . . . . . . . 355--362
Zhiwei Yang and
Yingkun Nie and
Gang Yang and
Yuangang Zu and
Yujie Fu and
Lijun Zhou Synergistic effects in the designs of
neuraminidase ligands: Analysis from
docking and molecular dynamics studies 363--374
Jurgis Sapijanskas and
Michel Loreau Cascading extinctions, functional
complementarity, and selection in
two-trophic-level model communities: a
trait-based mechanistic approach . . . . 375--387
José Rui Ferreira Marques and
Rute R. da Fonseca and
Brett Drury and
André Melo Conformational characterization of
disulfide bonds: a tool for protein
classification . . . . . . . . . . . . . 388--395
Tanja Stadler Sampling-through-time in birth-death
trees . . . . . . . . . . . . . . . . . 396--404
Gina D'Suze and
Carlos Sevcik Scorpion venom complexity fractal
analysis. Its relevance for comparing
venoms . . . . . . . . . . . . . . . . . 405--416
Even Tjòrve and
Kathleen M. C. Tjòrve A unified approach to the Richards-model
family for use in growth analyses: Why
we need only two model forms . . . . . . 417--425
A. Arazi and
A. U. Neumann Modeling immune complex-mediated
autoimmune inflammation . . . . . . . . 426--436
J. Potvin and
J. A. Goldbogen and
R. E. Shadwick Scaling of lunge feeding in rorqual
whales: An integrated model of
engulfment duration . . . . . . . . . . 437--453
Natasha K. Martin and
Eamonn A. Gaffney and
Robert A. Gatenby and
Philip K. Maini Leaky vessels as a potential source of
stromal acidification in tumours . . . . 454--460
Natasha K. Martin and
Eamonn A. Gaffney and
Robert A. Gatenby and
Philip K. Maini Tumour-stromal interactions in
acid-mediated invasion: a mathematical
model . . . . . . . . . . . . . . . . . 461--470
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 265--470 (7 December 2010) . . . . ??
S. A. Pedro and
J. M. Tchuenche HIV/AIDS dynamics: Impact of economic
classes with transmission from poor
clinical settings . . . . . . . . . . . 471--485
Vlastimil K\vrivan Evolutionary stability of optimal
foraging: Partial preferences in the
diet and patch models . . . . . . . . . 486--494
Xi Zhang and
Chen Guo and
Wen Zhang and
Huai Cao and
Huazhen Xie and
Kan Wang and
Ciquan Liu A folding ``framework structure'' of
\bionameTetrahymena group I intron . . . 495--501
András Szilágyi and
Géza Meszéna Coexistence in a fluctuating environment
by the effect of relative nonlinearity:
a minimal model . . . . . . . . . . . . 502--512
Cristina Stan and
Constantin P. Cristescu and
Eugen I. Scarlat Similarity analysis for DNA sequences
based on chaos game representation. Case
study: The albumin . . . . . . . . . . . 513--518
Boaz Tamir and
Avner Priel Reversibility and efficiency in coding
protein information . . . . . . . . . . 519--525
Daniel Campos and
Vicenç Méndez and
Isaac Llopis Persistent random motion: Uncovering
cell migration dynamics . . . . . . . . 526--534
Antonio J. Golubski and
Christopher A. Klausmeier Control in mutualisms: Combined
implications of partner choice and
bargaining roles . . . . . . . . . . . . 535--545
A. Ram\'ìrez and
J. Grasa and
A. Alonso and
F. Soteras and
R. Osta and
M. J. Muñoz and
B. Calvo Active response of skeletal muscle: In
vivo experimental results and model
formulation . . . . . . . . . . . . . . 546--553
Marc Barthélemy and
Claude Godr\`eche and
Jean-Marc Luck Fluctuation effects in metapopulation
models: Percolation and pandemic
threshold . . . . . . . . . . . . . . . 554--564
Alison K. McLean and
Fabio Luciani and
Mark M. Tanaka Trade-offs in resource allocation in the
intracellular life-cycle of hepatitis C
virus . . . . . . . . . . . . . . . . . 565--572
Micha\l Arbilly and
Uzi Motro and
Marcus W. Feldman and
Arnon Lotem Co-evolution of learning complexity and
social foraging strategies . . . . . . . 573--581
Rodrick Wallace Protein folding disorders: Toward a
basic biological paradigm . . . . . . . 582--594
Pascal Zongo and
Anne-France Viet and
Pierre Magal and
Catherine Beaumont A spatio-temporal model to describe the
spread of \bionameSalmonella within a
laying flock . . . . . . . . . . . . . . 595--604
Elias Zintzaras and
Mauro Santos and
Eörs Szathmáry Selfishness versus functional
cooperation in a stochastic protocell
model . . . . . . . . . . . . . . . . . 605--613
A. Cangiani and
R. Natalini A spatial model of cellular molecular
trafficking including active transport
along microtubules . . . . . . . . . . . 614--625
Julian King and
Helin Koc and
Karl Unterkofler and
Pawe\l Mochalski and
Alexander Kupferthaler and
Gerald Teschl and
Susanne Teschl and
Hartmann Hinterhuber and
Anton Amann Physiological modeling of isoprene
dynamics in exhaled breath . . . . . . . 626--637
Erika T. Camacho and
Miguel A. Colón Vélez and
Daniel J. Hernández and
Ubaldo Rodr\'ìguez Bernier and
Jon Van Laarhoven and
Stephen Wirkus A mathematical model for photoreceptor
interactions . . . . . . . . . . . . . . 638--646
Xinsheng Liu and
Wanlin Guo Persistent cooperators in nature . . . . 647--652
Benedikt Obermayer and
Erwin Frey Error thresholds for self- and
cross-specific enzymatic replication . . 653--662
Daniele Pietra and
Alice Borghini and
Maria Cristina Breschi and
Anna Maria Bianucci Enhancer and competitive allosteric
modulation model for G-protein-coupled
receptors . . . . . . . . . . . . . . . 663--675
Michael Doebeli and
Iaroslav Ispolatov A model for the evolutionary
diversification of religions . . . . . . 676--684
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 471--684 (21 December 2010) . . . ??
Denise Kirschner Fifty years of JTB: Past, present and
future: a letter from the
Editors-in-Chief . . . . . . . . . . . . iii--iv
Jie Lou and
Robert J. Smith Modelling the effects of adherence to
the HIV fusion inhibitor enfuvirtide . . 1--13
Jian Zu and
Masayasu Mimura and
Yasuhiro Takeuchi Adaptive evolution of foraging-related
traits in a predator--prey community . . 14--29
Joe Yuichiro Wakano and
Christoph Hauert Pattern formation and chaos in spatial
ecological public goodsgames . . . . . . 30--38
Julia Korell and
Carolyn V. Coulter and
Stephen B. Duffull A statistical model for red blood cell
survival . . . . . . . . . . . . . . . . 39--49
Reiichiro Ishii and
Michael J. Crawley Herbivore-induced coexistence of
competing plant species . . . . . . . . 50--61
Jan-Åke Larsson and
Niclas Wadströmer and
Ola Hermanson and
Urban Lendahl and
Robert Forchheimer Modelling cell lineage using a
meta-Boolean tree model with a relation
to gene regulatory networks . . . . . . 62--76
Gion Fessel and
Jess G. Snedeker Equivalent stiffness after
glycosaminoglycan depletion in tendon
--- an ultra-structural finite element
model and corresponding experiments . . 77--83
Yun Kang and
Dieter Armbruster Dispersal effects on a discrete
two-patch model for plant-insect
interactions . . . . . . . . . . . . . . 84--97
Yumi Tanaka and
Kei'ichiro Iguchi and
Jin Yoshimura and
Nariyuki Nakagiri and
Kei-ichi Tainaka Historical effect in the territoriality
of ayu fish . . . . . . . . . . . . . . 98--104
Luís Almeida and
Patrizia Bagnerini and
Abderrahmane Habbal and
Stéphane Noselli and
Fanny Serman A mathematical model for dorsal closure 105--119
J. Stålhand and
A. Klarbring and
G. A. Holzapfel A mechanochemical 3D continuum model for
smooth muscle contraction under finite
strains . . . . . . . . . . . . . . . . 120--130
Hao Zhu Spatiotemporally modulated Vestigial
gradient by Wingless signaling
adaptively regulates cell division for
precise wing size control . . . . . . . 131--140
Kuiying Deng and
Herbert Gintis and
Tianguang Chu Strengthening strong reciprocity . . . . 141--145
R. J. P. Williams Chemical advances in evolution by and
changes in use of space during time . . 146--159
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--160 (7 January 2011) . . . . . ??
Grzegorz A. Rempala and
MichaL Seweryn and
Leszek Ignatowicz Model for comparative analysis of
antigen receptor repertoires . . . . . . 1--15
Jarad P. Mellard and
Kohei Yoshiyama and
Elena Litchman and
Christopher A. Klausmeier The vertical distribution of
phytoplankton in stratified water
columns . . . . . . . . . . . . . . . . 16--30
D. Okuonghae and
S. E. Omosigho Analysis of a mathematical model for
tuberculosis: What could be done to
increase case detection . . . . . . . . 31--45
Tobias Galla Imitation, internal absorption and the
reversal of local drift in stochastic
evolutionary games . . . . . . . . . . . 46--56
V. R. Chechetkin and
V. V. Lobzin Stability of the genetic code and
optimal parameters of amino acids . . . 57--63
Hao Lin and
Hui Ding Predicting ion channels and their types
by the dipeptide mode of pseudo amino
acid composition . . . . . . . . . . . . 64--69
Fridolin Groß and
Gerhard Metzner and
Ulrich Behn Mathematical modeling of allergy and
specific immunotherapy: Th1-Th2-Treg
interactions . . . . . . . . . . . . . . 70--78
D. Waxman Comparison and content of the
Wright--Fisher model of random genetic
drift, the diffusion approximation, and
an intermediate model . . . . . . . . . 79--87
Jiapu Zhang Comparison studies of the structural
stability of rabbit prion protein with
human and mouse prion proteins . . . . . 88--95
Stephen Davis and
Stephen J. Bent Loop analysis for pathogens: niche
partitioning in the transmission graph
for pathogens of the North American tick
Ixodes scapularis . . . . . . . . . . . 96--103
Bo Liu and
Shiwei Yan and
Qi Wang Intrinsic noise and Hill dynamics in the
p53 system . . . . . . . . . . . . . . . 104--108
Carlos Grilo and
Luís Correia Effects of asynchronism on evolutionary
games . . . . . . . . . . . . . . . . . 109--122
Guosen Xie and
Zhongxi Mo Three 3D graphical representations of
DNA primary sequences based on the
classifications of DNA bases and their
applications . . . . . . . . . . . . . . 123--130
Flora S. Bacelar and
Andrew White and
Mike Boots Life history and mating systems select
for male biased parasitism mediated
through natural selection and ecological
feedbacks . . . . . . . . . . . . . . . 131--137
Xiuwei Zhu and
Xiaobo Zhou and
Michael T. Lewis and
Ling Xia and
Stephen Wong Cancer stem cell, niche and EGFR decide
tumor development and treatment
response: a bio-computational simulation
study . . . . . . . . . . . . . . . . . 138--149
Bart Haegeman and
Michel Loreau A mathematical synthesis of niche and
neutral theories in community ecology 150--165
Stephen Duncan and
Cameron Hepburn and
Antonis Papachristodoulou Optimal harvesting of fish stocks under
a time-varying discount rate . . . . . . 166--173
Ruoying Chen and
Zhiwang Zhang and
Di Wu and
Peng Zhang and
Xinyang Zhang and
Yong Wang and
Yong Shi Prediction of protein interaction hot
spots using rough set-based multiple
criteria linear programming . . . . . . 174--180
John Hughes and
William O. Hancock and
John Fricks A matrix computational approach to
kinesin neck linker extension . . . . . 181--194
Alfonsas Juska Minimal models of growth and decline of
microbial populations . . . . . . . . . 195--200
Marco Archetti Contract theory for the evolution of
cooperation: The right incentives
attract the right partners . . . . . . . 201--207
Pooya Zakeri and
Behzad Moshiri and
Mehdi Sadeghi Prediction of protein submitochondria
locations based on data fusion of
various features of sequences . . . . . 208--216
Yujuan Huang and
Lianping Yang and
Tianming Wang Phylogenetic analysis of DNA sequences
based on the generalized pseudo-amino
acid composition . . . . . . . . . . . . 217--223
Tomohiko Konno A condition for cooperation in a game on
complex networks . . . . . . . . . . . . 224--233
Hana M. Dobrovolny and
Ronald Gieschke and
Brian E. Davies and
Nelson L. Jumbe and
Catherine A. A. Beauchemin Neuraminidase inhibitors for treatment
of human and avian strain influenza: a
comparative modeling study . . . . . . . 234--244
Leo van Iersel and
Steven Kelk When two trees go to war . . . . . . . . 245--255
Rachata Muneepeerakul and
Sandro Azaele and
Simon A. Levin and
Andrea Rinaldo and
Ignacio Rodriguez-Iturbe Evolution of dispersal in explicitly
spatial metacommunities . . . . . . . . 256--265
Joanne Mann and
Mick Roberts Modelling the epidemiology of hepatitis
B in New Zealand . . . . . . . . . . . . 266--272
Claire M. Postlethwaite and
Michael M. Walker A geometric model for initial
orientation errors in pigeon navigation 273--279
Qingfeng Chen and
Gang Li and
Yi-Ping Phoebe Chen Interval-based distance function for
identifying RNA structure candidates . . 280--286
Hervé Seligmann Pathogenic mutations in antisense
mitochondrial tRNAs . . . . . . . . . . 287--296
Mayumi Seto and
Yoh Iwasa Regime shift and robustness of
organism-created environments: a model
for microbial ecosystems . . . . . . . . 297--306
Gert Roos and
Sam Van Wassenbergh and
Peter Aerts and
Anthony Herrel and
Dominique Adriaens Effects of snout dimensions on the
hydrodynamics of suction feeding in
juvenile and adult seahorses . . . . . . 307--317
Jun Nakabayashi and
Akira Sasaki A mathematical model of the
intracellular replication and within
host evolution of hepatitis type B
virus: Understanding the long time
course of chronic hepatitis . . . . . . 318--329
José A. Capitán and
José A. Cuesta Species assembly in model ecosystems, I:
Analysis of the population model and the
invasion dynamics . . . . . . . . . . . 330--343
José A. Capitán and
José A. Cuesta and
Jordi Bascompte Species assembly in model ecosystems,
II: Results of the assembly process . . 344--355
T. O. Richardson and
E. J. H. Robinson and
K. Christensen and
J. H. Jensen and
K. Christensen and
H. J. Jensen and
N. R. Franks and
A. B. Sendova-Franks Comment on P. Nouvellet, J. P. Bacon, D.
Waxman, ``Testing the level of ant
activity associated with quorum sensing:
An empirical approach leading to the
establishment and test of a null-model'' 356--358
Lewis Wolpert Positional information and patterning
revisited . . . . . . . . . . . . . . . 359--365
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--366 (21 January 2011) . . . . . ??
G. W. Horgan The behaviour of a neutral model of
weight regulated only by body mass . . . 1--6
Philip Newey Not one odour but two: a new model for
nestmate recognition . . . . . . . . . . 7--12
Petri P. Kärenlampi Age distribution of trees in stationary
forest system . . . . . . . . . . . . . 13--18
Laura Fumanelli and
Mimmo Iannelli and
Hussnain Ahmed Janjua and
Olivier Jousson Mathematical modeling of bacterial
virulence and host-pathogen interactions
in the \bionameDictyostelium/Pseudomonas
system . . . . . . . . . . . . . . . . . 19--24
S. Hu and
T. Biben and
X. Wang and
P. Jurdic and
J.-C. Géminard Internal dynamics of actin structures
involved in the cell motility and
adhesion: Modeling of the podosomes at
the molecular level . . . . . . . . . . 25--30
Alexandra Pokhilko and
Jason A. Ramos and
Hans Holtan and
Don R. Maszle and
Rajnish Khanna and
Andrew J. Millar Ubiquitin ligase switch in plant
photomorphogenesis: a hypothesis . . . . 31--41
Nina Alphey and
Michael B. Bonsall and
Luke Alphey Modeling resistance to genetic control
of insects . . . . . . . . . . . . . . . 42--55
Krishna Kumar Kandaswamy and
Kuo-Chen Chou and
Thomas Martinetz and
Steffen Möller and
P. N. Suganthan and
S. Sridharan and
Ganesan Pugalenthi AFP-Pred: a random forest approach for
predicting antifreeze proteins from
sequence-derived properties . . . . . . 56--62
Yong Min and
Xiaogang Jin and
Ming Chen and
Zhengzheng Pan and
Ying Ge and
Jie Chang Pathway knockout and redundancy in
metabolic networks . . . . . . . . . . . 63--69
Jonas Bühler and
Gregor Huber and
Friederike Schmid and
Peter Blümler Analytical model for long-distance
tracer-transport in plants . . . . . . . 70--79
Sarah Cobey and
Mercedes Pascual Consequences of host heterogeneity,
epitope immunodominance, and immune
breadth for strain competition . . . . . 80--87
Poonsap Na Nakorn and
Witcha Treesuwan and
Kiattawee Choowongkomon and
Supa Hannongbua and
Nonlawat Boonyalai In vitro and in silico binding study of
the peptide derived from HIV-1 CA-CTD
and LysRS as a potential HIV-1 blocking
site . . . . . . . . . . . . . . . . . . 88--97
Na Gao and
Hikaru Aono and
Hao Liu Perturbation analysis of 6DoF flight
dynamics and passive dynamic stability
of hovering fruit fly \bionameDrosophila
melanogaster . . . . . . . . . . . . . . 98--111
E. E. van Loon and
J. Shamoun-Baranes and
W. Bouten and
S. L. Davis Understanding soaring bird migration
through interactions and decisions at
the individual level . . . . . . . . . . 112--126
Atsushi Yamauchi and
Yutaka Kobayashi Joint evolution of sex ratio and
reproductive group size under local mate
competition with inbreeding depression 127--133
Giulia Menconi and
Aldamaria Puliti and
Isabella Sbrana and
Valerio Conti and
Roberto Marangoni A top-down linguistic approach to the
analysis of genomic sequences: The
metabotropic glutamate receptors 1 and 5
in human and in mouse as a case study 134--142
Jinzhi Lei and
Michael C. Mackey Multistability in an age-structured
model of hematopoiesis: Cyclical
neutropenia . . . . . . . . . . . . . . 143--153
Carel Pretorius and
Peter Dodd and
Robin Wood An investigation into the statistical
properties of TB episodes in a South
African community with high HIV
prevalence . . . . . . . . . . . . . . . 154--163
Marco Arieli Herrera-Valdez and
Joceline Lega Reduced models for the pacemaker
dynamics of cardiac cells . . . . . . . 164--176
Gilles Didier and
Elisabeth Remy and
Claudine Chaouiya Mapping multivalued onto Boolean
dynamics . . . . . . . . . . . . . . . . 177--184
James A. R. Marshall Queller's rule ok: Comment on van Veelen
`When inclusive fitness is right and
when it can be wrong' . . . . . . . . . 185--188
Matthijs van Veelen A rule is not a rule if it changes from
case to case (a reply to Marshall's
comment) . . . . . . . . . . . . . . . . 189--195
Tuyen Quang Le and
Doyoung Byun and
Saputra and
Jin Hwan Ko and
Hoon Choel Park and
Minjun Kim Corrigendum to ``Numerical investigation
of the aerodynamic characteristics of a
hovering Coleopteran insect'' [J. Theor.
Biol. \bf 266 (2010) 485--495] . . . . . 196--196
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--196 (7 February 2011) . . . . . ??
Paul E. Parham and
Edwin Michael Outbreak properties of epidemic models:
The roles of temporal forcing and
stochasticity on pathogen invasion
dynamics . . . . . . . . . . . . . . . . 1--9
Maqsood Hayat and
Asifullah Khan Predicting membrane protein types by
fusing composite protein sequence
features into pseudo amino acid
composition . . . . . . . . . . . . . . 10--17
Bozidarka L. Zari\'c and
Vesna B. Jovanovi\'c and
Srdan D. Stojanovi\'c Non-covalent interactions across subunit
interfaces in Sm proteins . . . . . . . 18--26
Eric N. Powell and
John M. Klinck and
Eileen E. Hofmann Generation time and the stability of
sex-determining alleles in oyster
populations as deduced using a
gene-based population dynamics model . . 27--43
Guisong Chang and
Tianming Wang Genome analysis with the conditional
multinomial distribution profile . . . . 44--50
G. Malherbe and
David Holcman Stochastic modeling of gene activation
and applications to cell regulation . . 51--63
James R. Edwards and
Mary R. Myerscough Intelligent decisions from the hive
mind: Foragers and nectar receivers of
\bionameApis mellifera collaborate to
optimise active forager numbers . . . . 64--77
Zoran Konkoli Multiparticle reaction noise
characteristics . . . . . . . . . . . . 78--86
Samuel Soubeyrand and
Lionel Roques and
Jérôme Coville and
Julien Fayard Patchy patterns due to group dispersal 87--99
Anna Fedor and
Péter Ittzés and
Eörs Szathmáry Parsing recursive sentences with a
connectionist model including a neural
stack and synaptic gating . . . . . . . 100--105
Alexander E. Zook and
Anna Eklof and
Ute Jacob and
Stefano Allesina Food webs: Ordering species according to
body size yields high degree of
intervality . . . . . . . . . . . . . . 106--113
Christopher C. Howells and
William T. Baumann and
David C. Samuels and
Carla V. Finkielstein The Bcl-$2$-associated death promoter
(BAD) lowers the threshold at which the
Bcl-$2$-interacting domain death agonist
(BID) triggers mitochondria
disintegration . . . . . . . . . . . . . 114--123
Takuya Sekiguchi and
Mayuko Nakamaru How inconsistency between attitude and
behavior persists through cultural
transmission . . . . . . . . . . . . . . 124--135
Miguel M. de Sousa and
Cristian R. Munteanu and
Alejandro Pazos and
Nuno A. Fonseca and
Rui Camacho and
A. L. Magalhães Amino acid pair- and triplet-wise
groupings in the interior of $ \alpha
$-helical segments in proteins . . . . . 136--144
Navid Safaeian and
Mathieu Sellier and
Tim David A computational model of hemodynamic
parameters in cortical capillary
networks . . . . . . . . . . . . . . . . 145--156
A. Milgram The stability of the Boubaker
polynomials expansion scheme
(BPES)-based solution to Lotka--Volterra
problem . . . . . . . . . . . . . . . . 157--158
Ryosuke Omori and
Ben Adams Disrupting seasonality to control
disease outbreaks: The case of koi
herpes virus . . . . . . . . . . . . . . 159--165
Lorenzo Isella and
Juliette Stehlé and
Alain Barrat and
Ciro Cattuto and
Jean-François Pinton and
Wouter Van den Broeck What's in a crowd? Analysis of
face-to-face behavioral networks . . . . 166--180
L. Bourouiba and
A. Teslya and
J. Wu Highly pathogenic avian influenza
outbreak mitigated by seasonal low
pathogenic strains: Insights from
dynamic modeling . . . . . . . . . . . . 181--201
Sandip Ghosal and
Yoshio Fukui Does buckling instability of the
pseudopodium limit how well an amoeba
can climb? . . . . . . . . . . . . . . . 202--204
Zhiyuan Li and
Ming Ni and
Jikun Li and
Yuping Zhang and
Qi Ouyang and
Chao Tang Decision making of the p53 network:
Death by integration . . . . . . . . . . 205--211
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--212 (21 February 2011) . . . . ??
Thomas House and
Matt J. Keeling Epidemic prediction and control in
clustered populations . . . . . . . . . 1--7
Lang Cao and
Hisashi Ohtsuki and
Bing Wang and
Kazuyuki Aihara Evolution of cooperation on adaptively
weighted networks . . . . . . . . . . . 8--15
Bing-Shuo Chen and
Sheng-Nan Wu Functional role of the activity of
ATP-sensitive potassium channels in
electrical behavior of hippocampal
neurons: Experimental and theoretical
studies . . . . . . . . . . . . . . . . 16--25
Zhao-Hui Qi and
Ruo-Yan Wei A combination dimensionality reduction
approach to codon position patterns of
eubacteria based on their complete
genomes . . . . . . . . . . . . . . . . 26--34
Rubén J. Requejo and
Juan Camacho Evolution of cooperation mediated by
limiting resources: Connecting resource
based models and evolutionary game
theory . . . . . . . . . . . . . . . . . 35--41
Amitabha Bose and
Victoria Booth Co-existent activity patterns in
inhibitory neuronal networks with
short-term synaptic depression . . . . . 42--54
Pasquale Laise and
Francesca Di Patti and
Duccio Fanelli and
Marika Masselli and
Annarosa Arcangeli Deterministic and stochastic aspects of
VEGF-A production and the cooperative
behavior of tumoral cell colony . . . . 55--63
W. C. H. Parr and
A. Ruto and
C. Soligo and
H. J. Chatterjee Allometric shape vector projection: a
new method for the identification of
allometric shape characters and
trajectories applied to the human
astragalus (talus) . . . . . . . . . . . 64--71
Martin Kroon Influence of dispersion in myosin
filament orientation and anisotropic
filament contractions in smooth muscle 72--82
Leonid B. Katsnelson and
Tatiana Sulman and
Olga Solovyova and
Vladimir S. Markhasin Role of myocardial viscoelasticity in
disturbances of electrical and
mechanical activity in calcium
overloaded cardiomyocytes: Mathematical
modeling . . . . . . . . . . . . . . . . 83--95
Chetan D. Pahlajani and
Paul J. Atzberger and
Mustafa Khammash Stochastic reduction method for
biological chemical kinetics using
time-scale separation . . . . . . . . . 96--112
Martin Hartvig and
Ken H. Andersen and
Jan E. Beyer Food web framework for size-structured
populations . . . . . . . . . . . . . . 113--122
Hiroshi Nishiura and
Hisashi Inaba Estimation of the incubation period of
influenza A (H1N1-2009) among imported
cases: Addressing censoring using
outbreak data at the origin of
importation . . . . . . . . . . . . . . 123--130
Mehmet A. Orman and
Francois Berthiaume and
Ioannis P. Androulakis and
Marianthi G. Ierapetritou Pathway analysis of liver metabolism
under stressed condition . . . . . . . . 131--140
Frank J. Poelwijk and
Sorin Tanase-Nicola and
Daniel J. Kiviet and
Sander J. Tans Reciprocal sign epistasis is a necessary
condition for multi-peaked fitness
landscapes . . . . . . . . . . . . . . . 141--144
Kelly E. Murphy and
Cameron L. Hall and
Scott W. McCue and
D. L. Sean McElwain A two-compartment mechanochemical model
of the roles of transforming growth
factor $ \beta $ and tissue tension in
dermal wound healing . . . . . . . . . . 145--159
Sergio M. Vallina and
Corinne Le Quéré Stability of complex food webs:
Resilience, resistance and the average
interaction strength . . . . . . . . . . 160--173
Kazuhiro Maeda and
Hiroyuki Kurata Quasi-multiparameter sensitivity measure
for robustness analysis of complex
biochemical networks . . . . . . . . . . 174--186
Yukio-Pegio Gunji and
Tomohiro Shirakawa and
Takayuki Niizato and
Masaki Yamachiyo and
Iori Tani An adaptive and robust biological
network based on the vacant-particle
transportation model . . . . . . . . . . 187--200
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--200 (7 March 2011) . . . . . . ??
Andrew E. Noble and
Nico M. Temme and
William F. Fagan and
Timothy H. Keitt A sampling theory for asymmetric
communities . . . . . . . . . . . . . . 1--14
Marc Sturrock and
Alan J. Terry and
Dimitris P. Xirodimas and
Alastair M. Thompson and
Mark A. J. Chaplain Spatio-temporal modelling of the Hes1
and p53-Mdm2 intracellular signalling
pathways . . . . . . . . . . . . . . . . 15--31
Junfeng Tang and
Shurong Zhou The importance of niche differentiation
for coexistence on large scales . . . . 32--36
Julie C. Blackwood and
Alan Hastings The effect of time delays on Caribbean
coral-algal interactions . . . . . . . . 37--43
M. Puckeridge and
B. D. Fulcher and
A. J. K. Phillips and
P. A. Robinson Incorporation of caffeine into a
quantitative model of fatigue and sleep 44--54
Yixian Song and
Stefan Scheu and
Barbara Drossel Geographic parthenogenesis in a
consumer-resource model for sexual
reproduction . . . . . . . . . . . . . . 55--62
Alberto d'Onofrio and
Piero Manfredi and
Piero Poletti The impact of vaccine side effects on
the natural history of immunization
programmes: An imitation-game approach 63--71
Kouroush Sadegh Zadeh An integro-partial differential equation
for modeling biofluids flow in fractured
biomaterials . . . . . . . . . . . . . . 72--79
J. Krishnan and
Aiman Alam-Nazki An investigation of design principles
underlying repulsive and attractive
gradient sensing and their switching . . 80--99
Livingstone Morford A theoretical application of selectable
markers in bacterial episomes for a DNA
cryptosystem . . . . . . . . . . . . . . 100--102
Hedia Fgaier and
Hermann J. Eberl Antagonistic control of microbial
pathogens under iron limitations by
siderophore producing bacteria in a
chemostat setup . . . . . . . . . . . . 103--114
Catherine Coutand and
Jean-Denis Mathias and
Georges Jeronimidis and
Jean-François Destrebecq TWIG: a model to simulate the
gravitropic response of a tree axis in
the frame of elasticity and
viscoelasticity, at intra-annual time
scale . . . . . . . . . . . . . . . . . 115--129
Soyoka Muko and
Yoh Iwasa Optimal choice of species and size class
for transplanting coral community . . . 130--137
Efrat Sheffer and
Hezi Yizhaq and
Moshe Shachak and
Ehud Meron Mechanisms of vegetation-ring formation
in water-limited systems . . . . . . . . 138--146
Joshua L. Payne and
Rupert Mazzucco and
Ulf Dieckmann The evolution of conditional dispersal
and reproductive isolation along
environmental gradients . . . . . . . . 147--155
Cédric Sueur and
Jean-Louis Deneubourg and
Odile Petit and
Iain D. Couzin Group size, grooming and fission in
primates: a modeling approach based on
group structure . . . . . . . . . . . . 156--166
Guillermin Agüero-Chapin and
Gustavo A. de la Riva and
Reinaldo Molina-Ruiz and
Aminael Sánchez-Rodr\'ìguez and
Gisselle Pérez-Machado and
V\'ìtor Vasconcelos and
Agostinho Antunes Non-linear models based on simple
topological indices to identify RNase
III protein members . . . . . . . . . . 167--178
Shuhei Ikemoto and
Fabio DallaLibera and
Hiroshi Ishiguro Stochastic resonance emergence from a
minimalistic behavioral rule . . . . . . 179--187
Subhasis Banerjee and
Indrani Bose Transient pulse formation in jasmonate
signaling pathway . . . . . . . . . . . 188--196
Jorge Peña and
Enea Pestelacci and
André Berchtold and
Marco Tomassini Participation costs can suppress the
evolution of upstream reciprocity . . . 197--206
Laura De Vargas Roditi and
Franziska Michor Evolutionary dynamics of BRCA1
alterations in breast tumorigenesis . . 207--215
Andrew M. Oster and
Balbir Thomas and
David Terman and
Christopher P. Fall The low conductance mitochondrial
permeability transition pore confers
excitability and CICR wave propagation
in a computational model . . . . . . . . 216--231
Adi Livnat and
Christos Papadimitriou and
Marcus W. Feldman An analytical contrast between fitness
maximization and selection for
mixability . . . . . . . . . . . . . . . 232--234
C. J. Evans and
R. M. Phillips and
P. F. Jones and
P. M. Loadman and
B. D. Sleeman and
C. J. Twelves and
S. W. Smye Corrigendum to ``A mathematical model of
doxorubicin penetration through
multicellular layers'' [J. Theor. Biol.
\bf 257 (2009) 598--608] . . . . . . . . 235--235
Kuo-Chen Chou Some remarks on protein attribute
prediction and pseudo amino acid
composition . . . . . . . . . . . . . . 236--247
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--248 (21 March 2011) . . . . . . ??
K. J. Palmer and
M. S. Ridout and
B. J. T. Morgan Kinetic models of guanidine
hydrochloride-induced curing of the
yeast [ PSI + ] prion . . . . . . . . . 1--11
Daniela Calvetti and
Erkki Somersalo Dynamic activation model for a
glutamatergic neurovascular unit . . . . 12--29
Francisco C. Santos and
Jorge M. Pacheco and
Brian Skyrms Co-evolution of pre-play signaling and
cooperation . . . . . . . . . . . . . . 30--35
Romain Rieger and
Ridha Hambli and
Rachid Jennane Modeling of biological doses and
mechanical effects on bone transduction 36--42
Lionel Roques and
Samuel Soubeyrand and
Jérôme Rousselet A statistical-reaction-diffusion
approach for analyzing expansion
processes . . . . . . . . . . . . . . . 43--51
Peng Wang and
William L. Olbricht Fluid mechanics in the perivascular
space . . . . . . . . . . . . . . . . . 52--57
Natasha K. Martin and
Peter Vickerman and
Matthew Hickman Mathematical modelling of hepatitis C
treatment for injecting drug users . . . 58--66
Vlastimil K\vrivan On the Gause predator--prey model with a
refuge: a fresh look at the history . . 67--73
Michelle E. Lander and
Miles L. Logsdon and
Thomas R. Loughlin and
Glenn R. Van Blaricom Spatial patterns and scaling behaviors
of Steller sea lion (\bionameEumetopias
jubatus) distributions and their
environment . . . . . . . . . . . . . . 74--83
Michael C. Mackey and
Marta Tyran-Kami\'nska and
Romain Yvinec Molecular distributions in gene
regulatory dynamics . . . . . . . . . . 84--96
J. W. Schofield and
E. A. Gaffney and
R. A. Gatenby and
P. K. Maini Tumour angiogenesis: The gap between
theory and experiments . . . . . . . . . 97--102
James E. Lyon and
Sagar A. Pandit and
Carel P. van Schaik and
Gauri R. Pradhan Mating strategies in primates: a game
theoretical approach to infanticide . . 103--108
John Kang and
Robert L. Steward and
YongTae Kim and
Russell S. Schwartz and
Philip R. LeDuc and
Kathleen M. Puskar Response of an actin filament network
model under cyclic stretching through a
coarse grained Monte Carlo approach . . 109--119
W. A. Comisar and
D. J. Mooney and
J. J. Linderman Integrin organization: Linking adhesion
ligand nanopatterns with altered cell
responses . . . . . . . . . . . . . . . 120--130
D. Waxman A compact result for the time-dependent
probability of fixation at a neutral
locus . . . . . . . . . . . . . . . . . 131--135
Yu-Yun Chen and
Sze-Bi Hsu Synchronized reproduction promotes
species coexistence through reproductive
facilitation . . . . . . . . . . . . . . 136--144
Andrew T. Fenley and
Suman K. Banik and
Rahul V. Kulkarni Computational modeling of differences in
the quorum sensing induced luminescence
phenotypes of \bionameVibrio harveyi and
\bionameVibrio cholerae . . . . . . . . 145--153
Christopher Pagnutti and
Madhur Anand and
Mohamed Azzouz Estimating gap lifetime and memory from
a simple model of forest canopy dynamics 154--160
Sergio Castellano and
Paolo Cermelli Sampling and assessment accuracy in mate
choice: a random-walk model of
information processing in mating
decision . . . . . . . . . . . . . . . . 161--169
Richard A. Boyle and
Timothy M. Lenton and
Andrew J. Watson Symbiotic physiology promotes
homeostasis in Daisyworld . . . . . . . 170--182
William H. James Further support for a hypothesis on the
reported offspring sex ratios of
hepatitis B carriers . . . . . . . . . . 183--184
Yara-Elena Sánchez-Corrales and
Elena R. Álvarez-Buylla and
Luis Mendoza Corrigendum to ``The \bionameArabidopsis
thaliana flower organ specification gene
regulatory network determines a robust
differentiation process'' [J. Theor.
Biol. \bf 264 (2010) 971--983] . . . . . 185--185
María Luz Cárdenas and
Juan-Carlos Letelier and
Claudio Gutierrez and
Athel Cornish-Bowden and
Jorge Soto-Andrade Corrigendum to ``Closure to efficient
causation, computability and artificial
life'' [J. Theor. Biol. \bf 263 (2010)
79--92] . . . . . . . . . . . . . . . . 186--186
Mike Mesterton-Gibbons and
Sergey Gavrilets and
Janko Gravner and
Erol Akçay Models of coalition or alliance
formation . . . . . . . . . . . . . . . 187--204
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--204 (7 April 2011) . . . . . . ??
Emily Hackett-Jones and
Andrew White and
Christina A. Cobbold The evolution of developmental timing in
natural enemy systems . . . . . . . . . 1--11
Marieke Jesse and
Hans Heesterbeek Divide and conquer? Persistence of
infectious agents in spatial
metapopulations of hosts . . . . . . . . 12--20
D. L. Gonzalez and
S. Giannerini and
R. Rosa Circular codes revisited: a statistical
approach . . . . . . . . . . . . . . . . 21--28
Chrisantha Fernando Symbol manipulation and rule learning in
spiking neuronal networks . . . . . . . 29--41
G. Alsmeyer and
C. Gutiérrez and
R. Martínez Limiting genotype frequencies of
Y-linked genes through bisexual
branching processes with blind choice 42--51
Vera Afreixo and
Carlos A. C. Bastos and
Armando J. Pinho and
Sara P. Garcia and
Paulo J. S. G. Ferreira Genome analysis with distance to the
nearest dissimilar nucleotide . . . . . 52--58
Peter S. Kim and
Peter P. Lee T cell state transition produces an
emergent change detector . . . . . . . . 59--69
Michael Kücken and
Baruch Rinkevich and
Lee Shaish and
Andreas Deutsch Nutritional resources as positional
information for morphogenesis in the
stony coral \bionameStylophora
pistillata . . . . . . . . . . . . . . . 70--77
Tuomas Nurmi and
Kalle Parvinen Joint evolution of specialization and
dispersal in structured metapopulations 78--92
Michael Assaf and
Mauro Mobilia Fixation of a deleterious allele under
mutation pressure and finite selection
intensity . . . . . . . . . . . . . . . 93--103
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--104 (21 April 2011) . . . . . . ??
Etienne Sirot and
Olivier Pays On the dynamics of predation risk
perception for a vigilant forager . . . 1--7
D. A. Smith The interaction energy of charged
filaments in an electrolyte: Results for
all filament spacings . . . . . . . . . 8--15
Christian Guill and
Barbara Drossel and
Wolfram Just and
Eddy Carmack A three-species model explaining cyclic
dominance of Pacific salmon . . . . . . 16--21
Wen Duan and
Kiho Lee and
Allan E. Herbison and
James Sneyd A mathematical model of adult GnRH
neurons in mouse brain and its
bifurcation analysis . . . . . . . . . . 22--34
Aiping Xu and
Jan Dolfing and
Thomas P. Curtis and
Gary Montague and
Elaine Martin Maintenance affects the stability of a
two-tiered microbial `food chain'? . . . 35--41
Nikolaus Berndt and
Sabrina Hoffmann and
Jan Benda and
Hermann-Georg Holzhütter The influence of the chloride currents
on action potential firing and volume
regulation of excitable cells studied by
a kinetic model . . . . . . . . . . . . 42--49
Hui-Shen Shen Nonlinear analysis of lipid tubules by
nonlocal beam model . . . . . . . . . . 50--56
H. Diaz and
A. A. Ramirez and
A. Olarte and
C. Clavijo A model for the control of malaria using
genetically modified vectors . . . . . . 57--66
Giuseppina Albano and
Virginia Giorno and
Patricia Román-Román and
Francisco Torres-Ruiz Inferring the effect of therapy on
tumors showing stochastic Gompertzian
growth . . . . . . . . . . . . . . . . . 67--77
Matthijs van Veelen The replicator dynamics with $n$ players
and population structure . . . . . . . . 78--85
Bouchra Aylaj and
Flavie Luciani and
Veronique Delmas and
Lionel Larue and
Florian De Vuyst Melanoblast proliferation dynamics
during mouse embryonic development.
Modeling and validation . . . . . . . . 86--98
Jianxiong Huang and
Xiangcheng Mi and
Keping Ma A genome evolution-based framework for
measures of originality for clades . . . 99--105
Amber M. Smith and
Jonathan A. McCullers and
Frederick R. Adler Mathematical model of a three-stage
innate immune response to a pneumococcal
lung infection . . . . . . . . . . . . . 106--116
Sayaki U. Suzuki and
Akira Sasaki How does the resistance threshold in
spatially explicit epidemic dynamics
depend on the basic reproductive ratio
and spatial correlation of crop
genotypes? . . . . . . . . . . . . . . . 117--125
Alexander Filippov and
Valentin L. Popov and
Stanislav N. Gorb Shear induced adhesion: Contact
mechanics of biological spatula-like
attachment devices . . . . . . . . . . . 126--131
Abbas Mahdavi and
Samad Jahandideh Application of density similarities to
predict membrane protein types based on
pseudo-amino acid composition . . . . . 132--137
Josep L. Garcia-Domingo and
Joan Saldaña Extinction threshold for spatial forest
dynamics with height structure . . . . . 138--149
Brendan O'Fallon Two optimal mutation rates in obligate
pathogens subject to deleterious
mutation . . . . . . . . . . . . . . . . 150--158
Ronald A. J. van Elburg Stochastic continuous time neurite
branching models with tree and segment
dependent rates . . . . . . . . . . . . 159--173
Qi Dai and
Xiaoqing Liu and
Yuhua Yao and
Fukun Zhao Numerical characteristics of word
frequencies and their application to
dissimilarity measure for sequence
comparison . . . . . . . . . . . . . . . 174--180
A. Yu. Morozov and
M. W. Adamson Evolution of virulence driven by
predator--prey interaction: Possible
consequences for population dynamics . . 181--191
Yuta Shiino and
Osamu Kuwazuru Theoretical approach to the functional
optimisation of spiriferide brachiopod
shell: Optimum morphology of sulcus . . 192--198
Judy Day and
Avner Friedman and
Larry S. Schlesinger Modeling the host response to inhalation
anthrax . . . . . . . . . . . . . . . . 199--208
Alexandre G. de Brevern and
Agnel Praveen Joseph Species specific amino acid
sequence-protein local structure
relationships: An analysis in the light
of a structural alphabet . . . . . . . . 209--217
Margaret Watts and
Joel Tabak and
Charles Zimliki and
Arthur Sherman and
Richard Bertram Slow variable dominance and phase
resetting in phantom bursting . . . . . 218--228
Humberto González-D\'ìaz and
Francisco Prado-Prado and
Eduardo Sobarzo-Sánchez and
Mohamed Haddad and
Séverine Maurel Chevalley and
Alexis Valentin and
Joëlle Quetin-Leclercq and
Mar\'ìa A. Dea-Ayuela and
Mar\'ìa Teresa Gomez-Muños and
Cristian R. Munteanu and
Juan José Torres-Labandeira and
Xerardo Garc\'ìa-Mera and
Ricardo A. Tapia and
Florencio M. Ubeira NL MIND-BEST: a web server for ligands
and proteins discovery ---
Theoretic-experimental study of proteins
of \bionameGiardia lamblia and new
compounds active against
\bionamePlasmodium falciparum . . . . . 229--249
Kerry A. Landman and
Anthony E. Fernando and
Dongcheng Zhang and
Donald F. Newgreen Building stable chains with motile
agents: Insights into the morphology of
enteric neural crest cell migration . . 250--268
David C. Krakauer and
James P. Collins and
Douglas Erwin and
Jessica C. Flack and
Walter Fontana and
Manfred D. Laubichler and
Sonja J. Prohaska and
Geoffrey B. West and
Peter F. Stadler The challenges and scope of theoretical
biology . . . . . . . . . . . . . . . . 269--276
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--276 (7 May 2011) . . . . . . . ??
S. Das and
P. K. Gupta A mathematical model on fractional
Lotka--Volterra equations . . . . . . . 1--6
Robert E. Nordon and
Kap-Hyoun Ko and
Ross Odell and
Timm Schroeder Multi-type branching models to describe
cell differentiation programs . . . . . 7--18
Zhen Wang and
Aleksandra Murks and
Wen-Bo Du and
Zhi-Hai Rong and
Matjaz Perc Coveting thy neighbors fitness as a
means to resolve social dilemmas . . . . 19--26
Svetlana Bunimovich-Mendrazitsky and
Jean Claude Gluckman and
Joel Chaskalovic A mathematical model of combined
bacillus Calmette--Guerin (BCG) and
interleukin (IL)-2 immunotherapy of
superficial bladder cancer . . . . . . . 27--40
G. Kember and
J. A. Armour and
M. Zamir Neural control of heart rate: The role
of neuronal networking . . . . . . . . . 41--47
Karthik Panchanathan Two wrongs don't make a right: The
initial viability of different
assessment rules in the evolution of
indirect reciprocity . . . . . . . . . . 48--54
Stanca M. Ciupe and
Patrick De Leenheer and
Thomas B. Kepler Paradoxical suppression of poly-specific
broadly neutralizing antibodies in the
presence of strain-specific neutralizing
antibodies following HIV infection . . . 55--66
Bo Jiang and
Xiao Zhang and
Yijun Zuo and
Guolian Kang A powerful truncated tail strength
method for testing multiple null
hypotheses in one dataset . . . . . . . 67--73
Koichi Saeki and
Yoh Iwasa T cell anergy as a strategy to reduce
the risk of autoimmunity . . . . . . . . 74--82
Akihiko Mougi and
Yoh Iwasa Unique coevolutionary dynamics in a
predator--prey system . . . . . . . . . 83--89
Leah R. Johnson and
Cheryl J. Briggs Parameter inference for an individual
based model of chytridiomycosis in frogs 90--98
Peter A. Abrams and
Lasse Ruokolainen How does adaptive consumer movement
affect population dynamics in
consumer-resource metacommunities with
homogeneous patches? . . . . . . . . . . 99--110
Ping Xie A model for the dynamics of mammalian
family X DNA polymerases . . . . . . . . 111--122
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--122 (21 May 2011) . . . . . . . ??
Jaime Iranzo and
Javier Román and
Angel Sánchez The spatial Ultimatum game revisited . . 1--10
S. K. Pandey and
M. K. Chaube and
Dharmendra Tripathi Peristaltic transport of multilayered
power-law fluids with distinct
viscosities: a mathematical model for
intestinal flows . . . . . . . . . . . . 11--19
H. M. T. Boer and
C. Stötzel and
S. Röblitz and
P. Deuflhard and
R. F. Veerkamp and
H. Woelders A simple mathematical model of the
bovine estrous cycle: Follicle
development and endocrine interactions 20--31
Nik J. Cunniffe and
Christopher A. Gilligan A theoretical framework for biological
control of soil-borne plant pathogens:
Identifying effective strategies . . . . 32--43
Kyle N. Armstrong and
Leonard J. Kerry Modelling the prey detection performance
of \bionameRhinonicteris aurantia
(\bionameChiroptera: Hipposideridae) in
different atmospheric conditions
discounts the notional role of relative
humidity in adaptive evolution . . . . . 44--54
Naoki Masuda and
Mitsuhiro Nakamura Numerical analysis of a reinforcement
learning model with the dynamic
aspiration level in the iterated
Prisoner's dilemma . . . . . . . . . . . 55--62
Ken Binmore and
Larry Samuelson Sex and evolutionary stability . . . . . 63--73
J. V. Greenman and
V. B. Pasour Phase control of resonant systems:
Interference, chaos and high periodicity 74--86
Ajit Kumar and
Kresimir Josi\'c Reduced models of networks of coupled
enzymatic reactions . . . . . . . . . . 87--106
Frederick Chen and
Miaohua Jiang and
Scott Rabidoux and
Stephen Robinson Public avoidance and epidemics: Insights
from an economic model . . . . . . . . . 107--119
Jinya Otsuka The large-scale evolution by generating
new genes from gene duplication;
similarity and difference between
monoploid and diploid organisms . . . . 120--126
Xiaoguang Du and
Shurong Zhou and
Rampal S. Etienne Negative density dependence can offset
the effect of species competitive
asymmetry: a niche-based mechanism for
neutral-like patterns . . . . . . . . . 127--134
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--134 (7 June 2011) . . . . . . . ??
Wonju Jeon and
Sang-Hee Lee Simulation study of territory size
distributions in subterranean termites 1--8
Emmanuel Hanert and
Eva Schumacher and
Eric Deleersnijder Front dynamics in fractional-order
epidemic models . . . . . . . . . . . . 9--16
Jiapu Zhang and
Jie Sun and
Changzhi Wu Optimal atomic-resolution structures of
prion AGAAAAGA amyloid fibrils . . . . . 17--28
D. Napoletani and
M. Signore and
T. Sauer and
L. Liotta and
E. Petricoin Homologous control of protein signaling
networks . . . . . . . . . . . . . . . . 29--43
Tinevimbo Shiri and
Alex Welte Modelling the impact of acute infection
dynamics on the accumulation of HIV-1
mutations . . . . . . . . . . . . . . . 44--54
R. Keinj and
T. Bastogne and
P. Vallois Multinomial model-based formulations of
TCP and NTCP for radiotherapy treatment
planning . . . . . . . . . . . . . . . . 55--62
T. Ishikawa and
T. Sato and
G. Mohit and
Y. Imai and
T. Yamaguchi Transport phenomena of microbial flora
in the small intestine with peristalsis 63--73
David E. Hiebeler and
Nicholas E. Millett Pair and triplet approximation of a
spatial lattice population model with
multiscale dispersal using Markov chains
for estimating spatial autocorrelation 74--82
Bo Zhao and
Victor Duan and
Stephen S.-T. Yau A novel clustering method via
nucleotide-based Fourier power spectrum
analysis . . . . . . . . . . . . . . . . 83--89
Yan Cai and
Shixiong Xu and
Jie Wu and
Quan Long Coupled modelling of tumour
angiogenesis, tumour growth and blood
perfusion . . . . . . . . . . . . . . . 90--101
J. J. Poos and
Å. Brännström and
U. Dieckmann Harvest-induced maturation evolution
under different life-history trade-offs
and harvesting regimes . . . . . . . . . 102--112
Alex Arenas and
Juan Camacho and
José A. Cuesta and
Rubén J. Requejo The joker effect: Cooperation driven by
destructive agents . . . . . . . . . . . 113--119
Sungim Whang and
Sunhwa Choi and
Eunok Jung A dynamic model for tuberculosis
transmission and optimal treatment
strategies in South Korea . . . . . . . 120--131
Yvonne Schmitz and
Olaf Wolkenhauer and
Katja Rateitschak Nucleo-cytoplasmic shuttling of APC can
maximize $ \beta $-catenin/TCF
concentration . . . . . . . . . . . . . 132--142
Sangwook Wu and
Shubin Liu and
Charles H. Davis and
Darrel W. Stafford and
John D. Kulman and
Lee G. Pedersen A hetero-dimer model for concerted
action of vitamin K carboxylase and
vitamin K reductase in vitamin K cycle 143--149
Rebecca H. Chisholm and
Barry D. Hughes and
Kerry A. Landman and
Georg Mayer and
Paul M. Whitington When are cellular oscillators sufficient
for sequential segmentation? . . . . . . 150--160
Stefano Allesina Predicting trophic relations in
ecological networks: a test of the
Allometric Diet Breadth Model . . . . . 161--168
Owen L. Petchey and
Andrew P. Beckerman and
Jens O. Riede and
Philip H. Warren Fit, efficiency, and biology: Some
thoughts on judging food web models . . 169--171
Alex Escobar Qualia as the fundamental nature of
visual awareness . . . . . . . . . . . . 172--176
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--176 (21 June 2011) . . . . . . ??
Zimei Wu and
C.-K. Chui and
G.-S. Hong and
Stephen Chang Physiological analysis on oscillatory
behavior of glucose-insulin regulation
by model with delays . . . . . . . . . . 1--9
Zhao-Hui Qi and
Ling Li and
Zhi-Meng Zhang and
Xiao-Qin Qi Self-similarity analysis of eubacteria
genome based on weighted graph . . . . . 10--18
Jacques Demongeot and
Adrien Elena and
Mathilde Noual and
Sylvain Sené and
Florence Thuderoz ``Immunetworks'', intersecting circuits
and dynamics . . . . . . . . . . . . . . 19--33
R. J. Allen and
I. D. L. Bogle and
A. J. Ridley A model of localised Rac1 activation in
endothelial cells due to fluid flow . . 34--42
Yuanshi Wang and
Donald L. DeAngelis Transitions of interaction outcomes in a
uni-directional consumer-resource system 43--49
Simeone Marino and
Mohammed El-Kebir and
Denise Kirschner A hybrid multi-compartment model of
granuloma formation and T cell priming
in Tuberculosis . . . . . . . . . . . . 50--62
Takuya Okabe Physical phenomenology of phyllotaxis 63--75
Joost C. M. Uitdehaag Bet hedging based cooperation can limit
kin selection and form a basis for
mutualism . . . . . . . . . . . . . . . 76--87
Rinat Sergeev and
Caroline Colijn and
Ted Cohen Models to understand the
population-level impact of mixed strain
\bionameM. tuberculosis infections . . . 88--100
Li Tai Fang The end-to-end distance of RNA as a
randomly self-paired polymer . . . . . . 101--107
Jianquan Li and
Yali Yang SIR-SVS epidemic models with continuous
and impulsive vaccination strategies . . 108--116
Michael Stich and
Susanna C. Manrubia Motif frequency and evolutionary search
times in RNA populations . . . . . . . . 117--126
Soyoka Muko and
Yoh Iwasa Long-term effect of coral
transplantation: Restoration goals and
the choice of species . . . . . . . . . 127--138
Willem H. Mulder Probability distributions of ancestries
and genealogical distances on
stochastically generated rooted binary
trees . . . . . . . . . . . . . . . . . 139--145
Amotz Zahavi and
Marina Perel The information encoded by the sex
steroid hormones testosterone and
estrogen: a hypothesis . . . . . . . . . 146--149
Filippo Stefanoni and
Maurizio Ventre and
Francesco Mollica and
Paolo A. Netti A numerical model for durotaxis . . . . 150--158
Mark T. Holder and
Mike Steel Estimating phylogenetic trees from
pairwise likelihoods and posterior
probabilities of substitution counts . . 159--166
F. Nyabadza and
Z. Mukandavire Modelling HIV/AIDS in the presence of an
HIV testing and screening campaign . . . 167--179
Clément de Loubens and
Albert Magnin and
Marion Doyennette and
Ioan Cristian Tréléa and
Isabelle Souchon A biomechanical model of swallowing for
understanding the influence of saliva
and food bolus viscosity on flavor
release . . . . . . . . . . . . . . . . 180--188
J. C. Flores Diffusion coefficient of Modern Humans
outcompeting Neanderthals . . . . . . . 189--190
P. Nouvellet and
J. P. Bacon and
D. Waxman Testing the level of ant activity
associated with quorum sensing: An
empirical approach leading to the
establishment and test of a null-model
(response to the comment of Richardson
et al.) . . . . . . . . . . . . . . . . 191--193
Niall J. MacKay Mass scale and curvature in metabolic
scaling: Comment on: T. Kolokotrones et
al., Curvature in metabolic scaling,
Nature \bf 464 (2010) 753--756 . . . . . 194--196
Eric J. Deeds and
Van Savage and
Walter Fontana Curvature in metabolic scaling: a reply
to MacKay . . . . . . . . . . . . . . . 197--198
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--198 (7 July 2011) . . . . . . . ??
Baldvin Einarsson and
Björn Birnir and
Sven Sigur\ethsson A dynamic energy budget (DEB) model for
the energy usage and reproduction of the
Icelandic capelin (\bionameMallotus
villosus) . . . . . . . . . . . . . . . 1--8
Erika T. Camacho and
Stephen Wirkus and
Pamela A. Marshall Mathematical modeling of fungal
infection in immune compromised
individuals: Implications for drug
treatment . . . . . . . . . . . . . . . 9--17
Hassan Mohabatkar and
Majid Mohammad Beigi and
Abolghasem Esmaeili Prediction of GABA A receptor proteins
using the concept of Chou's pseudo-amino
acid composition and support vector
machine . . . . . . . . . . . . . . . . 18--23
Colin R. Tosh Which conditions promote negative
density dependent selection on prey
aggregations? . . . . . . . . . . . . . 24--30
Vicenç Méndez and
Isaac Llopis and
Daniel Campos and
Werner Horsthemke Effect of environmental fluctuations on
invasion fronts . . . . . . . . . . . . 31--38
Zachariah Gompert and
Keith Willmott and
Marianne Elias Heterogeneity in predator micro-habitat
use and the maintenance of Müllerian
mimetic diversity . . . . . . . . . . . 39--46
Pat Barclay Competitive helping increases with the
size of biological markets and invades
defection . . . . . . . . . . . . . . . 47--55
Masanari Asano and
Masanori Ohya and
Yoshiharu Tanaka and
Irina Basieva and
Andrei Khrennikov Quantum-like model of brain's
functioning: Decision making from
decoherence . . . . . . . . . . . . . . 56--64
Yasuhiro Inoue and
Shunsuke Tsuda and
Koji Nakagawa and
Masaki Hojo and
Taiji Adachi Modeling myosin-dependent rearrangement
and force generation in an actomyosin
network . . . . . . . . . . . . . . . . 65--73
Antti Häkkinen and
Shannon Healy and
Howard T. Jacobs and
Andre S. Ribeiro Genome wide study of NF-Y type CCAAT
boxes in unidirectional and
bidirectional promoters in human and
mouse . . . . . . . . . . . . . . . . . 74--83
Mathieu Lemay and
Enno de Lange and
Jan P. Kucera Effects of stochastic channel gating and
distribution on the cardiac action
potential . . . . . . . . . . . . . . . 84--96
Yvonne Blum and
Aleksandra Birn-Jeffery and
Monica A. Daley and
Andre Seyfarth Does a crouched leg posture enhance
running stability and robustness? . . . 97--106
Guohua Huang and
Houqing Zhou and
Yongfan Li and
Lixin Xu Alignment-free comparison of genome
sequences by a new numerical
characterization . . . . . . . . . . . . 107--112
Philip J. Aston and
Gianne Derks and
Adewale Raji and
Balaji M. Agoram and
Piet H. van der Graaf Mathematical analysis of the
pharmacokinetic-pharmacodynamic (PKPD)
behaviour of monoclonal antibodies:
Predicting in vivo potency . . . . . . . 113--121
Markus Böl and
Heiko Stark and
Nadja Schilling On a phenomenological model for fatigue
effects in skeletal muscles . . . . . . 122--132
Jianjun Bi and
Huilan Yang and
Huacheng Yan and
Rengang Song and
Jianyong Fan Knowledge-based virtual screening of
HLA-A*0201-restricted CD8 + T-cell
epitope peptides from herpes simplex
virus genome . . . . . . . . . . . . . . 133--139
Svetlana Bunimovich-Mendrazitsky and
Jean Claude Gluckman and
Joel Chaskalovic Corrigendum to ``A mathematical model of
combined bacillus Calmette--Guerin (BCG)
and interleukin(IL)-2 immunotherapy of
superficial bladder cancer'' [J. Theor.
Biol. \bf 277(1) (2011) 27--40] . . . . 140--140
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--140 (21 July 2011) . . . . . . ??
J. Grasman and
H. M. Salomons and
S. Verhulst Stochastic modeling of length-dependent
telomere shortening in \bionameCorvus
monedula . . . . . . . . . . . . . . . . 1--6
Stephen M. Gatesy and
Nancy S. Pollard Apples, oranges, and angles: Comparative
kinematic analysis of disparate limbs 7--13
Cortland K. Griswold A model of the physiological basis of a
multivariate phenotype that is mediated
by Ca$^{2+}$ signaling and controlled by
ryanodine receptor composition . . . . . 14--22
Jacqueline García and
Néstor Torres Mathematical modelling and assessment of
the pH homeostasis mechanisms in
\bionameAspergillus niger while in
citric acid producing conditions . . . . 23--35
Paolo Sibani and
Simon Christiansen Non-stationary aging dynamics in ant
societies . . . . . . . . . . . . . . . 36--40
M. L. Smith and
G. M. Yanega and
A. Ruina Elastic instability model of rapid beak
closure in hummingbirds . . . . . . . . 41--51
C. Gh. Buzea and
M. Agop and
Evelina Moraru and
Bogdan A. Stana and
Manuela G\^ìr\ctu and
D. Iancu Some implications of Scale Relativity
theory in avascular stages of growth of
solid tumors in the presence of an
immune system response . . . . . . . . . 52--64
Jamie X. Luo and
Matthew S. Turner Functionality and metagraph
disintegration in Boolean networks . . . 65--70
Vladislav V. Khrustalev and
Eugene V. Barkovsky Percent of highly immunogenic amino acid
residues forming B-cell epitopes is
higher in homologous proteins encoded by
GC-rich genes . . . . . . . . . . . . . 71--79
Sylvain Goutelle and
Laurent Bourguignon and
Roger W. Jelliffe and
John E. Conte and
Pascal Maire Mathematical modeling of pulmonary
tuberculosis therapy: Insights from a
prototype model with rifampin . . . . . 80--92
Hans Joachim Poethke and
Andreas Gros and
Thomas Hovestadt The ability of individuals to assess
population density influences the
evolution of emigration propensity and
dispersal distance . . . . . . . . . . . 93--99
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--100 (7 August 2011) . . . . . . ??
Shunsuke Ooyama and
Tatsuo Shibata Hierarchical organization of noise
generates spontaneous signal in
\bionameParamecium cell . . . . . . . . 1--9
A. M. Al-Jumaily and
Y. Du Fading memory model for airway smooth
muscle dynamic response . . . . . . . . 10--13
Michael Renton and
Art Diggle and
Sudheesh Manalil and
Stephen Powles Does cutting herbicide rates threaten
the sustainability of weed management in
cropping systems? . . . . . . . . . . . 14--27
Juan A. Subirana and
Xavier Messeguer The distribution of alternating AT
sequences in eukaryotic genomes suggests
a role in homologous chromosome
recognition in meiosis . . . . . . . . . 28--34
Qi Ma and
Anders Johansson and
David J. T. Sumpter A first principles derivation of animal
group size distributions . . . . . . . . 35--43
Ya-Nan Zhang and
Xiao-Yong Pan and
Yan Huang and
Hong-Bin Shen Adaptive compressive learning for
prediction of protein--protein
interactions from primary sequence . . . 44--52
Frithjof Lutscher and
Gunog Seo The effect of temporal variability on
persistence conditions in rivers . . . . 53--59
I. Roterman and
L. Konieczny and
W. Jurkowski and
K. Prymula and
M. Banach Two-intermediate model to characterize
the structure of fast-folding proteins 60--70
Xiao Liu and
Yubo Fan and
Xiaoyan Deng Effect of the endothelial glycocalyx
layer on arterial LDL transport under
normal and high pressure . . . . . . . . 71--81
Cordoleani Flora and
Nerini David and
Gauduchon Mathias and
Morozov Andrew and
Poggiale Jean-Christophe Structural sensitivity of biological
models revisited . . . . . . . . . . . . 82--91
Natalya Kurochkina and
Tsering Choekyi Helix-helix interfaces and ligand
binding . . . . . . . . . . . . . . . . 92--102
Anuradha Chauhan and
Stephan Lorenzen and
Hanspeter Herzel and
Samuel Bernard Regulation of mammalian cell cycle
progression in the regenerating liver 103--112
Eelco Eggen and
M. Niels de Keijzer and
Bela M. Mulder Self-regulation in tip-growth: The role
of cell wall ageing . . . . . . . . . . 113--121
Yongfeng Li and
Francis A. Cucinotta Modeling non-homologous end joining . . 122--135
Mina Youssef and
Caterina Scoglio An individual-based approach to SIR
epidemics in contact networks . . . . . 136--144
Daniel Strömbom Collective motion from local attraction 145--151
Daniele Muraro and
Helen Byrne and
John King and
Ute Voß and
Joseph Kieber and
Malcolm Bennett The influence of cytokinin-auxin
cross-regulation on cell-fate
determination in \bionameArabidopsis
thaliana root development . . . . . . . 152--167
J. Hugon and
J.-C. Rostain and
B. Gardette A new biophysical decompression model
for estimating the risk of articular
bends during and after decompression . . 168--179
Chaitanya S. Gokhale and
Arne Traulsen Strategy abundance in evolutionary
many-player games with multiple
strategies . . . . . . . . . . . . . . . 180--191
Carsten Magnus and
Roland R. Regoes Restricted occupancy models for
neutralization of HIV virions and
populations . . . . . . . . . . . . . . 192--202
Sarah D. Olson and
Susan S. Suarez and
Lisa J. Fauci Coupling biochemistry and hydrodynamics
captures hyperactivated sperm motility
in a simple flagellar model . . . . . . 203--216
Uphar Chamoli and
Stephen Wroe Allometry in the distribution of
material properties and geometry of the
felid skull: Why larger species may need
to change and how they may achieve it 217--226
Philip J. Murray and
Philip K. Maini and
Ruth E. Baker The clock and wavefront model revisited 227--238
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--238 (21 August 2011) . . . . . ??
Tomás Kulich and
Jaroslav Flegr Positive effects of multiple gene
control on the spread of altruism by
group selection . . . . . . . . . . . . 1--6
Aina Astudillo Fernandez and
Jean Louis Deneubourg On following behaviour as a mechanism
for collective movement . . . . . . . . 7--15
Xia Jingbo and
Zhang Silan and
Shi Feng and
Xiong Huijuan and
Hu Xuehai and
Niu Xiaohui and
Li Zhi Using the concept of pseudo amino acid
composition to predict resistance gene
against \booktitleXanthomonas oryzae pv.
oryzae in rice: An approach from chaos
games representation . . . . . . . . . . 16--23
Sheng-Feng Shen and
H. Kern Reeve and
Sandra L. Vehrencamp Parental care, cost of reproduction and
reproductive skew: a general costly
young model . . . . . . . . . . . . . . 24--31
Ian S. Dunn RNA templating of molecular assembly and
covalent modification patterning in
early molecular evolution and modern
biosystems . . . . . . . . . . . . . . . 32--41
Xuan Xiao and
Zhi-Cheng Wu and
Kuo-Chen Chou iLoc-Virus: a multi-label learning
classifier for identifying the
subcellular localization of virus
proteins with both single and multiple
sites . . . . . . . . . . . . . . . . . 42--51
Don Klinkenberg and
Hiroshi Nishiura The correlation between infectivity and
incubation period of measles, estimated
from households with two cases . . . . . 52--60
Eliezer Z. Prisman and
Amiram Gafni and
Antonio Finelli A stochastic approach to risk management
for prostate cancer patients on active
surveillance . . . . . . . . . . . . . . 61--70
P. Mettikolla and
N. Calander and
R. Luchowski and
I. Gryczynski and
Z. Gryczynski and
J. Zhao and
D. Szczesna-Cordary and
J. Borejdo Cross-bridge kinetics in myofibrils
containing familial hypertrophic
cardiomyopathy R58Q mutation in the
regulatory light chain of myosin . . . . 71--81
Nicolae Radu Zabet Negative feedback and physical limits of
genes . . . . . . . . . . . . . . . . . 82--91
Qinqin Wu and
Weiqiang Zhou and
Jiajun Wang and
Hong Yan Correlation between the flexibility and
periodic dinucleotide patterns in yeast
nucleosomal DNA sequences . . . . . . . 92--98
Jianquan Li and
Paolo Fergola and
Zhien Ma Effects of allelochemicals produced by
one population in a chemostat-like
environment . . . . . . . . . . . . . . 99--105
Xuemei Liu and
Lin Wan and
Jing Li and
Gesine Reinert and
Michael S. Waterman and
Fengzhu Sun New powerful statistics for
alignment-free sequence comparison under
a pattern transfer model . . . . . . . . 106--116
Diego Lopez and
Sébastien Michelin and
Emmanuel de Langre Flow-induced pruning of branched systems
and brittle reconfiguration . . . . . . 117--124
Andy Gardner Kin selection under blending inheritance 125--129
Aurélie Courcoul and
Hervé Monod and
Mirjam Nielen and
Don Klinkenberg and
Lenny Hogerwerf and
François Beaudeau and
Elisabeta Vergu Modelling the effect of heterogeneity of
shedding on the within herd
\bionameCoxiella burnetii spread and
identification of key parameters by
sensitivity analysis . . . . . . . . . . 130--141
Guo-Ping Zhou The disposition of the LZCC protein
residues in wenxiang diagram provides
new insights into the protein--protein
interaction mechanism . . . . . . . . . 142--148
Jiapu Zhang and
David Y. Gao and
John Yearwood A novel canonical dual computational
approach for prion AGAAAAGA amyloid
fibril molecular modeling . . . . . . . 149--157
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--158 (7 September 2011) . . . . ??
Naoyuki Iseki and
Akira Sasaki and
Hirokazu Toju Arms race between weevil rostrum length
and camellia pericarp thickness:
Geographical cline and theory . . . . . 1--9
Andrés Chavarría-Krauser and
Du Yejie A model of plasma membrane flow and
cytosis regulation in growing pollen
tubes . . . . . . . . . . . . . . . . . 10--24
Xianning Liu and
Xiaoping Chen and
Yasuhiro Takeuchi Dynamics of an SIQS epidemic model with
transport-related infection and
exit-entry screenings . . . . . . . . . 25--35
Konstantin Krepkin and
José Costa Defining the role of cooperation in
early tumor progression . . . . . . . . 36--45
Mario Cammarano Co-dominance and succession in forest
dynamics: The role of interspecific
differences in crown transmissivity . . 46--57
Matthew D. Herron and
Michael Doebeli Adaptive diversification of a plastic
trait in a predictably fluctuating
environment . . . . . . . . . . . . . . 58--68
Lei Zhang and
Ning Zhang and
Ji-Shou Ruan and
Tao Zhang Studies on the rules of $ \beta $-strand
alignment in a protein $ \beta $-sheet
structure . . . . . . . . . . . . . . . 69--76
Xiaojuan Shen Conformation and sequence evidence for
two-fold symmetry in left-handed
beta-helix fold . . . . . . . . . . . . 77--83
Gregory Herschlag and
Laura Miller Reynolds number limits for jet
propulsion: a numerical study of
simplified jellyfish . . . . . . . . . . 84--95
Zoran Konkoli Spontaneous noise reduction in a
strongly cooperative reaction model . . 96--102
Noreen Akhtar and
Muaz Niazi and
Farah Mustafa and
Amir Hussain A discrete event system specification
(DEVS)-based model of consanguinity . . 103--112
Maria Abou Chakra and
Jonathon Richard Stone Holotestoid: a computational model for
testing hypotheses about echinoid
skeleton form and growth . . . . . . . . 113--125
T. Chyou and
G. F. Liddell and
M. G. Paulin An upper-body can improve the stability
and efficiency of passive dynamic
walking . . . . . . . . . . . . . . . . 126--135
Shev MacNamara and
Ruth E. Baker and
Philip K. Maini Distinguishing graded and ultrasensitive
signalling cascade kinetics by the shape
of morphogen gradients in
\bionameDrosophila . . . . . . . . . . . 136--146
Maria-Grazia Ascenzi and
Christian Blanco and
Ian Drayer and
Hannah Kim and
Ryan Wilson and
Kelsey N. Retting and
Karen M. Lyons and
George Mohler Effect of localization, length and
orientation of chondrocytic primary
cilium on murine growth plate
organization . . . . . . . . . . . . . . 147--155
P. A. Robinson Neural field theory of synaptic
plasticity . . . . . . . . . . . . . . . 156--163
Elizabeth M. Cherry and
Flavio H. Fenton Effects of boundaries and geometry on
the spatial distribution of action
potential duration in cardiac tissue . . 164--176
Ludvik Bass and
Michael Sòrensen and
Ole Lajord Munk and
Susanne Keiding Analogue tracers and lumped constant in
capillary beds . . . . . . . . . . . . . 177--181
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Pages 1--182 (21 September 2011) . . . . ??
Petros T. Damos and
Nikos T. Papadopoulos and
Alexandros Rigas and
Matilda Savopoulou-Soultani Energetic loads and informational
entropy during insect metamorphosis:
Measuring structural variability and
self-organization . . . . . . . . . . . 1--12
Anonymous Pages 1--114 (7 October 2011) . . . . . 1--114
Hannah Farr and
Tim David Models of neurovascular coupling via
potassium and EET signalling . . . . . . 13--23
Xiaobo Shi and
Xiuzhen Hu and
Shaobo Li and
Xingxing Liu Prediction of $ \beta $-turn types in
protein by using composite vector . . . 24--30
D. Havelka and
M. Cifra and
O. Kucera and
J. Pokorný and
J. Vrba High-frequency electric field and
radiation characteristics of cellular
microtubule network . . . . . . . . . . 31--40
Bernd Lütkenhöner and
Türker Basel An analytical model of the vestibular
evoked myogenic potential . . . . . . . 41--49
Cory Simon and
Niño Yosinao A mathematical model to distinguish
sociological and biological
susceptibility factors in disease
transmission in the context of H1N1/09
influenza . . . . . . . . . . . . . . . 50--56
Akira Tsuda and
Fiona E. Laine-Pearson and
Peter E. Hydon Why chaotic mixing of particles is
inevitable in the deep lung . . . . . . 57--66
Petra Kochová and
Robert Cimrman and
Jirí Janácek and
Kirsti Witter and
Zbynek Tonar How to assess, visualize and compare the
anisotropy of linear structures
reconstructed from optical sections ---
a study based on histopathological
quantification of human brain
microvessels . . . . . . . . . . . . . . 67--78
Wan J. Hsieh and
Hsiuying Wang Human microRNA target identification by
RRSM . . . . . . . . . . . . . . . . . . 79--84
Y. Liu and
W. Zhang and
C. Wang and
G. S. Kassab A linearized and incompressible
constitutive model for arteries . . . . 85--91
Xuefeng Zhao and
Yi Liu and
Wei Zhang and
Chong Wang and
Ghassan S. Kassab A novel arterial constitutive model in a
commercial finite element package:
Application to balloon angioplasty . . . 92--99
Juan-Carlos Letelier and
María Luz Cárdenas and
Athel Cornish-Bowden From L'Homme Machine to metabolic
closure: Steps towards understanding
life . . . . . . . . . . . . . . . . . . 100--113
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Christina Pawlowitsch and
Panayotis Mertikopoulos and
Nikolaus Ritt Neutral stability, drift, and the
diversification of languages . . . . . . 1--12
Anonymous Pages 1--170 (21 October 2011) . . . . . 1--170
L. M. Peinado Cortés and
J. C. Vanegas Acosta and
D. A. Garzón Alvarado A mechanobiological model of epiphysis
structures formation . . . . . . . . . . 13--25
Arild O. Gautestad Memory matters: Influence from a
cognitive map on animal space use . . . 26--36
Jeromos Vukov and
Francisco C. Santos and
Jorge M. Pacheco Escaping the tragedy of the commons via
directed investments . . . . . . . . . . 37--41
Shinsuke Suzuki and
Hiromichi Kimura Oscillatory dynamics in the coevolution
of cooperation and mobility . . . . . . 42--47
Elena Agliari and
Adriano Barra and
Francesco Guerra and
Francesco Moauro A thermodynamic perspective of immune
capabilities . . . . . . . . . . . . . . 48--63
Yoshihiro Nakamura and
Shoichi Awa and
Hitoshi Kato and
Yoichi M. Ito and
Akira Kamiya and
Takashi Igarashi Model combining hydrodynamics and
fractal theory for analysis of in vivo
peripheral pulmonary and systemic
resistance of shunt cardiac defects . . 64--73
Denis Michel Hierarchical cooperativity mediated by
chromatin remodeling; the model of the
MMTV transcription regulation . . . . . 74--81
Florian Centler and
Ingo Fetzer and
Martin Thullner Modeling population patterns of
chemotactic bacteria in homogeneous
porous media . . . . . . . . . . . . . . 82--91
Scheila de Avila e Silva and
Sergio Echeverrigaray and
Günther J. L. Gerhardt BacPP: Bacterial promoter prediction ---
a tool for accurate sigma-factor
specific assignment in enterobacteria 92--99
Binsheng Gong and
Tao Liu and
Xiaoyu Zhang and
Xi Chen and
Jiang Li and
Hongchao Lv and
Yi Zou and
Xia Li and
Shaoqi Rao Disease embryo development network
reveals the relationship between disease
genes and embryo development genes . . . 100--108
Tatsuya Sasaki and
Tatsuo Unemi Replicator dynamics in public goods
games with reward funds . . . . . . . . 109--114
Jenny Vuong and
Christian Hellmich Bone fibrillogenesis and mineralization:
Quantitative analysis and implications
for tissue elasticity . . . . . . . . . 115--130
Marco Tektonidis and
Haralambos Hatzikirou and
Arnaud Chauvi\`ere and
Matthias Simon and
Karl Schaller and
Andreas Deutsch Identification of intrinsic in vitro
cellular mechanisms for glioma invasion 131--147
Emily J. Hackett-Jones and
Kerry A. Landman and
Donald F. Newgreen and
Dongcheng Zhang On the role of differential adhesion in
gangliogenesis in the enteric nervous
system . . . . . . . . . . . . . . . . . 148--159
Henry P. Mirsky and
Mark J. Miller and
Jennifer J. Linderman and
Denise E. Kirschner Systems biology approaches for
understanding cellular mechanisms of
immunity in lymph nodes during infection 160--170
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Jennifer J. H. Reynolds and
Andrew White and
Jonathan A. Sherratt and
Mike Boots The population dynamical consequences of
density-dependent prophylaxis . . . . . 1--8
Anonymous Pages 1--104 (7 November 2011) . . . . . 1--104
Dobromir T. Dimitrov and
Marie-Claude Boily and
Rebecca F. Baggaley and
Benoit Masse Modeling the gender-specific impact of
vaginal microbicides on HIV transmission 9--20
Or Givan and
Nehemia Schwartz and
Assaf Cygelberg and
Lewi Stone Predicting epidemic thresholds on
complex networks: Limitations of
mean-field approaches . . . . . . . . . 21--28
Junling Ma and
Jonathan Dushoff and
David J. D. Earn Age-specific mortality risk from
pandemic influenza . . . . . . . . . . . 29--34
H. Frederik Nijhout Dependence of morphometric allometries
on the growth kinetics of body parts . . 35--43
Christina Vasalou and
Michael A. Henson A multicellular model for differential
regulation of circadian signals in the
core and shell regions of the
suprachiasmatic nucleus . . . . . . . . 44--56
Elias D. C. Neto and
Viviane M. de Oliveira and
Alexandre Rosas and
Paulo R. A. Campos The effect of spatially correlated
environments on genetic diversity-area
relationships . . . . . . . . . . . . . 57--65
David Murrugarra and
Reinhard Laubenbacher Regulatory patterns in molecular
interaction networks . . . . . . . . . . 66--72
Emmanuel Benard and
Christian J. Michel A generalization of substitution
evolution models of nucleotides to
genetic motifs . . . . . . . . . . . . . 73--83
Robert A. Laird Green-beard effect predicts the
evolution of traitorousness in the
two-tag Prisoner's dilemma . . . . . . . 84--91
Wentian Li On parameters of the human genome . . . 92--104
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
William C. Jordan-Cooley and
Romuald N. Lipcius and
Leah B. Shaw and
Jian Shen and
Junping Shi Bistability in a differential equation
model of oyster reef height and sediment
accumulation . . . . . . . . . . . . . . 1--11
Anonymous Pages 1--270 (21 November 2011) . . . . 1--270
Mariana Lozada and
Paola D'Adamo and
Miguel Angel Fuentes Beneficial effects of human altruism . . 12--16
K. Wendelsdorf and
G. Dean and
Shuhua Hu and
S. Nordone and
H. T. Banks Host immune responses that promote
initial HIV spread . . . . . . . . . . . 17--35
Ajeet K. Sharma and
Debashish Chowdhury Stochastic theory of protein synthesis
and polysome: Ribosome profile on a
single mRNA transcript . . . . . . . . . 36--46
Etienne Couturier and
Sylvain Courrech du Pont and
Stéphane Douady The filling law: a general framework for
leaf folding and its consequences on
leaf shape diversity . . . . . . . . . . 47--64
Arthur F. T. Mak and
Yanyan Yu and
Linda P. C. Kwan and
Lei Sun and
Eric W. C. Tam Deformation and reperfusion damages and
their accumulation in subcutaneous
tissues during loading and unloading: a
theoretical modeling of deep tissue
injuries . . . . . . . . . . . . . . . . 65--73
C. De Michele and
F. Accatino and
R. Vezzoli and
R. J. Scholes Savanna domain in the herbivores-fire
parameter space exploiting a
tree-grass-soil water dynamic model . . 74--82
J. V. Ross Invasion of infectious diseases in
finite homogeneous populations . . . . . 83--89
Alexander P. Petroff and
Ting-Di Wu and
Biqing Liang and
Jeannie Mui and
Jean-Luc Guerquin-Kern and
Hojatollah Vali and
Daniel H. Rothman and
Tanja Bosak Reaction-diffusion model of nutrient
uptake in a biofilm: Theory and
experiment . . . . . . . . . . . . . . . 90--95
Elizabeth S. Allman and
James H. Degnan and
John A. Rhodes Determining species tree topologies from
clade probabilities under the coalescent 96--106
Timothy D. Harrington and
Nariman Naber and
Adam G. Larson and
Roger Cooke and
Sarah E. Rice and
Edward Pate Analysis of the interaction of the Eg5
Loop5 with the nucleotide site . . . . . 107--115
Yun Kang and
Rebecca Clark and
Michael Makiyama and
Jennifer Fewell Mathematical modeling on obligate
mutualism: Interactions between
leaf-cutter ants and their fungus garden 116--127
Jean-Baptiste André and
Nicolas Baumard Social opportunities and the evolution
of fairness . . . . . . . . . . . . . . 128--135
Michael Lutianov and
Shailesh Naire and
Sally Roberts and
Jan-Herman Kuiper A mathematical model of cartilage
regeneration after cell therapy . . . . 136--150
Yo Horikawa Exponential transient propagating
oscillations in a ring of spiking
neurons with unidirectional slow
inhibitory synaptic coupling . . . . . . 151--159
Sladjana Spasic and
Aleksandar Kalauzi and
Srdjan Kesic and
Milica Obradovic and
Jasna Saponjic Surrogate data modeling the relationship
between high frequency amplitudes and
Higuchi fractal dimension of EEG signals
in anesthetized rats . . . . . . . . . . 160--166
Alan Veliz-Cuba Reduction of Boolean network models . . 167--172
Bin Tang and
M. J. Brennan On the dynamic behaviour of the
``click'' mechanism in dipteran flight 173--180
Maíra Aguiar and
Sebastien Ballesteros and
Bob W. Kooi and
Nico Stollenwerk The role of seasonality and import in a
minimalistic multi-strain dengue model
capturing differences between primary
and secondary infections: Complex
dynamics and its implications for data
analysis . . . . . . . . . . . . . . . . 181--196
Giorgio Guzzetta and
Marco Ajelli and
Zhenhua Yang and
Stefano Merler and
Cesare Furlanello and
Denise Kirschner Modeling socio-demography to capture
tuberculosis transmission dynamics in a
low burden setting . . . . . . . . . . . 197--205
Guifang Fu and
Zhong Wang and
Jiahan Li and
Rongling Wu A mathematical framework for functional
mapping of complex phenotypes using
delay differential equations . . . . . . 206--216
Cassie S. Mitchell and
Robert H. Lee Synaptic glutamate spillover increases
NMDA receptor reliability at the
cerebellar glomerulus . . . . . . . . . 217--224
Lin Hua and
Ping Zhou and
Hong Liu and
Lin Li and
Zheng Yang and
Zhi-cheng Liu Mining susceptibility gene modules and
disease risk genes from SNP data by
combining network topological properties
with support vector regression . . . . . 225--236
Eli E. Goldwyn and
Alan Hastings The roles of the Moran effect and
dispersal in synchronizing oscillating
populations . . . . . . . . . . . . . . 237--246
Anna Maria Spagnuolo and
Victor DiRita and
Denise Kirschner A model for \bionameVibrio cholerae
colonization of the human intestine . . 247--258
S. Towers and
K. Vogt Geisse and
Y. Zheng and
Z. Feng Antiviral treatment for pandemic
influenza: Assessing potential
repercussions using a seasonally forced
SIR model . . . . . . . . . . . . . . . 259--268
Liene Daukste and
Britta Basse and
Bruce C. Baguley and
David J. N. Wall Corrigendum to ``Using a stem cell and
progeny model to illustrate the
relationship between cell cycle times of
in vivo human tumour cell tissue
populations, in vitro primary cultures
and the cell lines derived from them''
[J. Theor. Biol. \bf 260 (2009)
563--571] . . . . . . . . . . . . . . . 269--269
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Darya Yu. Orlova and
Vyacheslav I. Borisov and
Vladimir S. Kozhevnikov and
Valeri P. Maltsev and
Andrei V. Chernyshev Distribution function approach to the
study of the kinetics of IgM antibody
binding to Fc$ \gamma $RIIIb (CD16b)
receptors on neutrophils by flow
cytometry . . . . . . . . . . . . . . . 1--6
Anonymous Pages 1--104 (7 December 2011) . . . . . 1--104
Alan J. Terry and
Mark A. J. Chaplain Spatio-temporal modelling of the NF-$
\kappa $B intracellular signalling
pathway: The roles of diffusion, active
transport, and cell geometry . . . . . . 7--26
Feng Cheng and
Dan Theodorescu and
Ira G. Schulman and
Jae K. Lee In vitro transcriptomic prediction of
hepatotoxicity for early drug discovery 27--36
David Kleinhans and
Per R. Jonsson On the impact of dispersal asymmetry on
metapopulation persistence . . . . . . . 37--45
Clément Chatelain and
Pasquale Ciarletta and
Martine Ben Amar Morphological changes in early melanoma
development: Influence of nutrients,
growth inhibitors and cell-adhesion
mechanisms . . . . . . . . . . . . . . . 46--59
Thomas J. Anastasio Data-driven modeling of Alzheimer
Disease pathogenesis . . . . . . . . . . 60--72
Yoshitaka Kamimura Population stochasticity, random
determination of handedness, and the
genetic basis of antisymmetry . . . . . 73--80
Ronald M. Nelson and
Jaco M. Greeff Sex ratio dependent dispersal when sex
ratios vary between patches . . . . . . 81--87
Harmen de Weerd and
Rineke Verbrugge Evolution of altruistic punishment in
heterogeneous populations . . . . . . . 88--103
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Maud V. P. Charron and
Henri Seegers and
Michel Langlais and
Pauline Ezanno Seasonal spread and control of
Bluetongue in cattle . . . . . . . . . . 1--9
Anonymous Pages 1--128 (21 December 2011) . . . . 1--128
Carl L. Gardner and
Jeremiah R. Jones Electrodiffusion model simulation of the
potassium channel . . . . . . . . . . . 10--13
Robert W. Whittlesey Wake-based unsteady modeling of the
aquatic beetle \bionameDytiscus
marginalis . . . . . . . . . . . . . . . 14--21
Guillermo Peris and
Andrés Marzal Normalized global alignment for protein
sequences . . . . . . . . . . . . . . . 22--28
J. C. Flores and
Mauro Bologna and
Deterlino Urzagasti A mathematical model for the Andean
Tiwanaku civilization collapse: Climate
variations . . . . . . . . . . . . . . . 29--32
J. S. Gill and
C. M. Salafia and
D. Grebenkov and
D. D. Vvedensky Modeling oxygen transport in human
placental terminal villi . . . . . . . . 33--41
Ingo Schiffner and
Johann Baumeister and
Roswitha Wiltschko Mathematical analysis of the
navigational process in homing pigeons 42--46
Vladimir Sukhov and
Vladimir Nerush and
Lyubov Orlova and
Vladimir Vodeneev Simulation of action potential
propagation in plants . . . . . . . . . 47--55
Lamwah Chow and
Meng Fan and
Zhilan Feng Dynamics of a multigroup epidemiological
model with group-targeted vaccination
strategies . . . . . . . . . . . . . . . 56--64
B. Göbel and
M. Chung and
K. M. Oltmanns and
A. Peters and
D. Langemann Robust modeling of appetite regulation 65--75
Lasse Ruokolainen and
Peter A. Abrams and
Kevin S. McCann and
Brian J. Shuter The roles of spatial heterogeneity and
adaptive movement in stabilizing (or
destabilizing) simple metacommunities 76--87
Julia Korell and
Carolyn V. Coulter and
Stephen B. Duffull Evaluation of red blood cell labelling
methods based on a statistical model for
red blood cell survival . . . . . . . . 88--98
Robert L. Unckless The potential role of the X chromosome
in the emergence of male-killing from
mutualistic endosymbionts . . . . . . . 99--104
Amin Mehrabian and
Younane Abousleiman General solutions to poroviscoelastic
model of hydrocephalic human brain
tissue . . . . . . . . . . . . . . . . . 105--118
C. M. Field and
D. K. Summers Multicopy plasmid stability: Revisiting
the dimer catastrophe . . . . . . . . . 119--127
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
D. Maxin and
L. Berec and
M. Covello and
J. Jessee and
M. Zimmer The impact of sexually abstaining groups
on persistence of sexually transmitted
infections in populations with ephemeral
pair bonds . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--128 (7 January 2012) . . . . . 1--128
Susanne W. Lipfert and
Michael Günther and
Daniel Renjewski and
Sten Grimmer and
Andre Seyfarth A model-experiment comparison of system
dynamics for human walking and running 11--17
Ken-ichi Hironaka and
Yoh Iwasa and
Yoshihiro Morishita Multiple feedback loops achieve robust
localization of wingless expression in
\bionameDrosophila notum development . . 18--29
Seth Bullock An evolutionary advantage for
extravagant honesty . . . . . . . . . . 30--38
Morgiane Richard and
Matthew Fryett and
Samantha Miller and
Ian Booth and
Celso Grebogi and
Alessandro Moura Optimality in DNA repair . . . . . . . . 39--43
Gesham Magombedze and
Nicola Mulder A mathematical representation of the
development of Mycobacterium
tuberculosis active, latent and dormant
stages . . . . . . . . . . . . . . . . . 44--59
Mahmood Amiri and
Fariba Bahrami and
Mahyar Janahmadi Functional contributions of astrocytes
in synchronization of a neuronal network
model . . . . . . . . . . . . . . . . . 60--70
R. M. T. Fleming and
C. M. Maes and
M. A. Saunders and
Y. Ye and
B. Ò. Palsson A variational principle for computing
nonequilibrium fluxes and potentials in
genome-scale biochemical networks . . . 71--77
Qi Dai and
Xiaodong Guo and
Lihua Li Sequence comparison via polar
coordinates representation and curve
tree . . . . . . . . . . . . . . . . . . 78--85
J. R. Fernández and
J. M. García-Aznar and
R. Martínez Piezoelectricity could predict sites of
formation/resorption in bone remodelling
and modelling . . . . . . . . . . . . . 86--92
Maqsood Hayat and
Asifullah Khan MemHyb: Predicting membrane protein
types by hybridizing SAAC and PSSM . . . 93--102
Todd R. Young and
Bastien Fernandez and
Richard Buckalew and
Gregory Moses and
Erik M. Boczko Clustering in cell cycle dynamics with
general response/signaling feedback . . 103--115
Matthijs van Veelen and
Martin A. Nowak Multi-player games on the cycle . . . . 116--128
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Robert P. Gove and
William Chen and
Nicholas B. Zweber and
Rebecca Erwin and
Jan Rychtá\vr and
David L. Remington Effects of causal networks on the
structure and stability of resource
allocation trait correlations . . . . . 1--14
Anonymous Pages 1--236 (21 January 2012) . . . . . 1--236
Wen Jiang and
Adam M. Sullivan and
Chunlei Su and
Xiaopeng Zhao An agent-based model for the
transmission dynamics of
\bionameToxoplasma gondii . . . . . . . 15--26
Dmitrii Polev Transcriptional noise as a driver of
gene evolution . . . . . . . . . . . . . 27--33
Bruce P. Ayati Microbial dormancy in batch cultures as
a function of substrate-dependent
mortality . . . . . . . . . . . . . . . 34--40
Yong Cheng Poh and
Arthur Beyder and
Peter R. Strege and
Gianrico Farrugia and
Martin L. Buist Quantification of gastrointestinal
sodium channelopathy . . . . . . . . . . 41--48
Guoqing Liu and
Jia Liu and
Xiangjun Cui and
Lu Cai Sequence-dependent prediction of
recombination hotspots in
\bionameSaccharomyces cerevisiae . . . . 49--54
Sedigheh Mahdavi and
Ali Mohades and
Ali Salehzadeh Yazdi and
Samad Jahandideh and
Ali Masoudi-Nejad Computational analysis of RNA-protein
interaction interfaces via the Voronoi
diagram . . . . . . . . . . . . . . . . 55--64
Fabio Borgogno and
Paolo D'Odorico and
Francesco Laio and
Luca Ridolfi Stochastic resonance and coherence
resonance in groundwater-dependent plant
ecosystems . . . . . . . . . . . . . . . 65--73
Jin-Long Lu and
Xue-Hai Hu and
Dong-Gang Hu A new hybrid fractal algorithm for
predicting thermophilic nucleotide
sequences . . . . . . . . . . . . . . . 74--81
Michael Günther and
Tom Weihmann Climbing in hexapods: a plain model for
heavy slopes . . . . . . . . . . . . . . 82--86
Duygu Balcan and
Alessandro Vespignani Invasion threshold in structured
populations with recurrent mobility
patterns . . . . . . . . . . . . . . . . 87--100
Mehmet A. Orman and
Ioannis P. Androulakis and
Francois Berthiaume and
Marianthi G. Ierapetritou Metabolic network analysis of perfused
livers under fed and fasted states:
Incorporating thermodynamic and
futile-cycle-associated regulatory
constraints . . . . . . . . . . . . . . 101--110
Changjing Zhuge and
Jinzhi Lei and
Michael C. Mackey Neutrophil dynamics in response to
chemotherapy and G-CSF . . . . . . . . . 111--120
Suyu Mei Multi-kernel transfer learning based on
Chou's PseAAC formulation for protein
submitochondria localization . . . . . . 121--130
Jung Min Lee and
Donghoon Choi and
Giphil Cho and
Yongkuk Kim The effect of public health
interventions on the spread of influenza
among cities . . . . . . . . . . . . . . 131--142
Zhijun Qiu and
Xicheng Wang Prediction of protein--protein
interaction sites using patch-based
residue characterization . . . . . . . . 143--150
Shoma Tanabe and
Naoki Masuda Evolution of cooperation facilitated by
reinforcement learning with adaptive
aspiration levels . . . . . . . . . . . 151--160
Xia Wang and
Yanni Xiao and
Junrui Wang and
Xinxin Lu A mathematical model of effects of
environmental contamination and presence
of volunteers on hospital infections in
China . . . . . . . . . . . . . . . . . 161--173
Pablo Riera-Fernández and
Cristian R. Munteanu and
Manuel Escobar and
Francisco Prado-Prado and
Raquel Mart\'ìn-Romalde and
David Pereira and
Karen Villalba and
Aliuska Duardo-Sánchez and
Humberto González-D\'ìaz New Markov--Shannon Entropy models to
assess connectivity quality in complex
networks: From molecular to cellular
pathway, Parasite--Host, Neural,
Industry, and Legal--Social networks . . 174--188
Noël Bonneuil Multiallelic polymorphism maintained
under unpredictable migration and
selection . . . . . . . . . . . . . . . 189--196
Ratchada Sopakayang and
Raffaella De Vita and
Albert Kwansa and
Joseph W. Freeman Elastic and viscoelastic properties of a
type I collagen fiber . . . . . . . . . 197--205
Omri Tal The cumulative effect of genetic markers
on classification performance: Insights
from simple models . . . . . . . . . . . 206--218
Raluca Apostu and
Michael C. Mackey Mathematical model of GAL regulon
dynamics in \bionameSaccharomyces
cerevisiae . . . . . . . . . . . . . . . 219--235
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Roger Cropp and
John Norbury Constructing ecologies . . . . . . . . . 1--8
Anonymous Pages 1--186 (7 February 2012) . . . . . 1--186
Erol Akçay Incentives in the family II: Behavioral
dynamics and the evolution of non-costly
signaling . . . . . . . . . . . . . . . 9--18
Hal Whitehead and
David Lusseau Animal social networks as substrate for
cultural behavioural diversity . . . . . 19--28
Mohammad Reza Rahbar and
Iraj Rasooli and
Seyed Latif Mousavi Gargari and
Gunnar Sandstrom and
Jafar Amani and
Yaser Fattahian and
Abolfazl Jahangiri and
Marziyeh Jalali A potential in silico antibody-antigen
based diagnostic test for precise
identification of \bionameAcinetobacter
baumannii . . . . . . . . . . . . . . . 29--39
Jan Molácek and
Mark Denny and
John W. M. Bush The fine art of surfacing: Its efficacy
in broadcast spawning . . . . . . . . . 40--47
Hiroshi Nishiura and
Ping Yan and
Candace K. Sleeman and
Charles J. Mode Estimating the transmission potential of
supercritical processes based on the
final size distribution of minor
outbreaks . . . . . . . . . . . . . . . 48--55
Mark Robertson-Tessi and
Ardith El-Kareh and
Alain Goriely A mathematical model of tumor-immune
interactions . . . . . . . . . . . . . . 56--73
Sarah L. Fann and
Stuart R. Borrett Environ centrality reveals the tendency
of indirect effects to homogenize the
functional importance of species in
ecosystems . . . . . . . . . . . . . . . 74--86
Bernd Lütkenhöner and
Türker Basel Deconvolution of the vestibular evoked
myogenic potential . . . . . . . . . . . 87--97
Istvan Karsai and
Michael D. Phillips Regulation of task differentiation in
wasp societies: a bottom-up model of the
``common stomach'' . . . . . . . . . . . 98--113
Masoomeh Taghipoor and
Philippe Lescoat and
Jean-René Licois and
Christine Georgelin and
Guy Barles Mathematical modeling of transport and
degradation of feedstuffs in the small
intestine . . . . . . . . . . . . . . . 114--121
Takuyo Aita and
Yuzuru Husimi Biophysical connection between
evolutionary dynamics and thermodynamics
in in vitro evolution . . . . . . . . . 122--129
S. Dalessi and
A. Neves and
S. Bergmann Modeling morphogen gradient formation
from arbitrary realistically shaped
sources . . . . . . . . . . . . . . . . 130--138
Pavel Kozlovsky and
Amit Gefen The relative contributions of propulsive
forces and receptor-ligand binding
forces during early contact between
spermatozoa and zona pellucida of
oocytes . . . . . . . . . . . . . . . . 139--143
Xue Zhong and
Jason Droesch and
Randal Fox and
Eva M. Top and
Stephen M. Krone On the meaning and estimation of plasmid
transfer rates for surface-associated
and well-mixed bacterial populations . . 144--152
John M. Marshall and
Bruce A. Hay Confinement of gene drive systems to
local populations: a comparative
analysis . . . . . . . . . . . . . . . . 153--171
Gil Iosilevskii and
Yannis P. Papastamatiou and
Carl G. Meyer and
Kim N. Holland Energetics of the yo-yo dives of
predatory sharks . . . . . . . . . . . . 172--181
Simcha Lev-Yadun and
Gadi Katzir Mirror images: Fish versus terrestrial
animals . . . . . . . . . . . . . . . . 182--184
Zhi-gang Shen and
Qi-xue Fan and
Margaret Anne Hurley and
Cong-xin Xie and
Wei Yang and
Yun-long Zhang A letter to the editor about the article
``A model for environmental sex reversal
in fish'' . . . . . . . . . . . . . . . 185--185
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Ole Lajord Munk Model-independent plot of dynamic PET
data facilitates data interpretation and
model selection . . . . . . . . . . . . 1--8
Anonymous Pages 1--204 (21 February 2012) . . . . 1--204
Bartholomäus V. Hirt and
Jonathan A. D. Wattis and
Simon P. Preston and
Charles A. Laughton The effects of a telomere destabilizing
agent on cancer cell-cycle dynamics ---
integrated modelling and experiments . . 9--22
Magnus G. Fagerlind and
Jeremy S. Webb and
Nicolas Barraud and
Diane McDougald and
Andreas Jansson and
Patric Nilsson and
Mikael Harlén and
Staffan Kjelleberg and
Scott A. Rice Dynamic modelling of cell death during
biofilm development . . . . . . . . . . 23--36
Nuris Figueroa-Morales and
Kalet León and
Roberto Mulet Stochastic approximation to the T cell
mediated specific response of the immune
system . . . . . . . . . . . . . . . . . 37--46
Sanyi Tang and
Yanni Xiao and
Lin Yuan and
Robert A. Cheke and
Jianhong Wu Campus quarantine (Fengxiao) for curbing
emergent infectious diseases: Lessons
from mitigating A/H1N1 in Xi'an, China 47--58
Graham M. Donovan and
Grant Lythe T-cell movement on the reticular network 59--67
László Zsolt Garamszegi and
Sándor Zseb\Hok and
János Török The relationship between syllable
repertoire similarity and pairing
success in a passerine bird species with
complex song . . . . . . . . . . . . . . 68--76
Ilmari Karonen Stable trimorphic coexistence in a
lattice model of spatial competition
with two site types . . . . . . . . . . 77--85
T. G. Vaughan and
P. D. Drummond and
A. J. Drummond Within-host demographic fluctuations and
correlations in early retroviral
infection . . . . . . . . . . . . . . . 86--99
Valentina Baldazzi and
Delphine Ropers and
Johannes Geiselmann and
Daniel Kahn and
Hidde de Jong Importance of metabolic coupling for the
dynamics of gene expression following a
diauxic shift in \bionameEscherichia
coli . . . . . . . . . . . . . . . . . . 100--115
PaweL Kocieniewski and
James R. Faeder and
Tomasz Lipniacki The interplay of double phosphorylation
and scaffolding in MAPK pathways . . . . 116--124
Lianping Yang and
Xiangde Zhang and
Hegui Zhu Alignment free comparison: Similarity
distribution between the DNA primary
sequences based on the shortest absent
word . . . . . . . . . . . . . . . . . . 125--131
Wim Hordijk and
Mike Steel Predicting template-based catalysis
rates in a simple catalytic reaction
model . . . . . . . . . . . . . . . . . 132--138
Diego A. Oyarzún and
Madalena Chaves and
Marit Hoff-Hoffmeyer-Zlotnik Multistability and oscillations in
genetic control of metabolism . . . . . 139--153
J. V. Greenman and
V. B. Pasour Threshold dynamics for periodically
forced ecological systems: The control
of population invasion and exclusion . . 154--167
Rangarajan Sudarsan and
Cody Thompson and
Peter G. Kevan and
Hermann J. Eberl Flow currents and ventilation in
Langstroth beehives due to brood
thermoregulation efforts of honeybees 168--193
Eunha Shim and
John J. Grefenstette and
Steven M. Albert and
Brigid E. Cakouros and
Donald S. Burke A game dynamic model for vaccine
skeptics and vaccine believers: Measles
as an example . . . . . . . . . . . . . 194--203
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
William A. Pruett and
Robert L. Hester and
Thomas G. Coleman The apparent hysteresis in
hormone-agonist relationships . . . . . 1--5
Anonymous Pages 1--102 (7 March 2012) . . . . . . 1--102
Herman Pontzer Relating ranging ecology, limb length,
and locomotor economy in terrestrial
animals . . . . . . . . . . . . . . . . 6--12
Chen Jia and
Xu-Feng Liu and
Min-Ping Qian and
Da-Quan Jiang and
Yu-Ping Zhang Kinetic behavior of the general modifier
mechanism of Botts and Morales with
non-equilibrium binding . . . . . . . . 13--20
Dov A. Pechenick and
Joshua L. Payne and
Jason H. Moore The influence of assortativity on the
robustness of signal-integration logic
in gene regulatory networks . . . . . . 21--32
Lei Zhang and
Fengchun Tian and
Shiyuan Wang and
Xiao Liu A novel coding method for gene mutation
correction during protein translation
process . . . . . . . . . . . . . . . . 33--40
Alberto d'Onofrio Spatiotemporal effects of a possible
chemorepulsion of tumor cells by immune
system effectors . . . . . . . . . . . . 41--48
Takuyo Aita and
Yuzuru Husimi Toward an evolutionary containment of
evolving pathogen-receptors by using an
ensemble of multiple mutant ligands:
From the viewpoint of fitness landscape
in sequence space . . . . . . . . . . . 49--55
Wataru Nakahashi and
Shiro Horiuchi Evolution of ape and human mating
systems . . . . . . . . . . . . . . . . 56--64
Stilianos Louca and
Sébastien Ibanez and
Didier Piau and
Laurence Després Specialized nursery pollination
mutualisms as evolutionary traps
stabilized by antagonistic traits . . . 65--83
Arno Steinacher and
Ottoline Leyser and
Richard H. Clayton A computational model of auxin and pH
dynamics in a single plant cell . . . . 84--94
Bo Chen and
Ping Ji Numericalization of the self adaptive
spectral rotation method for coding
region prediction . . . . . . . . . . . 95--102
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
M. A. K. Bulelzai and
Johan L. A. Dubbeldam Long time evolution of atherosclerotic
plaques . . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--188 (21 March 2012) . . . . . . 1--188
Luis J. Gilarranz and
Jordi Bascompte Spatial network structure and
metapopulation persistence . . . . . . . 11--16
Robert M. McMeeking and
Eduard Arzt and
Rüdiger Wehner Cataglyphis desert ants improve their
mobility by raising the gaster . . . . . 17--25
Joshua G. Schraiber and
Angela N. Kaczmarczyk and
Ricky Kwok and
Miran Park and
Rachel Silverstein and
Florentine U. Rutaganira and
Taruna Aggarwal and
Michael A. Schwemmer and
Carole L. Hom and
Richard K. Grosberg and
Sebastian J. Schreiber Constraints on the use of
lifespan-shortening \bionameWolbachia to
control dengue fever . . . . . . . . . . 26--32
Tanja Stadler and
Mike Steel Distribution of branch lengths and
phylogenetic diversity under homogeneous
speciation models . . . . . . . . . . . 33--40
Loredana G. Marcu and
Eva Bezak Neoadjuvant cisplatin for head and neck
cancer: Simulation of a novel schedule
for improved therapeutic ratio . . . . . 41--47
Marco Del Giudice Sex ratio dynamics and fluctuating
selection on personality . . . . . . . . 48--60
Hiroshi Kori and
Yoji Kawamura and
Naoki Masuda Structure of cell networks critically
determines oscillation regularity . . . 61--72
D. A. Rolls and
G. Daraganova and
R. Sacks-Davis and
M. Hellard and
R. Jenkinson and
E. McBryde and
P. E. Pattison and
G. L. Robins Modelling hepatitis C transmission over
a social network of injecting drug users 73--87
Marcello Delitala and
Tommaso Lorenzi A mathematical model for the dynamics of
cancer hepatocytes under therapeutic
actions . . . . . . . . . . . . . . . . 88--102
Andrew M. Bate and
Frank M. Hilker Rabbits protecting birds: Hypopredation
and limitations of hyperpredation . . . 103--115
Marguerite Robinson and
Nikolaos I. Stilianakis and
Yannis Drossinos Spatial dynamics of airborne infectious
diseases . . . . . . . . . . . . . . . . 116--126
Michael Hackenberg and
Antonio Rueda and
Pedro Carpena and
Pedro Bernaola-Galván and
Guillermo Barturen and
José L. Oliver Clustering of DNA words and biological
function: a proof of principle . . . . . 127--136
Yunjiao Wang and
Pawe\l Paszek and
Caroline A. Horton and
Hong Yue and
Michael R. H. White and
Douglas B. Kell and
Mark R. Muldoon and
David S. Broomhead A systematic survey of the response of a
model NF-$ \kappa $B signalling pathway
to TNF$ \alpha $ stimulation . . . . . . 137--147
Eduardo Liz and
Pawe\l Pilarczyk Global dynamics in a stage-structured
discrete-time population model with
harvesting . . . . . . . . . . . . . . . 148--165
Alexander M. Zöllner and
Adrian Buganza Tepole and
Ellen Kuhl On the biomechanics and mechanobiology
of growing skin . . . . . . . . . . . . 166--175
Saeil C. Murtada and
Anders Arner and
Gerhard A. Holzapfel Experiments and mechanochemical modeling
of smooth muscle contraction:
Significance of filament overlap . . . . 176--186
Ha Youn Lee and
Elena E. Giorgi and
Brandon F. Keele and
Brian Gaschen and
Gayathri S. Athreya and
Jesus F. Salazar-Gonzalez and
Kimmy T. Pham and
Paul A. Goepfert and
J. Michael Kilby and
Michael S. Saag and
Eric L. Delwart and
Michael P. Busch and
Beatrice H. Hahn and
George M. Shaw and
Bette T. Korber and
Tanmoy Bhattacharya and
Alan S. Perelson Corrigendum to ``Modeling sequence
evolution in acute HIV-1 infection'' [J.
Theor. Biol. \bf 261 (2009) 341--360] 187--187
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
K. C. Harding and
M. Begon and
A. Eriksson and
B. Wennberg Increased migration in host-pathogen
metapopulations can cause host
extinction . . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--156 (7 April 2012) . . . . . . 1--156
João A. Moreira and
Flávio L. Pinheiro and
Ana Nunes and
Jorge M. Pacheco Evolutionary dynamics of collective
action when individual fitness derives
from group decisions taken in the past 8--15
J. G. Sumner and
J. Fernández-Sánchez and
P. D. Jarvis Lie Markov models . . . . . . . . . . . 16--31
Vladimir Vainstein and
Oleg U. Kirnasovsky and
Yuri Kogan and
Zvia Agur Strategies for cancer stem cell
elimination: Insights from mathematical
modeling . . . . . . . . . . . . . . . . 32--41
Bahman Vahidi and
Nasser Fatouraee A biomechanical simulation of ureteral
flow during peristalsis using
intraluminal morphometric data . . . . . 42--50
Hervé Seligmann An overlapping genetic code for
frameshifted overlapping genes in
\bionameDrosophila mitochondria:
Antisense antitermination tRNAs UAR
insert serine . . . . . . . . . . . . . 51--76
Leonard G. Stepanskiy Sonication-induced unfolding proteins 77--81
Sara-Jane Dunn and
Alexander G. Fletcher and
S. Jonathan Chapman and
David J. Gavaghan and
James M. Osborne Modelling the role of the basement
membrane beneath a growing epithelial
monolayer . . . . . . . . . . . . . . . 82--91
S. Fischer and
P. Kurbatova and
N. Bessonov and
O. Gandrillon and
V. Volpert and
F. Crauste Modeling erythroblastic islands: Using a
hybrid model to assess the function of
central macrophage . . . . . . . . . . . 92--106
Marcus J. Tindall and
Louise Dyson and
Kieran Smallbone and
Philip K. Maini Modelling acidosis and the cell cycle in
multicellular tumour spheroids . . . . . 107--115
Tobias Siebert and
Michael Günther and
Reinhard Blickhan A 3D-geometric model for the deformation
of a transversally loaded muscle . . . . 116--121
Sayyed R. Mousavi Improved haplotype assembly using Xor
genotypes . . . . . . . . . . . . . . . 122--130
Sander P. van Noort and
Ricardo Águas and
Sébastien Ballesteros and
M. Gabriela M. Gomes The role of weather on the relation
between influenza and influenza-like
illness . . . . . . . . . . . . . . . . 131--137
Takashi Saitou and
Mahemuti Rouzimaimaiti and
Naohiko Koshikawa and
Motoharu Seiki and
Kazuhisa Ichikawa and
Takashi Suzuki Mathematical modeling of invadopodia
formation . . . . . . . . . . . . . . . 138--146
Jong-Hoon Kim and
James S. Koopman HIV transmissions by stage in dynamic
sexual partnerships . . . . . . . . . . 147--153
Michael S. Andersen and
John Rasmussen and
Michael Damsgaard Letter to the Editor . . . . . . . . . . 154--155
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Martin A. Nowak Evolving cooperation . . . . . . . . . . 1--8
Marco Archetti and
István Scheuring Review: Game theory of public goods in
one-shot social dilemmas without
assortment . . . . . . . . . . . . . . . 9--20
Robert Axelrod Launching ``The Evolution of
Cooperation'' . . . . . . . . . . . . . 21--24
Karl Sigmund Moral assessment in indirect reciprocity 25--30
James A. Damore and
Jeff Gore Understanding microbial cooperation . . 31--41
Ingela Alger and
Jörgen W. Weibull A generalization of Hamilton's rule ---
Love others how much? . . . . . . . . . 42--54
Burton Simon and
Jeffrey A. Fletcher and
Michael Doebeli Hamilton's rule in multi-level selection
models . . . . . . . . . . . . . . . . . 55--63
Matthijs van Veelen and
Julián García and
Maurice W. Sabelis and
Martijn Egas Group selection and inclusive fitness
are not equivalent; the Price equation
vs. models and statistics . . . . . . . 64--80
György Szabó and
Attila Szolnoki Selfishness, fraternity, and
other-regarding preference in spatial
evolutionary games . . . . . . . . . . . 81--87
Francisco C. Santos and
Flávio L. Pinheiro and
Tom Lenaerts and
Jorge M. Pacheco The role of diversity in the evolution
of cooperation . . . . . . . . . . . . . 88--96
Benjamin Allen and
Arne Traulsen and
Corina E. Tarnita and
Martin A. Nowak How mutation affects evolutionary games
on graphs . . . . . . . . . . . . . . . 97--105
Christoph Hauert and
Lorens A. Imhof Evolutionary games in deme structured,
finite populations . . . . . . . . . . . 106--112
Tore Ellingsen and
Jack Robles The evolution of parental investment:
Re-examining the anisogamy argument . . 113--119
Arne Traulsen and
Floyd A. Reed From genes to games: Cooperation and
cyclic dominance in meiotic drive . . . 120--125
Matteo Cavaliere and
Sean Sedwards and
Corina E. Tarnita and
Martin A. Nowak and
Attila Csikász-Nagy Prosperity is associated with
instability in dynamical networks . . . 126--138
Manfred Milinski and
Bettina Rockenbach On the interaction of the stick and the
carrot in social dilemmas . . . . . . . 139--143
Ross Cressman and
Jie-Wen Song and
Bo-Yu Zhang and
Yi Tao Cooperation and evolutionary dynamics in
the public goods game with institutional
incentives . . . . . . . . . . . . . . . 144--151
Alessandro Tavoni and
Maja Schlüter and
Simon Levin The survival of the conformist: Social
pressure and renewable resource
management . . . . . . . . . . . . . . . 152--161
Andrew M. Colman and
Lindsay Browning and
Briony D. Pulford Spontaneous similarity discrimination in
the evolution of cooperation . . . . . . 162--171
David G. Rand The promise of Mechanical Turk: How
online labor markets can help theorists
run behavioral experiments . . . . . . . 172--179
Partha Dasgupta Dark matters: Exploitation as
cooperation . . . . . . . . . . . . . . 180--187
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Ryota Iijima On delayed discrete evolutionary
dynamics . . . . . . . . . . . . . . . . 1--6
Anonymous Pages 1--376 (7 May 2012) . . . . . . . 1--376
Michael Knudsen and
Elisenda Feliu and
Carsten Wiuf Exact analysis of intrinsic qualitative
features of phosphorelays using
mathematical models . . . . . . . . . . 7--18
Gang Du and
Mao Sun Aerodynamic effects of corrugation and
deformation in flapping wings of
hovering hoverflies . . . . . . . . . . 19--28
Yuta Shiino and
Osamu Kuwazuru and
Yutaro Suzuki and
Satoshi Ono Swimming capability of the remopleuridid
trilobite \bionameHypodicranotus
striatus: Hydrodynamic functions of the
exoskeleton and the long, forked
hypostome . . . . . . . . . . . . . . . 29--38
Qiang Hou and
Zhen Jin and
Shigui Ruan Dynamics of rabies epidemics and the
impact of control efforts in Guangdong
Province, China . . . . . . . . . . . . 39--47
John Vandermeer and
Senay Yitbarek Self-organized spatial pattern
determines biodiversity in spatial
competition . . . . . . . . . . . . . . 48--56
Olaf Wolkenhauer and
Darryl Shibata and
Mihajlo D. Mesarovi\'c The role of theorem proving in systems
biology . . . . . . . . . . . . . . . . 57--61
James N. McNair and
J. Denis Newbold Turbulent particle transport in streams:
Can exponential settling be reconciled
with fluid mechanics? . . . . . . . . . 62--80
Kenta Suzuki and
Takehito Yoshida Non-random spatial coupling induces
desynchronization, chaos and
multistability in a
predator--prey-resource system . . . . . 81--90
J. Chifman and
A. Kniss and
P. Neupane and
I. Williams and
B. Leung and
Z. Deng and
P. Mendes and
V. Hower and
F. M. Torti and
S. A. Akman and
S. V. Torti and
R. Laubenbacher The core control system of intracellular
iron homeostasis: a mathematical model 91--99
Lin Wang and
Xiao Wang Influence of temporary migration on the
transmission of infectious diseases in a
migrants' home village . . . . . . . . . 100--109
Jun Nakabayashi A compartmentalization model of
hepatitis C virus replication: An
appropriate distribution of HCV RNA for
the effective replication . . . . . . . 110--117
Alexander G. Fletcher and
Christopher J. W. Breward and
S. Jonathan Chapman Mathematical modeling of monoclonal
conversion in the colonic crypt . . . . 118--133
Emmanuel Hanert Front dynamics in a two-species
competition model driven by Lévy flights 134--142
Gabriel Piedrafita and
Athel Cornish-Bowden and
Federico Morán and
Francisco Montero Size matters: Influence of stochasticity
on the self-maintenance of a simple
model of metabolic closure . . . . . . . 143--151
Sang Woo Park and
Marcos Intaglietta and
Daniel M. Tartakovsky Impact of endothelium roughness on blood
flow . . . . . . . . . . . . . . . . . . 152--160
Samantha M. Tracht and
Sara Y. Del Valle and
Brian K. Edwards Economic analysis of the use of
facemasks during pandemic (H1N1) 2009 161--172
Geoffrey V. Martin and
Yeoheung Yun and
Laura Conforti Modulation of T cell activation by
localized K$^+$ accumulation at the
immunological synapse --- a mathematical
model . . . . . . . . . . . . . . . . . 173--182
Jinliang Yang and
Rui Gao and
Max Q.-H. Meng and
Tzyh-Jong Tarn Colored Petri nets to model gene
mutation and amino acids classification 183--192
Gergely Horváth and
Jaromír Kovárík and
Friederike Mengel Limited memory can be beneficial for the
evolution of cooperation . . . . . . . . 193--205
Soheila Montaseri and
Nasrollah Moghadam-Charkari and
Fatemeh Zare-Mirakabad A heuristic approach to RNA-RNA
interaction prediction . . . . . . . . . 206--211
David G. Rand and
Martin A. Nowak Evolutionary dynamics in finite
populations can explain the full range
of cooperative behaviors observed in the
centipede game . . . . . . . . . . . . . 212--221
Annalisa J. Swan and
Alys R. Clark and
Merryn H. Tawhai A computational model of the topographic
distribution of ventilation in healthy
human lungs . . . . . . . . . . . . . . 222--231
Joshua R. Porter and
John S. Burg and
Peter J. Espenshade and
Pablo A. Iglesias Identifying a static nonlinear structure
in a biological system using noisy,
sparse data . . . . . . . . . . . . . . 232--241
Michael A. Berthaume and
Paul C. Dechow and
Jose Iriarte-Diaz and
Callum F. Ross and
David S. Strait and
Qian Wang and
Ian R. Grosse Probabilistic finite element analysis of
a craniofacial finite element model . . 242--253
Ioannis A. Papadakis and
Kiriakos Kotzabasis and
Konstadia Lika Modeling the dynamic modulation of light
energy in photosynthetic algae . . . . . 254--264
Nathaniel Hallinan The generalized time variable
reconstructed birth-death process . . . 265--276
Cassie S. Mitchell and
Robert H. Lee Cargo distributions differentiate
pathological axonal transport
impairments . . . . . . . . . . . . . . 277--291
Heather A. Barker and
Mark Broom and
Jan Rychtár A game theoretic model of
kleptoparasitism with strategic arrivals
and departures of beetles at dung pats 292--298
Jelena Gruji\'c and
José A. Cuesta and
Angel Sánchez On the coexistence of cooperators,
defectors and conditional cooperators in
the multiplayer iterated Prisoner's
Dilemma . . . . . . . . . . . . . . . . 299--308
Jennifer A. Flegg and
Helen M. Byrne and
Mark B. Flegg and
D. L. Sean McElwain Wound healing angiogenesis: The clinical
implications of a simple mathematical
model . . . . . . . . . . . . . . . . . 309--316
Jichen Shi and
Jian Xu and
Xiaorong Zhang and
Ling Yang Positive feedback induced memory effect
in ischemic preconditioning . . . . . . 317--323
J. M. García-Manso and
J. M. Martín-González and
D. Vaamonde and
M. E. Da Silva-Grigoletto The limitations of scaling laws in the
prediction of performance in endurance
events . . . . . . . . . . . . . . . . . 324--329
Onur Kerimo\uglu and
Dietmar Straile and
Frank Peeters Role of phytoplankton cell size on the
competition for nutrients and light in
incompletely mixed systems . . . . . . . 330--343
Callie J. Miller and
G. Bard Ermentrout and
Lance A. Davidson Rotational model for actin filament
alignment by myosin . . . . . . . . . . 344--359
Brittany A. Niccum and
Roby Poteau and
Glen E. Hamman and
Jan C. Varada and
Jewgeni H. Dshalalow and
Richard R. Sinden On an unbiased and consistent estimator
for mutation rates . . . . . . . . . . . 360--367
Andrew D. Higginson and
Michael P. Speed and
Graeme D. Ruxton Effects of anti-predator defence through
toxin sequestration on use of
alternative food microhabitats by small
herbivores . . . . . . . . . . . . . . . 368--375
Flora Cordoleani and
David Nerini and
Mathias Gauduchon and
Andrew Morozov and
Jean-Christophe Poggiale Corrigendum to ``Structural sensitivity
of biological models revisited'' [J.
Theor. Biol. \bf 283 (2011) 82--91] . . 376--376
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
W. C. H. Parr and
S. Wroe and
U. Chamoli and
H. S. Richards and
M. R. McCurry and
P. D. Clausen and
C. McHenry Toward integration of geometric
morphometrics and computational
biomechanics: New methods for 3D virtual
reconstruction and quantitative analysis
of Finite Element Models . . . . . . . . 1--14
Anonymous Pages 1--174 (21 May 2012) . . . . . . . 1--174
Fernando López-Caamal and
Míriam R. García and
Richard H. Middleton and
Heinrich J. Huber Positive feedback in the Akt/mTOR
pathway and its implications for growth
signal progression in skeletal muscle
cells: An analytical study . . . . . . . 15--27
Ridha Hambli and
Abdelwahed Barkaoui Physically based 3D finite element model
of a single mineralized collagen
microfibril . . . . . . . . . . . . . . 28--41
Valery I. Lim and
James F. Curran and
Maria B. Garber Hydration shells of molecules in
molecular association: a mechanism for
biomolecular recognition . . . . . . . . 42--48
A. K. Misra and
Vishal Singh A delay mathematical model for the
spread and control of water borne
diseases . . . . . . . . . . . . . . . . 49--56
Michael Weiss A model for transit time distributions
through organs that accounts for fractal
heterogeneity . . . . . . . . . . . . . 57--61
Lars Olof Björn and
Per Uvdal and
Shaoshan Li Ecological importance of the thermal
emissivity of avian eggshells . . . . . 62--66
M. Mercker and
M. Ptashnyk and
J. Kühnle and
D. Hartmann and
M. Weiss and
W. Jäger A multiscale approach to curvature
modulated sorting in biological
membranes . . . . . . . . . . . . . . . 67--82
Leonardo Martins and
Jarno Mäkelä and
Antti Häkkinen and
Meenakshisundaram Kandhavelu and
Olli Yli-Harja and
José M. Fonseca and
Andre S. Ribeiro Dynamics of transcription of closely
spaced promoters in \bionameEscherichia
coli, one event at a time . . . . . . . 83--94
Timothy Steckmann and
Zubair Awan and
Bernard S. Gerstman and
Prem P. Chapagain Kinetics of peptide secondary structure
conversion during amyloid $ \beta
$-protein fibrillogenesis . . . . . . . 95--102
Micael Ehn and
Kevin Laland Adaptive strategies for cumulative
cultural learning . . . . . . . . . . . 103--111
M. P. Adams and
D. G. Mallet and
G. J. Pettet Active regulation of the epidermal
calcium profile . . . . . . . . . . . . 112--121
Paul Macklin and
Mary E. Edgerton and
Alastair M. Thompson and
Vittorio Cristini Patient-calibrated agent-based modelling
of ductal carcinoma in situ (DCIS): From
microscopic measurements to macroscopic
predictions of clinical progression . . 122--140
Davide Vergni and
Sandro Iannaccone and
Stefano Berti and
Massimo Cencini Invasions in heterogeneous habitats in
the presence of advection . . . . . . . 141--152
Ren Jiu-sheng Effects of dispersion of fiber
orientation on the mechanical property
of the arterial wall . . . . . . . . . . 153--160
Krishnendu Chatterjee and
Damien Zufferey and
Martin A. Nowak Evolutionary game dynamics in
populations with different learners . . 161--173
James E. Lyon and
Sagar A. Pandit and
Carel P. van Schaik and
Gauri R. Pradhan Corrigendum to ``Mating strategies in
primates: a game theoretical approach to
infanticide'' [J. Theor. Biol. \bf 294
(2011) 103--108] . . . . . . . . . . . . 174--174
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
S. J. Payne and
C. N. J. Oakes and
C. S. Park Vasomotion does inhibit mass exchange
between axisymmetric blood vessels and
tissue . . . . . . . . . . . . . . . . . 1--5
Anonymous Pages 1--96 (7 June 2012) . . . . . . . 1--96
Akiko Satake and
Yoh Iwasa A stochastic model of chromatin
modification: Cell population coding of
winter memory in plants . . . . . . . . 6--17
Frederick Chen A mathematical analysis of public
avoidance behavior during epidemics
using game theory . . . . . . . . . . . 18--28
Yao Li and
Gaurav Dwivedi and
Wen Huang and
Melissa L. Kemp and
Yingfei Yi Quantification of degeneracy in
biological systems for characterization
of functional interactions between
modules . . . . . . . . . . . . . . . . 29--38
Pete C. Trimmer and
John M. McNamara and
Alasdair I. Houston and
James A. R. Marshall Does natural selection favour the
Rescorla--Wagner rule? . . . . . . . . . 39--52
Rosy Paola Cárdenas Sandoval and
Diego Alexander Garzón-Alvarado and
Angélica Maria Ramírez Martínez A mathematical model of the process of
ligament repair: Effect of cold therapy
and mechanical stress . . . . . . . . . 53--61
Sayed-Amir Marashi and
Laszlo David and
Alexander Bockmayr On flux coupling analysis of metabolic
subsystems . . . . . . . . . . . . . . . 62--69
Mark Broom and
Jan Rychtár A general framework for analysing
multiplayer games in networks using
territorial interactions as a case study 70--80
Dusan Ristanovi\'c and
Bojana Krstonosi\'c and
Nebojsa T. Milosevi\'c and
Radmila Gudovi\'c Mathematical modelling of
transformations of asymmetrically
distributed biological data: An
application to a quantitative
classification of spiny neurons of the
human putamen . . . . . . . . . . . . . 81--88
Arni S. R. Srinivasa Rao Understanding theoretically the impact
of reporting of disease cases in
epidemiology . . . . . . . . . . . . . . 89--95
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Olivia Prosper and
Nick Ruktanonchai and
Maia Martcheva Assessing the role of spatial
heterogeneity and human movement in
malaria dynamics and control . . . . . . 1--14
Anonymous Pages 1--154 (21 June 2012) . . . . . . 1--154
S. Suweis and
E. Bertuzzo and
L. Mari and
I. Rodriguez-Iturbe and
A. Maritan and
A. Rinaldo On species persistence-time
distributions . . . . . . . . . . . . . 15--24
Arturo Marín and
Héctor Tejero and
Juan Carlos Nuño and
Francisco Montero Characteristic time in quasispecies
evolution . . . . . . . . . . . . . . . 25--32
Louis C. Martineau Simple thermodynamic model of unassisted
proton shuttle uncoupling and prediction
of activity from calculated speciation,
lipophilicity, and molecular geometry 33--61
Andreas Kremling and
Dietrich Flockerzi Structural analysis of a core model for
carbohydrate uptake in
\bionameEscherichia coli . . . . . . . . 62--74
J. Kaiser and
T. Lemaire and
S. Naili and
V. Sansalone and
S. V. Komarova Do calcium fluxes within cortical bone
affect osteocyte mechanosensitivity? . . 75--86
Igor Pantic and
Ljubica Harhaji-Trajkovic and
Aleksandar Pantovic and
Nebojsa T. Milosevic and
Vladimir Trajkovic Changes in fractal dimension and
lacunarity as early markers of
UV-induced apoptosis . . . . . . . . . . 87--92
Michel Destrade and
Yi Liu and
Jeremiah G. Murphy and
Ghassan S. Kassab Uniform transmural strain in
pre-stressed arteries occurs at
physiological pressure . . . . . . . . . 93--97
Mark Westoby and
William K. Cornwell and
Daniel S. Falster An evolutionary attractor model for
sapwood cross section in relation to
leaf area . . . . . . . . . . . . . . . 98--109
Xiaofeng Yang and
Vladimir Mironov and
Qi Wang Modeling fusion of cellular aggregates
in biofabrication using phase field
theories . . . . . . . . . . . . . . . . 110--118
Michael L. Manapat and
David G. Rand and
Christina Pawlowitsch and
Martin A. Nowak Stochastic evolutionary dynamics resolve
the Traveler's Dilemma . . . . . . . . . 119--127
Chris A. Brackley and
David S. Broomhead and
M. Carmen Romano and
Marco Thiel A max-plus model of ribosome dynamics
during mRNA translation . . . . . . . . 128--140
Barbara Szomolay and
Tim D. Eubank and
Ryan D. Roberts and
Clay B. Marsh and
Avner Friedman Modeling the inhibition of breast cancer
growth by GM-CSF . . . . . . . . . . . . 141--151
Cenk Sumen and
Timothy E. Reddy and
Mark S. Alber and
Peter P. Lee Corrigendum to: ``Agent-based modeling
of the context dependency in T cell
recognition'' [J. Theor. Biol. \bf 236
(2005) 376--391] . . . . . . . . . . . . 152--153
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
F. García-Camacho and
A. Sánchez-Mirón and
E. Molina-Grima and
F. Camacho-Rubio and
J. C. Merchuck A mechanistic model of photosynthesis in
microalgae including photoacclimation
dynamics . . . . . . . . . . . . . . . . 1--15
Anonymous Pages 1--308 (7 July 2012) . . . . . . . 1--308
Mochamad Apri and
Maarten de Gee and
Jaap Molenaar Complexity reduction preserving
dynamical behavior of biochemical
networks . . . . . . . . . . . . . . . . 16--26
Konstantin G. Guria and
Anita R. Gagarina and
Georgy Th. Guria Instabilities in fibrinolytic regulatory
system. Theoretical analysis of blow-up
phenomena . . . . . . . . . . . . . . . 27--38
H. Youssefpour and
X. Li and
A. D. Lander and
J. S. Lowengrub Multispecies model of cell lineages and
feedback control in solid tumors . . . . 39--59
Joanne Simpson and
Mick Roberts Modelling heterogeneous host immune
response in a multi-strain system . . . 60--65
Kazuhiro Bessho and
Yoh Iwasa Variability in the evolutionarily stable
seasonal timing of germination and
maturation of annuals and the mode of
competition . . . . . . . . . . . . . . 66--80
Ping-an He and
Dan Li and
Yanping Zhang and
Xin Wang and
Yuhua Yao A 3D graphical representation of protein
sequences based on the Gray code . . . . 81--87
Guo-Liang Fan and
Qian-Zhong Li Predict mycobacterial proteins
subcellular locations by incorporating
pseudo-average chemical shift into the
general form of Chou's pseudo amino acid
composition . . . . . . . . . . . . . . 88--95
Ghasem Mahdevar and
Mehdi Sadeghi and
Abbas Nowzari-Dalini Transcription factor binding sites
detection by using alignment-based
approach . . . . . . . . . . . . . . . . 96--102
Kaihui Liu and
Ruiqi Wang MicroRNA-mediated regulation in the
mammalian circadian rhythm . . . . . . . 103--110
Cédric Gaucherel and
Henrik Jeldtoft Jensen Origins of evolution: Non-acquired
characters dominates over acquired
characters in changing environment . . . 111--120
Bing Wang and
Lang Cao and
Hideyuki Suzuki and
Kazuyuki Aihara Impacts of clustering on interacting
epidemics . . . . . . . . . . . . . . . 121--130
Pavel A. Prokharau and
Fred J. Vermolen and
José Manuel García-Aznar Model for direct bone apposition on
pre-existing surfaces, during
peri-implant osseointegration . . . . . 131--142
Sarah M. Roy and
Dominik Wodarz Infection of HIV-specific CD4 T helper
cells and the clonal composition of the
response . . . . . . . . . . . . . . . . 143--151
Giovanni Lo Iacono and
Frank van den Bosch and
Neil Paveley The evolution of plant pathogens in
response to host resistance: Factors
affecting the gain from deployment of
qualitative and quantitative resistance 152--163
Gerardo Presbitero and
Fergal J. O'Brien and
T. Clive Lee and
David Taylor Distribution of microcrack lengths in
bone in vivo and in vitro . . . . . . . 164--171
Thomas P. Prescott and
Antonis Papachristodoulou Guaranteed error bounds for structured
complexity reduction of biochemical
networks . . . . . . . . . . . . . . . . 172--182
Micha\l Krízek and
Pavel Krízek Why has nature invented three stop
codons of DNA and only one start codon? 183--187
Erica Staaterman and
Claire B. Paris and
Judith Helgers Orientation behavior in fish larvae: a
missing piece to Hjort's critical period
hypothesis . . . . . . . . . . . . . . . 188--196
Dashun Xu and
Gregory J. Sandland and
Dennis J. Minchella and
Zhilan Feng Interactions among virulence,
coinfection and drug resistance in a
complex life-cycle parasite . . . . . . 197--210
Saritha Namboodiri and
Alessandro Giuliani and
Achuthsankar S. Nair and
Pawan K. Dhar Looking for a sequence based allostery
definition: a statistical journey at
different resolution scales . . . . . . 211--218
N. Shayeghi and
T. Ng and
A. C. C. Coolen Direct Response Analysis in cellular
signalling networks . . . . . . . . . . 219--225
Graeme P. Boswell Modelling combat strategies in fungal
mycelia . . . . . . . . . . . . . . . . 226--234
Edward K. Agarwala and
Hillel J. Chiel and
Peter J. Thomas Pursuit of food versus pursuit of
information in a Markovian
perception-action loop model of foraging 235--272
Motohide Seki Intra-individual conflicts between
autosomal and X-linked altruistic genes:
Evolutionary perspectives of
sex-specific grandmothering . . . . . . 273--285
Kaare H. Jensen and
Kirstine Berg-Sòrensen and
Sòren M. M. Friis and
Tomas Bohr Analytic solutions and universal
properties of sugar loading models in
Münch phloem flow . . . . . . . . . . . . 286--296
Angela Yi-Chen Yeh and
Andy Gardner A general ploidy model for the evolution
of helping in viscous populations . . . 297--303
Juan C. Jiménez-Muñoz and
José A. Sobrino Comment on ``Ecological importance of
the thermal emissivity of avian
eggshells'' . . . . . . . . . . . . . . 304--307
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Zoran Konkoli Modeling reaction noise with a desired
accuracy by using the X level approach
reaction noise estimator (XARNES) method 1--14
Anonymous Pages 1--144 (21 July 2012) . . . . . . 1--144
Abolfazl Jahangiri and
Iraj Rasooli and
Mohammad Reza Rahbar and
Saeed Khalili and
Jafar Amani and
Kobra Ahmadi Zanoos Precise detection of \bionameL.
monocytogenes hitting its highly
conserved region possessing several
specific antibody binding sites . . . . 15--23
Siddhartha P. Chakrabarty and
John M. Murray Modelling hepatitis C virus infection
and the development of hepatocellular
carcinoma . . . . . . . . . . . . . . . 24--29
S. Parnell and
T. R. Gottwald and
W. R. Gilks and
F. van den Bosch Estimating the incidence of an epidemic
when it is first discovered and the
design of early detection monitoring . . 30--36
Bahram Hemmateenejad and
Ramin Miri and
Maryam Elyasi A segmented principal component
analysis-regression approach to QSAR
study of peptides . . . . . . . . . . . 37--44
Laurence Palk and
James Sneyd and
Kate Patterson and
Trevor J. Shuttleworth and
David I. Yule and
Oliver Maclaren and
Edmund J. Crampin Modelling the effects of calcium waves
and oscillations on saliva secretion . . 45--53
Scott A. McKinley and
Avanti Athreya and
John Fricks and
Peter R. Kramer Asymptotic analysis of microtubule-based
transport by multiple identical
molecular motors . . . . . . . . . . . . 54--69
Erika Asano and
Deby L. Cassill Modeling temperature-mediated
fluctuation in colony size in the fire
ant, Solenopsis invicta . . . . . . . . 70--77
Jan Kloppenborg Mòller and
Kirsten Riber Bergmann and
Lasse Engbo Christiansen and
Henrik Madsen Development of a restricted state space
stochastic differential equation model
for bacterial growth in rich media . . . 78--87
Asher Uziel and
Lewi Stone Determinants of periodicity in
seasonally driven epidemics . . . . . . 88--95
Akihiko Mougi Unusual predator--prey dynamics under
reciprocal phenotypic plasticity . . . . 96--102
Kamuela E. Yong and
Yi Li and
Stephen D. Hendrix Habitat choice of multiple pollinators
in almond trees and its potential effect
on pollen movement and productivity: a
theoretical approach using the
Shigesada--Kawasaki--Teramoto model . . 103--109
Elena Inarra and
Annick Laruelle Artificial distinction and real
discrimination . . . . . . . . . . . . . 110--117
Ralf Möller A model of ant navigation based on
visual prediction . . . . . . . . . . . 118--130
Timothy G. Bromage and
Russell T. Hogg and
Rodrigo S. Lacruz and
Chen Hou Primate enamel evinces long period
biological timing and regulation of life
history . . . . . . . . . . . . . . . . 131--144
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Changbing Tang and
Xiang Li and
Lang Cao and
Jingyuan Zhan The $ \sigma $ law of evolutionary
dynamics in community-structured
population . . . . . . . . . . . . . . . 1--6
Anonymous Pages 1--146 (7 August 2012) . . . . . . 1--146
Sebastian J. Plitzko and
Barbara Drossel and
Christian Guill Complexity-stability relations in
generalized food-web models with
realistic parameters . . . . . . . . . . 7--14
Rachele Allena and
Denis Aubry `Run-and-tumble' or `look-and-run'? A
mechanical model to explore the behavior
of a migrating amoeboid cell . . . . . . 15--31
Kai Ramsch and
Chris R. Reid and
Madeleine Beekman and
Martin Middendorf A mathematical model of foraging in a
dynamic environment by trail-laying
Argentine ants . . . . . . . . . . . . . 32--45
Andrew Allstadt and
Thomas Caraco and
F. Molnár and
G. Korniss Interference competition and invasion:
Spatial structure, novel weapons and
resistance zones . . . . . . . . . . . . 46--60
Kai A. Konrad and
Florian Morath Evolutionarily stable in-group
favoritism and out-group spite in
intergroup conflict . . . . . . . . . . 61--67
Junhong Zhou and
Dongdong Liu and
Xin Li and
Jing Ma and
Jue Zhang and
Jing Fang Pink noise: Effect on complexity
synchronization of brain activity and
sleep consolidation . . . . . . . . . . 68--72
Paul J. Hurtado Within-host dynamics of mycoplasma
infections: Conjunctivitis in wild
passerine birds . . . . . . . . . . . . 73--92
Cédric Sueur Viability of decision-making systems in
human and animal groups . . . . . . . . 93--103
Kevin Walters Parameter estimation for an immortal
model of colonic stem cell division
using approximate Bayesian computation 104--114
Samad Jahandideh and
Abbas Mahdavi RFCRYS: Sequence-based protein
crystallization propensity prediction by
means of random forest . . . . . . . . . 115--119
Florian T. Muijres and
Per Henningsson and
Melanie Stuiver and
Anders Hedenström Aerodynamic flight performance in
flap-gliding birds and bats . . . . . . 120--128
Ling Xue and
H. Morgan Scott and
Lee W. Cohnstaedt and
Caterina Scoglio A network-based meta-population approach
to model Rift Valley fever epidemics . . 129--144
Azim Jinha and
Rachid Ait-Haddou and
Motoshi Kaya and
Walter Herzog Response to Letter to the Editor
regarding Jinha et al. (2009) ``A
task-specific validation of homogeneous
non-linear optimization approaches'' . . 145--145
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Robert J. Vickerstaff and
Tobias Merkle Path integration mediated systematic
search: a Bayesian model . . . . . . . . 1--19
Anonymous Pages 1--212 (21 August 2012) . . . . . 1--212
Hisashi Ohtsuki Does synergy rescue the evolution of
cooperation? An analysis for homogeneous
populations with non-overlapping
generations . . . . . . . . . . . . . . 20--28
Andrew Morozov and
Alex Best Predation on infected host promotes
evolutionary branching of virulence and
pathogens' biodiversity . . . . . . . . 29--36
Shunsuke Sakurai and
Seido Nagano A molecular network underlying
spontaneous cAMP oscillation and
synchronization in \bionameDictyostelium 37--41
Pascal R. Buenzli and
Peter Pivonka and
Bruce S. Gardiner and
David W. Smith Modelling the anabolic response of bone
using a cell population model . . . . . 42--52
Sebastián Risau-Gusman and
Pablo M. Gleiser Modelling the effect of phosphorylation
on the circadian clock of
\bionameDrosophila . . . . . . . . . . . 53--61
Zijian Liu and
Shouming Zhong and
Zhidong Teng $n$ Species impulsive migration model
with Markovian switching . . . . . . . . 62--69
Chae Young Cha and
Akinori Noma Steady-state solutions of cell volume in
a cardiac myocyte model elaborated for
membrane excitation, ion homeostasis and
Ca$^{2+}$ dynamics . . . . . . . . . . . 70--81
Blerta Shtylla and
James P. Keener A mathematical model of ParA
filament-mediated chromosome movement in
Caulobacter crescentus . . . . . . . . . 82--95
Suncana Gecek and
Tarzan Legovi\'c Impact of maximum sustainable yield on
competitive community . . . . . . . . . 96--103
M. González and
C. Gutiérrez and
R. Martínez Extinction conditions for Y-linked
mutant-alleles through two-sex branching
processes with blind-mating structure 104--116
Friederike Mengel On the evolution of coarse categories 117--124
R. J. Dyson and
L. R. Band and
O. E. Jensen A model of crosslink kinetics in the
expanding plant cell wall: Yield stress
and enzyme action . . . . . . . . . . . 125--136
Aylin Günel Modelling the interactions between TLR4
and IFN$ \beta $ pathways . . . . . . . 137--148
Gang Huang and
Yasuhiro Takeuchi and
Andrei Korobeinikov HIV evolution and progression of the
infection to AIDS . . . . . . . . . . . 149--159
Yashar Sarbaz and
Farzad Towhidkhah and
Ayyoob Jafari and
Shahriar Gharibzadeh Do the chaotic features of gait change
in Parkinson's disease? . . . . . . . . 160--167
Julián García and
Arne Traulsen Leaving the loners alone: Evolution of
cooperation in the presence of
antisocial punishment . . . . . . . . . 168--173
Philippos K. Tsourkas and
Das Somkanya C. and
Paul Yu-Yang and
Wanli Liu and
Susan K. Pierce and
Subhadip Raychaudhuri Formation of BCR oligomers provides a
mechanism for B cell affinity
discrimination . . . . . . . . . . . . . 174--182
Miranda I. Teboh-Ewungkem and
Miao Wang Male fecundity and optimal gametocyte
sex ratios for \bionamePlasmodium
falciparum during incomplete
fertilization . . . . . . . . . . . . . 183--192
Jozef Nahalka Glycocodon theory-the first table of
glycocodons . . . . . . . . . . . . . . 193--204
Weihan Li and
Sandeep Krishna and
Simone Pigolotti and
Namiko Mitarai and
Mogens H. Jensen Switching between oscillations and
homeostasis in competing negative and
positive feedback motifs . . . . . . . . 205--210
Abid Ali Lashari and
Faiz Ahmad False mathematical reasoning in biology 211--211
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Gibin G. Powathil and
Kirsty E. Gordon and
Lydia A. Hill and
Mark A. J. Chaplain Modelling the effects of cell-cycle
heterogeneity on the response of a solid
tumour to chemotherapy: Biological
insights from a hybrid multiscale
cellular automaton model . . . . . . . . 1--19
Anonymous Pages 1--146 (7 September 2012) . . . . 1--146
Jan Bocianowski A comparison of two methods to estimate
additive-by-additive interaction of QTL
effects by a simulation study . . . . . 20--24
Tara N. Marriage and
Maria E. Orive Mutation-selection balance and mixed
mating with asexual reproduction . . . . 25--35
Tim Schellekens and
Tobias van Kooten Coexistence of two stage-structured
intraguild predators . . . . . . . . . . 36--44
K. B. Blyuss and
L. B. Nicholson The role of tunable activation
thresholds in the dynamics of
autoimmunity . . . . . . . . . . . . . . 45--55
Michael U. Kemp and
Judy Shamoun-Baranes and
E. Emiel van Loon and
James D. McLaren and
Adriaan M. Dokter and
Willem Bouten Quantifying flow-assistance and
implications for movement research . . . 56--67
James K. Miller and
Hope T. Badawy and
Curtis Clemons and
K. L. Kreider and
Pat Wilber and
Amy Milsted and
Gerald Young Development of the Pseudomonas
aeruginosa mushroom morphology and
cavity formation by iron-starvation: a
mathematical modeling study . . . . . . 68--78
Christoph K. Schmitt and
Christian Guill and
Barbara Drossel The robustness of cyclic dominance under
random fluctuations . . . . . . . . . . 79--87
Tamás Dávid-Barrett and
R. I. M. Dunbar Cooperation, behavioural synchrony and
status in social networks . . . . . . . 88--95
Dipjyoti Das and
Dibyendu Das and
Ashok Prasad Giant number fluctuations in microbial
ecologies . . . . . . . . . . . . . . . 96--104
Daqing Guo and
Chunguang Li Stochastic resonance in Hodgkin--Huxley
neuron induced by unreliable synaptic
transmission . . . . . . . . . . . . . . 105--114
Wim Hordijk and
Olivier Broennimann Dispersal routes reconstruction and the
minimum cost arborescence problem . . . 115--122
Sanyi Tang and
Yanni Xiao and
Ning Wang and
Hulin Wu Piecewise HIV virus dynamic model with
CD4 + T cell count-guided therapy: I . . 123--134
Yinxia Hu and
Tonghua Li and
Jiangming Sun and
Shengnan Tang and
Wenwei Xiong and
Dapeng Li and
Guanyan Chen and
Peisheng Cong Predicting Gram-positive bacterial
protein subcellular localization based
on localization motifs . . . . . . . . . 135--140
S. Lorente and
E. Cetkin and
T. Bello-Ochende and
J. P. Meyer and
A. Bejan The constructal-law physics of why
swimmers must spread their fingers and
toes . . . . . . . . . . . . . . . . . . 141--146
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
M. P. Curtis and
J. C. Kirkman-Brown and
T. J. Connolly and
E. A. Gaffney Modelling a tethered mammalian sperm
cell undergoing hyperactivation . . . . 1--10
Anonymous Pages 1--204 (21 September 2012) . . . . 1--204
Serik Sagitov and
Krzysztof Bartoszek Interspecies correlation for neutrally
evolving traits . . . . . . . . . . . . 11--19
Cinthia Marie Tanaka and
Yoh Iwasa Cultural evolution of a belief
controlling human mate choice: Dynamic
modeling of the hinoeuma superstition
in Japan . . . . . . . . . . . . . . . . 20--28
Liyan Song and
Yunbo Guo and
Qingkai Deng and
Jinming Li TH17 functional study in severe asthma
using agent based model . . . . . . . . 29--33
Mikolaj Rybi\'nski and
Anna Gambin Model-based selection of the robust
JAK-STAT activation mechanism . . . . . 34--46
Kenichi W. Okamoto and
Priyanga Amarasekare The biological control of disease
vectors . . . . . . . . . . . . . . . . 47--57
Atsushi Yamauchi and
Arndt Telschow Bistability of endosymbiont evolution of
genome size and host sex control . . . . 58--66
Damien Denis and
Jean-Sébastien Pierre and
Joan van Baaren and
Jacques J. M. van Alphen Physiological adaptations to climate
change in pro-ovigenic parasitoids . . . 67--77
I. Arnold Emerson and
K. M. Gothandam Residue centrality in alpha helical
polytopic transmembrane protein
structures . . . . . . . . . . . . . . . 78--87
Anders Johansson and
Kai Ramsch and
Martin Middendorf and
David J. T. Sumpter Tuning positive feedback for signal
detection in noisy dynamic environments 88--95
M. Broom and
R. N. Hughes and
M. T. Burrows and
G. D. Ruxton Evolutionarily stable sexual allocation
by both stressed and unstressed
potentially simultaneous hermaphrodites
within the same population . . . . . . . 96--102
Luigi Catacuzzeno and
Bernard Fioretti and
Fabio Franciolini A theoretical study on the role of
Ca$^{2+}$-activated K$^+$ channels in
the regulation of hormone-induced
Ca$^{2+}$ oscillations and their
synchronization in adjacent cells . . . 103--112
Vicenç Méndez and
Daniel Campos and
Ignacio Pagonabarraga and
Sergei Fedotov Density-dependent dispersal and
population aggregation patterns . . . . 113--120
Vincenzo Bonifaci and
Kurt Mehlhorn and
Girish Varma \bionamePhysarum can compute shortest
paths . . . . . . . . . . . . . . . . . 121--133
Krzysztof Argasinski The dynamics of sex ratio evolution
Dynamics of global population parameters 134--146
Amanda Galante and
Susanne Wisen and
Devaki Bhaya and
Doron Levy Modeling local interactions during the
motion of cyanobacteria . . . . . . . . 147--158
Olga Ilie and
Mark C. M. van Loosdrecht and
Cristian Picioreanu Mathematical modelling of tooth
demineralisation and pH profiles in
dental plaque . . . . . . . . . . . . . 159--175
Shweta Bansal and
Lauren Ancel Meyers The impact of past epidemics on future
disease dynamics . . . . . . . . . . . . 176--184
Erkki Somersalo and
Rossana Occhipinti and
Walter F. Boron and
Daniela Calvetti A reaction-diffusion model of CO 2
influx into an oocyte . . . . . . . . . 185--203
Pascal R. Buenzli and
Peter Pivonka and
Bruce S. Gardiner and
David W. Smith Corrigendum to ``Modelling the anabolic
response of bone using a cell population
model'' [J. Theor. Biol. \bf 307 (2012)
42--52] . . . . . . . . . . . . . . . . 204--204
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Massimo Di Giulio The `recently' split transfer RNA genes
may be close to merging the two halves
of the tRNA rather than having just
separated them . . . . . . . . . . . . . 1--2
Anonymous Pages 1--256 (7 October 2012) . . . . . 1--256
Yoram Louzoun and
Vitaly V. Ganusov Evolution of viral life-cycle in
response to cytotoxic T
lymphocyte-mediated immunity . . . . . . 3--13
Andrew P. McGovern and
Benjamin E. Powell and
Timothy J. T. Chevassut A dynamic multi-compartmental model of
DNA methylation with demonstrable
predictive value in hematological
malignancies . . . . . . . . . . . . . . 14--20
Junfen Shi and
Neil Curtis and
Laura C. Fitton and
Paul O'Higgins and
Michael J. Fagan Developing a musculoskeletal model of
the primate skull: Predicting muscle
activations, bite force, and joint
reaction forces using multibody dynamics
analysis and advanced optimisation
methods . . . . . . . . . . . . . . . . 21--30
József Garay and
Zoltán Varga and
Tomás Cabello and
Manuel Gámez Optimal nutrient foraging strategy of an
omnivore: Liebig's law determining
numerical response . . . . . . . . . . . 31--42
Maroussia Favre and
Didier Sornette Strong gender differences in
reproductive success variance, and the
times to the most recent common
ancestors . . . . . . . . . . . . . . . 43--54
Yasuyuki Suzuki and
Taishin Nomura and
Maura Casadio and
Pietro Morasso Intermittent control with ankle, hip,
and mixed strategies during quiet
standing: a theoretical proposal based
on a double inverted pendulum model . . 55--79
Suyu Mei Predicting plant protein subcellular
multi-localization by Chou's PseAAC
formulation based multi-label homolog
knowledge transfer learning . . . . . . 80--87
Marysa Laguë and
Nessy Tania and
Joel Heath and
Leah Edelstein-Keshet The effects of facilitation and
competition on group foraging in patches 88--96
Gregory A. Handy and
Bradford E. Peercy Extending the IP 3 receptor model to
include competition with partial
agonists . . . . . . . . . . . . . . . . 97--104
Giao T. Huynh and
Libin Rong Modeling the dynamics of virus shedding
into the saliva of Epstein--Barr virus
positive individuals . . . . . . . . . . 105--114
Ahmed Al-Jumaily and
Leizhi Chen Estimation of airway smooth muscle
stiffness changes due to length
oscillation using artificial neural
network . . . . . . . . . . . . . . . . 115--118
Criseida Zamora-Chimal and
Moisés Santillán and
Jesús Rodríguez-González Influence of the feedback loops in the
trp operon of \bionameB. subtilis on the
system dynamic response and noise
amplitude . . . . . . . . . . . . . . . 119--131
Inkyung Jung and
Dongsup Kim Histone modification profiles
characterize function-specific gene
regulation . . . . . . . . . . . . . . . 132--142
Yusur Al-Nuaimi and
Marc Goodfellow and
Ralf Paus and
Gerold Baier A prototypic mathematical model of the
human hair cycle . . . . . . . . . . . . 143--159
José Luis Fernández Theoretical approaches for detection of
sequence-specific Sister-Chromatid
Exchanges in interphase cells . . . . . 160--163
Lionel Xavier Dupuy and
Matthieu Vignes An algorithm for the simulation of the
growth of root systems on deformable
domains . . . . . . . . . . . . . . . . 164--174
Yixian Song and
Stefan Scheu and
Barbara Drossel Life histories and Cope's rule from an
explicit resource-consumer model based
on metabolic theory . . . . . . . . . . 175--182
William H. James Hypotheses on the stability and
variation of human sex ratios at birth 183--186
T. K. Kar and
Abhijit Ghorai and
Soovoojeet Jana Dynamics of pest and its predator model
with disease in the pest and optimal use
of pesticide . . . . . . . . . . . . . . 187--198
Lasse Ruokolainen and
Jörgen Ripa The strength of species interactions
modifies population responses to
environmental variation in competitive
communities . . . . . . . . . . . . . . 199--205
Joe Yuichiro Wakano and
Laurent Lehmann Evolutionary and convergence stability
for continuous phenotypes in finite
populations derived from two-allele
models . . . . . . . . . . . . . . . . . 206--215
Michael Netzer and
Karl G. Kugler and
Laurin A. J. Müller and
Klaus M. Weinberger and
Armin Graber and
Christian Baumgartner and
Matthias Dehmer A network-based feature selection
approach to identify metabolic
signatures in disease . . . . . . . . . 216--222
Shao-Ping Shi and
Jian-Ding Qiu and
Xing-Yu Sun and
Sheng-Bao Suo and
Shu-Yun Huang and
Ru-Ping Liang A method to distinguish between lysine
acetylation and lysine methylation from
protein sequences . . . . . . . . . . . 223--230
R. G. Brown and
A. F. James and
J. W. Pitchford and
M. J. Plank Habitat fragmentation: Simple models for
local persistence and the spread of
invasive species . . . . . . . . . . . . 231--238
R. G. M. van der Sman and
M. Sanders Prediction of postharvest firmness of
apple using biological switch model . . 239--248
Jianghong Dai Novel molecular fossils of bacteria:
Insights into hydrothermal origin of
life . . . . . . . . . . . . . . . . . . 249--256
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Thomas R. Johnston and
Mont Hubbard Optimization of the visco-elastic
parameters describing the heel-region of
a prosthesis . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--152 (21 October 2012) . . . . . 1--152
Naoki Masuda Ingroup favoritism and intergroup
cooperation under indirect reciprocity
based on group reputation . . . . . . . 8--18
Pierre Gabriel and
Shawn P. Garbett and
Vito Quaranta and
Darren R. Tyson and
Glenn F. Webb The contribution of age structure to
cell population responses to targeted
therapeutics . . . . . . . . . . . . . . 19--27
Benjamin Allen and
Martin A. Nowak Evolutionary shift dynamics on a cycle 28--39
Pooja Mishra and
Paras Nath Pandey Elman RNN based classification of
proteins sequences on account of their
mutual information . . . . . . . . . . . 40--45
Mathieu Moslonka-Lefebvre and
Sebastian Bonhoeffer and
Samuel Alizon Weighting for sex acts to understand the
spread of STI on networks . . . . . . . 46--53
Tetsuya Akita and
Shohei Takuno and
Hideki Innan Modeling evolutionary growth of a
microRNA-mediated regulation system . . 54--65
Meital Weiss and
Amotz Zahavi The information provided by the adrenal
cortical steroids: a hypothesis . . . . 66--68
D. E. Moulton and
A. Goriely and
R. Chirat Mechanical growth and morphogenesis of
seashells . . . . . . . . . . . . . . . 69--79
Alexandra Witthoft and
George Em Karniadakis A bidirectional model for communication
in the neurovascular unit . . . . . . . 80--93
Philipp M. Altrock and
Arne Traulsen and
Tobias Galla The mechanics of stochastic slowdown in
evolutionary games . . . . . . . . . . . 94--106
Simon T. Powers and
Daniel J. Taylor and
Joanna J. Bryson Punishment can promote defection in
group-structured populations . . . . . . 107--116
Ghanim Ullah and
William J. Bruno and
John E. Pearson Simplification of reversible Markov
chains by removal of states with low
equilibrium occupancy . . . . . . . . . 117--129
Robert L. Karp and
Mercedes Pérez Millán and
Tathagata Dasgupta and
Alicia Dickenstein and
Jeremy Gunawardena Complex-linear invariants of biochemical
networks . . . . . . . . . . . . . . . . 130--138
Yangqing Xu and
Jeremy Gunawardena Realistic enzymology for
post-translational modification:
Zero-order ultrasensitivity revisited 139--152
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Richard A. Boyle and
Hywel T. P. Williams and
Timothy M. Lenton Natural selection for costly nutrient
recycling in simulated microbial
metacommunities . . . . . . . . . . . . 1--12
Anonymous Pages 1--158 (7 November 2012) . . . . . 1--158
Christoforos Hadjichrysanthou and
Mark Broom and
Istvan Z. Kiss Approximating evolutionary dynamics on
networks using a Neighbourhood
Configuration model . . . . . . . . . . 13--21
N. J. McPherson and
R. A. Norman and
A. S. Hoyle and
J. E. Bron and
N. G. H. Taylor Stocking methods and parasite-induced
reductions in capture: Modelling Argulus
foliaceus in trout fisheries . . . . . . 22--33
S. M. White and
J. P. Burden and
P. K. Maini and
R. S. Hails Modelling the within-host growth of
viral infections in insects . . . . . . 34--43
Jessica Purcell and
Alan Brelsford and
Leticia Avilés Co-evolution between sociality and
dispersal: The role of synergistic
cooperative benefits . . . . . . . . . . 44--54
Tao Li and
Qian-Zhong Li Annotating the protein-RNA interaction
sites in proteins using evolutionary
information and protein backbone
structure . . . . . . . . . . . . . . . 55--64
Samad Jahandideh and
Vinodh Srinivasasainagendra and
Degui Zhi Comprehensive comparative analysis and
identification of RNA-binding protein
domains: Multi-class classification and
feature selection . . . . . . . . . . . 65--75
R. Keinj and
T. Bastogne and
P. Vallois Tumor growth modeling based on cell and
tumor lifespans . . . . . . . . . . . . 76--86
S. Towers and
G. Chowell Impact of weekday social contact
patterns on the modeling of influenza
transmission, and determination of the
influenza latent period . . . . . . . . 87--95
Neil Thomas and
Yasuhiro Imafuku Effect of elastic energy on the folding
of an RNA hairpin . . . . . . . . . . . 96--104
Wen-Lin Huang Ranking Gene Ontology terms for
predicting non-classical secretory
proteins in eukaryotes and prokaryotes 105--113
Valmir C. Barbosa and
Raul Donangelo and
Sergio R. Souza Quasispecies dynamics with network
constraints . . . . . . . . . . . . . . 114--119
Taina Immonen and
Richard Gibson and
Thomas Leitner and
Melanie A. Miller and
Eric J. Arts and
Erkki Somersalo and
Daniela Calvetti A hybrid stochastic-deterministic
computational model accurately describes
spatial dynamics and virus diffusion in
HIV-1 growth competition assay . . . . . 120--132
Perrine Pelosse and
Christopher M. Kribs-Zaleta The role of the ratio of vector and host
densities in the evolution of
transmission modes in vector-borne
diseases. The example of sylvatic
\bionameTrypanosoma cruzi . . . . . . . 133--142
Gary R. Mirams and
Alexander G. Fletcher and
Philip K. Maini and
Helen M. Byrne A theoretical investigation of the
effect of proliferation and adhesion on
monoclonal conversion in the colonic
crypt . . . . . . . . . . . . . . . . . 143--156
Joe Yuichiro Wakano and
Laurent Lehmann Corrigendum to ``Evolutionary and
convergence stability for continuous
phenotypes in finite populations derived
from two-allele models'' [J. Theor.
Biol. \bf 310 (2012) 206--215] . . . . . 157--157
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Jean-Sebastien Pierre and
Jean-Pierre Masson and
Eric Wajnberg Patch leaving rules: a stochastic
version of a well-known deterministic
motivational model . . . . . . . . . . . 1--11
Anonymous Pages 1--218 (21 November 2012) . . . . 1--218
Xiang-Sheng Wang and
Jianhong Wu and
Yong Yang Richards model revisited: Validation by
and application to infection dynamics 12--19
Takuya Okabe Systematic variations in divergence
angle . . . . . . . . . . . . . . . . . 20--41
Richard O. Prum and
Larry Samuelson The Hairy--Downy Game: a model of
interspecific social dominance mimicry 42--60
Pufeng Du and
Yang Tian and
Yan Yan Subcellular localization prediction for
human internal and organelle membrane
proteins with projected gene ontology
scores . . . . . . . . . . . . . . . . . 61--67
Christopher T. Richards and
Gregory S. Sawicki Elastic recoil can either amplify or
attenuate muscle-tendon power, depending
on inertial vs. fluid dynamic loading 68--78
Bertrand Collignon and
Jean Louis Deneubourg and
Claire Detrain Leader-based and self-organized
communication: Modelling group-mass
recruitment in ants . . . . . . . . . . 79--86
Jacopo Grilli and
Sandro Azaele and
Jayanth R. Banavar and
Amos Maritan Spatial aggregation and the species-area
relationship across scales . . . . . . . 87--97
Zigen Song and
Jian Xu Stability switches and multistability
coexistence in a delay-coupled neural
oscillators system . . . . . . . . . . . 98--114
Stephen R. Pring and
Markus Owen and
John R. King and
Kevin D. Sinclair and
Robert Webb and
Anthony P. F. Flint and
Philip C. Garnsworthy A mathematical model of the bovine
oestrous cycle: Simulating outcomes of
dietary and pharmacological
interventions . . . . . . . . . . . . . 115--126
Xiunan Wang and
Wendi Wang An HIV infection model based on a
vectored immunoprophylaxis experiment 127--135
Pearl P. Guan and
Weiqiang Zhou and
Hong Yan The relationship between geometric
patterns of hydrogen bonds and periodic
dinucleotides in nucleosome structures 136--141
N. Kazmi and
M. A. Hossain and
R. M. Phillips and
M. A. Al-Mamun and
R. Bass Avascular tumour growth dynamics and the
constraints of protein binding for drug
transportation . . . . . . . . . . . . . 142--152
Fabrizio Carten\`ì and
Addolorata Marasco and
Giuliano Bonanomi and
Stefano Mazzoleni and
Max Rietkerk and
Francesco Giannino Negative plant soil feedback explaining
ring formation in clonal plants . . . . 153--161
Richard M. Sibly and
Robert N. Curnow Evolution of discrimination in
populations at equilibrium between
selfishness and altruism . . . . . . . . 162--171
Iain S. Weaver and
James G. Dyke The importance of timescales for the
emergence of environmental
self-regulation . . . . . . . . . . . . 172--180
Christian H. Reick Self-similarity and scaling in two
models of phyllotaxis and the selection
of asymptotic divergence angles . . . . 181--200
Shuji Ishihara and
Kaoru Sugimura Bayesian inference of force dynamics
during morphogenesis . . . . . . . . . . 201--211
Ingemar Nåsell Recurrence conditions for childhood
infections . . . . . . . . . . . . . . . 212--216
Zhongxing Mai and
Haiyan Liu Corrigendum to ``Boolean network-based
analysis of the apoptosis network:
Irreversible apoptosis and stable
surviving'' [J. Theor. Biol. \bf 259 (4)
(2009) 760--769] . . . . . . . . . . . . 217--217
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
N. Garijo and
R. Manzano and
R. Osta and
M. A. Perez Stochastic cellular automata model of
cell migration, proliferation and
differentiation: Validation with in
vitro cultures of muscle satellite cells 1--9
Anonymous Pages 1--218 (7 December 2012) . . . . . 1--218
Kaveh Danesh and
Rick Durrett and
Laura J. Havrilesky and
Evan Myers A branching process model of ovarian
cancer . . . . . . . . . . . . . . . . . 10--15
Rebecca K. Borchering and
Hao Liu and
Mara C. Steinhaus and
Carl L. Gardner and
Yang Kuang A simple spatiotemporal rabies model for
skunk and bat interaction in northeast
Texas . . . . . . . . . . . . . . . . . 16--22
Pak-Wing Fok Mathematical model of intimal thickening
in atherosclerosis: Vessel stenosis as a
free boundary problem . . . . . . . . . 23--33
Patricia Román-Román and
Francisco Torres-Ruiz Inferring the effect of therapies on
tumor growth by using diffusion
processes . . . . . . . . . . . . . . . 34--56
Greg M. Thurber and
K. Dane Wittrup A mechanistic compartmental model for
total antibody uptake in tumors . . . . 57--68
Yann Le Cunff and
Khashayar Pakdaman Phenotype-genotype relation in Wagner's
canalization model . . . . . . . . . . . 69--83
Ron Sorace and
Natalia L. Komarova Accumulation of neutral mutations in
growing cell colonies with competition 84--94
José Antonio Vázquez and
José M. Lorenzo and
Pablo Fuciños and
Daniel Franco Evaluation of non-linear equations to
model different animal growths with mono
and bisigmoid profiles . . . . . . . . . 95--105
Stefan Geritz and
Mats Gyllenberg A mechanistic derivation of the
DeAngelis--Beddington functional
response . . . . . . . . . . . . . . . . 106--108
D. J. Kedziora and
R. G. Abeysuriya and
A. J. K. Phillips and
P. A. Robinson Physiologically based quantitative
modeling of unihemispheric sleep . . . . 109--119
Bhavin S. Khatri and
Andrew Free and
Rosalind J. Allen Oscillating microbial dynamics driven by
small populations, limited nutrient
supply and high death rates . . . . . . 120--129
Masanari Asano and
Irina Basieva and
Andrei Khrennikov and
Masanori Ohya and
Yoshiharu Tanaka and
Ichiro Yamato Quantum-like model of diauxie in
\bionameEscherichia coli: Operational
description of precultivation effect . . 130--137
Hideo Ezoe Evolutionary stability of one-to-many
mutualisms . . . . . . . . . . . . . . . 138--144
Eli Biton and
Hezi Gildor The seasonal effect in one-dimensional
Daisyworld . . . . . . . . . . . . . . . 145--156
Iain Martyn and
Mike Steel The impact and interplay of long and
short branches on phylogenetic
information content . . . . . . . . . . 157--163
Qing Zhang and
Hualin Shi Coupling chromosomal replication to cell
growth by the initiator protein DnaA in
\bionameEscherichia coli . . . . . . . . 164--172
R. M. T. Fleming and
I. Thiele Mass conserved elementary kinetics is
sufficient for the existence of a
non-equilibrium steady state
concentration . . . . . . . . . . . . . 173--181
Andrew L. Cohen and
Tanya L. Leise and
David K. Welsh Bayesian statistical analysis of
circadian oscillations in fibroblasts 182--191
Max Sajitz-Hermstein and
Zoran Nikoloski Restricted cooperative games on
metabolic networks reveal functionally
important reactions . . . . . . . . . . 192--203
Krzysztof Bartoszek and
Jason Pienaar and
Petter Mostad and
Staffan Andersson and
Thomas F. Hansen A phylogenetic comparative method for
studying multivariate adaptation . . . . 204--215
Willem H. Mulder Corrigendum to ``Probability
distributions of ancestries and
genealogical distances on stochastically
generated rooted binary trees'' [J.
Theor. Biol. \bf 280 (2011) 139--145] 216--217
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Linlin Su and
Roger Lui Advance of advantageous genes for a
multiple-allele population genetics
model . . . . . . . . . . . . . . . . . 1--8
Anonymous Pages 1--150 (21 December 2012) . . . . 1--150
Mark Broom and
Graeme D. Ruxton Perceptual advertisement by the prey of
stalking or ambushing predators . . . . 9--16
Ilya Potapov and
Jarno Mäkelä and
Olli Yli-Harja and
Andre S. Ribeiro Effects of codon sequence on the
dynamics of genetic networks . . . . . . 17--25
Gilles Didier and
Manuela Royer-Carenzi and
Michel Laurin The reconstructed evolutionary process
with the fossil record . . . . . . . . . 26--37
Hervé Seligmann Overlapping genes coded in the
3'-to-5'-direction in mitochondrial
genes and 3'-to-5' polymerization of
non-complementary RNA by an `invertase' 38--52
Omar Sierra Bello and
Janneth Gonzalez and
Francisco Capani and
George E. Barreto In silico docking reveals possible
Riluzole binding sites on Nav1.6 sodium
channel: Implications for amyotrophic
lateral sclerosis therapy . . . . . . . 53--63
Yongcui Wang and
Xianwen Ren and
Chunhua Zhang and
Naiyang Deng and
Xiangsun Zhang Interrogating noise in protein sequences
from the perspective of protein--protein
interactions prediction . . . . . . . . 64--70
J. Ackermann and
J. Einloft and
J. Nöthen and
I. Koch Reduction techniques for network
validation in systems biology . . . . . 71--80
Marta D. Santos and
Flávio L. Pinheiro and
Francisco C. Santos and
Jorge M. Pacheco Dynamics of $N$-person snowdrift games
in structured populations . . . . . . . 81--86
R. B. Roemer and
D. Booth and
A. A. Bhavsar and
G. H. Walter and
L. I. Terry Mathematical model of cycad cones'
thermogenic temperature responses:
Inverse calorimetry to estimate
metabolic heating rates . . . . . . . . 87--96
Grace Brooks and
Gabriel Provencher and
Jinzhi Lei and
Michael C. Mackey Neutrophil dynamics after chemotherapy
and G-CSF: The role of pharmacokinetics
in shaping the response . . . . . . . . 97--109
Chai Molina and
Lewi Stone Modelling the spread of diseases in
clustered networks . . . . . . . . . . . 110--118
Mariusz Pietruszka A biosynthesis/inactivation model for
enzymatic WLFs or non-enzymatically
mediated cell evolution . . . . . . . . 119--127
Irenaeus Wolff Retaliation and the role for punishment
in the evolution of cooperation . . . . 128--138
Mohd Suhail Rizvi and
Sovan Lal Das Role of membrane addition in animal cell
cytokinesis . . . . . . . . . . . . . . 139--143
Jacob Peedicayil A comparison of Erikson's Epigenetic
Principle with epigenetics . . . . . . . 144--145
B. Caudron and
J. L. Jestin Sequence criteria for the anti-parallel
character of protein beta-strands . . . 146--149
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Andrew M. Bate and
Frank M. Hilker predator--prey oscillations can shift
when diseases become endemic . . . . . . 1--8
Anonymous Pages 1--106 (7 January 2013) . . . . . 1--106
Luna Dimitrio and
Jean Clairambault and
Roberto Natalini A spatial physiological model for p53
intracellular dynamics . . . . . . . . . 9--24
Farida Chamchod and
John C. Beier Modeling Plasmodium vivax: Relapses,
treatment, seasonality, and G6PD
deficiency . . . . . . . . . . . . . . . 25--34
Gottfried Sachs Wind effects on bounding flight . . . . 35--41
Qin Liu and
Hai-Chao Han Mechanical buckling of arterioles in
collateral development . . . . . . . . . 42--48
Ping Xie Dynamics of tRNA occupancy and
dissociation during translation by the
ribosome . . . . . . . . . . . . . . . . 49--60
Kamil A. Barto\'n and
Thomas Hovestadt Prey density, value, and spatial
distribution affect the efficiency of
area-concentrated search . . . . . . . . 61--69
M. E. Hubbard and
H. M. Byrne Multiphase modelling of vascular tumour
growth in two spatial dimensions . . . . 70--89
James D. McLaren and
Judy Shamoun-Baranes and
Willem Bouten Stop early to travel fast: modelling
risk-averse scheduling among nocturnally
migrating birds . . . . . . . . . . . . 90--98
Michael A. Fishman and
Lilach Hadany Pollinators' mating rendezvous and the
evolution of floral advertisement . . . 99--106
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Kristina Crona and
Devin Greene and
Miriam Barlow The peaks and geometry of fitness
landscapes . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--430 (21 January 2013) . . . . . 1--430
Chen-Wei Liang and
Chien-Kuo Ku and
Jeng-Jong Liang A new scale-free network model for
simulating and predicting epidemics . . 11--19
Wing-Cheong Lo and
Edward W. Martin and
Charles L. Hitchcock and
Avner Friedman Mathematical model of colitis-associated
colon cancer . . . . . . . . . . . . . . 20--29
Susanne Schindler and
Olaf Breidbach and
Jürgen Jost Preferring the fittest mates: An
analytically tractable model . . . . . . 30--38
G. Kember and
J. A. Armour and
M. Zamir Dynamic neural networking as a basis for
plasticity in the control of heart rate 39--46
David E. Hiebeler and
Isaac J. Michaud and
Ben A. Wasserman and
Timothy D. Buchak Habitat association in populations on
landscapes with continuous-valued
heterogeneous habitat quality . . . . . 47--54
J. Goyens and
J. Reijniers and
B. Borremans and
H. Leirs Density thresholds for \bionameMopeia
virus invasion and persistence in its
host \bionameMastomys natalensis . . . . 55--61
Shan Gao and
Shuo Xu and
Yaping Fang and
Jianwen Fang Prediction of core cancer genes using
multi-task classification framework . . 62--70
Daniele Muraro and
Helen Byrne and
John King and
Malcolm Bennett The role of auxin and cytokinin
signalling in specifying the root
architecture of \bionameArabidopsis
thaliana . . . . . . . . . . . . . . . . 71--86
Gouhei Tanaka and
Kazuyuki Aihara Effects of seasonal variation patterns
on recurrent outbreaks in epidemic
models . . . . . . . . . . . . . . . . . 87--95
Etsuko Nonaka and
Kalle Parvinen and
Åke Brännström Evolutionary suicide as a consequence of
runaway selection for greater
aggregation tendency . . . . . . . . . . 96--104
Erika T. Camacho and
Stephen Wirkus Tracing the progression of retinitis
pigmentosa via photoreceptor
interactions . . . . . . . . . . . . . . 105--118
L. Soler and
A. Molenaar and
N. Merola and
P. D. Eckersall and
A. Gutiérrez and
J. J. Cerón and
V. Mulero and
T. A. Niewold Why working with porcine circulating
serum amyloid A is a pig of a job . . . 119--125
György Szabó and
Attila Szolnoki and
Lilla Czakó Coexistence of fraternity and egoism for
spatial social dilemmas . . . . . . . . 126--132
Guanghu Zhu and
Guanrong Chen and
Xin-Jian Xu and
Xinchu Fu Epidemic spreading on contact networks
with adaptive weights . . . . . . . . . 133--139
Joanna Jaruszewicz and
Pawe\l J. Zuk and
Tomasz Lipniacki Type of noise defines global attractors
in bistable molecular regulatory systems 140--151
Mark E. Laidre and
Alex Lamb and
Susanne Shultz and
Megan Olsen Making sense of information in noisy
networks: Human communication, gossip,
and distortion . . . . . . . . . . . . . 152--160
Tomotaka Matsumoto and
Akiko A. Yasumoto and
Kozue Nitta and
Tetsukazu Yahara and
Hidenori Tachida Difference in flowering time as an
isolating barrier . . . . . . . . . . . 161--167
Jan C. Biro and
Josephine M. K. Biro The concept of RNA-assisted protein
folding: Representation of amino acid
kinetics at the tRNA level . . . . . . . 168--174
Claire M. Postlethwaite and
Pieta Brown and
Todd E. Dennis A new multi-scale measure for analysing
animal movement data . . . . . . . . . . 175--185
Sachi Yamaguchi and
Satoko Seki and
Kota Sawada and
Satoshi Takahashi Small and poor females change sex: a
theoretical and empirical study on
protogynous sex change in a triggerfish
under varying resource abundance . . . . 186--191
Shuyan Ding and
Yang Li and
Xiwu Yang and
Tianming Wang A simple $k$-word interval method for
phylogenetic analysis of DNA sequences 192--199
Doris Z. Wang and
Hong Yan A graph spectrum based geometric
biclustering algorithm . . . . . . . . . 200--211
Junfeng Tang and
Shurong Zhou Hybrid niche-neutral models outperform
an otherwise equivalent neutral model
for fitting coral reef data . . . . . . 212--218
Zhijun Qiu and
Cuili Qin and
Min Jiu and
Xicheng Wang A simple iterative method to optimize
protein-ligand-binding residue
prediction . . . . . . . . . . . . . . . 219--223
Shanran Huang and
Jitao T. Huang Inter-residue interaction is a
determinant of protein folding kinetics 224--228
Michael Kücken and
Christophe Champod Merkel cells and the individuality of
friction ridge skin . . . . . . . . . . 229--237
Louise Riotte-Lambert and
Simon Benhamou and
Simon Chamaillé-Jammes Periodicity analysis of movement
recursions . . . . . . . . . . . . . . . 238--243
Spyros K. Stamatelos and
Ioannis P. Androulakis and
Ah-Ng Tony Kong and
Panos G. Georgopoulos A semi-mechanistic integrated
toxicokinetic-toxicodynamic (TK/TD)
model for arsenic(III) in hepatocytes 244--256
Joaquín Flores and
Alejandro Meza Romero and
Rui D. M. Travasso and
Eugenia Corvera Poiré Flow and anastomosis in vascular
networks . . . . . . . . . . . . . . . . 257--270
Yanni Xiao and
Sanyi Tang and
Yicang Zhou and
Robert J. Smith and
Jianhong Wu and
Ning Wang Predicting the HIV/AIDS epidemic and
measuring the effect of mobility in
mainland China . . . . . . . . . . . . . 271--285
Alessandra F. Lütz and
Sebastián Risau-Gusman and
Jeferson J. Arenzon Intransitivity and coexistence in four
species cyclic games . . . . . . . . . . 286--292
Gang Wu and
Keqiang Han and
Fenglin Lv Use of fast conformational sampling to
improve the characterization of VEGF
A-peptide interactions . . . . . . . . . 293--300
Marija Rosandi\'c and
Matko Glunci\'c and
Vladimir Paar Start/stop codon like trinucleotides
extensions in primate alpha satellites 301--309
Jeehyun Lee and
Jungeun Kim and
Hee-Dae Kwon Optimal control of an influenza model
with seasonal forcing and age-dependent
transmission rates . . . . . . . . . . . 310--320
Prabhakar Deonikar and
Mahendra Kavdia Contribution of membrane permeability
and unstirred layer diffusion to nitric
oxide-red blood cell interaction . . . . 321--330
Enrique Fernández-Blanco and
Vanessa Aguiar-Pulido and
Cristian Robert Munteanu and
Julian Dorado Random Forest classification based on
star graph topological indices for
antioxidant proteins . . . . . . . . . . 331--337
Shoma Tanabe and
Hideyuki Suzuki and
Naoki Masuda Indirect reciprocity with trinary
reputations . . . . . . . . . . . . . . 338--347
Akos Dobay and
Gabriella E. C. Gall and
Daniel J. Rankin and
Homayoun C. Bagheri Renaissance model of an epidemic with
quarantine . . . . . . . . . . . . . . . 348--358
Jost Neigenfind and
Sergio Grimbs and
Zoran Nikoloski On the relation between reactions and
complexes of (bio)chemical reaction
networks . . . . . . . . . . . . . . . . 359--365
Diego A. Garzón-Alvarado A hypothesis on the formation of the
primary ossification centers in the
membranous neurocranium: a mathematical
and computational model . . . . . . . . 366--376
Krishna Kumar Kandaswamy and
Ganesan Pugalenthi and
Kai-Uwe Kalies and
Enno Hartmann and
Thomas Martinetz EcmPred: Prediction of extracellular
matrix proteins based on random forest
with maximum relevance minimum
redundancy feature selection . . . . . . 377--383
Claire Morin and
Christian Hellmich and
Peter Henits Fibrillar structure and elasticity of
hydrating collagen: a quantitative
multiscale approach . . . . . . . . . . 384--393
Marco Scianna and
Luigi Preziosi Modeling the influence of nucleus
elasticity on cell invasion in fiber
networks and microchannels . . . . . . . 394--406
Denis Fils Nkoa Onana and
Boulchard Mewoli and
Djomangan Adama Ouattara Excitability in the host-pathogen
interactions of HIV infection and
emergence of viral load blips . . . . . 407--417
Ford Ballantyne IV Evaluating model fit to determine if
logarithmic transformations are
necessary in allometry: a comment on the
exchange between Packard (2009) and
Kerkhoff and Enquist (2009) . . . . . . 418--421
Alice Z. Hyun and
Paul Macklin Improved patient-specific calibration
for agent-based cancer modeling . . . . 422--424
Lan Zou and
Weinian Zhang and
Shigui Ruan Corrigendum to ``Modeling the
transmission dynamics and control of
Hepatitis B virus in China'' [J. Theor.
Biol. \bf 262 (2010) 330--338] . . . . . 425--427
Laurence Palk and
James Sneyd and
Trevor J. Shuttleworth and
David I. Yule and
Edmund J. Crampin Corrigendum to `A dynamic model of
saliva secretion' [J. Theor. Biol. \bf
266, 2010, 625--640] . . . . . . . . . . 428--428
Mathieu Moslonka-Lefebvre and
Sebastian Bonhoeffer and
Samuel Alizon Corrigendum to ``Weighting for sex acts
to understand the spread of STI on
networks'' [J. Theor. Biol. \bf 311
(2012) 46--53] . . . . . . . . . . . . . 429--429
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Yen-Kuang Chen and
Kuo-Bin Li Predicting membrane protein types by
incorporating protein topology, domains,
signal peptides, and physicochemical
properties into the general form of
Chou's pseudo amino acid composition . . 1--12
Anonymous Pages 1--226 (7 February 2013) . . . . . 1--226
Stefano Tealdi and
Carlo Camporeale and
Luca Ridolfi Inter-species competition-facilitation
in stochastic riparian vegetation
dynamics . . . . . . . . . . . . . . . . 13--21
Yijia Zhang and
Hongfei Lin and
Zhihao Yang and
Jian Wang and
Yanpeng Li Biomolecular event trigger detection
using neighborhood hash features . . . . 22--28
Yao-Wang Li and
Bo Li Characterization of
structure-antioxidant activity
relationship of peptides in free radical
systems using QSAR models: Key sequence
positions and their amino acid
properties . . . . . . . . . . . . . . . 29--43
P. K. Fung and
A. L. Haber and
P. A. Robinson Neural field theory of plasticity in the
cerebral cortex . . . . . . . . . . . . 44--57
Marco Archetti and
István Scheuring Trading public goods stabilizes
interspecific mutualism . . . . . . . . 58--67
F. J. Vermolen and
A. Gefen A semi-stochastic cell-based model for
in vitro infected `wound' healing
through motility reduction: a simulation
study . . . . . . . . . . . . . . . . . 68--80
T. K. Kar and
Bapan Ghosh Sustainability and economic consequences
of creating marine protected areas in
multispecies multiactivity context . . . 81--90
Xiwu Yang and
Tianming Wang A novel statistical measure for sequence
comparison on the basis of $k$-word
counts . . . . . . . . . . . . . . . . . 91--100
Kazutaka Kashima and
Hisashi Ohtsuki and
Akiko Satake Fission-fusion bat behavior as a
strategy for balancing the conflicting
needs of maximizing information accuracy
and minimizing infection risk . . . . . 101--109
Doriano Brogioli Looking for chemical reaction networks
exhibiting a drift along a manifold of
marginally stable states . . . . . . . . 110--123
Massimo Di Giulio A polyphyletic model for the origin of
tRNAs has more support than a
monophyletic model . . . . . . . . . . . 124--128
Djamila Moulay and
Yoann Pigné A metapopulation model for chikungunya
including populations mobility on a
large-scale network . . . . . . . . . . 129--139
Amirhossein Manzourolajdad and
Yingfeng Wang and
Timothy I. Shaw and
Russell L. Malmberg Information-theoretic uncertainty of
SCFG-modeled folding space of the
non-coding RNA . . . . . . . . . . . . . 140--163
Motahareh Moghtadaei and
Mohammad Reza Hashemi Golpayegani and
Reza Malekzadeh A variable structure fuzzy neural
network model of squamous dysplasia and
esophageal squamous cell carcinoma based
on a global chaotic optimization
algorithm . . . . . . . . . . . . . . . 164--172
Hesam Salehipour and
David J. Willis A coupled kinematics-energetics model
for predicting energy efficient flapping
flight . . . . . . . . . . . . . . . . . 173--196
Chenglong Yu and
Mo Deng and
Shiu-Yuen Cheng and
Shek-Chung Yau and
Rong L. He and
Stephen S.-T. Yau Protein space: a natural method for
realizing the nature of protein universe 197--204
Huijiang Gao and
Yongxin Liu and
Tingting Zhang and
Runqing Yang and
Huanmin Yang Statistical models for jointly analyzing
multiple allometries . . . . . . . . . . 205--209
I. Johanna Stamper and
Xujing Wang Mathematical modeling of insulin
secretion and the role of
glucose-dependent mobilization, docking,
priming and fusion of insulin granules 210--225
Zijian Liu and
Shouming Zhong and
Zhidong Teng Erratum to ``$n$ Species impulsive
migration model with Markovian
switching'': [J. Theor. Biol. 307 (2012)
62--69] . . . . . . . . . . . . . . . . 226--226
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Xuan Zhou and
Zhanchao Li and
Zong Dai and
Xiaoyong Zou Predicting promoters by
pseudo-trinucleotide compositions based
on discrete wavelets transform . . . . . 1--7
Anonymous Pages 1--148 (21 February 2013) . . . . 1--148
A. Arazi and
A. U. Neumann The role of positive feedback loops
involving anti-dsDNA and anti-anti-dsDNA
antibodies in autoimmune
glomerulonephritis . . . . . . . . . . . 8--22
Sridhar Ramakrishnan and
Srinivasan Rajaraman and
Srinivas Laxminarayan and
Nancy J. Wesensten and
Gary H. Kamimori and
Thomas J. Balkin and
Jaques Reifman A biomathematical model of the restoring
effects of caffeine on cognitive
performance during sleep deprivation . . 23--33
J. A. Fozard and
J. R. King and
M. J. Bennett Modelling auxin efflux carrier
phosphorylation and localization . . . . 34--49
Xiaotian Wu and
Venkata R. Duvvuri and
Yijun Lou and
Nicholas H. Ogden and
Yann Pelcat and
Jianhong Wu Developing a temperature-driven map of
the basic reproductive number of the
emerging tick vector of Lyme disease
Ixodes scapularis in Canada . . . . . . 50--61
K. Hu and
C. Thoens and
S. Bianco and
S. Edlund and
M. Davis and
J. Douglas and
J. H. Kaufman The effect of antibody-dependent
enhancement, cross immunity, and vector
population on the dynamics of dengue
fever . . . . . . . . . . . . . . . . . 62--74
A. J. K. Phillips and
P. A. Robinson and
E. B. Klerman Arousal state feedback as a potential
physiological generator of the ultradian
REM/NREM sleep cycle . . . . . . . . . . 75--87
Jun Li and
Fahima Nekka A rational quantitative approach to
determine the best dosing regimen for a
target therapeutic effect: a unified
formalism for antibiotic evaluation . . 88--95
Guillermo Abramson and
Luca Giuggioli and
Robert R. Parmenter and
V. M. Kenkre Quasi-one-dimensional waves in rodent
populations in heterogeneous habitats: a
consequence of elevational gradients on
spatio-temporal dynamics . . . . . . . . 96--101
Na Xu and
Mao Sun Lateral dynamic flight stability of a
model bumblebee in hovering and forward
flight . . . . . . . . . . . . . . . . . 102--115
Christian J. Michel and
Giuseppe Pirillo A permuted set of a trinucleotide
circular code coding the 20 amino acids
in variant nuclear codes . . . . . . . . 116--121
Mayumi Seto and
Noriko Takamura and
Yoh Iwasa Individual and combined suppressive
effects of submerged and floating-leaved
macrophytes on algal blooms . . . . . . 122--133
Marco Archetti Evolution of polygamous marriage by
maximization of inclusive fitness . . . 134--143
Athel Cornish-Bowden The physiological significance of
negative cooperativity revisited . . . . 144--147
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Sachi Yamaguchi and
Yoichi Yusa and
Kota Sawada and
Satoshi Takahashi Sexual systems and dwarf males in
barnacles: Integrating life history and
sex allocation theories . . . . . . . . 1--9
Anonymous Pages 1--170 (7 March 2013) . . . . . . 1--170
Corina E. Tarnita and
Clifford H. Taubes and
Martin A. Nowak Evolutionary construction by staying
together and coming together . . . . . . 10--22
Simon D. Angus and
Monika Joanna Piotrowska A numerical model of EMT6/Ro spheroid
dynamics under irradiation: Calibration
and estimation of the underlying
irradiation-induced cell survival
probability . . . . . . . . . . . . . . 23--32
Esteban A. Hernandez-Vargas and
Richard H. Middleton Modeling the three stages in HIV
infection . . . . . . . . . . . . . . . 33--40
Alok Sharma and
James Lyons and
Abdollah Dehzangi and
Kuldip K. Paliwal A feature extraction technique using
bi-gram probabilities of position
specific scoring matrix for protein fold
recognition . . . . . . . . . . . . . . 41--46
H. L. Mills and
A. Ganesh and
C. Colijn Pathogen spread on coupled networks:
Effect of host and network properties on
transmission thresholds . . . . . . . . 47--57
Folashade B. Agusto and
Sara Y. Del Valle and
Kbenesh W. Blayneh and
Calistus N. Ngonghala and
Maria J. Goncalves and
Nianpeng Li and
Ruijun Zhao and
Hongfei Gong The impact of bed-net use on malaria
prevalence . . . . . . . . . . . . . . . 58--65
Sabrina Ellenberger and
Stefan Schuster and
Johannes Wöstemeyer Correlation between sequence, structure
and function for trisporoid processing
proteins in the model zygomycete
\bionameMucor mucedo . . . . . . . . . . 66--75
Joo-Sung Maeng and
Jae-Hyung Park and
Seong-Min Jang and
Seog-Young Han A modeling approach to energy savings of
flying Canada geese using computational
fluid dynamics . . . . . . . . . . . . . 76--85
F. Lignet and
S. Benzekry and
S. Wilson and
F. Billy and
O. Saut and
M. Tod and
B. You and
A. Adda Berkane and
S. Kassour and
M. X. Wei and
E. Grenier and
B. Ribba Theoretical investigation of the
efficacy of antiangiogenic drugs
combined to chemotherapy in xenografted
mice . . . . . . . . . . . . . . . . . . 86--99
M. Vela-Pérez and
M. A. Fontelos and
J. J. L. Velázquez Ant foraging and geodesic paths in
labyrinths: Analytical and computational
results . . . . . . . . . . . . . . . . 100--112
Pratha Sah and
Joseph Paul Salve and
Sutirth Dey Stabilizing biological populations and
metapopulations through Adaptive Limiter
Control . . . . . . . . . . . . . . . . 113--123
Danna R. Gifford and
Sijmen E. Schoustra Modelling colony population growth in
the filamentous fungus
\bionameAspergillus nidulans . . . . . . 124--130
Min Wu and
Hermann B. Frieboes and
Steven R. McDougall and
Mark A. J. Chaplain and
Vittorio Cristini and
John Lowengrub The effect of interstitial pressure on
tumor growth: Coupling with the blood
and lymphatic vascular systems . . . . . 131--151
Danilo Gullotto and
Mario Salvatore Nolassi and
Andrea Bernini and
Ottavia Spiga and
Neri Niccolai Probing the protein space for extending
the detection of weak homology folds . . 152--158
Kevin J. Kesseler and
Michael L. Blinov and
Timothy C. Elston and
William K. Kaufmann and
Dennis A. Simpson A predictive mathematical model of the
DNA damage G2 checkpoint . . . . . . . . 159--169
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Roslyn C. Henry and
Greta Bocedi and
Justin M. J. Travis Eco-evolutionary dynamics of range
shifts: Elastic margins and critical
thresholds . . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--100 (21 March 2013) . . . . . . 1--100
Susanna Röblitz and
Claudia Stötzel and
Peter Deuflhard and
Hannah M. Jones and
David-Olivier Azulay and
Piet H. van der Graaf and
Steven W. Martin A mathematical model of the human
menstrual cycle for the administration
of GnRH analogues . . . . . . . . . . . 8--27
Daniel Munther and
Jianhong Wu Enhanced surveillance on food-borne
disease outbreaks: Dynamics of
cross-contamination in biocidal wash
procedure . . . . . . . . . . . . . . . 28--35
Per Lundberg On the evolutionary stability of partial
migration . . . . . . . . . . . . . . . 36--39
Shade T. Shutters Towards a rigorous framework for
studying $2$-player continuous games . . 40--43
Yasser B. Ruiz-Blanco and
Yovani Marrero-Ponce and
Waldo Paz and
Yamila García and
Jesús Salgado Global stability of protein folding from
an empirical free energy function . . . 44--53
Cristina Stan and
Monica Teodora Cristescu and
Buimaga Iarinca Luiza and
C. P. Cristescu Investigation on series of length of
coding and non-coding DNA sequences of
bacteria using multifractal detrended
cross-correlation analysis . . . . . . . 54--62
Tuomas Nurmi and
Kalle Parvinen Evolution of specialization under
non-equilibrium population dynamics . . 63--77
Jianlei Zhang and
Tianguang Chu and
Franz J. Weissing Does insurance against punishment
undermine cooperation in the evolution
of public goods games? . . . . . . . . . 78--82
Julia Arciero and
G. Bard Ermentrout and
Richard Siggers and
Amin Afrazi and
David Hackam and
Yoram Vodovotz and
Jonathan Rubin Modeling the interactions of bacteria
and Toll-like receptor-mediated
inflammation in necrotizing
enterocolitis . . . . . . . . . . . . . 83--99
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Krzysztof Bartoszek and
Graham Jones and
Bengt Oxelman and
Serik Sagitov Time to a single hybridization event in
a group of species with unknown
ancestral history . . . . . . . . . . . 1--6
Anonymous Pages 1--94 (7 April 2013) . . . . . . . 1--94
C. Letellier and
F. Denis and
L. A. Aguirre What can be learned from a chaotic
cancer model? . . . . . . . . . . . . . 7--16
Jared Barber and
Mark Tronzo and
C. Harold Horvat and
Gilles Clermont and
Jeffrey Upperman and
Yoram Vodovotz and
Ivan Yotov A three-dimensional mathematical and
computational model of necrotizing
enterocolitis . . . . . . . . . . . . . 17--32
Hironori Fujita and
Masayoshi Kawaguchi Pattern formation by two-layer Turing
system with complementarysynthesis . . . 33--45
Karolina Safarzynska The coevolution of culture and
environment . . . . . . . . . . . . . . 46--57
Maymona Al-Husari and
Steven D. Webb Regulation of tumour intracellular pH: a
mathematical model examining the
interplay between H$^+$ and lactate . . 58--71
Brian B. Boutwell and
J. C. Barnes and
Raelynn Deaton and
Kevin M. Beaver On the evolutionary origins of
life-course persistent offending: a
theoretical scaffold for Moffitt's
developmental taxonomy . . . . . . . . . 72--80
Mike Steel and
Simone Linz and
Daniel H. Huson and
Michael J. Sanderson Identifying a species tree subject to
random lateral gene transfer . . . . . . 81--93
Aylin Günel Erratum to ``Modelling the interactions
between TLR4 and IFN$ \beta $ pathways''
[J. Theor. Biol. 307 (2012) 137--148] 94--94
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Motoshi Ichinose and
Masaru Iizuka and
Junko Kusumi and
Masasuke Takefu Models of compensatory molecular
evolution: Effects of back mutation . . 1--10
Anonymous Pages 1--90 (21 April 2013) . . . . . . 1--90
Charles M. Bishop and
Robin J. Spivey Integration of exercise response and
allometric scaling in endotherms . . . . 11--19
Stefano Giaimo Are some conventional measures of the
rate of ageing consistent with
antagonistic pleiotropy? . . . . . . . . 20--24
K. J. Painter and
T. Hillen Mathematical modelling of glioma growth:
The use of Diffusion Tensor Imaging
(DTI) data to predict the anisotropic
pathways of cancer invasion . . . . . . 25--39
Shibiao Wan and
Man-Wai Mak and
Sun-Yuan Kung GOASVM: a subcellular location predictor
by incorporating term-frequency gene
ontology into the general form of Chou's
pseudo-amino acid composition . . . . . 40--48
Zoe Cook and
Daniel W. Franks and
Elva J. H. Robinson Exploration versus exploitation in
polydomous ant colonies . . . . . . . . 49--56
R. A. Lintott and
R. A. Norman and
A. S. Hoyle The impact of increased dispersal in
response to disease control in patchy
environments . . . . . . . . . . . . . . 57--68
M. Broom and
G. D. Ruxton On the evolutionary stability of
zero-cost pooled-equilibrium signals . . 69--75
Ryo Oizumi and
Takenori Takada Optimal life schedule with stochastic
growth in age-size structured models:
Theory and an application . . . . . . . 76--89
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Hervé Seligmann Systematic asymmetric nucleotide
exchanges produce human mitochondrial
RNAs cryptically encoding for
overlapping protein coding genes . . . . 1--20
Anonymous Pages 1--108 (7 May 2013) . . . . . . . 1--108
Steven D. Webb and
Matt J. Keeling and
Mike Boots The role of spatial population structure
on the evolution of parasites with
acquired immunity and demography . . . . 21--31
Mike S. Fowler and
Lasse Ruokolainen Colonization, covariance and colour:
Environmental and ecological drivers of
diversity-stability relationships . . . 32--41
Gregory L. Wagner and
Eric Lauga Crawling scallop: Friction-based
locomotion with one degree of freedom 42--51
Olivier Maury and
Jean-Christophe Poggiale From individuals to populations to
communities: a dynamic energy budget
model of marine ecosystem size-spectrum
including life history diversity . . . . 52--71
P. K. Fung and
P. A. Robinson Neural field theory of calcium dependent
plasticity with applications to
transcranial magnetic stimulation . . . 72--83
Marisa C. Eisenberg and
Suzanne L. Robertson and
Joseph H. Tien Identifiability and estimation of
multiple transmission pathways in
cholera and waterborne disease . . . . . 84--102
Marianne Marcoux and
David Lusseau Network modularity promotes cooperation 103--108
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
M. Carmen Calzada and
Enrique Fernández-Cara and
Mercedes Marín Optimal control oriented to therapy for
a free-boundary tumor growth model . . . 1--11
Anonymous Pages 1--102 (21 May 2013) . . . . . . . 1--102
Junling Ma and
P. van den Driessche and
Frederick H. Willeboordse The importance of contact network
topology for the success of vaccination
strategies . . . . . . . . . . . . . . . 12--21
Didier Gonze Modeling the effect of cell division on
genetic oscillators . . . . . . . . . . 22--33
Attila Szolnoki and
Matjaz Perc Effectiveness of conditional punishment
for the evolution of public cooperation 34--41
Gregory Herschlag and
Guilherme J. M. Garcia and
Brian Button and
Robert Tarran and
Brandon Lindley and
Benjamin Reinhardt and
Timothy C. Elston and
M. Gregory Forest A mechanochemical model for
auto-regulation of lung airway surface
layer volume . . . . . . . . . . . . . . 42--51
Peter R. Wills Frameshifted prion proteins as
pathological agents: Quantitative
considerations . . . . . . . . . . . . . 52--61
Denis Michel Kinetic approaches to lactose operon
induction and bimodality . . . . . . . . 62--75
Peter Taylor Inclusive and personal fitness in
synergistic evolutionary games on graphs 76--82
Srinandan Dasmahapatra Model of haplotype and phenotype in the
evolution of a duplicated autoregulatory
activator . . . . . . . . . . . . . . . 83--102
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Joshua Greene and
Marc R. Birtwistle and
Leszek Ignatowicz and
Grzegorz A. Rempala Bayesian multivariate Poisson abundance
models for T-cell receptor data . . . . 1--10
Anonymous Pages 1--82 (7 June 2013) . . . . . . . 1--82
Ruian Ke and
Ken Haynes and
Jaroslav Stark Modelling the activation of alkaline pH
response transcription factor PacC in
\bionameAspergillus nidulans:
Involvement of a negative feedback loop 11--20
Alison Margolskee and
James F. Selgrade A lifelong model for the female
reproductive cycle with an antimüllerian
hormone treatment to delay menopause . . 21--35
S. Binny Priya and
Subhojit Saha and
Ramesh Anishetty and
Sharmila Anishetty A matrix based algorithm for
protein--protein interaction prediction
using domain-domain associations . . . . 36--42
Byron L. Long and
Rahul Rekhi and
Amada Abrego and
Jiwon Jung and
Amina A. Qutub Cells as state machines: Cell behavior
patterns arise during capillary
formation as a function of BDNF and VEGF 43--57
Xiaobo Li and
Scott C. Lenaghan and
Mingjun Zhang Evolutionary game based control for
biological systems with applications in
drug delivery . . . . . . . . . . . . . 58--69
Fabio Dercole and
Marco De Carli and
Fabio Della Rossa and
Alessandro V. Papadopoulos Overpunishing is not necessary to fix
cooperation in voluntary public goods
games . . . . . . . . . . . . . . . . . 70--81
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Frederick R. Adler and
Peter S. Kim Models of contrasting strategies of
rhinovirus immune manipulation . . . . . 1--10
Anonymous Pages 1--90 (21 June 2013) . . . . . . . 1--90
J. H. P. Dawes and
M. O. Souza A derivation of Holling's type I, II and
III functional responses in
predator--prey systems . . . . . . . . . 11--22
Christoph Grüter and
Roger Schürch and
Walter M. Farina Task-partitioning in insect societies:
Non-random direct material transfers
affect both colony efficiency and
information flow . . . . . . . . . . . . 23--33
Anjan K. Nandi and
Anindita Bhadra and
Annagiri Sumana and
Sujata A. Deshpande and
Raghavendra Gadagkar The evolution of complexity in social
organization --- a model using
dominance-subordinate behavior in two
social wasp species . . . . . . . . . . 34--44
Rob J. De Boer and
Alan S. Perelson Quantifying T lymphocyte turnover . . . 45--87
Jeremy G. Sumner Lie geometry of 2$ \times $2 Markov
matrices . . . . . . . . . . . . . . . . 88--90
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
A. Barton and
A. J. Fendrik Sustained vs. oscillating expressions of
Ngn2, Dll1 and Hes1: a model of neural
differentiation of embryonic
telencephalon . . . . . . . . . . . . . 1--8
Anonymous Pages 1--102 (7 July 2013) . . . . . . . 1--102
Tjalling Jager and
Benjamin T. Martin and
Elke I. Zimmer DEBkiss or the quest for the simplest
generic model of animal life history . . 9--18
Hengtong Wang and
Yueling Chen and
Yong Chen First-spike latency in Hodgkin's three
classes of neurons . . . . . . . . . . . 19--25
Badal Joshi and
Mainak Patel Encoding with synchrony: Phase-delayed
inhibition allows for reliable and
specific stimulus detection . . . . . . 26--32
Xiaoqing Zhao and
Hong Li and
Tonglaga Bao Analysis on the interaction between
post-spliced introns and corresponding
protein coding sequences in ribosomal
protein genes . . . . . . . . . . . . . 33--42
M. El-Kebir and
M. van der Kuip and
A. M. van Furth and
D. E. Kirschner Computational modeling of tuberculous
meningitis reveals an important role for
tumor necrosis factor-$ \alpha $ . . . . 43--53
Christopher A. Johnson and
Priyanga Amarasekare Competition for benefits can promote the
persistence of mutualistic interactions 54--64
Kang-Ling Liao and
Xue-Feng Bai and
Avner Friedman The role of CD200-CD200R in tumor immune
evasion . . . . . . . . . . . . . . . . 65--76
Micha\l Brylinski The utility of artificially evolved
sequences in protein threading and fold
recognition . . . . . . . . . . . . . . 77--88
E. van Leeuwen and
Å. Brännström and
V. A. A. Jansen and
U. Dieckmann and
A. G. Rossberg A generalized functional response for
predators that switch between multiple
prey species . . . . . . . . . . . . . . 89--98
João Carlos de Oliveira Guerra and
Pedro Licinio Erratum to ``The role played by exons in
genomic DNA sequence correlations'' [J.
Theor. Biol. \bf 264 (2010) 830--837] 99--99
Shoma Tanabe and
Hideyuki Suzuki and
Naoki Masuda Corrigendum to ``Indirect Reciprocity
with Trinary Reputations'' [J. Theor.
Biol. \bf 317 (2013) 338--347] . . . . . 100--101
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Yiliang Liu and
Qun Liu and
Zhenhai Liu Dynamical behaviors of a stochastic
delay logistic system with impulsive
toxicant input in a polluted environment 1--5
Anonymous Pages 1--100 (21 July 2013) . . . . . . 1--100
Bapan Ghosh and
T. K. Kar Possible ecosystem impacts of applying
maximum sustainable yield policy in food
chain models . . . . . . . . . . . . . . 6--14
Malte Lehmann and
Kim Sneppen Genetic Regulatory Networks that count
to 3 . . . . . . . . . . . . . . . . . . 15--19
Bradford W. Gutting and
David Marchette and
Robert Sherwood and
George A. Andrews and
Alison Director-Myska and
Stephen R. Channel and
Daniel Wolfe and
Alan E. Berger and
Ryan S. Mackie and
Brent J. Watson and
Andrey Rukhin Modeling low-dose mortality and disease
incubation period of inhalational
anthrax in the rabbit . . . . . . . . . 20--31
Ryosuke Omori and
Akira Sasaki Timing of the emergence of new
successful viral strains in seasonal
influenza . . . . . . . . . . . . . . . 32--38
Mikkel Meyer Andersen and
Poul Svante Eriksen and
Niels Morling The discrete Laplace exponential family
and estimation of Y-STR haplotype
frequencies . . . . . . . . . . . . . . 39--51
K. Psiuk-Maksymowicz Multiphase modelling of desmoplastic
tumour growth . . . . . . . . . . . . . 52--63
Seyed Jamaleddin Mousavi and
Mohamed Hamdy Doweidar and
Manuel Doblaré 3D computational modelling of cell
migration: a
mechano-chemo-thermo-electrotaxis
approach . . . . . . . . . . . . . . . . 64--73
Chris McCaig and
Andy Fenton and
Andrea Graham and
Carron Shankland and
Rachel Norman Using process algebra to develop
predator--prey models of within-host
parasite dynamics . . . . . . . . . . . 74--81
Elena E. Giorgi and
Bette T. Korber and
Alan S. Perelson and
Tanmoy Bhattacharya Modeling sequence evolution in HIV-1
infection with recombination . . . . . . 82--93
Safoora Karimi and
Mitra Dadvar and
Hamid Modarress and
Bahram Dabir A new correlation for inclusion of leaky
junctions in macroscopic modeling of
atherosclerotic lesion initiation . . . 94--100
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Tomasz Arod'z and
Przemyslaw M. Plonka Sequence and structure space model of
protein divergence driven by point
mutations . . . . . . . . . . . . . . . 1--8
Anonymous Pages 1--88 (7 August 2013) . . . . . . 1--88
Hsien-Tsai Wu and
Po-Chun Hsu and
Cheuk-Kwan Sun and
Hou-Jun Wang and
Cyuan-Cin Liu and
Hong-Ruei Chen and
An-Bang Liu and
Chieh-Ju Tang and
Men-Tzung Lo Assessment of autonomic dysfunction in
patients with type 2 diabetes using
reactive hyperemia . . . . . . . . . . . 9--17
Anne Kandler and
Stephen Shennan A non-equilibrium neutral model for
analysing cultural change . . . . . . . 18--25
Dov A. Pechenick and
Jason H. Moore and
Joshua L. Payne The influence of assortativity on the
robustness and evolvability of gene
regulatory networks upon gene birth . . 26--36
Reiji Suzuki and
Takaya Arita A simple computational model of the
evolution of a communicative trait and
its phenotypic plasticity . . . . . . . 37--44
Te Wu and
Feng Fu and
Yanling Zhang and
Long Wang Adaptive tag switching reinforces the
coevolution of contingent cooperation
and tag diversity . . . . . . . . . . . 45--55
Ronny Straube and
Carsten Conradi Reciprocal enzyme regulation as a source
of bistability in covalent modification
cycles . . . . . . . . . . . . . . . . . 56--74
D. Schokker and
A. Bannink and
M. A. Smits and
J. M. J. Rebel A mathematical model representing
cellular immune development and response
to \bionameSalmonella of chicken
intestinal tissue . . . . . . . . . . . 75--87
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Lin Hua and
Ping Zhou and
Lin Li and
Hong Liu and
Zheng Yang Prioritizing breast cancer subtype
related miRNAs using miRNA-mRNA
dysregulated relationships extracted
from their dual expression profiling . . 1--11
Anonymous Pages 1--90 (21 August 2013) . . . . . . 1--90
Joëlle De Caluwé and
Genevi\`eve Dupont The progression towards Alzheimer's
disease described as a bistable switch
arising from the positive loop between
amyloids and Ca$^{2+}$ . . . . . . . . . 12--18
Sahand Hormoz Stem cell population asymmetry can
reduce rate of replicative aging . . . . 19--27
Natasha P. Wilson and
Bradford Gates and
Mariajosé Castellanos Modeling the short time-scale dynamics
of $ \beta $-amyloid-neuron interactions 28--37
Janneke C. M. Heijne and
Sereina A. Herzog and
Christian L. Althaus and
Nicola Low and
Mirjam Kretzschmar Case and partnership reproduction
numbers for a curable sexually
transmitted infection . . . . . . . . . 38--47
Zhi-Xin Liu and
Song-lei Liu and
Hong-Qiang Yang and
Li-Hua Bao Using protein granularity to extract the
protein sequence features . . . . . . . 48--53
Tom Rosenström Bargaining models of depression and
evolution of cooperation . . . . . . . . 54--65
Pooja Rajdev and
David Thorsley and
Srinivasan Rajaraman and
Tracy L. Rupp and
Nancy J. Wesensten and
Thomas J. Balkin and
Jaques Reifman A unified mathematical model to quantify
performance impairment for both chronic
sleep restriction and total sleep
deprivation . . . . . . . . . . . . . . 66--77
S. Seirin Lee and
R. E. Baker and
E. A. Gaffney and
S. M. White Modelling Aedes aegypti mosquito control
via transgenic and sterile insect
techniques: Endemics and emerging
outbreaks . . . . . . . . . . . . . . . 78--90
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Hideo Ezoe and
Yusuke Ikegawa Coexistence of mutualists and
non-mutualists in a dual-lattice model 1--8
Anonymous Pages 1--290 (7 September 2013) . . . . 1--290
A. H. Antrup Co-evolution of institutions and
preferences: The case of the (human)
mating market . . . . . . . . . . . . . 9--19
Stéphanie Portet Dynamics of in vitro intermediate
filament length distributions . . . . . 20--29
Oleg V. Belov and
Ochbadrakh Chuluunbaatar and
Mikhail I. Kapralov and
Nasser H. Sweilam The role of the bacterial mismatch
repair system in SOS-induced
mutagenesis: a theoretical background 30--41
Jisca Huisman and
Jarle Tufto Modelling wild-domestic interbreeding:
How selection on a quantitative trait
affects gene flow at a neutral locus . . 42--51
Phuong T. T. Nguyen and
Alan J. Conley and
James Sneyd and
Rita S. F. Lee and
Tanya K. Soboleva and
Paul R. Shorten The role of enzyme compartmentalization
on the regulation of steroid synthesis 52--64
Luis F. Jover and
Michael H. Cortez and
Joshua S. Weitz Mechanisms of multi-strain coexistence
in host-phage systems with nested
infection networks . . . . . . . . . . . 65--77
Nicolas Houy Evolution of cooperation with similarity
to an archetype . . . . . . . . . . . . 78--88
H. A. Soula and
H. Julienne and
C. O. Soulage and
A. Géloën Modelling adipocytes size distribution 89--95
Mike Steel and
Wim Hordijk and
Joshua Smith Minimal autocatalytic networks . . . . . 96--107
Casimiro Corbacho and
Manuel Molina and
Manuel Mota and
Alfonso Ramos Birth--death branching models.
Application to African elephant
populations . . . . . . . . . . . . . . 108--116
A. M. Reynolds Selection pressures give composite
correlated random walks Lévy walk
characteristics . . . . . . . . . . . . 117--122
Patrick D. Shipman and
Sérgio H. Faria and
Christopher Strickland Towards a continuous population model
for natural language vowel shift . . . . 123--135
A. Carloni and
V. Poletti and
L. Fermo and
N. Bellomo and
M. Chilosi Heterogeneous distribution of mechanical
stress in human lung: a mathematical
approach to evaluate abnormal remodeling
in IPF . . . . . . . . . . . . . . . . . 136--140
Claudia Patricia Ruiz-Diaz and
Carlos Toledo-Hernández and
Alberto M. Sabat and
Mariano Marcano Immune response to a pathogen in corals 141--148
Cameron B. Gundersen and
Joy A. Umbach Synaptotagmins 1 and 2 as mediators of
rapid exocytosis at nerve terminals: The
dyad hypothesis . . . . . . . . . . . . 149--160
Carlos Rodríguez-Caso Can cell mortality determine division of
labor in tissue organization? . . . . . 161--170
Chu C. Y. Cyrus and
Ronald D. Lee On the evolution of intergenerational
division of labor, menopause and
transfers among adults and offspring . . 171--180
D. Donzelli and
C. De Michele and
R. J. Scholes Competition between trees and grasses
for both soil water and mineral nitrogen
in dry savannas . . . . . . . . . . . . 181--190
Anne Kandler and
Kevin N. Laland Tradeoffs between the strength of
conformity and number of conformists in
variable environments . . . . . . . . . 191--202
Luis Mier-y-Teran-Romero and
Ira B. Schwartz and
Derek A. T. Cummings Breaking the symmetry: Immune
enhancement increases persistence of
dengue viruses in the presence of
asymmetric transmission rates . . . . . 203--210
Niu Xiaohui and
Li Nana and
Xia Jingbo and
Chen Dingyan and
Peng Yuehua and
Xiao Yang and
Wei Weiquan and
Wang Dongming and
Wang Zengzhen Using the concept of Chou's pseudo amino
acid composition to predict protein
solubility: An approach with entropies
in information theory . . . . . . . . . 211--217
Johannes Neidhart and
Ivan G. Szendro and
Joachim Krug Exact results for amplitude spectra of
fitness landscapes . . . . . . . . . . . 218--227
Le Yang and
Tarynn M. Witten and
Ramana M. Pidaparti A biomechanical model of wound
contraction and scar formation . . . . . 228--248
Henrique C. Giacomini and
Brian J. Shuter and
Nigel P. Lester Predator bioenergetics and the prey size
spectrum: Do foraging costs determine
fish production? . . . . . . . . . . . . 249--260
Peter D. Sozou Kin selection and local competition in a
heterogeneous community . . . . . . . . 261--266
Lisa N. Murillo and
Michael S. Murillo and
Alan S. Perelson Towards multiscale modeling of influenza
infection . . . . . . . . . . . . . . . 267--290
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Kalle Parvinen and
Ulf Dieckmann Self-extinction through optimizing
selection . . . . . . . . . . . . . . . 1--9
Anonymous Pages 1--210 (21 September 2013) . . . . 1--210
Jiawei Luo and
Dan Song and
Cheng Liang and
Guanghui Li Model the evolution of protein
interaction network assisted with
protein age . . . . . . . . . . . . . . 10--17
Michele Bellingeri and
Simone Vincenzi Robustness of empirical food webs with
varying consumer's sensitivities to loss
of resources . . . . . . . . . . . . . . 18--26
Adriana T. Dawes and
David Iron Cortical geometry may influence
placement of interface between Par
protein domains in early
\bionameCaenorhabditis elegans embryos 27--37
S. Taskinen and
D. I. Warton Robust tests for one or more allometric
lines . . . . . . . . . . . . . . . . . 38--46
Jean-Christophe Leloup and
Albert Goldbeter Critical phase shifts slow down
circadian clock recovery: Implications
for jet lag . . . . . . . . . . . . . . 47--57
David M. McAvity and
Tristen Bristow and
Eric Bunker and
Alex Dreyer Perception without self-matching in
conditional tag based cooperation . . . 58--67
Hiroto Shoji and
Yasuhiro Nakatomi and
Chihiro Yokoyama and
Kenji Fukui and
Kazumitsu Hanai New index based on the physical
separation of motion into three
categories for characterizing the effect
of cocaine in mice . . . . . . . . . . . 68--77
Kai Wang and
Xueliang Zhang and
Zhen Jin and
Haimei Ma and
Zhidong Teng and
Lei Wang Modeling and analysis of the
transmission of \bionameEchinococcosis
with application to Xinjiang Uygur
Autonomous Region of China . . . . . . . 78--90
Óscar Angulo and
Rafael Bravo de la Parra and
Juan C. López-Marcos and
Miguel A. Zavala Stand dynamics and tree coexistence in
an analytical structured model: The role
of recruitment . . . . . . . . . . . . . 91--101
Graham M. Donovan Modelling airway smooth muscle passive
length adaptation via thick filament
length distributions . . . . . . . . . . 102--108
Massimo Di Giulio The origin of the genetic code in the
ocean abysses: New comparisons confirm
old observations . . . . . . . . . . . . 109--116
Yoh Iwasa and
Joung-Hun Lee Graduated punishment is efficient in
resource management if people are
heterogeneous . . . . . . . . . . . . . 117--125
Anneke S. De Vos and
Mirjam E. E. Kretzschmar The efficiency of targeted intervention
in limiting the spread of HIV and
Hepatitis C Virus among injecting drug
users . . . . . . . . . . . . . . . . . 126--134
Larry Bodgi and
Adeline Granzotto and
Clément Devic and
Guillaume Vogin and
Annick Lesne and
Jean-François Bottollier-Depois and
Jean-Marc Victor and
Mira Maalouf and
Georges Fares and
Nicolas Foray A single formula to describe
radiation-induced protein
relocalization: Towards a mathematical
definition of individual
radiosensitivity . . . . . . . . . . . . 135--145
Eric F. Lee and
Mark A. Matthews and
Andrew J. McElrone and
Ronald J. Phillips and
Kenneth A. Shackel and
Craig R. Brodersen Analysis of HRCT-derived xylem network
reveals reverse flow in some vessels . . 146--155
Ricardo Martínez-García and
Justin M. Calabrese and
Cristóbal López Spatial patterns in mesic savannas: The
local facilitation limit and the role of
demographic stochasticity . . . . . . . 156--165
Miguel Nakamura and
Pablo del Monte-Luna and
Daniel Lluch-Belda and
Salvador E. Lluch-Cota Statistical inference for extinction
rates based on last sightings . . . . . 166--173
M. Scianna and
C. G. Bell and
L. Preziosi A review of mathematical models for the
formation of vascular networks . . . . . 174--209
Ronny Straube and
Carsten Conradi Erratum to ``Reciprocal enzyme
regulation as a source of bistability in
covalent modification cycles'' [J.
Theor. Biol. \bf 330 (2013) 56--74] . . 210--210
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
J. Belmonte-Beitia and
T. E. Woolley and
J. G. Scott and
P. K. Maini and
E. A. Gaffney Modelling biological invasions:
Individual to population scales at
interfaces . . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--204 (7 October 2013) . . . . . 1--204
Mainak Patel and
Badal Joshi Decoding synchronized oscillations
within the brain: Phase-delayed
inhibition provides a robust mechanism
for creating a sharp synchrony filter 13--25
Sebastian Novak and
Krishnendu Chatterjee and
Martin A. Nowak Density games . . . . . . . . . . . . . 26--34
José A. Capitán and
Alex Arenas and
Roger Guimer\`a Degree of intervality of food webs: From
body-size data to models . . . . . . . . 35--44
Guo-Liang Fan and
Qian-Zhong Li Discriminating bioluminescent proteins
by incorporating average chemical shift
and evolutionary information into the
general form of Chou's pseudo amino acid
composition . . . . . . . . . . . . . . 45--51
Yanling Zhang and
Te Wu and
Xiaojie Chen and
Guangming Xie and
Long Wang Mixed strategy under generalized public
goods games . . . . . . . . . . . . . . 52--60
Gian Marco Palamara and
Gustav W. Delius and
Matthew J. Smith and
Owen L. Petchey Predation effects on mean time to
extinction under demographic
stochasticity . . . . . . . . . . . . . 61--70
Qihua Huang and
Laura Parshotam and
Hao Wang and
Caroline Bampfylde and
Mark A. Lewis A model for the impact of contaminants
on fish population dynamics . . . . . . 71--79
Lu-Lu Pan and
Yu Wang and
Jian-Hui Hu and
Zhao-Tang Ding and
Chen Li Analysis of codon use features of
stearoyl--acyl carrier protein
desaturase gene in \bionameCamellia
sinensis . . . . . . . . . . . . . . . . 80--86
Sunil Kumar Tripathi and
Ravikumar Muttineni and
Sanjeev Kumar Singh Extra precision docking, free energy
calculation and molecular dynamics
simulation studies of CDK2 inhibitors 87--100
Sachi Yamaguchi and
Kota Sawada and
Yoichi Yusa and
Yoh Iwasa Dwarf males and hermaphrodites can
coexist in marine sedentary species if
the opportunity to become a dwarf male
is limited . . . . . . . . . . . . . . . 101--108
Priya P. Panigrahi and
Tiratha Raj Singh Computational studies on Alzheimer's
disease associated pathways and
regulatory patterns using microarray
gene expression and network data:
Revealed association with aging and
other diseases . . . . . . . . . . . . . 109--121
Korinna T. Allhoff and
Barbara Drossel When do evolutionary food web models
generate complex networks? . . . . . . . 122--129
Motahareh Moghtadaei and
Mohammad Reza Hashemi Golpayegani and
Reza Malekzadeh Periodic and chaotic dynamics in a
map-based model of tumor-immune
interaction . . . . . . . . . . . . . . 130--140
William H. James Evolution and the variation of mammalian
sex ratios at birth: Reflections on
Trivers and Willard (1973) . . . . . . . 141--148
May Anne Mata and
Meghan Dutot and
Leah Edelstein-Keshet and
William R. Holmes A model for intracellular actin waves
explored by nonlinear local perturbation
analysis . . . . . . . . . . . . . . . . 149--161
David V. Foster and
Mary M. Rorick and
Tanja Gesell and
Laura M. Feeney and
Jacob G. Foster Dynamic landscapes: a model of context
and contingency in evolution . . . . . . 162--172
Ian Price and
Bard Ermentrout and
Ruben Zamora and
Bo Wang and
Nabil Azhar and
Qi Mi and
Gregory Constantine and
James R. Faeder and
Shirley Luckhart and
Yoram Vodovotz In vivo, in vitro, and in silico studies
suggest a conserved immune module that
regulates malaria parasite transmission
from mammals to mosquitoes . . . . . . . 173--186
Carl P. Simon and
Bethany Percha and
Rick Riolo and
Betsy Foxman Modeling bacterial colonization and
infection routes in health care
settings: Analytic and numerical
approaches . . . . . . . . . . . . . . . 187--199
Douglas S. Glazier Log-transformation is useful for
examining proportional relationships in
allometric scaling . . . . . . . . . . . 200--203
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Michel Droz and
Andrzej P\kekalski Model of annual plants dynamics with
facilitation and competition . . . . . . 1--12
Anonymous Pages 1--298 (21 October 2013) . . . . . 1--298
Xiaojie Chen and
Thilo Gross and
Ulf Dieckmann Shared rewarding overcomes defection
traps in generalized volunteer's
dilemmas . . . . . . . . . . . . . . . . 13--21
Jinbao Liao and
Zhenqing Li and
David E. Hiebeler and
Yoh Iwasa and
Jan Bogaert and
Ivan Nijs Species persistence in landscapes with
spatial variation in habitat quality: a
pair approximation model . . . . . . . . 22--30
Eric R. Lucas and
Jeremy Field Caste determination through mating in
primitively eusocial societies . . . . . 31--39
A. L. Addison and
J. A. Powell and
D. L. Six and
M. Moore and
B. J. Bentz The role of temperature variability in
stabilizing the mountain pine
beetle-fungus mutualism . . . . . . . . 40--50
Elizabeth M. Baptestini and
Marcus A. M. de Aguiar and
Yaneer Bar-Yam Conditions for neutral speciation via
isolation by distance . . . . . . . . . 51--56
Marcel Joly and
Darci Odloak Modeling interleukin-$2$-based
immunotherapy in AIDS pathogenesis . . . 57--78
Renato Vieira dos Santos and
Linaena Méricy da Silva The noise and the KISS in the cancer
stem cells niche . . . . . . . . . . . . 79--87
Daniel Angelo Longhi and
Francieli Dalcanton and
Gláucia Maria Falcão de Aragão and
Bruno Augusto Mattar Carciofi and
João Borges Laurindo Assessing the prediction ability of
different mathematical models for the
growth of \bionameLactobacillus
plantarum under non-isothermal
conditions . . . . . . . . . . . . . . . 88--96
Emanuel Andrada and
Christian Rode and
Reinhard Blickhan Grounded running in quails: Simulations
indicate benefits of observed fixed
aperture angle between legs before
touch-down . . . . . . . . . . . . . . . 97--107
B. Hernández-Gascón and
J. Grasa and
B. Calvo and
J. F. Rodríguez A $3$D electro-mechanical continuum
model for simulating skeletal muscle
contraction . . . . . . . . . . . . . . 108--118
B. Devipriya and
P. Kumaradhas Charge density distribution and the
electrostatic moments of CTPB in the
active site of p300 enzyme: a DFT and
charge density study . . . . . . . . . . 119--129
Atsushi Mochizuki and
Bernold Fiedler and
Gen Kurosawa and
Daisuke Saito Dynamics and control at feedback vertex
sets. II: a faithful monitor to
determine the diversity of molecular
activities in regulatory networks . . . 130--146
Yuval Nov and
Danny Segev Optimal codon randomization via
mathematical programming . . . . . . . . 147--152
Vera Afreixo and
Carlos A. C. Bastos and
Sara P. Garcia and
João M. O. S. Rodrigues and
Armando J. Pinho and
Paulo J. S. G. Ferreira The breakdown of the word symmetry in
the human genome . . . . . . . . . . . . 153--159
Mark Broom and
Chris Cannings A dynamic network population model with
strategic link formation governed by
individual preferences . . . . . . . . . 160--168
Chang Gong and
Joshua T. Mattila and
Mark Miller and
JoAnne L. Flynn and
Jennifer J. Linderman and
D. Kirschner Predicting lymph node output efficiency
using systems biology . . . . . . . . . 169--184
Claire Morin and
Christian Hellmich Mineralization-driven bone tissue
evolution follows from fluid-to-solid
phase transformations in closed
thermodynamic systems . . . . . . . . . 185--197
Jonathan Nathan and
Jost von Hardenberg and
Ehud Meron Spatial instabilities untie the
exclusion-principle constraint on
species coexistence . . . . . . . . . . 198--204
Chao Huang and
Jing-Qi Yuan Predicting protein subchloroplast
locations with both single and multiple
sites via three different modes of
Chou's pseudo amino acid compositions 205--212
J. M. Dunn and
S. Davis and
A. Stacey and
M. A. Diuk-Wasser A simple model for the establishment of
tick-borne pathogens of \bionameIxodes
scapularis: a global sensitivity
analysis of $ R_0 $ . . . . . . . . . . 213--221
Philipp Thomas and
Arthur V. Straube and
Jens Timmer and
Christian Fleck and
Ramon Grima Signatures of nonlinearity in single
cell noise-induced oscillations . . . . 222--234
Sébastien Benzekry and
Philip Hahnfeldt Maximum tolerated dose versus metronomic
scheduling in the treatment of
metastatic cancers . . . . . . . . . . . 235--244
Sávio Torres de Farias Suggested phylogeny of tRNAs based on
the construction of ancestral sequences 245--248
Dusan Lazár Simulations show that a small part of
variable chlorophyll a fluorescence
originates in photosystem I and
contributes to overall fluorescence rise 249--264
Ying Liu and
Chunguang Li Stochastic resonance in feedforward-loop
neuronal network motifs in astrocyte
field . . . . . . . . . . . . . . . . . 265--275
Lianping Yang and
Xiangde Zhang and
Hegui Zhu Alignment free comparison: $k$ word
voting model and its applications . . . 276--282
J. M. González-Miranda On the effect of circadian oscillations
on biochemical cell signaling by NF-$
\kappa $B . . . . . . . . . . . . . . . 283--294
Andreas Sand and
Andreas Sand and
Mike Steel The standard lateral gene transfer model
is statistically consistent for
pectinate four-taxon trees . . . . . . . 295--298
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
G. Govan and
A. Xenos and
P. Frisco A critical study of network models for
neural networks and their dynamics . . . 1--10
Anonymous Pages 1--258 (7 November 2013) . . . . . 1--258
Chun-Wei Tung Prediction of pupylation sites using the
composition of $k$-spaced amino acid
pairs . . . . . . . . . . . . . . . . . 11--17
Hitoshi Koyano and
Dimitar Serbezov and
Hirohisa Kishino and
Tore Schweder Fractional parentage analysis and a
scale-free reproductive network of brown
trout . . . . . . . . . . . . . . . . . 18--35
Amir Rahimi and
Armin Madadkar-Sobhani and
Rouzbeh Touserkani and
Bahram Goliaei Efficacy of function specific
$3$D-motifs in enzyme classification
according to their EC-numbers . . . . . 36--43
M. Z. A. M. Jaffar and
F. A. Davidson Basic rules for polarised cell growth 44--51
Qi Dai and
Zhaofang Yan and
Zhuoxing Shi and
Xiaoqing Liu and
Yuhua Yao and
Pingan He Study of LZ-word distribution and its
application for sequence comparison . . 52--60
Christian Arnold and
Peter F. Stadler and
Sonja J. Prohaska Chromatin computation: Epigenetic
inheritance as a pattern reconstruction
problem . . . . . . . . . . . . . . . . 61--74
Kathryn J. Montovan and
Nathaniel Karst and
Laura E. Jones and
Thomas D. Seeley Local behavioral rules sustain the cell
allocation pattern in the combs of honey
bee colonies (\bionameApis mellifera) 75--86
Nicolas Bonello and
James Sampson and
John Burn and
Ian J. Wilson and
Gail McGrown and
Geoff P. Margison and
Mary Thorncroft and
Philip Crossbie and
Andrew C. Povey and
Mauro Santibanez-Koref and
Kevin Walters Bayesian inference supports a location
and neighbour-dependent model of DNA
methylation propagation at the MGMT gene
promoter in lung tumours . . . . . . . . 87--95
Wilfried Konrad and
Felix Flues and
Florian Schmich and
Thomas Speck and
Olga Speck An analytic model of the self-sealing
mechanism of the succulent plant
\bionameDelosperma cooperi . . . . . . . 96--109
Kouki Uchinomiya and
Yoh Iwasa Evolution of stalk/spore ratio in a
social amoeba: Cell-to-cell interaction
via a signaling chemical shaped by
cheating risk . . . . . . . . . . . . . 110--118
Ping Xie A dynamical model of programmed $ - 1 $
ribosomal frameshifting . . . . . . . . 119--131
Kylie J. Foster and
Stanley J. Miklavcic Mathematical modelling of the uptake and
transport of salt in plant roots . . . . 132--143
J. Müller and
B. A. Hense and
T. M. Fuchs and
M. Utz and
Ch. Pötzsche Bet-hedging in stochastically switching
environments . . . . . . . . . . . . . . 144--157
Tsutomu Takagi and
Yumiko Tamura and
Daniel Weihs Hydrodynamics and energy-saving swimming
techniques of Pacific bluefin tuna . . . 158--172
Mario Martínez Molina and
Marco A. Moreno-Armendáriz and
Juan Carlos Seck Tuoh Mora On the spatial dynamics and oscillatory
behavior of a predator--prey model based
on cellular automata and local particle
swarm optimization . . . . . . . . . . . 173--184
Sachit Butail and
Erik M. Bollt and
Maurizio Porfiri Analysis and classification of
collective behavior using generative
modeling and nonlinear manifold learning 185--199
Flora Cordoleani and
David Nerini and
Andrey Morozov and
Mathias Gauduchon and
Jean-Christophe Poggiale Scaling up the predator functional
response in heterogeneous environment:
When Holling type III can emerge? . . . 200--208
Marc Garbey and
Scott A. Berceli A dynamical system that describes vein
graft adaptation and failure . . . . . . 209--220
Elena Fimmel and
Alberto Danielli and
Lutz Strüngmann On dichotomic classes and bijections of
the genetic code . . . . . . . . . . . . 221--230
Abdulaziz Yousef and
Nasrollah Moghadam Charkari A novel method based on new adaptive LVQ
neural network for predicting
protein--protein interactions from
protein sequences . . . . . . . . . . . 231--239
Michael Doebeli and
Christoph Hauert and
Timothy Killingback A comment on ``Towards a rigorous
framework for studying $2$-player
continuous games'' by Shade T. Shutters,
Journal of Theoretical Biology 321,
40--43, 2013 . . . . . . . . . . . . . . 240--241
Justin G. Boyles and
Robin W. Warne A novel framework for predicting the use
of facultative heterothermy by
endotherms . . . . . . . . . . . . . . . 242--245
Mike Steel Consistency of Bayesian inference of
resolved phylogenetic trees . . . . . . 246--249
J. L. Boldrini and
R. C. Bassanezi and
A. C. Moretti and
F. J. Von Zuben and
W. A. C. Godoy and
C. J. Von Zuben and
S. F. dos Reis RETRACTED: Retraction notice to
``Non-local interactions and the
dynamics of dispersal in immature
insects'' . . . . . . . . . . . . . . . 250--250
J. L. Boldrini and
R. C. Bassanezi and
A. C. Moretti and
F. J. Von Zuben and
W. A. C. Godoy and
C. J. Von Zuben and
S. F. dos Reis Corrigendum to ``Non-local interactions
and the dynamics of dispersal in
immature insects'' [J. Theor. Biol. \bf
185 (4) (1997) 523--531] . . . . . . . . 251--251
J. L. Boldrini and
R. C. Bassanezi and
A. C. Moretti and
F. J. Von Zuben and
W. A. C. Godoy and
C. J. Von Zuben and
S. F. dos Reis Corrigendum to ``Non-local interactions
and the dynamics of dispersal in
immature insects'' [J. Theor. Biol. \bf
185 (4) (1997) 523--531] . . . . . . . . 252--258
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Alex Potapov and
Harshana Rajakaruna Allee threshold and stochasticity in
biological invasions: Colonization time
at low propagule pressure . . . . . . . 1--14
Anonymous Pages 1--190 (21 November 2013) . . . . 1--190
Monika Piwowar and
Mateusz Banach and
Leszek Konieczny and
Irena Roterman Structural role of exon-coded fragment
of polypeptide chains in selected
enzymes . . . . . . . . . . . . . . . . 15--23
F. H. S. Costa and
M. Campos and
O. E. Aiéllo and
M. A. A. da Silva Basic ingredients for mathematical
modeling of tumor growth in vitro:
Cooperative effects and search for space 24--29
A. Tosenberger and
F. Ataullakhanov and
N. Bessonov and
M. Panteleev and
A. Tokarev and
V. Volpert Modelling of thrombus growth in flow
with a DPD-PDE method . . . . . . . . . 30--41
Raluca Eftimie Simultaneous use of different
communication mechanisms leads to
spatial sorting and unexpected
collective behaviours in animal groups 42--53
Wan J. Hsieh and
Hsiuying Wang RRSM with a data-dependent threshold for
miRNA target prediction . . . . . . . . 54--60
Xiwu Yang and
Tianming Wang Linear regression model of short
$k$-word: a similarity distance suitable
for biological sequences with various
lengths . . . . . . . . . . . . . . . . 61--70
Xuan Xiao and
Jian-Liang Min and
Pu Wang and
Kuo-Chen Chou iCDI-PseFpt: Identify the channel-drug
interaction in cellular networking with
PseAAC and molecular fingerprints . . . 71--79
Jiu-Sheng Ren Growth and residual stresses of arterial
walls . . . . . . . . . . . . . . . . . 80--88
Michele Starnini and
Anna Machens and
Ciro Cattuto and
Alain Barrat and
Romualdo Pastor-Satorras Immunization strategies for epidemic
processes in time-varying contact
networks . . . . . . . . . . . . . . . . 89--100
V. Llaurens and
S. Billiard and
M. Joron The effect of dominance on polymorphism
in Müllerian mimicry . . . . . . . . . . 101--110
Amaury Lambert and
Mike Steel Predicting the loss of phylogenetic
diversity under non-stationary
diversification models . . . . . . . . . 111--124
Stephen Tully and
Monica Cojocaru and
Chris T. Bauch Coevolution of risk perception, sexual
behaviour, and HIV transmission in an
agent-based model . . . . . . . . . . . 125--132
Anca R\vadulescu and
Paul Adams Hebbian crosstalk and input segregation 133--149
M. A. Al-Mamun and
L. J. Brown and
M. A. Hossain and
C. Fall and
L. Wagstaff and
R. Bass A hybrid computational model for the
effects of maspin on cancer cell
dynamics . . . . . . . . . . . . . . . . 150--160
Daniel Franco and
Frank M. Hilker Adaptive limiter control of unimodal
population maps . . . . . . . . . . . . 161--173
Caterina Thomaseth and
Patrick Weber and
Thomas Hamm and
Kenji Kashima and
Nicole Radde Modeling sphingomyelin synthase 1 driven
reaction at the Golgi apparatus can
explain data by inclusion of a positive
feedback mechanism . . . . . . . . . . . 174--180
Daisuke Takahashi and
Åke Brännström and
Rupert Mazzucco and
Atsushi Yamauchi and
Ulf Dieckmann Abrupt community transitions and cyclic
evolutionary dynamics in complex food
webs . . . . . . . . . . . . . . . . . . 181--189
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Simone Pigolotti and
Massimo Cencini Species abundances and lifetimes: From
neutral to niche-stabilized communities 1--8
Anonymous Pages 1--112 (7 December 2013) . . . . . 1--112
Jeremy D. Scheff and
Steve E. Calvano and
Ioannis P. Androulakis Predicting critical transitions in a
model of systemic inflammation . . . . . 9--15
C. J. Thompson and
T. E. Lee and
L. Stone and
M. A. McCarthy and
M. A. Burgman Inferring extinction risks from sighting
records . . . . . . . . . . . . . . . . 16--22
James A. Strother A computational model of flow between
the microscale respiratory structures of
fish gills . . . . . . . . . . . . . . . 23--40
Chiara Poletto and
Michele Tizzoni and
Vittoria Colizza Human mobility and time spent at
destination: Impact on spatial epidemic
spreading . . . . . . . . . . . . . . . 41--58
Brian R. Lawn and
Mark B. Bush and
Amir Barani and
Paul J. Constantino and
Stephen Wroe Inferring biological evolution from
fracture patterns in teeth . . . . . . . 59--65
J. Lefevre and
D. J. Marshall and
A. N. Combes and
A. L. Ju and
M. H. Little and
N. A. Hamilton Modelling cell turnover in a complex
tissue during development . . . . . . . 66--79
Ana Mar\'ìa Velasco and
Arturo Becerra and
Ricardo Hernández-Morales and
Luis Delaye and
Mar\'ìa Eugenia Jiménez-Corona and
Samuel Ponce-de-Leon and
Antonio Lazcano Low complexity regions (LCRs) contribute
to the hypervariability of the HIV-1
gp120 protein . . . . . . . . . . . . . 80--86
Pilhwa Lee and
Eric A. Sobie and
Charles S. Peskin Computer simulation of voltage sensitive
calcium ion channels in a dendritic
spine . . . . . . . . . . . . . . . . . 87--93
Yann Guédon and
Yassin Refahi and
Fabrice Besnard and
Etienne Farcot and
Christophe Godin and
Teva Vernoux Pattern identification and
characterization reveal permutations of
organs as a key genetically controlled
property of post-meristematic
phyllotaxis . . . . . . . . . . . . . . 94--110
Suyu Mei Corrigendum to ``Predicting plant
protein subcellular multi-localization
by Chou's PseAAC formulation based
multi-label homolog knowledge transfer
learning'' [J. Theor. Biol. \bf 310
(2012) 80--87] . . . . . . . . . . . . . 111--111
Suyu Mei Corrigendum to ``Multi-kernel transfer
learning based on Chou's PseAAC
formulation for protein submitochondria
localization'' [J. Theor. Biol. \bf 293
(2012) 121--130] . . . . . . . . . . . . 112--112
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Stefan A. H. Geritz and
Éva Kisdi and
Christopher A. Klausmeier Introduction to special issue . . . . . 1--2
Olof Leimar and
Akira Sasaki and
Michael Doebeli and
Ulf Dieckmann Limiting similarity, species packing,
and the shape of competition kernels . . 3--13
Colin T. Kremer and
Christopher A. Klausmeier Coexistence in a variable environment:
Eco-evolutionary perspectives . . . . . 14--25
Xiao Xiao and
Gregor F. Fussmann Armstrong--McGehee mechanism revisited:
Competitive exclusion and coexistence of
nonlinear consumers . . . . . . . . . . 26--35
Lasse Ruokolainen and
Kevin McCann Environmental weakening of trophic
interactions drives stability in
stochastic food webs . . . . . . . . . . 36--46
Robert D. Holt and
Michael Barfield Direct plant-predator interactions as
determinants of food chain dynamics . . 47--57
Ahmad R. Kamran-Disfani and
Antonio J. Golubski Lateral cascade of indirect effects in
food webs with different types of
adaptive behavior . . . . . . . . . . . 58--69
Sara A. Reynolds and
Chad E. Brassil When can a single-species,
density-dependent model capture the
dynamics of a consumer-resource system? 70--83
William T. Gibson and
William G. Wilson Individual-based chaos: Extensions of
the discrete logistic model . . . . . . 84--92
Yolanda E. Morbey Protandry, sexual size dimorphism, and
adaptive growth . . . . . . . . . . . . 93--99
Henrique C. Giacomini and
Brian J. Shuter Adaptive responses of energy storage and
fish life histories to climatic
gradients . . . . . . . . . . . . . . . 100--111
Vlastimil K\vrivan Behavioral refuges and predator--prey
coexistence . . . . . . . . . . . . . . 112--121
Hiroyuki Matsuda and
Peter A. Abrams Is feedback control effective for
ecosystem-based fisheries management? 122--128
Yuuya Tachiki and
Yoh Iwasa Coevolution of mast seeding in trees and
extended diapause of seed predators . . 129--139
Eva Kisdi and
Stefan A. H. Geritz and
Barbara Boldin Evolution of pathogen virulence under
selective predation: a construction
method to find eco-evolutionary cycles 140--150
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Kylie J. Foster and
Stanley J. Miklavcic On the competitive uptake and transport
of ions through differentiated root
tissues . . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--294 (7 January 2014) . . . . . 1--294
Jan Teichmann and
Mark Broom and
Eduardo Alonso The application of temporal difference
learning in optimal diet models . . . . 11--16
Andy M. Reynolds and
Patrick Schultheiss and
Ken Cheng Does the Australian desert ant
\bionameMelophorus bagoti approximate a
Lévy search by an intrinsic bi-modal
walk? . . . . . . . . . . . . . . . . . 17--22
S. P. Vega Royero and
G. J. Sibona Can we heal Chagas infection? . . . . . 23--29
Ping He and
Wei Wu and
Hai-Dong Wang and
Ke-Long Liao and
Wei Zhang and
Feng-Lin Lv and
Kang Yang Why ligand cross-reactivity is high
within peptide recognition domain
families? A case study on human c-Src
SH3 domain . . . . . . . . . . . . . . . 30--37
Geoffrey A. M. Hunter and
James P. Keener Mechanisms underlying the additive and
redundant Qrr phenotypes in
\bionameVibrio harveyi and
\bionameVibrio cholerae . . . . . . . . 38--49
Tamer Oraby and
Olga Vasilyeva and
Daniel Krewski and
Frithjof Lutscher Modeling seasonal behavior changes and
disease transmission with application to
chronic wasting disease . . . . . . . . 50--59
Margarete Utz and
Jonathan M. Jeschke and
Volker Loeschcke and
Wilfried Gabriel Phenotypic plasticity with instantaneous
but delayed switches . . . . . . . . . . 60--72
József Garay and
Vill\Ho Csiszár and
Tamás F. Móri Under multilevel selection: ``When shall
you be neither spiteful nor envious?'' 73--84
Muhammad Tahir and
Asifullah Khan and
Hüseyin Kaya Protein subcellular localization in
human and hamster cell lines: Employing
local ternary patterns of fluorescence
microscopy images . . . . . . . . . . . 85--95
Evgeny A. Shavlyugin and
Leonid G. Hanin and
Mikhail A. Khanin Dynamics of pathologic clot formation: a
mathematical model . . . . . . . . . . . 96--104
Suyu Mei SVM ensemble based transfer learning for
large-scale membrane proteins
discrimination . . . . . . . . . . . . . 105--110
Axel Kowald and
Marcus Dawson and
Thomas B. L. Kirkwood Mitochondrial mutations and ageing: Can
mitochondrial deletion mutants
accumulate via a size based replication
advantage? . . . . . . . . . . . . . . . 111--118
H. W. Kwon and
M. Y. Choi Generalized hydromechanical model for
stomatal responses to hydraulic
perturbations . . . . . . . . . . . . . 119--130
Sarah M. Roy and
Dominik Wodarz Tissue architecture, feedback
regulation, and resilience to viral
infection . . . . . . . . . . . . . . . 131--138
Michiko Nosaka and
Katsuki Hirata and
Ryotarou Tsuji and
Syunya Sunaba Planes formed with four intron-positions
in tertiary structures of retinol
binding protein and calpain domain VI 139--145
Qian Liu and
Yi-Ping Phoebe Chen and
Jinyan Li $k$-Partite cliques of protein
interactions: a novel subgraph topology
for functional coherence analysis on PPI
networks . . . . . . . . . . . . . . . . 146--154
Hervé Seligmann Putative anticodons in mitochondrial
tRNA sidearm loops: Pocketknife tRNAs? 155--163
P. K. Fung and
P. A. Robinson Neural field theory of synaptic
metaplasticity with applications to
theta burst stimulation . . . . . . . . 164--176
Eili Y. Klein The impact of heterogeneous transmission
on the establishment and spread of
antimalarial drug resistance . . . . . . 177--185
Nicola J. R. Plowes and
Kai Ramsch and
Martin Middendorf and
Bert Hölldobler An empirically based simulation of group
foraging in the harvesting ant,
\bionameMessor pergandei . . . . . . . . 186--198
Rui Dilão The regulation of gene expression in
eukaryotes: Bistability and oscillations
in repressilator models . . . . . . . . 199--208
M. Doyennette and
I. Déléris and
G. Féron and
E. Guichard and
I. Souchon and
I. C. Trelea Main individual and product
characteristics influencing in-mouth
flavour release during eating masticated
food products with different textures:
Mechanistic modelling and experimental
validation . . . . . . . . . . . . . . . 209--221
Yue Wu and
Clare A. Saddler and
Frank Valckenborgh and
Mark M. Tanaka Dynamics of evolutionary rescue in
changing environments and the emergence
of antibiotic resistance . . . . . . . . 222--231
Sven Kurbel Hypothesis of homeothermy evolution on
isolated South China Craton that moved
from equator to cold north latitudes
250--200 Myr ago . . . . . . . . . . . . 232--237
Erica J. Graham and
Frederick R. Adler Long-term models of oxidative stress and
mitochondrial damage in insulin
resistance progression . . . . . . . . . 238--250
Fulton E. Rockwell and
N. Michele Holbrook and
Abraham D. Stroock Leaf hydraulics I: Scaling transport
properties from single cells to tissues 251--266
Fulton E. Rockwell and
N. Michele Holbrook and
Abraham D. Stroock Leaf hydraulics II: Vascularized tissues 267--284
Wes Maciejewski Reproductive value in graph-structured
populations . . . . . . . . . . . . . . 285--293
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Marco Archetti Evolutionary dynamics of the Warburg
effect: Glycolysis as a collective
action problem among cancer cells . . . 1--8
Anonymous Pages 1--142 (21 January 2014) . . . . . 1--142
Lo\"\ic Tadrist and
Marc Saudreau and
Emmanuel de Langre Wind and gravity mechanical effects on
leaf inclination angles . . . . . . . . 9--16
Allen Cheung Animal path integration: a model of
positional uncertainty along tortuous
paths . . . . . . . . . . . . . . . . . 17--33
Zohre Hajisharifi and
Moien Piryaiee and
Majid Mohammad Beigi and
Mandana Behbahani and
Hassan Mohabatkar Predicting anticancer peptides with
Chou's pseudo amino acid composition and
investigating their mutagenicity via
Ames test . . . . . . . . . . . . . . . 34--40
Shishi Luo A unifying framework reveals key
properties of multilevel selection . . . 41--52
Sameer Jade and
Kelli H. Tamvada and
David S. Strait and
Ian R. Grosse Finite element analysis of a femur to
deconstruct the paradox of bone
curvature . . . . . . . . . . . . . . . 53--63
Nao Takashina and
Akihiko Mougi Effects of marine protected areas on
overfished fishing stocks with multiple
stable states . . . . . . . . . . . . . 64--70
Shengli Zhang and
Yunyun Liang and
Xiguo Yuan Improving the prediction accuracy of
protein structural class: Approached
with alternating word frequency and
normalized Lempel--Ziv complexity . . . 71--77
Kristo Abner and
Tõnis Aaviksaar and
Kaarel Adamberg and
Raivo Vilu Single-cell model of prokaryotic cell
cycle . . . . . . . . . . . . . . . . . 78--87
C. T. Wannige and
D. Kulasiri and
S. Samarasinghe A nutrient dependant switch explains
mutually exclusive existence of meiosis
and mitosis initiation in budding yeast 88--101
Ying Xu and
Jiang-Nan Yang Cooperation promotes the evolution of
separate sexes from hermaphrodites with
unitary growth . . . . . . . . . . . . . 102--110
Erida Gjini and
Daniel T. Haydon and
J. David Barry and
Christina A. Cobbold Revisiting the diffusion approximation
to estimate evolutionary rates of gene
family diversification . . . . . . . . . 111--122
Maria Abou Chakra and
Arne Traulsen Under high stakes and uncertainty the
rich should lend the poor a helping hand 123--130
Jonas Bühler and
Eric von Lieres and
Gregor Huber A class of compartmental models for
long-distance tracer transport in plants 131--142
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
John H. M. Thornley and
Anthony J. Parsons Allocation of new growth between shoot,
root and mycorrhiza in relation to
carbon, nitrogen and phosphate supply:
Teleonomy with maximum growth rate . . . 1--14
Anonymous Pages 1--106 (7 February 2014) . . . . . 1--106
Martial L. Ndeffo Mbah and
David P. Durham and
Jan Medlock and
Alison P. Galvani Country- and age-specific optimal
allocation of dengue vaccines . . . . . 15--22
Elsje Pienaar and
Maria Lerm A mathematical model of the initial
interaction between Mycobacterium
tuberculosis and macrophages . . . . . . 23--32
A. C. Fowler and
H. F. Winstanley and
M. J. McGuinness and
L. B. Cribbin Oscillations in soil bacterial redox
reactions . . . . . . . . . . . . . . . 33--38
Keita Honjo and
Akiko Satake N-player mosquito net game: Individual
and social rationality in the misuse of
insecticide-treated nets . . . . . . . . 39--46
L. Berec and
D. Maxin Why have parasites promoting mating
success been observed so rarely? . . . . 47--61
Helen Kettle and
Ruairi Donnelly and
Harry J. Flint and
Glenn Marion pH feedback and phenotypic diversity
within bacterial functional groups of
the human gut . . . . . . . . . . . . . 62--69
Jiapu Zhang and
Yuanli Zhang Molecular dynamics studies on the NMR
and X-ray structures of rabbit prion
proteins . . . . . . . . . . . . . . . . 70--82
Koji Kawamura and
Laurence Hibrand-Saint Oyant and
Fabrice Foucher and
Tatiana Thouroude and
Sébastien Loustau Kernel methods for phenotyping complex
plant architecture . . . . . . . . . . . 83--92
Henrik Sjödin and
Åke Brännström and
Mårten Söderquist and
Göran Englund Population-level consequences of
heterospecific density-dependent
movements in predator--prey systems . . 93--106
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Stanca M. Ciupe and
Elissa J. Schwartz Understanding virus-host dynamics
following EIAV infection in SCID horses 1--8
Anonymous Pages 1--210 (21 February 2014) . . . . 1--210
Jozef Nahalka Protein--RNA recognition: Cracking the
code . . . . . . . . . . . . . . . . . . 9--15
Severo Vázquez-Prieto and
Humberto González-Díaz and
Esperanza Paniagua and
Román Vilas and
Florencio M. Ubeira A QSPR-like model for multilocus
genotype networks of \bionameFasciola
hepatica in Northwest Spain . . . . . . 16--24
Michele M. Ciulla and
Federico De Marco and
Elisa Montelatici and
Lorenza Lazzari and
Gianluca L. Perrucci and
Fabio Magrini Assessing cytokines' talking patterns
following experimental myocardial damage
by applying Shannon's information theory 25--31
Clément Calenge and
Sophie Rossi Bayesian modelling of hunting data may
improve the understanding of
host-parasite systems: Wild boar
diseases and vaccination as an example 32--43
Basil N. Yakimov and
Dmitry I. Iudin and
Leonid A. Solntsev and
David B. Gelashvili Multifractal analysis of neutral
community spatial structure . . . . . . 44--53
Rachael Miller Neilan and
Kenneth Rose Simulating the effects of fluctuating
dissolved oxygen on growth,
reproduction, and survival of fish and
shrimp . . . . . . . . . . . . . . . . . 54--68
Fabio Zucca Persistent and susceptible bacteria with
individual deaths . . . . . . . . . . . 69--78
Jonathan F. Li and
John Lowengrub The effects of cell compressibility,
motility and contact inhibition on the
growth of tumor cell clusters using the
Cellular Potts Model . . . . . . . . . . 79--91
A. G. Yakovlev and
V. A. Shuvalov Modeling of reversible charge separation
in reaction centers of photosynthesis:
An incoherent approach . . . . . . . . . 92--101
Nils Christian and
Alexander Skupin and
Silvia Morante and
Karl Jansen and
Giancarlo Rossi and
Oliver Ebenhöh Mesoscopic behavior from microscopic
Markov dynamics and its application to
calcium release channels . . . . . . . . 102--112
Sweta Kumari and
Arumugam Mohana Priya and
Sajitha Lulu and
Mohammad Tauqueer Molecular modeling, simulation and
virtual screening of ribosomal
phosphoprotein P1 from
\bionamePlasmodium falciparum . . . . . 113--119
Emmanuel A. Mpolya and
Kenta Yashima and
Hisashi Ohtsuki and
Akira Sasaki Epidemic dynamics of a vector-borne
disease on a villages-and-city star
network with commuters . . . . . . . . . 120--126
Vlastimil K\vrivan Competition in di- and tri-trophic food
web modules . . . . . . . . . . . . . . 127--137
Lester Ingber and
Marco Pappalepore and
Ronald R. Stesiak Electroencephalographic field influence
on calcium momentum waves . . . . . . . 138--153
Rajasekaran Mahalingam and
Hung-Pin Peng and
An-Suei Yang Prediction of FMN-binding residues with
three-dimensional probability
distributions of interacting atoms on
protein surfaces . . . . . . . . . . . . 154--161
Peter A. Abrams The evolutionary and behavioral
modification of consumer responses to
environmental change . . . . . . . . . . 162--173
Shuhei Ohnishi and
Takashi Yamakawa and
Tatsuro Akamine On the analytical solution for the
Pütter--Bertalanffy growth equation . . . 174--177
Oliver P. Hauser and
Arne Traulsen and
Martin A. Nowak Heterogeneity in background fitness acts
as a suppressor of selection . . . . . . 178--185
Xiao-Hui Niu and
Xue-Hai Hu and
Feng Shi and
Jing-Bo Xia Predicting DNA binding proteins using
support vector machine with hybrid
fractal features . . . . . . . . . . . . 186--192
Shimaila Ali and
Jin Duan and
Trevor C. Charles and
Bernard R. Glick A bioinformatics approach to the
determination of genes involved in
endophytic behavior in
\bionameBurkholderia spp. . . . . . . . 193--198
Hong Wang and
Xi-cheng Wang Parameter estimation for metabolic
networks with two stage Bregman
regularization homotopy inversion
algorithm . . . . . . . . . . . . . . . 199--207
Kohji Sato Minimum dynamic core in consciousness 208--210
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
P. K. Jithinraj and
Ushasi Roy and
Manoj Gopalakrishnan Zero-order ultrasensitivity: a study of
criticality and fluctuations under the
total quasi-steady state approximation
in the linear noise regime . . . . . . . 1--11
Anonymous Pages 1--88 (7 March 2014) . . . . . . . 1--88
Liang Kong and
Lichao Zhang and
Jinfeng Lv Accurate prediction of protein
structural classes by incorporating
predicted secondary structure
information into the general form of
Chou's pseudo amino acid composition . . 12--18
Xiaowu Liu and
Riqiang Deng and
Jinwen Wang and
Xunzhang Wang COStar: a D-star Lite-based dynamic
search algorithm for codon optimization 19--30
Guo-Sheng Han and
Zu-Guo Yu and
Vo Anh A two-stage SVM method to predict
membrane protein types by incorporating
amino acid classifications and
physicochemical properties into a
general form of Chou's PseAAC . . . . . 31--39
Alberto Antonioni and
Marco Tomassini and
Pierre Buesser Random diffusion and cooperation in
continuous two-dimensional space . . . . 40--48
Marco Campenn\`\i and
Gabriele Schino Partner choice promotes cooperation: The
two faces of testing with agent-based
models . . . . . . . . . . . . . . . . . 49--55
S. Sutradhar and
R. Paul Tug-of-war between opposing molecular
motors explains chromosomal oscillation
during mitosis . . . . . . . . . . . . . 56--69
R. G. Abeysuriya and
C. J. Rennie and
P. A. Robinson Prediction and verification of nonlinear
sleep spindle harmonic oscillations . . 70--77
Yan Xu and
Xiaobo Wang and
Yongcui Wang and
Yingjie Tian and
Xiaojian Shao and
Ling-Yun Wu and
Naiyang Deng Prediction of posttranslational
modification sites from amino acid
sequences with kernel methods . . . . . 78--87
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
David A. Kessler and
Nadav M. Shnerb Neutral-like abundance distributions in
the presence of selection in a
continuous fitness landscape . . . . . . 1--11
Anonymous Pages 1--110 (21 March 2014) . . . . . . 1--110
Elsa W. Birch and
Madeleine Udell and
Markus W. Covert Incorporation of flexible objectives and
time-linked simulation with flux balance
analysis . . . . . . . . . . . . . . . . 12--21
Mauricio A. Fuentes The mechanical cost of transport of fast
running animals . . . . . . . . . . . . 22--31
Juan A. Bonachela and
Simon A. Levin Evolutionary comparison between viral
lysis rate and latent period . . . . . . 32--42
Marco Fidel Ávila and
Daniel Torrente and
Ricardo Cabezas and
Ludis Morales and
Luis Miguel Garc\'ìa-Segura and
Janneth Gonzalez and
George E. Barreto Structural insights from GRP78-NF-$
\kappa $B binding interactions: a
computational approach to understand a
possible neuroprotective pathway in
brain injuries . . . . . . . . . . . . . 43--51
Snigdhadip Dey and
Bedartha Goswami and
Amitabh Joshi Effects of symmetric and asymmetric
dispersal on the dynamics of
heterogeneous metapopulations: Two-patch
systems revisited . . . . . . . . . . . 52--60
E. Fabian Cardozo and
Rutao Luo and
Michael J. Piovoso and
Ryan Zurakowski Spatial modeling of HIV cryptic viremia
and $2$-LTR formation during raltegravir
intensification . . . . . . . . . . . . 61--69
Koh Hashimoto Multigame effect in finite populations
induces strategy linkage between two
games . . . . . . . . . . . . . . . . . 70--77
K. de Borst and
T. K. Bader Structure-function relationships in
hardwood --- Insight from
micromechanical modelling . . . . . . . 78--91
Syi Hidden patterns of reciprocity . . . . . 92--98
D. Hala and
D. B. Huggett In silico predicted structural and
functional robustness of piscine
steroidogenesis . . . . . . . . . . . . 99--108
Lewis Wolpert A relaxed modification of the Rappaport
model for cytokinesis . . . . . . . . . 109--109
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Satoshi Yamashita and
Tatsuo Michiue Quantitative analysis of cell
arrangement indicates early
differentiation of the neural region
during Xenopus gastrulation . . . . . . 1--7
Anonymous Pages 1--108 (7 April 2014) . . . . . . 1--108
Maqsood Hayat and
Muhammad Tahir and
Sher Afzal Khan Prediction of protein structure classes
using hybrid space of multi-profile
Bayes and bi-gram probability feature
spaces . . . . . . . . . . . . . . . . . 8--15
Hiroshi Toyoizumi and
Jeremy Field Dynamics of social queues . . . . . . . 16--22
Jorge Peña and
Laurent Lehmann and
Georg Nöldeke Gains from switching and evolutionary
stability in multi-player matrix games 23--33
Tadasu Matsuo and
Marko Jusup and
Yoh Iwasa The conflict of social norms may cause
the collapse of cooperation: Indirect
reciprocity with opposing attitudes
towards in-group favoritism . . . . . . 34--46
Keisuke Ejima and
Kazuyuki Aihara and
Hiroshi Nishiura Probabilistic differential diagnosis of
Middle East respiratory syndrome (MERS)
using the time from immigration to
illness onset among imported cases . . . 47--53
Takuya Sekiguchi and
Mayuko Nakamaru How intergenerational interaction
affects attitude-behavior inconsistency 54--66
E. Georgelin and
N. Loeuille Dynamics of coupled mutualistic and
antagonistic interactions, and their
implications for ecosystem management 67--74
Karl E. Zelik and
Tzu-Wei P. Huang and
Peter G. Adamczyk and
Arthur D. Kuo The role of series ankle elasticity in
bipedal walking . . . . . . . . . . . . 75--85
T. Glimm and
R. Bhat and
S. A. Newman Modeling the morphodynamic galectin
patterning network of the developing
avian limb skeleton . . . . . . . . . . 86--108
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Bo Wu A novel method to study aging in
bacteria that reproduce by
morphologically symmetric fission . . . 1--6
Anonymous Pages 1--190 (21 April 2014) . . . . . . 1--190
Sachi Yamaguchi and
Jens T. Hòeg and
Yoh Iwasa Evolution of sex determination and
sexually dimorphic larval sizes in
parasitic barnacles . . . . . . . . . . 7--16
Duncan S. Barrack and
Rüdiger Thul and
Markus R. Owen Modelling the coupling between
intracellular calcium release and the
cell cycle during cortical brain
development . . . . . . . . . . . . . . 17--32
C. Boëte and
F. B. Agusto and
R. G. Reeves Impact of mating behaviour on the
success of malaria control through a
single inundative release of transgenic
mosquitoes . . . . . . . . . . . . . . . 33--43
Samuel Zambrano and
Marco E. Bianchi and
Alessandra Agresti A simple model of NF-$ \kappa $B
dynamics reproduces experimental
observations . . . . . . . . . . . . . . 44--53
Geert Biermans and
Nele Horemans and
Niel Hens and
Jordi Vives i Batlle and
Hildegarde Vandenhove and
Ann Cuypers A dynamic dosimetry model for
radioactive exposure scenarios in
\bionameArabidopsis thaliana . . . . . . 54--62
Yan Li and
Andreas Handel Modeling inoculum dose dependent
patterns of acute virus infections . . . 63--73
Laureano Castro and
Miguel A. Toro Cumulative cultural evolution: The role
of teaching . . . . . . . . . . . . . . 74--83
Xiaomei Li and
Xindong Wu and
Gongqing Wu Robust feature generation for protein
subchloroplast location prediction with
a weighted GO transfer model . . . . . . 84--94
Reijer Lenstra Evolution of the genetic code through
progressive symmetry breaking . . . . . 95--108
Yuhua Yao and
Shoujiang Yan and
Jianning Han and
Qi Dai and
Ping-an He A novel descriptor of protein sequences
and its application . . . . . . . . . . 109--117
K. M. Aquino and
P. A. Robinson and
P. M. Drysdale Spatiotemporal hemodynamic response
functions derived from physiology . . . 118--136
Kuikui Gao and
Xu Zhang and
Enmin Feng and
Zhilong Xiu Sensitivity analysis and parameter
identification of nonlinear hybrid
systems for glycerol transport
mechanisms in continuous culture . . . . 137--143
Nurul S. Abdul Latif and
Graeme C. Wake and
Tony Reglinski and
Philip A. G. Elmer Modelling induced resistance to plant
diseases . . . . . . . . . . . . . . . . 144--150
S. M. Ashrafur Rahman and
Naveen K. Vaidya and
Xingfu Zou Impact of Tenofovir gel as a PrEP on HIV
infection: a mathematical model . . . . 151--159
Joseph Reynolds and
Inês F. Amado and
Antonio A. Freitas and
Grant Lythe and
Carmen Molina-París A mathematical perspective on CD4 + T
cell quorum-sensing . . . . . . . . . . 160--175
Maarten J. Wensink and
Tomasz F. Wrycza and
Annette Baudisch No senescence despite declining
selection pressure: Hamilton's result in
broader perspective . . . . . . . . . . 176--181
Stefan Müller and
Georg Regensburger and
Ralf Steuer Enzyme allocation problems in kinetic
metabolic networks: Optimal solutions
are elementary flux modes . . . . . . . 182--190
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
David Gomez and
Rahul Marathe and
Veronika Bierbaum and
Stefan Klumpp Modeling stochastic gene expression in
growing cells . . . . . . . . . . . . . 1--11
Anonymous Pages 1--122 (7 May 2014) . . . . . . . 1--122
Chenglong Yu and
Rong Lucy He and
Stephen S.-T. Yau Viral genome phylogeny based on
Lempel--Ziv complexity and Hausdorff
distance . . . . . . . . . . . . . . . . 12--20
Martin Ritchie and
Luc Berthouze and
Thomas House and
Istvan Z. Kiss Higher-order structure and epidemic
dynamics in clustered networks . . . . . 21--32
Karsten Alexander Lettmann and
Matthias Hardtke-Wolenski The importance of liver microcirculation
in promoting autoimmune hepatitis via
maintaining an inflammatory cytokine
milieu --- a mathematical model study 33--46
Kaustubh Dhole and
Gurdeep Singh and
Priyadarshini P. Pai and
Sukanta Mondal Sequence-based prediction of
protein--protein interaction sites with
L1-logreg classifier . . . . . . . . . . 47--54
Guang Hu and
Wenying Yan and
Jianhong Zhou and
Bairong Shen Residue interaction network analysis of
Dronpa and a DNA clamp . . . . . . . . . 55--64
Wataru Nakahashi and
Marcus W. Feldman Evolution of division of labor:
Emergence of different activities among
group members . . . . . . . . . . . . . 65--79
Radu Dumitru Moleriu and
Daniela Zaharie and
Lavinia Cristina Moatar-Moleriu and
Alexandra Teodora Gruia and
Ani Aurora Mic and
Felix Aurel Mic Insights into the mechanisms of thymus
involution and regeneration by modeling
the glucocorticoid-induced perturbation
of thymocyte populations dynamics . . . 80--99
Bin Liang and
Mao Sun Dynamic flight stability of a hovering
model dragonfly . . . . . . . . . . . . 100--112
Sang Joon Lee and
Seung Chul Lee and
Bo Heum Kim Liquid-intake flow around the tip of
butterfly proboscis . . . . . . . . . . 113--121
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Tai-Hsien Wu and
Rurng-Sheng Guo and
Guo-Wei He and
Ying-Ming Liu and
Dewei Qi Simulation of swimming of a flexible
filament using the generalized
lattice-spring lattice-Boltzmann method 1--11
Anonymous Pages 1--172 (21 May 2014) . . . . . . . 1--172
Carlos Fernandez-Lozano and
Marcos Gestal and
Humberto González-D\'ìaz and
Julián Dorado and
Alejandro Pazos and
Cristian R. Munteanu Markov mean properties for cell
death-related protein classification . . 12--21
Burton Simon Continuous-time models of group
selection, and the dynamical
insufficiency of kin selection models 22--31
Mochamad Apri and
Johannes Kromdijk and
Pieter H. B. de Visser and
Maarten de Gee and
Jaap Molenaar Modelling cell division and
endoreduplication in tomato fruit
pericarp . . . . . . . . . . . . . . . . 32--43
Daniel Maykranz and
Andre Seyfarth Compliant ankle function results in
landing-take off asymmetry in legged
locomotion . . . . . . . . . . . . . . . 44--49
Zhen Wang and
Attila Szolnoki and
Matjaz Perc Rewarding evolutionary fitness with
links between populations promotes
cooperation . . . . . . . . . . . . . . 50--56
H. G. Kilian and
D. Bartkowiak and
M. Kazda and
D. Kaufmann Modelling the growth of plants with a
uniform growth logistics . . . . . . . . 57--65
V. S. K. Manem and
M. Kohandel and
N. L. Komarova and
S. Sivaloganathan Spatial invasion dynamics on random and
unstructured meshes: Implications for
heterogeneous tumor populations . . . . 66--73
Álvaro G. López and
Juan Sabuco and
Jesús M. Seoane and
Jorge Duarte and
Cristina Januário and
Miguel A. F. Sanjuán Avoiding healthy cells extinction in a
cancer model . . . . . . . . . . . . . . 74--81
Lei Yang and
Jizhe Wang and
Huiping Wang and
Yingli Lv and
Yongchun Zuo and
Wei Jiang Analysis and identification of toxin
targets by topological properties in
protein--protein interaction network . . 82--91
Laura Cantini and
Claudia Cianci and
Duccio Fanelli and
Emma Massi and
Luigi Barletti Linear noise approximation for
stochastic oscillations of intracellular
calcium . . . . . . . . . . . . . . . . 92--99
Naoki Masuda Evolution via imitation among
like-minded individuals . . . . . . . . 100--108
Clemente F. Arias and
Miguel A. Herrero and
Francisco J. Acosta and
Cristina Fernandez-Arias A mathematical model for a T cell fate
decision algorithm during immune
response . . . . . . . . . . . . . . . . 109--120
Navid Nezafat and
Younes Ghasemi and
Gholamreza Javadi and
Mohammad Javad Khoshnoud and
Eskandar Omidinia A novel multi-epitope peptide vaccine
against cancer: An in silico approach 121--134
Mark A. Gilbert and
Steven M. White and
James M. Bullock and
Eamonn A. Gaffney Spreading speeds for stage structured
plant populations in fragmented
landscapes . . . . . . . . . . . . . . . 135--149
Bonhi S. Bhattacharya and
Peter K. Sweby and
Anne-Marie Minihane and
Kim G. Jackson and
Marcus J. Tindall A mathematical model of the sterol
regulatory element binding protein 2
cholesterol biosynthesis pathway . . . . 150--162
Simon Benhamou Path integration and coordinate systems 163--166
Massimo Di Giulio The split genes of \bionameNanoarchaeum
equitans have not originated in its
lineage and have been merged in another
\bionameNanoarchaeota: a reply to Podar
et al. . . . . . . . . . . . . . . . . . 167--169
P. K. Jithinraj and
Ushasi Roy and
Manoj Gopalakrishnan Corrigendum to ``Zero-order
ultrasensitivity: a study of criticality
and fluctuations under the total
quasi-steady state approximation in the
linear noise regime'' [J. Theor. Biol.
\bf 344 (2014) 1--11] . . . . . . . . . 170--170
Axel Kowald and
Marcus Dawson and
Thomas B. L. Kirkwood Erratum to ``Mitochondrial mutations and
ageing: Can mitochondrial deletion
mutants accumulate via a size based
replication advantage?'' [J. Theor.
Biol. \bf 340 (2014) 111--118] . . . . . 171--171
Elsje Pienaar and
Maria Lerm Erratum to ``A mathematical model of the
initial interaction between
Mycobacterium tuberculosis and
macrophages'' [J. Theoret. Biol. \bf 342
(2014) 23--32] . . . . . . . . . . . . . 172--172
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Yasuyuki Suzuki and
Daichi Sakai and
Taishin Nomura and
Yoshito Hirata and
Kazuyuki Aihara A new protocol for intermittent androgen
suppression therapy of prostate cancer
with unstable saddle-point dynamics . . 1--16
Anonymous Pages 1--112 (7 June 2014) . . . . . . . 1--112
Mototaka Minakuchi and
Seido Nagano Stable territory formation in ecology
and its potential generality in pattern
formations . . . . . . . . . . . . . . . 17--23
Samir Okasha and
John A. Weymark and
Walter Bossert Inclusive fitness maximization: An
axiomatic approach . . . . . . . . . . . 24--31
Jin-Tu Sun and
Bin Ao and
Sheng Zhang and
Zhitong Bing and
Lei Yang Evolving protein--protein interaction
networks: a model based on duplication
and mutation at different rates . . . . 32--36
Christian A. Yates Discrete and continuous models for
tissue growth and shrinkage . . . . . . 37--48
Sayyed R. Mousavi and
Ilnaz Khodadadi and
Hossein Falsafain and
Reza Nadimi and
Nasser Ghadiri Maximum likelihood model based on minor
allele frequencies and weighted Max-SAT
formulation for haplotype assembly . . . 49--56
B. Fallqvist and
A. Kulachenko and
M. Kroon Modelling of cross-linked actin networks
--- Influence of geometrical parameters
and cross-link compliance . . . . . . . 57--69
R. I. Hickson and
M. G. Roberts How population heterogeneity in
susceptibility and infectivity
influences epidemic dynamics . . . . . . 70--80
María J. Cáceres and
Beno\^\it Perthame Beyond blow-up in excitatory integrate
and fire neuronal networks: Refractory
period and spontaneous activity . . . . 81--89
Stephen D. McIntyre and
Virendra Kakade and
Yoichiro Mori and
Elena G. Tolkacheva Heart rate variability and alternans
formation in the heart: The role of
feedback in cardiac dynamics . . . . . . 90--97
Carmen Lía Murall and
Kevin S. McCann and
Chris T. Bauch Revising ecological assumptions about
Human papillomavirus interactions and
type replacement . . . . . . . . . . . . 98--109
Mikkel Meyer Andersen and
Poul Svante Eriksen and
Niels Morling Corrigendum to ``The discrete Laplace
exponential family and estimation of
Y-STR haplotype frequencies'' [J. Theor.
Biol. \bf 329 (2013) 39--51] . . . . . . 110--110
P. K. Jithinraj and
Ushasi Roy and
Manoj Gopalakrishnan Erratum to ``Zero-order
ultrasensitivity: a study of criticality
and fluctuations under the total
quasi-steady state approximation in the
linear noise regime'' [J. Theor. Biol.
\bf 344 (2014) 1--11] . . . . . . . . . 111--111
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Tuhin K. Roy and
Timothy W. Secomb Theoretical analysis of the determinants
of lung oxygen diffusing capacity . . . 1--8
Anonymous Pages 1--96 (21 June 2014) . . . . . . . 1--96
James P. Grover and
Feng-Bin Wang Competition and allelopathy with
resource storage: Two resources . . . . 9--24
Hiroto Yonenoh and
Eizo Akiyama Selection of opponents in the prisoner's
dilemma in dynamic networks: An
experimental approach . . . . . . . . . 25--36
Sonali Shinde and
Milsee Mol and
Virashree Jamdar and
Shailza Singh Molecular modeling and molecular
dynamics simulations of GPI 14 in
Leishmania major: Insight into the
catalytic site for active site directed
drug design . . . . . . . . . . . . . . 37--46
M. Fribourg and
B. Hartmann and
M. Schmolke and
N. Marjanovic and
R. A. Albrecht and
A. Garc\'ìa-Sastre and
S. C. Sealfon and
C. Jayaprakash and
F. Hayot Model of influenza A virus infection:
Dynamics of viral antagonism and innate
immune response . . . . . . . . . . . . 47--57
Long-Fei Li and
Cheng Xiang and
Ya-Bing Zhu and
Kai-Rong Qin Modeling of progesterone-induced
intracellular calcium signaling in human
spermatozoa . . . . . . . . . . . . . . 58--66
Hannah Woodall and
Ben Adams Partial cross-enhancement in models for
dengue epidemiology . . . . . . . . . . 67--73
Yoram Louzoun and
Chuan Xue and
Gregory B. Lesinski and
Avner Friedman A mathematical model for pancreatic
cancer growth and treatments . . . . . . 74--82
Joe Yuichiro Wakano and
Laurent Lehmann Evolutionary branching in
deme-structured populations . . . . . . 83--95
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Yanni Xiao and
Xiaodan Sun and
Sanyi Tang and
Jianhong Wu Transmission potential of the novel
avian influenza A (H7N9) infection in
mainland China . . . . . . . . . . . . . 1--5
Anonymous Pages 1--108 (7 July 2014) . . . . . . . 1--108
Wataru Nakahashi The effect of cultural interaction on
cumulative cultural evolution . . . . . 6--15
D. J. G. Agnew and
J. E. F. Green and
T. M. Brown and
M. J. Simpson and
B. J. Binder Distinguishing between mechanisms of
cell aggregation using pair-correlation
functions . . . . . . . . . . . . . . . 16--23
Francisco Encinas-Viso and
Tomás A. Revilla and
Rampal S. Etienne Shifts in pollinator population
structure may jeopardize pollination
service . . . . . . . . . . . . . . . . 24--30
MunJu Kim and
Damon Reed and
Katarzyna A. Rejniak The formation of tight tumor clusters
affects the efficacy of cell cycle
inhibitors: a hybrid model study . . . . 31--50
Reiji Suzuki and
Takaya Arita Emergence of a dynamic resource
partitioning based on the coevolution of
phenotypic plasticity in sympatric
species . . . . . . . . . . . . . . . . 51--59
Amaury Lambert and
Helen K. Alexander and
Tanja Stadler Phylogenetic analysis accounting for
age-dependent death and sampling with
applications to epidemics . . . . . . . 60--70
Carlos Llensa and
David Juher and
Joan Saldaña On the early epidemic dynamics for
pairwise models . . . . . . . . . . . . 71--81
Sivan Leviyang Constructing lower-bounds for CTL escape
rates in early SIV infection . . . . . . 82--91
Aaron G. Lim and
Philip K. Maini HTLV-I infection: a dynamic struggle
between viral persistence and host
immunity . . . . . . . . . . . . . . . . 92--108
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
H. Berends and
W. J. J. Gerrits and
J. France and
J. L. Ellis and
S. M. van Zijderveld and
J. Dijkstra Evaluation of the SF 6 tracer technique
for estimating methane emission rates
with reference to dairy cows using a
mechanistic model . . . . . . . . . . . 1--8
Anonymous Pages 1--178 (21 July 2014) . . . . . . 1--178
Xiao Ding and
Chang-Chang Cao and
Xiao Sun Intrinsic correlation of
oligonucleotides: a novel genomic
signature for metagenome analysis . . . 9--18
Shuyan Ding and
Shoujiang Yan and
Shuhua Qi and
Yan Li and
Yuhua Yao A protein structural classes prediction
method based on PSI-BLAST profile . . . 19--23
Linghua Zhou and
Yong Shen and
Weimiao Wu and
Zuoheng Wang and
Wei Hou and
Sheng Zhu and
Rongling Wu A model for computing genes governing
marital dissolution through sentimental
dynamics . . . . . . . . . . . . . . . . 24--33
Christopher M. Kribs-Zaleta Graphical analysis of evolutionary
trade-off in sylvatic
\bionameTrypanosoma cruzi transmission
modes . . . . . . . . . . . . . . . . . 34--43
Ericka Mochan and
David Swigon and
G. Bard Ermentrout and
Sarah Lukens and
Gilles Clermont A mathematical model of intrahost
pneumococcal pneumonia infection
dynamics in murine strains . . . . . . . 44--54
Lorenzo Peruzzi and
Katia Francesca Caparelli and
Gianni Bedini A new index for the quantification of
chromosome number variation: An
application to selected animal and plant
groups . . . . . . . . . . . . . . . . . 55--60
Qinbin He and
Zengrong Liu Investigation of oscillation
accumulation triggered genetic switch in
gene regulatory networks . . . . . . . . 61--66
L. E. Brown and
J. R. King and
M. Loose Two different network topologies yield
bistability in models of mesoderm and
anterior mesendoderm specification in
amphibians . . . . . . . . . . . . . . . 67--77
Zhipeng Gao and
Hongmei Guo and
Weiyi Chen Initial tension of the human extraocular
muscles in the primary eye position . . 78--83
Peter S. Kim and
John S. McQueen and
James E. Coxworth and
Kristen Hawkes Grandmothering drives the evolution of
longevity in a probabilistic model . . . 84--94
Deborah C. Markham and
Matthew J. Simpson and
Philip K. Maini and
Eamonn A. Gaffney and
Ruth E. Baker Comparing methods for modelling
spreading cell fronts . . . . . . . . . 95--103
Sang-Woo Lee and
Francois Gabriel Feugier and
Yoshihiro Morishita Canalization-based vein formation in a
growing leaf . . . . . . . . . . . . . . 104--120
Benjamin D. Robertson and
Gregory S. Sawicki Exploiting elasticity: Modeling the
influence of neural control on mechanics
and energetics of ankle muscle-tendons
during human hopping . . . . . . . . . . 121--132
Mayuko Iwamoto and
Daishin Ueyama and
Ryo Kobayashi The advantage of mucus for adhesive
locomotion in gastropods . . . . . . . . 133--141
Olivia Prosper and
Nick Ruktanonchai and
Maia Martcheva Optimal vaccination and bednet
maintenance for the control of malaria
in a region with naturally acquired
immunity . . . . . . . . . . . . . . . . 142--156
Sylvie Lorthois and
Paul Duru and
Ian Billanou and
Michel Quintard and
Pierre Celsis Kinetic modeling in the context of
cerebral blood flow quantification by
H$_2 $$ ^15$ O positron emission
tomography : The meaning of the
permeability coefficient in R e n k i n
- - C r o n e's model revisited at
capillary scale . . . . . . . . . . . . 157--169
Yunjun Zhang and
Qi Ouyang and
Zhi Geng Refining network reconstruction based on
functional reliability . . . . . . . . . 170--178
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
A. Gómez-Corral and
M. López García Control strategies for a stochastic
model of host-parasite interaction in a
seasonal environment . . . . . . . . . . 1--11
Anonymous Pages 1--146 (7 August 2014) . . . . . . 1--146
Andrii Mironchenko and
Jan Kozlowski Optimal allocation patterns and optimal
seed mass of a perennial plant . . . . . 12--24
David V. McLeod and
Geoff Wild The relationship between ecology and the
optimal helping strategy in cooperative
breeders . . . . . . . . . . . . . . . . 25--34
Konstadia Lika and
Starrlight Augustine and
Laure Pecquerie and
Sebastiaan A. L. M. Kooijman The bijection from data to parameter
space with the standard DEB model
quantifies the supply-demand spectrum 35--47
Jing Yan and
Yan Xu and
Brian Hu and
Sammy Alnajm and
Lina Liu and
Yin Lu and
Zhiguang Sun and
Feng Cheng TIBS: a web database to browse gene
expression in irritable bowel syndrome 48--53
Konstantin Ristl and
Sebastian J. Plitzko and
Barbara Drossel Complex response of a food-web module to
symmetric and asymmetric migration
between several patches . . . . . . . . 54--59
Malikeh Nabaei and
Nasser Fatouraee Microstructural modelling of cerebral
aneurysm evolution through effective
stress mediated destructive remodelling 60--71
Chundi Vinay Kumar and
K. M. Kumar and
Rayapadi Swetha and
Sudha Ramaiah and
Anand Anbarasu Protein aggregation due to nsSNP
resulting in P56S VABP protein is
associated with amyotrophic lateral
sclerosis . . . . . . . . . . . . . . . 72--80
Julie Simons and
Sarah Olson and
Ricardo Cortez and
Lisa Fauci The dynamics of sperm detachment from
epithelium in a coupled
fluid-biochemical model of
hyperactivated motility . . . . . . . . 81--94
Marco Zoli Twist versus nonlinear stacking in short
DNA molecules . . . . . . . . . . . . . 95--104
Joanna Kawka and
Dominik Sturm and
Sabrina Pleier and
Stefan Pfister and
Anna Marciniak-Czochra Revealing the role of SGK1 in the
dynamics of medulloblastoma using a
mathematical model . . . . . . . . . . . 105--112
Marianne Rooman and
Jaroslav Albert and
Mitia Duerinckx Stochastic noise reduction upon
complexification: Positively correlated
birth-death type systems . . . . . . . . 113--123
Bradford P. Taylor and
Michael H. Cortez and
Joshua S. Weitz The virus of my virus is my friend:
Ecological effects of virophage with
alternative modes of coinfection . . . . 124--136
James Lyons and
Neela Biswas and
Alok Sharma and
Abdollah Dehzangi and
Kuldip K. Paliwal Protein fold recognition by alignment of
amino acid residues using kernelized
dynamic time warping . . . . . . . . . . 137--145
Sweta Kumari and
Arumugam MohanaPriya and
Sajitha Lulu and
Mohammad Tauqueer Corrigendum to ``Molecular modeling,
simulation and virtual screening of
ribosomal phosphoprotein P1 from
\bionamePlasmodium falciparum'' [J.
Theor. Biol. \bf 343 (2014) 113--119] 146--146
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Babak Sharifimajd and
Jonas Stålhand A continuum model for
excitation-contraction of smooth muscle
under finite deformations . . . . . . . 1--9
Anonymous Pages 1--242 (21 August 2014) . . . . . 1--242
Jasmine Foo and
Franziska Michor Evolution of acquired resistance to
anti-cancer therapy . . . . . . . . . . 10--20
R. G. Kasimova and
D. Tishin and
Yu.V. V. Obnosov and
G. M. Dlussky and
F. B. Baksht and
A. R. Kacimov Ant mound as an optimal shape in
constructal design: Solar irradiation
and circadian brood/fungi-warming
sorties . . . . . . . . . . . . . . . . 21--32
William H. James An update on the hypothesis that one
cause of autism is high intrauterine
levels of testosterone of maternal
origin . . . . . . . . . . . . . . . . . 33--39
Can Huang and
Ming Wu and
Jun Du and
Di Liu and
Christina Chan Systematic modeling for the insulin
signaling network mediated by IRS 1 and
IRS 2 . . . . . . . . . . . . . . . . . 40--52
David A. Smith Electrostatic forces or structural
scaffolding: What stabilizes the lattice
spacing of relaxed skinned muscle
fibers? . . . . . . . . . . . . . . . . 53--60
Scott Forbes Pregnancy sickness and parent-offspring
conflict over thyroid function . . . . . 61--67
Nadia Ursino Eco-hydrology driven fire regime in
savanna . . . . . . . . . . . . . . . . 68--76
A. Barton and
A. J. Fendrik and
E. Rotondo A stochastic model of neurogenesis
controlled by a single factor . . . . . 77--82
Christian J. Michel A genetic scale of reading frame coding 83--94
Wenying Yan and
Maomin Sun and
Guang Hu and
Jianhong Zhou and
Wenyu Zhang and
Jiajia Chen and
Biao Chen and
Bairong Shen Amino acid contact energy networks
impact protein structure and evolution 95--104
Lichao Zhang and
Xiqiang Zhao and
Liang Kong Predict protein structural class for
low-similarity sequences by evolutionary
difference information into the general
form of Chou's pseudo amino acid
composition . . . . . . . . . . . . . . 105--110
M. V. Simkin and
V. P. Roychowdhury Stochastic modeling of a serial killer 111--116
Mitsuhiro Nakamura and
Hisashi Ohtsuki Indirect reciprocity in three types of
social dilemmas . . . . . . . . . . . . 117--127
Sen Li and
Jie Yang System analysis of synonymous codon
usage biases in archaeal virus genomes 128--139
K. M. Mitchell and
A. M. Foss and
H. J. Prudden and
Z. Mukandavire and
M. Pickles and
J. R. Williams and
H. C. Johnson and
B. M. Ramesh and
R. Washington and
S. Isac and
S. Rajaram and
A. E. Phillips and
J. Bradley and
M. Alary and
S. Moses and
C. M. Lowndes and
C. H. Watts and
M.-C. Boily and
P. Vickerman Who mixes with whom among men who have
sex with men? Implications for modelling
the HIV epidemic in southern India . . . 140--150
Ryan Lukeman Ordering dynamics in collectively
swimming Surf Scoters . . . . . . . . . 151--159
Xue Gong and
Gregory Moses and
Alexander B. Neiman and
Todd Young Noise-induced dispersion and breakup of
clusters in cell cycle dynamics . . . . 160--169
Jasmine Foo and
Kevin Leder and
Marc D. Ryser Multifocality and recurrence risk: a
quantitative model of field
cancerization . . . . . . . . . . . . . 170--184
Sayed-Amir Marashi and
Mojtaba Tefagh A mathematical approach to emergent
properties of metabolic networks:
Partial coupling relations, hyperarcs
and flux ratios . . . . . . . . . . . . 185--193
Min Wu and
Hermann B. Frieboes and
Mark A. J. Chaplain and
Steven R. McDougall and
Vittorio Cristini and
John S. Lowengrub The effect of interstitial pressure on
therapeutic agent transport: Coupling
with the tumor blood and lymphatic
vascular systems . . . . . . . . . . . . 194--207
Gregg S. Davis and
Simeone Marino and
Carl F. Marrs and
Janet R. Gilsdorf and
Suzanne Dawid and
Denise E. Kirschner Phase variation and host immunity
against high molecular weight (HMW)
adhesins shape population dynamics of
nontypeable Haemophilus influenzae
within human hosts . . . . . . . . . . . 208--218
Kirti M. Yenkie and
Urmila Diwekar Optimal control for predicting
customized drug dosage for
superovulation stage of in vitro
fertilization . . . . . . . . . . . . . 219--228
Suhua Zhang and
Yafei Chen and
Hailong An and
Hui Liu and
Junwei Li and
Chunli Pang and
Qing Ji and
Yong Zhan A novel biophysical model on calcium and
voltage dual dependent gating of
calcium-activated chloride channel . . . 229--235
Graeme D. Ruxton and
David M. Wilkinson Energetic arguments predict
larger-bodied animals will be
increasingly confined to flat
environments . . . . . . . . . . . . . . 236--238
David S. Tourigny Geometric phase shifts in biological
oscillators . . . . . . . . . . . . . . 239--242
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
G. Sander van Doorn and
Thomas Riebli and
Michael Taborsky Coaction versus reciprocity in
continuous-time models of cooperation 1--10
Anonymous Pages 1--222 (7 September 2014) . . . . 1--222
Jason Lloyd-Price and
Huy Tran and
Andre S. Ribeiro Dynamics of small genetic circuits
subject to stochastic partitioning in
cell division . . . . . . . . . . . . . 11--19
Ying-Hen Hsieh and
Junli Liu and
Yun-Huei Tzeng and
Jianhong Wu Impact of visitors and hospital staff on
nosocomial transmission and spread to
community . . . . . . . . . . . . . . . 20--29
Sukanta Mondal and
Priyadarshini P. Pai Chou's pseudo amino acid composition
improves sequence-based antifreeze
protein prediction . . . . . . . . . . . 30--35
Sarah Schoenmakers and
Christian Hilbe and
Bernd Blasius and
Arne Traulsen Sanctions as honest signals --- The
evolution of pool punishment by public
sanctioning institutions . . . . . . . . 36--46
Abdullah A. Al-Shammari and
Eamonn A. Gaffney and
Stuart Egginton Modelling capillary oxygen supply
capacity in mixed muscles: Capillary
domains revisited . . . . . . . . . . . 47--61
Adrián González-Casanova and
Eneas Aguirre-von-Wobeser and
Guadalupe Esp\'ìn and
Luis Serv\'ìn-González and
Noemi Kurt and
Dario Span\`o and
Jochen Blath and
Gloria Soberón-Chávez Strong seed-bank effects in bacterial
evolution . . . . . . . . . . . . . . . 62--70
Katrina K. Treloar and
Matthew J. Simpson and
D. L. Sean McElwain and
Ruth E. Baker Are in vitro estimates of cell
diffusivity and cell proliferation rate
sensitive to assay geometry? . . . . . . 71--84
Thy-Hou Lin and
Tsung-Lin Tsai Constructing a linear QSAR for some
metabolizable drugs by human or pig
flavin-containing monooxygenases using
some molecular features selected by a
genetic algorithm trained SVM . . . . . 85--97
Hyeong-Chai Jeong and
Seung-Yoon Oh and
Benjamin Allen and
Martin A. Nowak Optional games on cycles and complete
graphs . . . . . . . . . . . . . . . . . 98--112
Thomas P. Prescott and
Antonis Papachristodoulou Layered decomposition for the model
order reduction of timescale separated
biochemical reaction networks . . . . . 113--122
Zhilan Feng and
John W. Glasser and
Andrew N. Hill and
Mikael A. Franko and
Rose-Marie Carlsson and
Hans Hallander and
Peet Tüll and
Patrick Olin Modeling rates of infection with
transient maternal antibodies and waning
active immunity: Application to
\bionameBordetella pertussis in Sweden 123--132
O. C. Collins and
K. S. Govinder Incorporating heterogeneity into the
transmission dynamics of a waterborne
disease model . . . . . . . . . . . . . 133--143
Esther Ibáñez-Marcelo and
Tomás Alarcón The topology of robustness and
evolvability in evolutionary systems
with genotype-phenotype map . . . . . . 144--162
Sudipta Tung and
Abhishek Mishra and
Sutirth Dey A comparison of six methods for
stabilizing population dynamics . . . . 163--173
Carrie A. Manore and
Kyle S. Hickmann and
Sen Xu and
Helen J. Wearing and
James M. Hyman Comparing dengue and chikungunya
emergence and endemic transmission in
\bionameA. aegypti and \bionameA.
albopictus . . . . . . . . . . . . . . . 174--191
Richard J. Strilka and
Scott B. Armen and
Matthew C. Indeck Qualitative analysis of subcutaneous
Lispro and regular insulin injections
for stress hyperglycemia: a pilot
numerical study . . . . . . . . . . . . 192--200
Marcelo Pires and
Frank Raischel and
Sandra H. Vaz and
Andreia Cruz-Silva and
Ana M. Sebastião and
Pedro G. Lind Modeling the functional network of
primary intercellular Ca$^{2+}$ wave
propagation in astrocytes and its
application to study drug effects . . . 201--212
Mohammad Reza Bakhtiarizadeh and
Mohammad Moradi-Shahrbabak and
Mansour Ebrahimi and
Esmaeil Ebrahimie Neural network and SVM classifiers
accurately predict lipid binding
proteins, irrespective of sequence
homology . . . . . . . . . . . . . . . . 213--222
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Qiang Li and
Furong Lu and
Guohong Deng and
Kaifa Wang Modeling the effects of covalently
closed circular DNA and dendritic cells
in chronic HBV infection . . . . . . . . 1--9
Anonymous Pages 1--272 (21 September 2014) . . . . 1--272
Leslie Braziel Jones and
Timothy W. Secomb and
Mark W. Dewhirst and
Ardith W. El-Kareh The additive damage model: a
mathematical model for cellular
responses to drug combinations . . . . . 10--20
Sonia L. Mestizo Gutiérrez and
Marisol Herrera Rivero and
Nicandro Cruz Ramírez and
Elena Hernández and
Gonzalo E. Aranda-Abreu Decision trees for the analysis of genes
involved in Alzheimer's disease
pathology . . . . . . . . . . . . . . . 21--25
Omer Markovitch and
Doron Lancet Multispecies population dynamics of
prebiotic compositional assemblies . . . 26--34
Da Zhou and
Yue Wang and
Bin Wu A multi-phenotypic cancer model with
cell plasticity . . . . . . . . . . . . 35--45
Jing Chen and
Aleksey Zinger The robustness of zero-determinant
strategies in Iterated Prisoner's
Dilemma games . . . . . . . . . . . . . 46--54
Carlos G. Schrago The limiting distribution of the
effective population size of the
ancestor of humans and chimpanzees . . . 55--61
Naviyn Prabhu Balakrishnan and
Lakshminarayanan Samavedham and
Gade Pandu Rangaiah Personalized mechanistic models for
exercise, meal and insulin interventions
in children and adolescents with type 1
diabetes . . . . . . . . . . . . . . . . 62--73
Yoshihiro Morishita and
Takayuki Suzuki Bayesian inference of whole-organ
deformation dynamics from limited
space-time point data . . . . . . . . . 74--85
James R. Moore The benefits of diversity: Heterogeneous
DC populations allow for both immunity
and tolerance . . . . . . . . . . . . . 86--102
Bo Deng and
Alex Estes and
Brett Grieb and
Douglas Richard and
Brittney Hinds and
Eileen Hebets A male spider's ornamentation
polymorphism maintained by opposing
selection with two niches . . . . . . . 103--111
Atefeh Ghorbaniaghdam and
Olivier Henry and
Mario Jolicoeur An in-silico study of the regulation of
CHO cells glycolysis . . . . . . . . . . 112--122
Albert J. Markvoort and
Sam Sinai and
Martin A. Nowak Computer simulations of cellular group
selection reveal mechanism for
sustaining cooperation . . . . . . . . . 123--133
Qianqian Ma and
Caner Kazanci How much of the storage in the ecosystem
is due to cycling? . . . . . . . . . . . 134--142
Abhay Sharma Bioinformatic analysis revealing
association of exosomal mRNAs and
proteins in epigenetic inheritance . . . 143--149
N. Ringa and
C. T. Bauch Dynamics and control of foot-and-mouth
disease in endemic countries: a pair
approximation model . . . . . . . . . . 150--159
Angelo Pavesi Prediction of the determinants of
thermal stability by linear discriminant
analysis: The case of the glutamate
dehydrogenase protein family . . . . . . 160--168
Avijit Podder and
Nidhi Jatana and
N. Latha Human Dopamine Receptors Interaction
Network (DRIN): a systems biology
perspective on topology, stability and
functionality of the network . . . . . . 169--183
Hildur Knútsdóttir and
Eirikur Pálsson and
Leah Edelstein-Keshet Mathematical model of
macrophage-facilitated breast cancer
cells invasion . . . . . . . . . . . . . 184--199
H. Henke and
P. A. Robinson and
P. M. Drysdale and
P. N. Loxley Spatiotemporally varying visual
hallucinations: I. Corticothalamic
theory . . . . . . . . . . . . . . . . . 200--209
H. Henke and
P. A. Robinson and
P. M. Drysdale Spatiotemporally varying visual
hallucinations: II. Spectral
classification and comparison with
theory . . . . . . . . . . . . . . . . . 210--219
Duncan A. Rouch Evolution of the first genetic cells and
the universal genetic code: a hypothesis
based on macromolecular coevolution of
RNA and proteins . . . . . . . . . . . . 220--244
Katy J. Rubin and
Katherine Lawler and
Peter Sollich and
Tony Ng Memory effects in biochemical networks
as the natural counterpart of extrinsic
noise . . . . . . . . . . . . . . . . . 245--267
Anatoly S. Buchelnikov and
Maxim P. Evstigneev Quantitative correlation of the in vitro
biological effect with parameters of
molecular complexation in
mutagen-interceptor systems . . . . . . 268--271
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Sae-Il Murtada and
Gerhard A. Holzapfel Investigating the role of smooth muscle
cells in large elastic arteries: a
finite element analysis . . . . . . . . 1--10
Anonymous Pages 1--246 (7 October 2014) . . . . . 1--246
Sridhar Ramakrishnan and
Srinivas Laxminarayan and
Nancy J. Wesensten and
Gary H. Kamimori and
Thomas J. Balkin and
Jaques Reifman Dose-dependent model of caffeine effects
on human vigilance during total sleep
deprivation . . . . . . . . . . . . . . 11--24
Hengtong Wang and
Yongjuan Sun and
Yichen Li and
Yong Chen Influence of autapse on mode-locking
structure of a Hodgkin--Huxley neuron
under sinusoidal stimulus . . . . . . . 25--30
Upuli Gunasinghe and
Damminda Alahakoon and
Susan Bedingfield Extraction of high quality $k$-words for
alignment-free sequence comparison . . . 31--51
Benedikt Bauer and
Reiner Siebert and
Arne Traulsen Cancer initiation with epistatic
interactions between driver and
passenger mutations . . . . . . . . . . 52--60
Lei Yang and
Yingli Lv and
Tao Li and
Yongchun Zuo and
Wei Jiang Human proteins characterization with
subcellular localizations . . . . . . . 61--73
James M. Trauer and
Justin T. Denholm and
Emma S. McBryde Construction of a mathematical model for
tuberculosis transmission in highly
endemic regions of the Asia-pacific . . 74--84
Xiao Chen and
Qinke Peng and
Libin Han and
Tao Zhong and
Tao Xu An effective haplotype assembly
algorithm based on hypergraph
partitioning . . . . . . . . . . . . . . 85--92
Suma Ghosh and
Jessica L. Waite and
Dale H. Clayton and
Frederick R. Adler Can antibodies against flies alter
malaria transmission in birds by
changing vector behavior? . . . . . . . 93--101
Timothy O. Lamberton and
Nicholas D. Condon and
Jennifer L. Stow and
Nicholas A. Hamilton On linear models and parameter
identifiability in experimental
biological systems . . . . . . . . . . . 102--121
Hui Zhang and
Meng Gao and
Wenting Wang and
Zhiguang Liu Evolutionary prisoner's dilemma game on
graphs and social networks with external
constraint . . . . . . . . . . . . . . . 122--131
Shibin Mathew and
John Bartels and
Ipsita Banerjee and
Yoram Vodovotz Global sensitivity analysis of a
mathematical model of acute inflammation
identifies nonlinear dependence of
cumulative tissue damage on host
interleukin-6 responses . . . . . . . . 132--148
George W. A. Constable and
Alan J. McKane Population genetics on islands connected
by an arbitrary network: An analytic
approach . . . . . . . . . . . . . . . . 149--165
Kenichi W. Okamoto and
Priyanga Amarasekare and
Ian T. D. Petty Modeling oncolytic virotherapy: Is
complete tumor-tropism too much of a
good thing? . . . . . . . . . . . . . . 166--178
Nicolas E. Humphries and
David W. Sims Optimal foraging strategies: Lévy walks
balance searching and patch exploitation
under a very broad range of conditions 179--193
S. Diehl and
E. Henningsson and
A. Heyden and
S. Perna A one-dimensional moving-boundary model
for tubulin-driven axonal growth . . . . 194--207
L. C. B. Faria and
A. S. L. Rocha and
R. Palazzo Transmission of intra-cellular genetic
information: a system proposal . . . . . 208--231
David Neill Evolution of lifespan . . . . . . . . . 232--245
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Massimo Di Giulio and
Marco Moracci and
Beatrice Cobucci-Ponzano RNA editing and modifications of RNAs
might have favoured the evolution of the
triplet genetic code from an ennuplet
code . . . . . . . . . . . . . . . . . . 1--5
Anonymous Pages 1--238 (21 October 2014) . . . . . 1--238
Mateusz Banach and
Leszek Konieczny and
Irena Roterman The fuzzy oil drop model, based on
hydrophobicity density distribution,
generalizes the influence of water
environment on protein structure and
function . . . . . . . . . . . . . . . . 6--17
Changchuan Yin and
Ying Chen and
Stephen S.-T. Yau A measure of DNA sequence similarity by
Fourier Transform with applications on
hierarchical clustering . . . . . . . . 18--28
Marius Kempe and
Stephen J. Lycett and
Alex Mesoudi From cultural traditions to cumulative
culture: parameterizing the differences
between human and nonhuman culture . . . 29--36
Stefan A. H. Geritz and
Mats Gyllenberg The DeAngelis--Beddington functional
response and the evolution of timidity
of the prey . . . . . . . . . . . . . . 37--44
Andrew J. Black and
Thomas House and
Matt J. Keeling and
Joshua V. Ross The effect of clumped population
structure on the variability of
spreading dynamics . . . . . . . . . . . 45--53
L. A. Crompton and
J. France and
C. K. Reynolds and
J. A. N. Mills and
M. D. Hanigan and
J. L. Ellis and
A. Bannink and
B. J. Bequette and
J. Dijkstra An isotope dilution model for
partitioning phenylalanine and tyrosine
uptake by the mammary gland of lactating
dairy cows . . . . . . . . . . . . . . . 54--60
Peter E. Larsen and
Leland J. Cseke and
R. Michael Miller and
Frank R. Collart Modeling forest ecosystem responses to
elevated carbon dioxide and ozone using
artificial neural networks . . . . . . . 61--71
Robert L. Bertrand Lag phase-associated iron accumulation
is likely a microbial counter-strategy
to host iron sequestration: Role of the
ferric uptake regulator (fur) . . . . . 72--79
T. Knipfer and
J. Fei and
G. A. Gambetta and
K. A. Shackel and
M. A. Matthews A revised and unified
pressure-clamp/relaxation theory for
studying plant cell water relations with
pressure probes: In-situ determination
of cell volume for calculation of
volumetric elastic modulus and hydraulic
conductivity . . . . . . . . . . . . . . 80--91
Christoph Koke and
Takuma Kanesaki and
Jörg Grosshans and
Ulrich S. Schwarz and
Carina M. Dunlop A computational model of nuclear
self-organisation in syncytial embryos 92--100
S. M. Kissler and
C. Cichowitz and
S. Sankaranarayanan and
D. M. Bortz Determination of personalized diabetes
treatment plans using a two-delay model 101--111
Ofri Mann and
Moshe Kiflawi Social foraging with partial (public)
information . . . . . . . . . . . . . . 112--119
Loris Nanni and
Alessandra Lumini and
Sheryl Brahnam A set of descriptors for identifying the
protein-drug interaction in cellular
networking . . . . . . . . . . . . . . . 120--128
R. Leander and
E. J. Allen and
S. P. Garbett and
D. R. Tyson and
V. Quaranta Derivation and experimental comparison
of cell-division probability densities 129--135
Junsong Zhao and
Kimberly D. Siegmund and
Darryl Shibata and
Paul Marjoram Ancestral inference in tumors: How much
can we know? . . . . . . . . . . . . . . 136--145
Xiao-Sheng Cheng and
Heping Zhang and
Xian'an Jin and
Wen-Yuan Qiu Ear decomposition of $3$-regular
polyhedral links with applications . . . 146--154
Hidetsugu Sakaguchi and
Satomi Maeyama Competitive aggregation dynamics using
phase wave signals . . . . . . . . . . . 155--160
Marianne Robert and
Laurent Dagorn and
Jean Louis Deneubourg The aggregation of tuna around floating
objects: What could be the underlying
social mechanisms? . . . . . . . . . . . 161--170
Guoli Yang and
Jincai Huang and
Weiming Zhang Older partner selection promotes the
prevalence of cooperation in
evolutionary games . . . . . . . . . . . 171--183
Zhixia Ying and
Jinbao Liao and
Shichang Wang and
Hui Lu and
Yongjie Liu and
Liang Ma and
Zhenqing Li Species coexistence in a
lattice-structured habitat: Effects of
species dispersal and interactions . . . 184--191
Yuriy Mitrokhin Two faces of entropy and information in
biological systems . . . . . . . . . . . 192--198
David S. Boukal and
Ulf Dieckmann and
Katja Enberg and
Mikko Heino and
Christian Jòrgensen Life-history implications of the
allometric scaling of growth . . . . . . 199--207
Andrew D. Higginson and
John M. McNamara and
Alasdair I. Houston The starvation-predation trade-off
shapes the strategic use of protein for
energy during fasting . . . . . . . . . 208--219
Alistair M. Middleton and
Christian Fleck and
Ramon Grima A continuum approximation to an
off-lattice individual-cell based model
of cell migration and adhesion . . . . . 220--232
Alan Grafen Total reproductive values for females
and for males in sexual diploids are not
equal . . . . . . . . . . . . . . . . . 233--235
Andy Gardner Total reproductive value of juvenile
females is twice that of juvenile males
under X-linkage and haplodiploidy . . . 236--237
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Jason W. Olejarz and
Martin A. Nowak Evolution of staying together in the
context of diffusible public goods . . . 1--12
Anonymous Pages 1--318 (7 November 2014) . . . . . 1--318
Christoph K. Schmitt and
Christian Guill and
Eddy Carmack and
Barbara Drossel Effect of introducing a competitor on
cyclic dominance of sockeye salmon . . . 13--20
Louise Viger and
Fabrice Denis and
Martin Rosalie and
Christophe Letellier A cancer model for the angiogenic switch 21--33
Shibiao Wan and
Man-Wai Mak and
Sun-Yuan Kung R3P-Loc: a compact multi-label predictor
using ridge regression and random
projection for protein subcellular
localization . . . . . . . . . . . . . . 34--45
Charles Bordet and
Louis-Paul Rivest A stochastic Pella Tomlinson model and
its maximum sustainable yield . . . . . 46--53
Akihiko Mougi and
Michio Kondoh Stability of
competition-antagonism-mutualism hybrid
community and the role of community
network structure . . . . . . . . . . . 54--58
Xin Ma and
Xiao Sun Sequence-based predictor of ATP-binding
residues using random forest and
mRMR-IFS feature selection . . . . . . . 59--66
Luis U. Aguilera and
Jesús Rodríguez-González Studying HIV latency by modeling the
interaction between HIV proteins and the
innate immune response . . . . . . . . . 67--77
Hongqiang Lv and
Jiuqiang Han and
Jun Liu and
Jiguang Zheng and
Dexing Zhong and
Ruiling Liu ISDTool 2.0: a computational model for
predicting immunosuppressive domain of
retroviruses . . . . . . . . . . . . . . 78--82
M. Legu\`ebe and
A. Silve and
L. M. Mir and
C. Poignard Conducting and permeable states of cell
membrane submitted to high voltage
pulses: Mathematical and numerical
studies validated by the experiments . . 83--94
H. Nguyen and
P. Dayan and
G. J. Goodhill The influence of receptor positioning on
chemotactic information . . . . . . . . 95--101
Stefania Tron and
Francesco Laio and
Luca Ridolfi Effect of water table fluctuations on
phreatophytic root distribution . . . . 102--108
Loris Nanni and
Sheryl Brahnam and
Alessandra Lumini Prediction of protein structure classes
by incorporating different protein
descriptors into general Chou's pseudo
amino acid composition . . . . . . . . . 109--116
Wes Maciejewski and
Gregory J. Puleo Environmental evolutionary graph theory 117--128
Whan Ghang and
Martin A. Nowak Stochastic evolution of staying together 129--136
Sunpeng Wang and
Libin Rong Stochastic population switch may explain
the latent reservoir stability and
intermittent viral blips in HIV patients
on suppressive therapy . . . . . . . . . 137--148
Jan Humplik and
Alison L. Hill and
Martin A. Nowak Evolutionary dynamics of infectious
diseases in finite populations . . . . . 149--162
Oliver P. Hauser and
Martin A. Nowak and
David G. Rand Punishment does not promote cooperation
under exploration dynamics when
anti-social punishment is possible . . . 163--171
Tomer J. Czaczkes How to not get stuck --- negative
feedback due to crowding maintains
flexibility in ant foraging . . . . . . 172--180
Julián García and
Matthijs van Veelen and
Arne Traulsen Evil green beards: Tag recognition can
also be used to withhold cooperation in
structured populations . . . . . . . . . 181--186
Kenta Ishimoto and
Eamonn A. Gaffney A study of spermatozoan swimming
stability near a surface . . . . . . . . 187--199
Yonggang Pei and
Qinghui Gao and
Juntao Li and
Xiting Zhao Identifying local co-regulation
relationships in gene expression data 200--207
Pierre Artoisenet and
Laure-Anne Minsart Statistical genetics in traditionally
cultivated crops . . . . . . . . . . . . 208--221
Emily Harvey and
Jeffrey Heys and
Tomás Gedeon Quantifying the effects of the division
of labor in metabolic pathways . . . . . 222--242
Paul Smolen and
Douglas A. Baxter and
John H. Byrne Simulations suggest pharmacological
methods for rescuing long-term
potentiation . . . . . . . . . . . . . . 243--250
Raziel Davison and
Carol L. Boggs and
Annette Baudisch Resource allocation as a driver of
senescence: Life history tradeoffs
produce age patterns of mortality . . . 251--262
Yann Le Cunff and
Khashayar Pakdaman Reproduction cost reduces demographic
stochasticity and enhances
inter-individual compatibility . . . . . 263--270
W. J. Chivers and
W. Gladstone and
R. D. Herbert and
M. M. Fuller predator--prey systems depend on a prey
refuge . . . . . . . . . . . . . . . . . 271--278
Matthijs van Veelen and
Shishi Luo and
Burton Simon A simple model of group selection that
cannot be analyzed with inclusive
fitness . . . . . . . . . . . . . . . . 279--289
Hiroshi C. Ito and
Ulf Dieckmann Evolutionary branching under slow
directional evolution . . . . . . . . . 290--314
Elchanan Mossel and
Mike Steel Majority rule has transition ratio 4 on
Yule trees under a $2$-state symmetric
model . . . . . . . . . . . . . . . . . 315--318
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Eric Maréchal and
Olivier Bastien Modeling of regulatory loops controlling
galactolipid biosynthesis in the inner
envelope membrane of chloroplasts . . . 1--13
Ying Chen and
John S. Lowengrub Tumor growth in complex, evolving
microenvironmental geometries: a diffuse
domain approach . . . . . . . . . . . . 14--30
Angelean O. Hendrix and
James F. Selgrade Bifurcation analysis of a menstrual
cycle model reveals multiple mechanisms
linking testosterone and classical PCOS 31--40
Pia Domschke and
Dumitru Trucu and
Alf Gerisch and
Mark A. J. Chaplain Mathematical modelling of cancer
invasion: Implications of cell adhesion
variability for tumour infiltrative
growth patterns . . . . . . . . . . . . 41--60
Leithen K. M'Gonigle and
Philip B. Greenspoon Allee effects and species co-existence
in an environment where resource
abundance varies . . . . . . . . . . . . 61--68
Dieter Armbruster and
John Nagy and
Jon Young Three level signal transduction cascades
lead to reliably timed switches . . . . 69--80
Xinyang Deng and
Zhen Wang and
Qi Liu and
Yong Deng and
Sankaran Mahadevan A belief-based evolutionarily stable
strategy . . . . . . . . . . . . . . . . 81--86
L. G. Bowden and
P. K. Maini and
D. E. Moulton and
J. B. Tang and
X. T. Wang and
P. Y. Liu and
H. M. Byrne An ordinary differential equation model
for full thickness wounds and the
effects of diabetes . . . . . . . . . . 87--100
Saumitra V. Joshi and
Sat. Ghosh On the air cleansing efficiency of an
extended green wall: a CFD analysis of
mechanistic details of transport
processes . . . . . . . . . . . . . . . 101--110
Pengbi Cui and
Zhi-Xi Wu Selfish punishment with avoiding
mechanism can alleviate both first-order
and second-order social dilemma . . . . 111--123
Mathew P. Dafilis and
Federico Frascoli and
Jodie McVernon and
Jane M. Heffernan and
James M. McCaw The dynamical consequences of seasonal
forcing, immune boosting and demographic
change in a model of disease
transmission . . . . . . . . . . . . . . 124--132
Toshio Sekimura and
Yuta Fujihashi and
Yasuhiro Takeuchi A model for population dynamics of the
mimetic butterfly \bionamePapilio
polytes in the Sakishima Islands, Japan 133--140
Xiuli Cen and
Zhilan Feng and
Yulin Zhao Emerging disease dynamics in a model
coupling within-host and between-host
systems . . . . . . . . . . . . . . . . 141--151
Tilahun Melak and
Sunita Gakkhar Potential non homologous protein targets
of mycobacterium tuberculosis H37Rv
identified from protein--protein
interaction network . . . . . . . . . . 152--158
Noriyuki P. Tani and
Alan Blatt and
David A. Quint and
Ajay Gopinathan Optimal cooperative searching using
purely repulsive interactions . . . . . 159--164
Sanhita Ray and
Anjan Kr. Dasgupta Probiotics as cheater cells: Parameter
space clustering for individualized
prescription . . . . . . . . . . . . . . 165--174
Huihua Ge and
Guangya Zhang RETRACTED: Identifying halophilic
proteins based on random forests with
preprocessing of the pseudo-amino acid
composition . . . . . . . . . . . . . . 175--175
Maulika S. Patel and
Himanshu S. Mazumdar Knowledge base and neural network
approach for protein secondary structure
prediction . . . . . . . . . . . . . . . 182--189
Jessica B. McGillen and
Catherine J. Kelly and
Alicia Mart\'ìnez-González and
Natasha K. Martin and
Eamonn A. Gaffney and
Philip K. Maini and
V\'ìctor M. Pérez-Garc\'ìa Glucose-lactate metabolic cooperation in
cancer: Insights from a spatial
mathematical model and implications for
targeted therapy . . . . . . . . . . . . 190--203
Massimo Di Giulio The genetic code did not originate from
an mRNA codifying polyglycine because
the proto-mRNAs already codified for an
amino acid number greater than one . . . 204--205
Mitsuhiro Nakamura and
Hisashi Ohtsuki Erratum to ``Indirect reciprocity in
three types of social dilemmas'' [J.
Theor. Biol. \bf 355 (2014) 117--127] 206--206
Huihua Ge and
Guangya Zhang Retraction notice to ``Identifying
halophilic proteins based on random
forests with preprocessing of the
pseudo-amino acid composition'' [J.
Theor. Biol. \bf 361 (2014) 175--181] R1
Anonymous Pages R1---R2, 1--206 (21 November 2014) R1-
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Xing-Ming Zhao and
Luonan Chen Network-based biomarkers for complex
diseases . . . . . . . . . . . . . . . . 1--2
Jian-lei Gu and
Yao Lu and
Cong Liu and
Hui Lu Multiclass classification of sarcomas
using pathway based feature selection
method . . . . . . . . . . . . . . . . . 3--8
Guimin Qin and
Xing-Ming Zhao A survey on computational approaches to
identifying disease biomarkers based on
molecular networks . . . . . . . . . . . 9--16
Yung-Hao Wong and
Ru-Hong Chen and
Bor-Sen Chen Core and specific network markers of
carcinogenesis from multiple cancer
samples . . . . . . . . . . . . . . . . 17--34
Wanwei Zhang and
Tao Zeng and
Luonan Chen EdgeMarker: Identifying differentially
correlated molecule pairs as
edge-biomarkers . . . . . . . . . . . . 35--43
Xiaogang Wu and
Mohammad Al Hasan and
Jake Yue Chen Pathway and network analysis in
proteomics . . . . . . . . . . . . . . . 44--52
Y. X. Rachel Wang and
Haiyan Huang Review on statistical methods for gene
network reconstruction using expression
data . . . . . . . . . . . . . . . . . . 53--61
Duojiao Wu and
Xiaoping Liu and
Chen Liu and
Zhiping Liu and
Ming Xu and
Ruiming Rong and
Mengjia Qian and
Luonan Chen and
Tongyu Zhu Network analysis reveals roles of
inflammatory factors in different
phenotypes of kidney transplant patients 62--68
Jie Hu and
Xiaomei Zhu and
Xinan Wang and
Ruoshi Yuan and
Wei Zheng and
Minjuan Xu and
Ping Ao Two programmed replicative lifespans of
\bionameSaccharomyces cerevisiae formed
by the endogenous molecular-cellular
network . . . . . . . . . . . . . . . . 69--74
Xinguo Lu and
Yong Deng and
Lei Huang and
Bingtao Feng and
Bo Liao A co-expression modules based gene
selection for cancer recognition . . . . 75--82
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
C. J. Baker and
M. Sterling and
P. Berry A generalised model of crop lodging . . 1--12
Anonymous Pages 1--454 (21 December 2014) . . . . 1--454
Leonid Berezansky and
Elena Braverman and
Lev Idels Effect of treatment on the global
dynamics of delayed pathological
angiogenesis models . . . . . . . . . . 13--21
Benoit Crouzy and
Katharina Edmaier and
Paolo Perona Biomechanics of plant anchorage at early
development stage . . . . . . . . . . . 22--29
I. R. R\uadulescu and
D. Cândea and
A. Halanay A study on stability and medical
implications for a complex delay model
for CML with cell competition and
treatment . . . . . . . . . . . . . . . 30--40
Hamid Laga and
Sebastian Kurtek and
Anuj Srivastava and
Stanley J. Miklavcic Landmark-free statistical analysis of
the shape of plant leaves . . . . . . . 41--52
Jessica B. Langebrake and
Gabriel E. Dilanji and
Stephen J. Hagen and
Patrick De Leenheer Traveling waves in response to a
diffusing quorum sensing signal in
spatially-extended bacterial colonies 53--61
Kris De Jaegher and
Stephanie Rosenkranz and
Utz Weitzel Economic principles in communication: An
experimental study . . . . . . . . . . . 62--73
M. J. McGuinness and
L. B. Cribbin and
H. F. Winstanley and
A. C. Fowler Modelling spatial oscillations in soil
borehole bacteria . . . . . . . . . . . 74--79
Mengyang Sun and
Xianrui Cheng and
Joshua E. S. Socolar Regulatory logic and pattern formation
in the early sea urchin embryo . . . . . 80--92
Koji Noshita Quantification and geometric analysis of
coiling patterns in gastropod shells
based on $3$D and $2$D image data . . . 93--104
Frederick Chen and
Flavio Toxvaerd The economics of vaccination . . . . . . 105--117
Zuzanna Szyma\'nska and
Martin Parisot and
Miroslaw Lachowicz Mathematical modeling of the
intracellular protein dynamics: The
importance of active transport along
microtubules . . . . . . . . . . . . . . 118--128
C. J. Thompson and
T. E. Lee and
M. A. McCarthy Species distributions and area
relationships . . . . . . . . . . . . . 129--133
Claire M. Postlethwaite and
Michael M. Walker A model for navigational errors in
complex environmental fields . . . . . . 134--144
Jia Wen and
YuYan Zhang and
Stephen S. T. Yau $k$-mer Sparse matrix model for genetic
sequence and its applications in
sequence comparison . . . . . . . . . . 145--150
Yangchen Lin and
William J. Sutherland Interaction modification effects on
ecological networks are affected by
ratio dependence and network topology 151--157
Amlan Barua and
Jhankar Acharya and
Saroj Ghaskadbi and
Pranay Goel The relationship between fasting plasma
glucose and HbA 1c during intensive
periods of glucose control in
antidiabetic therapy . . . . . . . . . . 158--163
Vladimir Borzan and
Boris Tomasevi\'c and
Sven Kurbel Hypothesis: Possible respiratory
advantages for heterozygote carriers of
cystic fibrosis linked mutations during
dusty climate of last glaciation . . . . 164--168
Siddhartha Sen and
H. Paul Voorheis Protein folding: Understanding the role
of water and the low Reynolds number
environment as the peptide chain emerges
from the ribosome and folds . . . . . . 169--187
Chandrajit Lahiri and
Shrikant Pawar and
Radhakrishnan Sabarinathan and
Md. Izhar Ashraf and
Yamini Chand and
Dipshikha Chakravortty Interactome analyses of
\bionameSalmonella pathogenicity islands
reveal SicA indispensable for virulence 188--197
Imraan A. Faruque and
J. Sean Humbert Wing motion transformation to evaluate
aerodynamic coupling in flapping wing
flight . . . . . . . . . . . . . . . . . 198--204
Andrea Becchetti Empirically founded genotype-phenotype
maps from mammalian cyclic
nucleotide-gated ion channels . . . . . 205--215
Hervé Seligmann Species radiation by DNA replication
that systematically exchanges
nucleotides? . . . . . . . . . . . . . . 216--222
Jianshe Yu and
Qiwen Sun and
Moxun Tang The nonlinear dynamics and fluctuations
of mRNA levels in cross-talking pathway
activated transcription . . . . . . . . 223--234
Shiliang Feng and
Weiping Zhu Bidirectional molecular transport shapes
cell polarization in a two-dimensional
model of eukaryotic chemotaxis . . . . . 235--246
Calistus N. Ngonghala and
Sara Y. Del Valle and
Ruijun Zhao and
Jemal Mohammed-Awel Quantifying the impact of decay in
bed-net efficacy on malaria transmission 247--261
Benjamin R. Morin and
Charles Perrings and
Simon Levin and
Ann Kinzig Disease risk mitigation: The equivalence
of two selective mixing strategies on
aggregate contact patterns and resulting
epidemic spread . . . . . . . . . . . . 262--270
Ya Guo and
Jinglu Tan Fourier transform of delayed
fluorescence as an indicator of
herbicide concentration . . . . . . . . 271--276
Peter van Heijster and
Heather Hardway and
Tasso J. Kaper and
Cynthia A. Bradham A computational model for BMP movement
in sea urchin embryos . . . . . . . . . 277--289
Louisa Roselius and
Dirk Langemann and
Johannes Müller and
Burkhard A. Hense and
Stefan Filges and
Dieter Jahn and
Richard Münch Modelling and analysis of a
gene-regulatory feed-forward loop with
basal expression of the second regulator 290--299
Duncan Taylor and
Jo-Anne Bright and
John Buckleton The `factor of two' issue in mixed DNA
profiles . . . . . . . . . . . . . . . . 300--306
Stephanie R. Taylor and
Allyson Cheever and
Sarah M. Harmon Velocity response curves demonstrate the
complexity of modeling entrainable
clocks . . . . . . . . . . . . . . . . . 307--317
R. El Cheikh and
S. Bernard and
N. El Khatib Modeling circadian clock-cell cycle
interaction effects on cell population
growth rates . . . . . . . . . . . . . . 318--331
Javier García-Algarra and
Javier Galeano and
Juan Manuel Pastor and
José María Iriondo and
José J. Ramasco Rethinking the logistic approach for
population dynamics of mutualistic
interactions . . . . . . . . . . . . . . 332--343
Bevan L. Cheeseman and
Donald F. Newgreen and
Kerry A. Landman Spatial and temporal dynamics of cell
generations within an invasion wave: a
link to cell lineage tracing . . . . . . 344--356
Elisa Calistri and
Marcello Buiatti and
Roberto Livi Variation and constraints in
species-specific promoter sequences . . 357--366
Yolandy Lemmer and
Anne Grobler and
Clint Moody and
Hendrik Viljoen A model of isoniazid treatment of
tuberculosis . . . . . . . . . . . . . . 367--373
N. Terranova and
P. Rebuzzini and
G. Mazzini and
E. Borella and
C. A. Redi and
M. Zuccotti and
S. Garagna and
P. Magni Mathematical modeling of growth and
death dynamics of mouse embryonic stem
cells irradiated with $ \gamma $-rays 374--380
Allison T. Neal and
Peter D. Taylor Local mate competition and transmission
bottlenecks: a new model for
understanding malaria parasite and other
sex ratios . . . . . . . . . . . . . . . 381--389
Xuebing Zhang and
Hongyong Zhao Bifurcation and optimal harvesting of a
diffusive predator--prey system with
delays and interval biological
parameters . . . . . . . . . . . . . . . 390--403
William H. James and
John Valentine A further note on the rises in sex ratio
at birth during and just after the two
World Wars . . . . . . . . . . . . . . . 404--411
Jian Zhang and
Pingping Sun and
Xiaowei Zhao and
Zhiqiang Ma PECM: Prediction of extracellular matrix
proteins using the concept of Chou's
pseudo amino acid composition . . . . . 412--418
Lei Zhao and
Martin Lascoux and
David Waxman Exact simulation of conditioned
Wright--Fisher models . . . . . . . . . 419--426
Tauanne D. Amarante and
Jafferson K. L. da Silva and
Guilherme J. M. Garcia Effects of airway surface liquid height
on the kinetics of extracellular
nucleotides in airway epithelia . . . . 427--435
Mark A. Gilbert and
Eamonn A. Gaffney and
James M. Bullock and
Steven M. White Spreading speeds for plant populations
in landscapes with low environmental
variation . . . . . . . . . . . . . . . 436--452
Rakesh K. Jain and
Paolo A. Netti Letter to the editor regarding recent
article by Wu et al. [J. Theor. Biol.
\bf 355 (2014) pp. 194--207] . . . . . . 453--453
Henrique C. Giacomini and
Brian J. Shuter Corrigendum to ``Adaptive responses of
energy storage and fish life histories
to climatic gradients'' [J. Theor. Biol.
\bf 339 (2013) 100--111] . . . . . . . . 454--454
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Kazuo Yamazaki and
Simcha Lev-Yadun Dense white trichome production by
plants as possible mimicry of arthropod
silk or fungal hyphae that deter
herbivory . . . . . . . . . . . . . . . 1--6
Anonymous Pages 1--438 (7 January 2015) . . . . . 1--438
Aleksandr N. Bugay and
Evgeny A. Krasavin and
Aleksandr Yu. Parkhomenko and
Maria A. Vasilyeva Modeling nucleotide excision repair and
its impact on UV-induced mutagenesis
during SOS-response in bacterial cells 7--20
Teeraphan Laomettachit and
Teerasit Termsaithong and
Anuwat Sae-Tang and
Orawan Duangphakdee Decision-making in honeybee swarms based
on quality and distance information of
candidate nest sites . . . . . . . . . . 21--30
André E. R. Soares and
Carlos G. Schrago The influence of taxon sampling on
Bayesian divergence time inference under
scenarios of rate heterogeneity among
lineages . . . . . . . . . . . . . . . . 31--39
Irina Kareva Immune evasion through competitive
inhibition: The shielding effect of
cancer non-stem cells . . . . . . . . . 40--48
K. Dormanns and
E. M. J. van Disseldorp and
R. G. Brown and
T. David Neurovascular coupling and the influence
of luminal agonists via the endothelium 49--70
Nikolaos E. Ioannidis and
Kiriakos Kotzabasis Could structural similarity of specific
domains between animal globins and plant
antenna proteins provide hints important
for the photoprotection mechanism? . . . 71--79
R. Penta and
D. Ambrosi The role of the microvascular tortuosity
in tumor transport phenomena . . . . . . 80--97
Mohammad Ganjtabesh and
Soheila Montaseri and
Fatemeh Zare-Mirakabad Using temperature effects to predict the
interactions between two RNAs . . . . . 98--102
A. Verdian Doghaei and
M. R. Housaindokht and
M. R. Bozorgmehr Molecular crowding effects on
conformation and stability of
G-quadruplex DNA structure: Insights
from molecular dynamics simulation . . . 103--112
Elena Fimmel and
Lutz Strüngmann On the hierarchy of trinucleotide
$n$-circular codes and their
corresponding amino acids . . . . . . . 113--120
G. A. Arango-Argoty and
J. A. Jaramillo-Garzón and
G. Castellanos-Domínguez Feature extraction by statistical
contact potentials and wavelet transform
for predicting subcellular localizations
in gram negative bacterial proteins . . 121--130
Vlastimil K\vrivan and
Debaldev Jana Effects of animal dispersal on
harvesting with protected areas . . . . 131--138
Weifan Liu and
Sarah D. Olson Compartment calcium model of frog
skeletal muscle during activation . . . 139--153
Marco Tomassini and
Alberto Antonioni Lévy flights and cooperation among mobile
individuals . . . . . . . . . . . . . . 154--161
Julian Z. Xue and
Artem Kaznatcheev and
Andre Costopoulos and
Frederic Guichard Fidelity drive: a mechanism for
chaperone proteins to maintain stable
mutation rates in prokaryotes over
evolutionary time . . . . . . . . . . . 162--167
Ido Filin The relation between maternal phenotype
and offspring size, explained by
overhead material costs of reproduction 168--178
Aslan Massahi and
Pinar Çalik In-silico determination of
\bionamePichia pastoris signal peptides
for extracellular recombinant protein
production . . . . . . . . . . . . . . . 179--188
H. A. Soula and
A. Géloën and
C. O. Soulage Model of adipose tissue cellularity
dynamics during food restriction . . . . 189--196
Xiaofeng Liu and
Ning Xu and
Aimin Jiang Tortuosity entropy: a measure of spatial
complexity of behavioral changes in
animal movement . . . . . . . . . . . . 197--205
Giuseppina Albano and
Virginia Giorno and
Patricia Román-Román and
Sergio Román-Román and
Francisco Torres-Ruiz Estimating and determining the effect of
a therapy on tumor dynamics by means of
a modified Gompertz diffusion process 206--219
D. E. Moulton and
A. Goriely and
R. Chirat The morpho-mechanical basis of ammonite
form . . . . . . . . . . . . . . . . . . 220--230
Yusuke Ikegawa and
Hideo Ezoe and
Toshiyuki Namba Effects of generalized and specialized
adaptive defense by shared prey on
intra-guild predation . . . . . . . . . 231--241
Xuesong Liu and
Qiuhui Pan and
Yibin Kang and
Mingfeng He Fixation probabilities in evolutionary
games with the Moran and Fermi processes 242--248
Julie A. Shay and
Christopher Huynh and
Paul G. Higgs The origin and spread of a cooperative
replicase in a prebiotic chemical system 249--259
Masashi Tachikawa and
Atsushi Mochizuki Nonlinearity in cytoplasm viscosity can
generate an essential symmetry breaking
in cellular behaviors . . . . . . . . . 260--265
Jong-Hoon Kim and
Seong-Hwan Rho Transmission dynamics of oral polio
vaccine viruses and vaccine-derived
polioviruses on networks . . . . . . . . 266--274
Willem H. Mulder and
Forrest W. Crawford On the distribution of interspecies
correlation for Markov models of
character evolution on Yule trees . . . 275--283
Abdollah Dehzangi and
Rhys Heffernan and
Alok Sharma and
James Lyons and
Kuldip Paliwal and
Abdul Sattar Gram-positive and Gram-negative protein
subcellular localization by
incorporating evolutionary-based
descriptors into Chou's general PseAAC 284--294
Qiang Zhang and
Hong Li and
Xiaoqing Zhao and
Yan Zheng and
Deliang Zhou Distribution bias of the sequence
matching between exons and introns in
exon joint and EJC binding region in
\bionameC. elegans . . . . . . . . . . . 295--304
Lena-Maria Holtz and
Dieter Wolf-Gladrow and
Silke Thoms Numerical cell model investigating
cellular carbon fluxes in
\bionameEmiliania huxleyi . . . . . . . 305--315
William H. James Hypothesis: High levels of maternal
adrenal androgens are a major cause of
miscarriage and other forms of
reproductive suboptimality . . . . . . . 316--320
Michael G. Elliot Identical inferences about correlated
evolution arise from ancestral state
reconstruction and independent contrasts 321--325
Peter J. Enyeart and
Zachary B. Simpson and
Andrew D. Ellington A microbial model of economic trading
and comparative advantage . . . . . . . 326--343
Susmita Bag and
Sudha Ramaiah and
Anand Anbarasu fabp4 is central to eight obesity
associated genes: a functional gene
network-based polymorphic study . . . . 344--354
Martin Jansen and
Peter Pfaffelhuber Stochastic gene expression with delay 355--363
Roohollah Shamloo-Dashtpagerdi and
Hooman Razi and
Massumeh Aliakbari and
Angelica Lindlöf and
Mahdi Ebrahimi and
Esmaeil Ebrahimie A novel pairwise comparison method for
in silico discovery of statistically
significant cis-regulatory elements in
eukaryotic promoter regions: Application
to \bionameArabidopsis . . . . . . . . . 364--376
C. Finn McQuaid and
Nicholas F. Britton Parasite species richness and its effect
on persistence in food webs . . . . . . 377--382
A. S. Serov and
C. M. Salafia and
P. Brownbill and
D. S. Grebenkov and
M. Filoche Optimal villi density for maximal oxygen
uptake in the human placenta . . . . . . 383--396
S. Sircar and
E. Aisenbrey and
S. J. Bryant and
D. M. Bortz Determining equilibrium osmolarity in
poly(ethylene glycol)/chondrotin sulfate
gels mimicking articular cartilage . . . 397--406
Yasser B. Ruiz-Blanco and
Yovani Marrero-Ponce and
Pablo J. Prieto and
Jesús Salgado and
Yamila Garc\'ìa and
Clivia M. Sotomayor-Torres A Hooke's law-based approach to protein
folding rate . . . . . . . . . . . . . . 407--417
Pascal R. Buenzli Osteocytes as a record of bone formation
dynamics: a mathematical model of
osteocyte generation in bone matrix . . 418--427
Ira Aviram and
Avinoam Rabinovitch and
Arieh Zaritsky Maximizing yields of virulent phage: The
T4/\bionameEscherichia coli system as a
test case . . . . . . . . . . . . . . . 428--432
ZhuoHua Shen and
Justin Seipel Animals prefer leg stiffness values that
may reduce the energetic cost of
locomotion . . . . . . . . . . . . . . . 433--438
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Whan Ghang and
Martin A. Nowak Indirect reciprocity with optional
interactions . . . . . . . . . . . . . . 1--11
Anonymous Pages 1--496 (21 January 2015) . . . . . 1--496
Yoshinori Hayakawa and
Masashi Tachikawa and
Atsushi Mochizuki Mathematical study for the mechanism of
vascular and spot patterns by auxin and
pin dynamics in plant development . . . 12--22
Maria R. Fumagalli and
Matteo Osella and
Philippe Thomen and
Francois Heslot and
Marco Cosentino Lagomarsino Speed of evolution in large asexual
populations with diminishing returns . . 23--31
Reza Zohouri Aram and
Nasrollah Moghadam Charkari A two-layer classification framework for
protein fold recognition . . . . . . . . 32--39
Katarína Bod'ová and
David Paydarfar and
Daniel B. Forger Characterizing spiking in noisy type II
neurons . . . . . . . . . . . . . . . . 40--54
Rachel A. Taylor and
Andrew White and
Jonathan A. Sherratt Seasonal forcing in a host-macroparasite
system . . . . . . . . . . . . . . . . . 55--66
Rodrigo Wiff and
Mauricio A. Barrientos and
Andrés C. Milessi and
J. C. Quiroz and
John Harwood Modelling production per unit of food
consumed in fish populations . . . . . . 67--75
George P. Malanson and
Lynn M. Resler Neighborhood functions alter unbalanced
facilitation on a stress gradient . . . 76--83
Christoforos Hadjichrysanthou and
Kieran J. Sharkey Epidemic control analysis: Designing
targeted intervention strategies against
epidemics propagated on contact networks 84--95
Ravindra Kumar and
Abhishikha Srivastava and
Bandana Kumari and
Manish Kumar Prediction of $ \beta $-lactamase and
its class by Chou's pseudo-amino acid
composition and support vector machine 96--103
Jaspreet Toor and
Alex Best The evolution of host resistance to
disease in the presence of predators . . 104--111
Zhijie Jack Tseng and
John J. Flynn Convergence analysis of a finite element
skull model of \bionameHerpestes
javanicus (\bionameCarnivora, Mammalia):
Implications for robust comparative
inferences of biomechanical function . . 112--148
Robert A. Laird and
Brandon S. Schamp Competitive intransitivity, population
interaction structure, and strategy
coexistence . . . . . . . . . . . . . . 149--158
Jinhui Zhang and
Yong Li and
Xinan Zhang Mathematical modeling of tuberculosis
data of China . . . . . . . . . . . . . 159--163
Christian J. Michel An extended genetic scale of reading
frame coding . . . . . . . . . . . . . . 164--174
Man Xi and
Guohong Yun and
B. Narsu A mathematical model on stress-strain of
the epimysium of skeletal muscles . . . 175--180
András Szarka and
Tibor Balogh In silico aided thoughts on
mitochondrial vitamin C transport . . . 181--189
Judit Oláh and
Vic Norris and
Judit Ovádi Modeling of sensing potency of
cytoskeletal systems decorated with
metabolic enzymes . . . . . . . . . . . 190--196
Zaheer Ullah Khan and
Maqsood Hayat and
Muazzam Ali Khan Discrimination of acidic and alkaline
enzyme using Chou's pseudo amino acid
composition in conjunction with
probabilistic neural network model . . . 197--203
Pietro Landi and
Cang Hui and
Ulf Dieckmann Fisheries-induced disruptive selection 204--216
Daniel J. Cleather and
Dominic F. L. Southgate and
Anthony M. J. Bull The role of the biarticular hamstrings
and gastrocnemius muscles in closed
chain lower limb extension . . . . . . . 217--225
Timothy O. Lamberton and
James Lefevre and
Kieran M. Short and
Ian M. Smyth and
Nicholas A. Hamilton Comparing and distinguishing the
structure of biological branching . . . 226--237
Sona John and
Kavita Jain Effect of drift, selection and
recombination on the equilibrium
frequency of deleterious mutations . . . 238--246
Aurélie Carlier and
Liesbet Geris and
Nick van Gastel and
Geert Carmeliet and
Hans Van Oosterwyck Oxygen as a critical determinant of bone
fracture healing --- a multiscale model 247--264
Xu Xue and
Wang Yongjun and
Li Zhihong Folding of SAM-II riboswitch explored by
replica-exchange molecular dynamics
simulation . . . . . . . . . . . . . . . 265--269
Emanuel A. Fronhofer and
Hans Joachim Poethke and
Ulf Dieckmann Evolution of dispersal distance:
Maternal investment leads to bimodal
dispersal kernels . . . . . . . . . . . 270--279
Yasser Aboelkassem and
Dragana Savic and
Stuart G. Campbell Mathematical modeling of aortic valve
dynamics during systole . . . . . . . . 280--288
Lars Ole Schwen and
Weiwei Wei and
Felix Gremse and
Josef Ehling and
Lei Wang and
Uta Dahmen and
Tobias Preusser Algorithmically generated rodent hepatic
vascular trees in arbitrary detail . . . 289--300
Alexander M. Zöllner and
Jacquelynn M. Pok and
Emily J. McWalter and
Garry E. Gold and
Ellen Kuhl On high heels and short muscles: a
multiscale model for sarcomere loss in
the gastrocnemius muscle . . . . . . . . 301--310
Victoria Romeo Aznar and
Mar\'ìa Sol De Majo and
Sylvia Fischer and
Diego Francisco and
Mario A. Natiello and
Hernán G. Solari A model for the development of
\bionameAedes (Stegomyia) aegypti as a
function of the available food . . . . . 311--324
John Walmsley and
Gary R. Mirams and
Joe Pitt-Francis and
Blanca Rodriguez and
Kevin Burrage Application of stochastic
phenomenological modelling to
cell-to-cell and beat-to-beat
electrophysiological variability in
cardiac tissue . . . . . . . . . . . . . 325--336
Jianquan Li and
Ke Men and
Yali Yang and
Duan Li Dynamical analysis on a chronic
hepatitis C virus infection model with
immune response . . . . . . . . . . . . 337--346
Toshinori Okuyama Demographic stochasticity alters the
outcome of exploitation competition . . 347--351
N. Panitchob and
K. L. Widdows and
I. P. Crocker and
M. A. Hanson and
E. D. Johnstone and
C. P. Please and
C. P. Sibley and
J. D. Glazier and
R. M. Lewis and
B. G. Sengers Computational modelling of amino acid
exchange and facilitated transport in
placental membrane vesicles . . . . . . 352--364
Pierre Barbillon and
Mathieu Thomas and
Isabelle Goldringer and
Frédéric Hospital and
Stéphane Robin Network impact on persistence in a
finite population dynamic diffusion
model: Application to an emergent seed
exchange network . . . . . . . . . . . . 365--376
Rui Li and
Liufang Xu and
Hualin Shi Strategy of tuning gene expression ratio
in prokaryotic cell from perspective of
noise and correlation . . . . . . . . . 377--389
C. Baker and
N. Dowson and
P. Thomas and
S. Rose Modelling of FDG metabolism in liver
voxels . . . . . . . . . . . . . . . . . 390--402
Y. He and
D. Kulasiri and
S. Samarasinghe Modelling the dynamics of CaMKII-NMDAR
complex related to memory formation in
synapses: The possible roles of
threonine 286 autophosphorylation of
CaMKII in long term potentiation . . . . 403--419
L. Barberis and
M. A. Pasquale and
C. A. Condat Joint fitting reveals hidden
interactions in tumor growth . . . . . . 420--432
T. Abdalrahman and
S. Scheiner and
C. Hellmich Is trabecular bone permeability governed
by molecular ordering-induced fluid
viscosity gain? Arguments from
re-evaluation of experimental data in
the framework of homogenization theory 433--444
Fabio Vittorio De Blasio and
Lee Hsiang Liow and
Tore Schweder and
Birgitte Freiesleben De Blasio A model for global diversity in response
to temperature change over geological
time scales, with reference to planktic
organisms . . . . . . . . . . . . . . . 445--456
David Juher and
Istvan Z. Kiss and
Joan Saldaña Analysis of an epidemic model with
awareness decay on regular random
networks . . . . . . . . . . . . . . . . 457--468
Steffen Waldherr and
Diego A. Oyarzún and
Alexander Bockmayr Dynamic optimization of metabolic
networks coupled with gene expression 469--485
Xinzhu Wei and
Lei Zhao and
Martin Lascoux and
David Waxman Population structure and the rate of
evolution . . . . . . . . . . . . . . . 486--495
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Xiaowei Wu and
Hongxiao Zhu Fast maximum likelihood estimation of
mutation rates using a birth-death
process . . . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--130 (7 February 2015) . . . . . 1--130
Taigang Liu and
Peiying Tao and
Xiaowei Li and
Yufang Qin and
Chunhua Wang Prediction of subcellular location of
apoptosis proteins combining tri-gram
encoding based on PSSM and recursive
feature elimination . . . . . . . . . . 8--12
Claudia Lenk and
Frank M. Weber and
Martin Bauer and
Mario Einax and
Philipp Maass and
Gunnar Seeman Initiation of atrial fibrillation by
interaction of pacemakers with
geometrical constraints . . . . . . . . 13--23
Jennifer Hoyal Cuthill The size of the character state space
affects the occurrence and detection of
homoplasy: Modelling the probability of
incompatibility for unordered
phylogenetic characters . . . . . . . . 24--32
Takuma Hatano and
Yoshito Hirata and
Hideyuki Suzuki and
Kazuyuki Aihara Comparison between mathematical models
of intermittent androgen suppression for
prostate cancer . . . . . . . . . . . . 33--45
Korinna T. Allhoff and
Eva Marie Weiel and
Tobias Rogge and
Barbara Drossel On the interplay of speciation and
dispersal: An evolutionary food web
model in space . . . . . . . . . . . . . 46--56
Nathan Mellor and
Benjamin Péret and
Silvana Porco and
Ilkka Sairanen and
Karin Ljung and
Malcolm Bennett and
John King Modelling of \bionameArabidopsis LAX3
expression suggests auxin homeostasis 57--70
P. Straka and
S. Fedotov Transport equations for subdiffusion
with nonlinear particle interaction . . 71--83
Xiong Li and
Bo Liao and
Haowen Chen A new technique for generating
pathogenic barcodes in breast cancer
susceptibility analysis . . . . . . . . 84--90
John M. Murray and
Ashish Goyal In silico single cell dynamics of
hepatitis B virus infection and
clearance . . . . . . . . . . . . . . . 91--102
Colin Phipps and
Hamid Molavian and
Mohammad Kohandel A microscale mathematical model for
metabolic symbiosis: Investigating the
effects of metabolic inhibition on ATP
turnover in tumors . . . . . . . . . . . 103--114
Oleg V. Belov and
Eugene A. Krasavin and
Marina S. Lyashko and
Munkhbaatar Batmunkh and
Nasser H. Sweilam A quantitative model of the major
pathways for radiation-induced DNA
double-strand break repair . . . . . . . 115--130
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Joung-Hun Lee and
Karl Sigmund and
Ulf Dieckmann and
Yoh Iwasa Games of corruption: How to suppress
illegal logging . . . . . . . . . . . . 1--13
Anonymous Pages 1--296 (21 February 2015) . . . . 1--296
Christopher H. Remien Modeling the dynamics of stable isotope
tissue-diet enrichment . . . . . . . . . 14--20
Ning Wei and
Yoichiro Mori and
Elena G. Tolkacheva The role of short term memory and
conduction velocity restitution in
alternans formation . . . . . . . . . . 21--28
A. Ghorbanpour Arani and
M. Abdollahian and
M. H. Jalaei Vibration of bioliquid-filled
microtubules embedded in cytoplasm
including surface effects using modified
couple stress theory . . . . . . . . . . 29--38
J. D. Day and
E. K. LeGrand Synergy of local, regional, and systemic
non-specific stressors for host defense
against pathogens . . . . . . . . . . . 39--48
J. V. Greenman and
B. Adams The exclusion problem in seasonally
forced epidemiological systems . . . . . 49--60
Oyita Udiani and
Noa Pinter-Wollman and
Yun Kang Identifying robustness in the regulation
of collective foraging of ant colonies
using an interaction-based model with
backward bifurcation . . . . . . . . . . 61--75
Kirti M. Yenkie and
Urmila Diwekar Uncertainty in clinical data and
stochastic model for in vitro
fertilization . . . . . . . . . . . . . 76--85
Racheal L. Cooper and
Rebecca A. Segal and
Robert F. Diegelmann and
Angela M. Reynolds Modeling the effects of systemic
mediators on the inflammatory phase of
wound healing . . . . . . . . . . . . . 86--99
Snigdhadip Dey and
Bedartha Goswami and
Amitabh Joshi A possible mechanism for the attainment
of out-of-phase periodic dynamics in two
chaotic subpopulations coupled at low
dispersal rate . . . . . . . . . . . . . 100--110
Wen Si and
Weinian Zhang Control exponential growth of tumor
cells with slow spread of oncolytic
virus . . . . . . . . . . . . . . . . . 111--129
Meredith Root-Bernstein and
Robert Root-Bernstein The ribosome as a missing link in the
evolution of life . . . . . . . . . . . 130--158
Andrew J. Black and
J. V. Ross Computation of epidemic final size
distributions . . . . . . . . . . . . . 159--165
Elsje Pienaar and
Nicholas A. Cilfone and
Philana Ling Lin and
Véronique Dartois and
Joshua T. Mattila and
J. Russell Butler and
JoAnne L. Flynn and
Denise E. Kirschner and
Jennifer J. Linderman A computational tool integrating host
immunity with antibiotic dynamics to
study tuberculosis treatment . . . . . . 166--179
Yongxue Chen and
Yongxian Wen Global dynamic analysis of a H7N9
avian--human influenza model in an
outbreak region . . . . . . . . . . . . 180--188
Atsushi Mochizuki and
Bernold Fiedler Sensitivity of chemical reaction
networks: a structural approach. 1.
Examples and the carbon metabolic
network . . . . . . . . . . . . . . . . 189--202
Phillip Schumm and
Caterina Scoglio and
Qian Zhang and
Duygu Balcan Global epidemic invasion thresholds in
directed cattle subpopulation networks
having source, sink, and transit nodes 203--221
John Wei Lau and
David N. Levy and
Dominik Wodarz Contribution of HIV-1 genomes that do
not integrate to the basic reproductive
ratio of the virus . . . . . . . . . . . 222--229
Daniel Bearup and
Sergei Petrovskii On time scale invariance of random walks
in confined space . . . . . . . . . . . 230--245
Paul Rauwolf and
Dominic Mitchell and
Joanna J. Bryson Value homophily benefits cooperation but
motivates employing incorrect social
information . . . . . . . . . . . . . . 246--261
James M. Greene and
Doron Levy and
King Leung Fung and
Paloma S. Souza and
Michael M. Gottesman and
Orit Lavi Modeling intrinsic heterogeneity and
growth of cancer cells . . . . . . . . . 262--277
Yanrui Ding and
Xueqin Wang and
Zhaolin Mou Communities in the iron superoxide
dismutase amino acid network . . . . . . 278--285
K. Korvasová and
E. A. Gaffney and
P. K. Maini and
M. A. Ferreira and
V. Klika Investigating the Turing conditions for
diffusion-driven instability in the
presence of a binding immobile substrate 286--295
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Hang Qi and
Shoufeng Ma and
Ning Jia and
Guangchao Wang Experiments on individual strategy
updating in iterated snowdrift game
under random rematching . . . . . . . . 1--12
Anonymous Pages 1--144 (7 March 2015) . . . . . . 1--144
Julian Krick and
Josef Daniel Ackerman Adding ecology to particle capture
models: Numerical simulations of capture
on a moving cylinder in crossflow . . . 13--26
Tomás Aquino and
Diogo Bolster and
Ana Nunes Characterization of the endemic
equilibrium and response to mutant
injection in a multi-strain disease
model . . . . . . . . . . . . . . . . . 27--36
M. A. Morales and
J. F. Rojas and
J. Oliveros and
A. A. Hernández S. A new mechanochemical model: Coupled
Ginzburg--Landau and Swift--Hohenberg
equations in biological patterns of
marine animals . . . . . . . . . . . . . 37--54
Audrey Addison and
James A. Powell and
Barbara J. Bentz and
Diana L. Six Integrating models to investigate
critical phenological overlaps in
complex ecological interactions: The
mountain pine beetle-fungus symbiosis 55--66
Giacomo Plazzotta and
Ted Cohen and
Caroline Colijn Magnitude and sources of bias in the
detection of mixed strain \bionameM.
tuberculosis infection . . . . . . . . . 67--73
József Garay and
Zoltán Varga and
Manuel Gámez and
Tomás Cabello Functional response and population
dynamics for fighting predator, based on
activity distribution . . . . . . . . . 74--82
Samantha Hartzell and
Mark S. Bartlett and
Lawrence Virgin and
Amilcare Porporato Nonlinear dynamics of the CAM circadian
rhythm in response to environmental
forcing . . . . . . . . . . . . . . . . 83--94
Gábor Závodszky and
György Károlyi and
György Paál Emerging fractal patterns in a real $3$D
cerebral aneurysm . . . . . . . . . . . 95--101
Francis G. Woodhouse and
Bruce S. Gardiner and
David W. Smith Short-term consolidation of articular
cartilage in the long-term context of
osteoarthritis . . . . . . . . . . . . . 102--112
Kelly C. Iarosz and
Fernando S. Borges and
Antonio M. Batista and
Murilo S. Baptista and
Regiane A. N. Siqueira and
Ricardo L. Viana and
Sergio R. Lopes Mathematical model of brain tumour with
glia-neuron interactions and
chemotherapy treatment . . . . . . . . . 113--121
Jaber Nasiri and
Mohammad Reza Naghavi and
Amir Hossein Kayvanjoo and
Mojtaba Nasiri and
Mansour Ebrahimi Precision assessment of some supervised
and unsupervised algorithms for genotype
discrimination in the genus
\bionamePisum using SSR molecular data 122--132
A. S. Serov and
C. M. Salafia and
M. Filoche and
D. S. Grebenkov Analytical theory of oxygen transport in
the human placenta . . . . . . . . . . . 133--144
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Lan Zou and
Shigui Ruan and
Weinian Zhang On the sexual transmission dynamics of
hepatitis B virus in China . . . . . . . 1--12
Anonymous Pages 1--110 (21 March 2015) . . . . . . 1--110
Mohammad H. Fatemi and
Afsane Heidari and
Sajjad Gharaghani QSAR prediction of HIV-1 protease
inhibitory activities using docking
derived molecular descriptors . . . . . 13--22
Matthew Spencer Size change, shape change, and the
growth space of a community . . . . . . 23--41
Henri Gouin The watering of tall trees ---
Embolization and recovery . . . . . . . 42--50
Chun Li and
Yan Yang and
Wenchao Fei and
Ping-an He and
Xiaoqing Yu and
Defu Zhang and
Shumin Yi and
Xuepeng Li and
Jin Zhu and
Changzhong Wang and
Zhifu Wang Prediction of success for polymerase
chain reactions using the Markov maximal
order model and support vector machine 51--58
Noel P. Quinn and
Josef D. Ackerman The effect of bottom roughness on scalar
transport in aquatic ecosystems:
Implications for reproduction and
recruitment in the benthos . . . . . . . 59--66
Himanshu Bhusan Samal and
Jyoti Prava and
Mrutyunjay Suar and
Rajani Kanta Mahapatra Comparative genomics study of
\bionameSalmonella Typhimurium LT2 for
the identification of putative
therapeutic candidates . . . . . . . . . 67--79
Natalya A. Kurochkina and
Michael J. Iadarola Helical assemblies: Structure
determinants . . . . . . . . . . . . . . 80--84
Caitlin Ross and
Jan Rychtár and
Olav Rueppell A structured population model suggests
that long life and post-reproductive
lifespan promote the evolution of
cooperation . . . . . . . . . . . . . . 85--94
Åsa Wohlin Numeral series hidden in the
distribution of atomic mass of amino
acids to codon domains in the genetic
code . . . . . . . . . . . . . . . . . . 95--109
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
J. M. Deutsch and
Ian P. Lewis Motor function in interpolar
microtubules during metaphase . . . . . 1--10
Anonymous Pages 1--210 (7 April 2015) . . . . . . 1--210
Ivan Grbatini\'c and
Dusica L. Mari\'c and
Nebojsa T. Milosevi\'c Neurons from the adult human dentate
nucleus: Neural networks in the neuron
classification . . . . . . . . . . . . . 11--20
Vlastimil K\vrivan and
Anupam Priyadarshi L-shaped prey isocline in the Gause
predator--prey experiments with a prey
refuge . . . . . . . . . . . . . . . . . 21--26
Kevin Doherty and
Martin Meere and
Petri T. Piiroinen Some mathematical models of
intermolecular autophosphorylation . . . 27--38
Robert H. Lee and
Cassie S. Mitchell Axonal transport cargo motor count
versus average transport velocity: Is
fast versus slow transport really single
versus multiple motor transport? . . . . 39--44
Hilla Behar and
Yoram Louzoun Commensal pathogens as a source of a
coexistence mechanism . . . . . . . . . 45--52
Dominik R. Bach A cost minimisation and Bayesian
inference model predicts startle reflex
modulation across species . . . . . . . 53--60
Tomotaka Matsumoto and
Akiko A. Yasumoto and
Kozue Nitta and
Shun K. Hirota and
Tetsukazu Yahara and
Hidenori Tachida Difference in flowering time can
initiate speciation of nocturnally
flowering species . . . . . . . . . . . 61--71
Daniel Franco and
Alfonso Ruiz-Herrera To connect or not to connect isolated
patches . . . . . . . . . . . . . . . . 72--80
Stuart T. Johnston and
Matthew J. Simpson and
Ruth E. Baker Modelling the movement of interacting
cell populations: a moment dynamics
approach . . . . . . . . . . . . . . . . 81--92
X. Zhao and
J. W. Kim and
P. A. Robinson Slow-wave oscillations in a
corticothalamic model of sleep and wake 93--102
Kenta Suzuki and
Takehito Yoshida Ecological resilience of population
cycles: a dynamic perspective of regime
shift . . . . . . . . . . . . . . . . . 103--115
Ya Guo and
Yesen Zhou and
Jinglu Tan Wavelet analysis of
pulse-amplitude-modulated chlorophyll
fluorescence for differentiation of
plant samples . . . . . . . . . . . . . 116--120
Samuel P. C. Brand and
Michael J. Tildesley and
Matthew J. Keeling Rapid simulation of spatial epidemics: a
spectral method . . . . . . . . . . . . 121--134
M. Pineda and
C. J. Weijer and
R. Eftimie Modelling cell movement, cell
differentiation, cell sorting and
proportion regulation in
\bionameDictyostelium discoideum
aggregations . . . . . . . . . . . . . . 135--150
Igor Pantic and
Sanja Dacic and
Predrag Brkic and
Irena Lavrnja and
Tomislav Jovanovic and
Senka Pantic and
Sanja Pekovic Discriminatory ability of fractal and
grey level co-occurrence matrix methods
in structural analysis of hippocampus
layers . . . . . . . . . . . . . . . . . 151--156
Denggui Fan and
Qingyun Wang Improving desynchronization of
Parkinsonian neuronal network via
triplet-structure coordinated reset
stimulation . . . . . . . . . . . . . . 157--170
Peter Dawson and
Ralph Gailis and
Alaster Meehan Detecting disease outbreaks using a
combined Bayesian network and particle
filter approach . . . . . . . . . . . . 171--183
Robin Aguilée and
Pierre de Villemereuil and
Jean-Michel Guillon Dispersal evolution and resource
matching in a spatially and temporally
variable environment . . . . . . . . . . 184--196
José A. L. da Silva From the RNA world to the RNA/protein
world: Contribution of some
riboswitch-binding species? . . . . . . 197--201
Shang-Hong Zhang Persistence and breakdown of strand
symmetry in the human genome . . . . . . 202--204
Himanshu Kaul and
Yiannis Ventikos Dynamic reciprocity revisited . . . . . 205--208
Mauricio A. Fuentes Corrigendum for ``The mechanical cost of
transport of fast running animals'' . . 209--209
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Rebecca M. Vandiver Buckling instability in arteries . . . . 1--8
Anonymous Pages 1--166 (21 April 2015) . . . . . . 1--166
Jun-ichi Ishihara and
Masashi Tachikawa and
Hideo Iwasaki and
Atsushi Mochizuki Mathematical study of pattern formation
accompanied by heterocyst
differentiation in multicellular
cyanobacterium . . . . . . . . . . . . . 9--23
Naser Babaei and
Metin U. Salamci Personalized drug administration for
cancer treatment using Model Reference
Adaptive Control . . . . . . . . . . . . 24--44
Peter A. Corning and
Eörs Szathmáry ``Synergistic selection'': a Darwinian
frame for the evolution of complexity 45--58
Surya Pratap Singh and
Dwijendra K. Gupta A comparative study of structural and
conformational properties of casein
kinase-1 isoforms: Insights from
molecular dynamics and principal
component analysis . . . . . . . . . . . 59--68
Krzysztof Bartoszek and
Serik Sagitov A consistent estimator of the
evolutionary rate . . . . . . . . . . . 69--78
Daniel Sánchez-Taltavull and
Tomás Alarcón Stochastic modelling of viral blips in
HIV-$1$-infected patients: Effects of
inhomogeneous density fluctuations . . . 79--89
Céline Van de Paer and
Pierre Saumitou-Laprade and
Philippe Vernet and
Sylvain Billiard The joint evolution and maintenance of
self-incompatibility with gynodioecy or
androdioecy . . . . . . . . . . . . . . 90--101
Linford J. B. Briant and
Julian F. R. Paton and
Anthony E. Pickering and
Alan R. Champneys Modelling the vascular response to
sympathetic postganglionic nerve
activity . . . . . . . . . . . . . . . . 102--116
Cody Koykka and
Geoff Wild The evolution of group dispersal with
leaders and followers . . . . . . . . . 117--126
Mauro Santos and
Eörs Szathmáry and
José F. Fontanari Phenotypic plasticity, the Baldwin
effect, and the speeding up of
evolution: The computational roots of an
illusion . . . . . . . . . . . . . . . . 127--136
Danielle Lyles and
Todd S. Rosenstock and
Alan Hastings Plant reproduction and environmental
noise: How do plants do it? . . . . . . 137--144
Helene C. Weigang and
Éva Kisdi Evolution of dispersal under a
fecundity-dispersal trade-off . . . . . 145--153
Eva A. Enns and
Margaret L. Brandeau Link removal for the control of
stochastically evolving epidemics over
networks: a comparison of approaches . . 154--165
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Lucy Ternent and
Rosemary J. Dyson and
Anne-Marie Krachler and
Sara Jabbari Bacterial fitness shapes the population
dynamics of antibiotic-resistant and
-susceptible bacteria in a model of
combined antibiotic and anti-virulence
treatment . . . . . . . . . . . . . . . 1--11
Anonymous Pages 1--222 (7 May 2015) . . . . . . . 1--222
Felix Filatov and
Alexander Shargunov Short nucleotide sequences in
herpesviral genomes identical to the
human DNA . . . . . . . . . . . . . . . 12--21
Chiho Kaito and
Ulf Dieckmann and
Akira Sasaki and
Fugo Takasu Beyond pairs: Definition and
interpretation of third-order structure
in spatial point patterns . . . . . . . 22--38
Joseph E. Hannon Bozorgmehr Quantifying protein sequences with
reference to the genetic code . . . . . 39--46
Koichi Ito and
Hisashi Ohtsuki and
Atsushi Yamauchi Relationship between aggregation of
rewards and the possibility of
polymorphism in continuous snowdrift
games . . . . . . . . . . . . . . . . . 47--53
Sebastian Novak and
Sylvia Cremer Fungal disease dynamics in insect
societies: Optimal killing rates and the
ambivalent effect of high social
interaction rates . . . . . . . . . . . 54--64
Tom Chou and
Yu Wang Fixation times in differentiation and
evolution in the presence of
bottlenecks, deserts, and oases . . . . 65--73
Abbas Moghimbeigi Two-part zero-inflated negative binomial
regression model for quantitative trait
loci mapping with count trait . . . . . 74--80
P. Kurbatova and
N. Bessonov and
V. Volpert and
H. A. W. M. Tiddens and
C. Cornu and
P. Nony and
D. Caudri Model of mucociliary clearance in cystic
fibrosis lungs . . . . . . . . . . . . . 81--88
Ellen van Velzen and
Rampal S. Etienne The importance of ecological costs for
the evolution of plant defense against
herbivory . . . . . . . . . . . . . . . 89--99
Chacha M. Issarow and
Nicola Mulder and
Robin Wood Modelling the risk of airborne
infectious disease using exhaled air . . 100--106
Maleeha Waqar and
Sidra Batool In silico analysis of binding of
neurotoxic venom ligands with
acetylcholinesterase for therapeutic use
in treatment of Alzheimer's disease . . 107--117
Guoli Yang and
Weiming Zhang and
Baoxin Xiu Neighbourhood reaction in the evolution
of cooperation . . . . . . . . . . . . . 118--127
Shaopeng Wang and
Anping Chen and
Stephen W. Pacala and
Jingyun Fang Density-dependent speciation alters the
structure and dynamics of neutral
communities . . . . . . . . . . . . . . 128--134
Tung Hoang and
Changchuan Yin and
Hui Zheng and
Chenglong Yu and
Rong Lucy He and
Stephen S.-T. Yau A new method to cluster DNA sequences
using Fourier power spectrum . . . . . . 135--145
H. T. Banks and
Kevin B. Flores and
Shuhua Hu and
Eric Rosenberg and
Maria Buzon and
Xu Yu and
Matthias Lichterfeld Immuno-modulatory strategies for
reduction of HIV reservoir cells . . . . 146--158
Sam Van Wassenbergh and
Steven W. Day and
L. Patricia Hernández and
Timothy E. Higham and
Tyler Skorczewski Suction power output and the inertial
cost of rotating the neurocranium to
generate suction in fish . . . . . . . . 159--167
Wolfhard von Thienen and
Dirk Metzler and
Volker Witte Modeling shortest path selection of the
ant Linepithema humile using
psychophysical theory and realistic
parameter values . . . . . . . . . . . . 168--178
Maël Montévil and
Matteo Mossio Biological organisation as closure of
constraints . . . . . . . . . . . . . . 179--191
Lena-Maria Holtz and
Dieter Wolf-Gladrow and
Silke Thoms Simulating the effects of light
intensity and carbonate system
composition on particulate organic and
inorganic carbon production in
\bionameEmiliania huxleyi . . . . . . . 192--204
Franck Jabot Why preferring parametric forecasting to
nonparametric methods? . . . . . . . . . 205--210
Charles T. Perretti and
Stephan B. Munch On estimating the reliability of
ecological forecasts . . . . . . . . . . 211--216
Allen Cheung and
Robert Vickerstaff Sensory and update errors which can
affect path integration . . . . . . . . 217--221
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Arik Kershenbaum and
Todd M. Freeberg and
David E. Gammon Estimating vocal repertoire size is like
collecting coupons: a theoretical
framework with heterogeneity in signal
abundance . . . . . . . . . . . . . . . 1--11
Anonymous Pages 1--132 (21 May 2015) . . . . . . . 1--132
Petra Kochová and
Robert Cimrman and
Milan Stengl and
Bohuslav Ostádal and
Zbynek Tonar A mathematical model of the carp heart
ventricle during the cardiac cycle . . . 12--25
Chung-Hao Lee and
Christopher A. Carruthers and
Salma Ayoub and
Robert C. Gorman and
Joseph H. Gorman and
Michael S. Sacks Quantification and simulation of
layer-specific mitral valve interstitial
cells deformation under physiological
loading . . . . . . . . . . . . . . . . 26--39
Danko Nikoli\'c Practopoiesis: Or how life fosters a
mind . . . . . . . . . . . . . . . . . . 40--61
Alan Grafen Biological fitness and the Price
Equation in class-structured populations 62--72
A. Barton and
A. J. Fendrik Retinogenesis: Stochasticity and the
competency model . . . . . . . . . . . . 73--81
Olga A. Filatova and
Patrick J. O. Miller An agent-based model of dialect
evolution in killer whales . . . . . . . 82--91
M. M. P. Cobben and
J. Verboom and
P. F. M. Opdam and
R. F. Hoekstra and
R. Jochem and
M. J. M. Smulders Spatial sorting and range shifts:
Consequences for evolutionary potential
and genetic signature of a dispersal
trait . . . . . . . . . . . . . . . . . 92--99
Fredrik Jansson What games support the evolution of an
ingroup bias? . . . . . . . . . . . . . 100--110
Elliott Sober and
Mike Steel How probable is common ancestry
according to different evolutionary
processes? . . . . . . . . . . . . . . . 111--116
Yoshiyuki Ogino and
Toru Asahi Model of complex chiral drug metabolic
systems and numerical simulation of the
remaining chirality toward analysis of
dynamical pharmacological activity . . . 117--131
Katarína Bod'ová and
David Paydarfar and
Daniel B. Forger Erratum to: ``Characterizing spiking in
noisy type II neurons'' [J. Theor. Biol.
\bf 365 (2015) 40--54] . . . . . . . . . 132--132
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Hideki Murakawa and
Hideru Togashi Continuous models for cell--cell
adhesion . . . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--182 (7 June 2015) . . . . . . . 1--182
Alexander Hoover and
Laura Miller A numerical study of the benefits of
driving jellyfish bells at their natural
frequency . . . . . . . . . . . . . . . 13--25
Bartosz Lisowski and
Lukasz Ku\'smierz and
Micha\l Zabicki and
Martin Bier ``Cargo-mooring'' as an operating
principle for molecular motors . . . . . 26--34
Julia Chifman and
Laura Kubatko Identifiability of the unrooted species
tree topology under the coalescent model
with time-reversible substitution
processes, site-specific rate variation,
and invariable sites . . . . . . . . . . 35--47
Marcus A. M. de Aguiar and
David M. Schneider and
Eduardo do Carmo and
Paulo R. A. Campos and
Ayana B. Martins Error catastrophe in populations under
similarity-essential recombination . . . 48--53
Benny Chor and
Mike Steel Do tree split probabilities determine
the branch lengths? . . . . . . . . . . 54--59
Xiaowei Zhao and
Qiao Ning and
Haiting Chai and
Zhiqiang Ma Accurate in silico identification of
protein succinylation sites using an
iterative semi-supervised learning
technique . . . . . . . . . . . . . . . 60--65
F. Crauste and
E. Terry and
I. Le Mercier and
J. Mafille and
S. Djebali and
T. Andrieu and
B. Mercier and
G. Kaneko and
C. Arpin and
J. Marvel and
O. Gandrillon Predicting pathogen-specific CD8 T cell
immune responses from a modeling
approach . . . . . . . . . . . . . . . . 66--82
Ian Price and
Ericka D. Mochan-Keef and
David Swigon and
G. Bard Ermentrout and
Sarah Lukens and
Franklin R. Toapanta and
Ted M. Ross and
Gilles Clermont The inflammatory response to influenza A
virus (H1N1): An experimental and
mathematical study . . . . . . . . . . . 83--93
Thijs Janzen and
Bart Haegeman and
Rampal S. Etienne A sampling formula for ecological
communities with multiple dispersal
syndromes . . . . . . . . . . . . . . . 94--106
Faez Iqbal Khan and
Algasan Govender and
Kugen Permaul and
Suren Singh and
Krishna Bisetty Thermostable chitinase II from
\bionameThermomyces lanuginosus SSBP:
Cloning, structure prediction and
molecular dynamics simulations . . . . . 107--114
Christian Hilbe and
Bin Wu and
Arne Traulsen and
Martin A. Nowak Evolutionary performance of
zero-determinant strategies in
multiplayer games . . . . . . . . . . . 115--124
Yovani Marrero-Ponce and
Ernesto Contreras-Torres and
César R. Garc\'ìa-Jacas and
Stephen J. Barigye and
Néstor Cubillán and
Ysa\'ìas J. Alvarado Novel $3$D bio-macromolecular bilinear
descriptors for protein science:
Predicting protein structural classes 125--137
Beverley J. Grieshaber and
John S. Terblanche A computational model of insect
discontinuous gas exchange: a
two-sensor, control systems approach . . 138--151
Sunmi Lee and
Carlos Castillo-Chavez The role of residence times in two-patch
dengue transmission dynamics and optimal
strategies . . . . . . . . . . . . . . . 152--164
Mathieu Moslonka-Lefebvre and
Hervé Monod and
Christopher A. Gilligan and
Elisabeta Vergu and
João A. N. Filipe Epidemics in markets with trade friction
and imperfect transactions . . . . . . . 165--178
Robert Sinclair Necessary relations for nucleotide
frequencies . . . . . . . . . . . . . . 179--182
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Robert Root-Bernstein Towards an integration of mathematical
models, theories and observations
concerning autoimmune diseases . . . . . 1--3
Koichi Saeki and
Hilje M. Doekes and
Rob J. De Boer Optimal T cell cross-reactivity and the
role of regulatory T cells . . . . . . . 4--12
K. B. Blyuss and
L. B. Nicholson Understanding the roles of activation
threshold and infections in the dynamics
of autoimmune disease . . . . . . . . . 13--20
Elena Agliari and
Adriano Barra and
Gino Del Ferraro and
Francesco Guerra and
Daniele Tantari Anergy in self-directed B lymphocytes: a
statistical mechanics perspective . . . 21--31
Igor Menshikov and
Liubov Beduleva and
Maksim Frolov and
Nadezhda Abisheva and
Tatyana Khramova and
Elena Stolyarova and
Kseniya Fomina The idiotypic network in the regulation
of autoimmunity: Theoretical and
experimental studies . . . . . . . . . . 32--39
Melvin Cohn Autoimmunity: Rationalizing possible
pathways from initiation to disease . . 40--51
Alfred I. Tauber Reconceiving autoimmunity: An overview 52--60
Nelson M. Vaz and
Claudia R. Carvalho On the origin of immunopathology . . . . 61--70
Noel R. Rose Molecular mimicry and clonal deletion: a
fresh look . . . . . . . . . . . . . . . 71--76
Majid Jaberi-Douraki and
Santiago Schnell and
Massimo Pietropaolo and
Anmar Khadra Unraveling the contribution of
pancreatic beta-cell suicide in
autoimmune type 1 diabetes . . . . . . . 77--87
William F. Pendergraft and
Anshul K. Badhwar and
Gloria A. Preston Autoantigen complementarity and its
contributions to hallmarks of autoimmune
disease . . . . . . . . . . . . . . . . 88--94
Stephen J. Merrill and
Ying Mu Thyroid autoimmunity as a window to
autoimmunity: An explanation for sex
differences in the prevalence of thyroid
autoimmunity . . . . . . . . . . . . . . 95--100
Robert Root-Bernstein and
DeLisa Fairweather Unresolved issues in theories of
autoimmune disease using myocarditis as
a framework . . . . . . . . . . . . . . 101--123
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Iftikhar Ali and
Zainab Sardar and
Awais Rasheed and
Tariq Mahmood Molecular characterization of the
puroindoline-$a$ and $b$ alleles in
synthetic hexaploid wheats and in silico
functional and structural insights into
Pina-D1 . . . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--134 (7 July 2015) . . . . . . . 1--134
Jia-Feng Yu and
Qing-Li Chen and
Jing Ren and
Yan-Ling Yang and
Ji-Hua Wang and
Xiao Sun Analysis of the multi-copied genes and
the impact of the redundant protein
coding sequences on gene annotation in
prokaryotic genomes . . . . . . . . . . 8--14
Hrvoje Siki\'c and
Yanrong Shi and
Snjezana Lubura and
Steven Bassnett A stochastic model of eye lens growth 15--31
Marisol Herrera-Rivero and
María Elena Hernández-Aguilar and
Gonzalo Emiliano Aranda-Abreu A strategy focused on MAPT, APP, NCSTN
and BACE1 to build blood classifiers for
Alzheimer's disease . . . . . . . . . . 32--38
Yusuke Kakizoe and
Satoru Morita and
Shinji Nakaoka and
Yasuhiro Takeuchi and
Kei Sato and
Tomoyuki Miura and
Catherine A. A. Beauchemin and
Shingo Iwami A conservation law for virus infection
kinetics in vitro . . . . . . . . . . . 39--47
Daniela Calvetti and
Yougan Cheng and
Erkki Somersalo A spatially distributed computational
model of brain cellular metabolism . . . 48--65
Zheng Y. X. Huang and
Frank van Langevelde and
Herbert H. T. Prins and
Willem F. de Boer Dilution versus facilitation: Impact of
connectivity on disease risk in
metapopulations . . . . . . . . . . . . 66--73
Fatemeh Hadaeghi and
Mohammad Reza Hashemi Golpayegani and
Greg Murray Towards a complex system understanding
of bipolar disorder: a map based model
of a complex winnerless competition . . 74--81
Michael J. Fox and
Behrouz Touri and
Jeff S. Shamma Dynamics in atomic signaling games . . . 82--90
Mikael Fortelius and
Stefan Geritz and
Mats Gyllenberg and
Jaakko Toivonen Adaptive dynamics on an environmental
gradient that changes over a geological
time-scale . . . . . . . . . . . . . . . 91--104
Gabriele Pedruzzi and
Kanury V. S. Rao and
Samrat Chatterjee Mathematical model of mycobacterium-host
interaction describes physiology of
persistence . . . . . . . . . . . . . . 105--117
L. M. Bilinsky and
M. C. Reed and
H. F. Nijhout The role of skeletal muscle in liver
glutathione metabolism during
acetaminophen overdose . . . . . . . . . 118--133
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Cicely Macnamara and
Raluca Eftimie Memory versus effector immune responses
in oncolytic virotherapies . . . . . . . 1--9
Anonymous Pages 1--118 (21 July 2015) . . . . . . 1--118
Fahimeh Golzari and
Saeed Jalili VR-BFDT: a variance reduction based
binary fuzzy decision tree induction
method for protein function prediction 10--24
L. Bolzoni and
A. Pugliese and
R. Ros\`a The role of heterogeneity on the
invasion probability of mosquito-borne
diseases in multi-host models . . . . . 25--35
Biao Tang and
Yanni Xiao and
Robert A. Cheke and
Ning Wang Piecewise virus-immune dynamic model
with HIV-1 RNA-guided therapy . . . . . 36--46
Jianhua Jia and
Zi Liu and
Xuan Xiao and
Bingxiang Liu and
Kuo-Chen Chou iPPI-Esml: An ensemble classifier for
identifying the interactions of proteins
by incorporating their physicochemical
properties and wavelet transforms into
PseAAC . . . . . . . . . . . . . . . . . 47--56
Aming Li and
Long Wang Evolutionary dynamics of synergistic and
discounted group interactions in
structured populations . . . . . . . . . 57--65
ZhuoHua Shen and
Justin Seipel The leg stiffnesses animals use may
improve the stability of locomotion . . 66--74
Tao Song and
Hong Gu Discovering short linear protein motif
based on selective training of profile
hidden Markov models . . . . . . . . . . 75--84
Duncan S. Barrack and
Rüdiger Thul and
Markus R. Owen Modelling cell cycle synchronisation in
networks of coupled radial glial cells 85--97
Ani Asatryan and
Dominik Wodarz and
Natalia L. Komarova New virus dynamics in the presence of
multiple infection . . . . . . . . . . . 98--109
Gottfried Sachs New model of flap-gliding flight . . . . 110--116
Arturo Tozzi How to turn an oscillation in a pink one 117--118
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
X. Woot de Trixhe and
W. Krzyzanski and
F. De Ridder and
A. Vermeulen vRNA structured population model for
Hepatitis C Virus dynamics . . . . . . . 1--11
Anonymous Pages 1--116 (7 August 2015) . . . . . . 1--116
Qihua Huang and
Hao Wang and
Mark A. Lewis The impact of environmental toxins on
predator--prey dynamics . . . . . . . . 12--30
Amir Lakizadeh and
Saeed Jalili and
Sayed-Amir Marashi PCD-GED: Protein complex detection
considering PPI dynamics based on time
series gene expression data . . . . . . 31--38
Tomás A. Revilla Numerical responses in resource-based
mutualisms: a time scale approach . . . 39--46
Steven J. Lade and
Miguel Coelho and
Iva M. Toli\'c and
Thilo Gross Fusion leads to effective segregation of
damage during cell division: An
analytical treatment . . . . . . . . . . 47--55
Bhavin S. Khatri and
Richard A. Goldstein A coarse-grained biophysical model of
sequence evolution and the population
size dependence of the speciation rate 56--64
Mahdieh B. Saraee and
Moharam H. Korayem Dynamic simulation and modeling of the
motion modes produced during the $3$D
controlled manipulation of biological
micro/nanoparticles based on the AFM . . 65--78
C. Selvaa Kumar and
Nikhil Gadewal and
Sudheer MM Mohammed Seminal role of deletion of amino acid
residues in H1-S2 and S-loop regions in
eukaryotic $ \beta $-tubulin
investigated from docking and dynamics
perspective . . . . . . . . . . . . . . 79--88
Shingo Gibo and
Hiroshi Ito Discrete and ultradiscrete models for
biological rhythms comprising a simple
negative feedback loop . . . . . . . . . 89--95
Fernando P. Santos and
Francisco C. Santos and
Ana Paiva and
Jorge M. Pacheco Evolutionary dynamics of group fairness 96--102
Benjamin Allen and
Martin A. Nowak Games among relatives revisited . . . . 103--116
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Jennifer A. Flegg and
Jessica Kasza and
Ian Darby and
Carolina D. Weller Healing of venous ulcers using
compression therapy: Predictions of a
mathematical model . . . . . . . . . . . 1--9
Anonymous Pages 1--98 (21 August 2015) . . . . . . 1--98
Yan Xu and
Ya-Xin Ding and
Jun Ding and
Ling-Yun Wu and
Nai-Yang Deng Phogly-PseAAC: Prediction of lysine
phosphoglycerylation in proteins
incorporating with position-specific
propensity . . . . . . . . . . . . . . . 10--15
P. Sáez and
M. Malv\`e and
M. A. Martínez A theoretical model of the endothelial
cell morphology due to different
waveforms . . . . . . . . . . . . . . . 16--23
V. S. Zubkov and
A. N. Combes and
K. M. Short and
J. Lefevre and
N. A. Hamilton and
I. M. Smyth and
M. H. Little and
H. M. Byrne A spatially-averaged mathematical model
of kidney branching morphogenesis . . . 24--37
Hanifeh Khayyeri and
Sara Barreto and
Damien Lacroix Primary cilia mechanics affects cell
mechanosensation: a computational study 38--46
Duncan Dauvergne and
Leah Edelstein-Keshet Application of quasi-steady state
methods to molecular motor transport on
microtubules in fungal hyphae . . . . . 47--58
Jianghong Dai and
Hong Qu and
Zhisheng Yu and
Jiangke Yang and
Hongxun Zhang Computational analysis of AnmK-like
kinase: New insights into the cell wall
metabolism of fungi . . . . . . . . . . 59--65
Saeed Khalili and
Mohammad Reza Rahbar and
Mohammad Haj Dezfulian and
Abolfazl Jahangiri In silico analyses of Wilms' tumor
protein to designing a novel
multi-epitope DNA vaccine against cancer 66--78
Yutaka Kobayashi and
Joe Yuichiro Wakano and
Hisashi Ohtsuki A paradox of cumulative culture . . . . 79--88
Gustavo V. Barroso and
David R. Luz On the limits of complexity in living
forms . . . . . . . . . . . . . . . . . 89--90
John Hartung Cancer might be a failed response to
renegade mitochondria . . . . . . . . . 91--93
Michel Koenig Phosphoribosylphosphate and
phosphoribosylnicotinate pairing with
phosphoribosylamine at the origin of the
RNA world . . . . . . . . . . . . . . . 94--97
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
L. J. Liu and
M. Schlesinger Interstitial hydraulic conductivity and
interstitial fluid pressure for
avascular or poorly vascularized tumors 1--8
Anonymous Pages 1--590 (7 September 2015) . . . . 1--590
Bin Shao and
Jiayi Wu and
Binghui Tian and
Qi Ouyang Minimum network constraint on reverse
engineering to develop biological
regulatory networks . . . . . . . . . . 9--15
M. H. Fatemi and
E. Mousa Shahroudi and
Z. Amini Development of quantitative interspecies
toxicity relationship modeling of
chemicals to fish . . . . . . . . . . . 16--23
Yu Liu and
Xue Liang and
Rongcun Yang Identification of peculiar and common
effects of histone modifications on
transcription . . . . . . . . . . . . . 24--39
Wahbi K. El-Bouri and
Stephen J. Payne Multi-scale homogenization of blood flow
in $3$-dimensional human cerebral
microvascular networks . . . . . . . . . 40--47
S. Sumathy and
S. V. M. Satyanarayana Model for bidirectional movement of
cytoplasmic dynein . . . . . . . . . . . 48--52
Duo-Fang Li and
Tian-Guang Cao and
Jin-Peng Geng and
Jian-Zhong Gu and
Hai-Long An and
Yong Zhan Statistical properties and error
threshold of quasispecies on single-peak
Gaussian-distributed fitness landscapes 53--59
Jonggul Lee and
Eunok Jung A spatial-temporal transmission model
and early intervention policies of 2009
A/H1N1 influenza in South Korea . . . . 60--73
Ronny Straube Analysis of substrate competition in
regulatory network motifs:
Stimulus-response curves, thresholds and
ultrasensitivity . . . . . . . . . . . . 74--82
Thomas E. Woolley and
Eamonn A. Gaffney and
James M. Oliver and
Sarah L. Waters and
Ruth E. Baker and
Alain Goriely Global contraction or local growth, bleb
shape depends on more than just cell
structure . . . . . . . . . . . . . . . 83--97
Gili Greenbaum Revisiting the time until fixation of a
neutral mutant in a finite population
--- a coalescent theory approach . . . . 98--102
Xiaofeng Wang and
Xiaojie Chen and
Long Wang Evolutionary dynamics of fairness on
graphs with migration . . . . . . . . . 103--114
Agustín Mercado-Reyes and
Pablo Padilla-Longoria and
Alfonso Arroyo-Santos Objects and processes: Two notions for
understanding biological information . . 115--122
Jacob D. Cooper and
Claudia Neuhauser and
Antony M. Dean and
Benjamin Kerr Tipping the mutation-selection balance:
Limited migration increases the
frequency of deleterious mutants . . . . 123--133
Taro Takaguchi and
Renaud Lambiotte Sufficient conditions of endemic
threshold on metapopulation networks . . 134--143
Christian Schmeiser and
Christoph Winkler The flatness of \bionameLamellipodia
explained by the interaction between
actin dynamics and membrane deformation 144--155
Christian J. Michel The maximal $ C^3 $ self-complementary
trinucleotide circular code X in genes
of bacteria, eukaryotes, plasmids and
viruses . . . . . . . . . . . . . . . . 156--177
Mohadeseh Lotfi and
Fatemeh Zare-Mirakabad and
Soheila Montaseri RNA secondary structure prediction based
on SHAPE data in helix regions . . . . . 178--182
Tetsuya Akita and
Masashi Kamo Theoretical lessons for increasing algal
biofuel: Evolution of oil accumulation
to avert carbon starvation in microalgae 183--191
Mauricio Salgado The evolution of paternal care can lead
to population growth in artificial
societies . . . . . . . . . . . . . . . 192--202
Marte Ròrvik Hòyem and
Frode Målòy and
Per Jakobsen and
Bjòrn Olav Brandsdal Stem cell regulation: Implications when
differentiated cells regulate symmetric
stem cell division . . . . . . . . . . . 203--219
Takeshi Matsuoka and
Shigenori Tanaka and
Kuniyoshi Ebina Systems approach to excitation-energy
and electron transfer reaction networks
in photosystem II complex: model studies
for chlorophyll a fluorescence induction
kinetics . . . . . . . . . . . . . . . . 220--237
Giorgio Guzzetta and
Marco Ajelli and
Zhenhua Yang and
Leonard N. Mukasa and
Naveen Patil and
Joseph H. Bates and
Denise E. Kirschner and
Stefano Merler Effectiveness of contact investigations
for tuberculosis control in Arkansas . . 238--246
Efrat Seri and
Nadav Shnerb Spatial patterns in the tropical forest
reveal connections between negative
feedback, aggregation and abundance . . 247--255
Sunhwa Choi and
Eunok Jung and
Seok-Min Lee Optimal intervention strategy for
prevention tuberculosis using a
smoking-tuberculosis model . . . . . . . 256--270
Renhua Song and
Daniel R. Catchpoole and
Paul J. Kennedy and
Jinyan Li Identification of lung cancer
miRNA-miRNA co-regulation networks
through a progressive data refining
approach . . . . . . . . . . . . . . . . 271--279
Lai Zhang and
Ken H. Andersen and
Ulf Dieckmann and
Åke Brännström Four types of interference competition
and their impacts on the ecology and
evolution of size-structured populations
and communities . . . . . . . . . . . . 280--290
Harsh Saini and
Gaurav Raicar and
Alok Sharma and
Sunil Lal and
Abdollah Dehzangi and
James Lyons and
Kuldip K. Paliwal and
Seiya Imoto and
Satoru Miyano Probabilistic expression of spatially
varied amino acid dimers into general
form of Chou's pseudo amino acid
composition for protein fold recognition 291--298
Marc Sturrock and
Wenrui Hao and
Judith Schwartzbaum and
Grzegorz A. Rempala A mathematical model of pre-diagnostic
glioma growth . . . . . . . . . . . . . 299--308
Benjamin J. Binder and
Kerry A. Landman and
Donald F. Newgreen and
Joshua V. Ross Incomplete penetrance: The role of
stochasticity in developmental cell
colonization . . . . . . . . . . . . . . 309--314
M. Ghaemi Bafghi and
M. R. Bassami and
Gh. R. Hashemi Tabar and
M. R. Saberi and
A. R. Haghparast and
H. Dehghani A bioinformatic approach to check the
spatial epitope structure of an
immunogenic protein coded by DNA vaccine
plasmids . . . . . . . . . . . . . . . . 315--320
Sebastian Höhna The time-dependent reconstructed
evolutionary process with a key-role for
mass-extinction events . . . . . . . . . 321--331
Atanaska Dobreva and
Ralf Paus and
N. G. Cogan Mathematical model for \bionamealopecia
areata . . . . . . . . . . . . . . . . . 332--345
José Luis Rodríguez-Fernández and
Mario García de Lacoba Plasma membrane-associated
superstructure: Have we overlooked a new
type of organelle in eukaryotic cells? 346--358
Ping Xie A unified model of nucleic acid
unwinding by the ribosome and the
hexameric and monomeric DNA helicases 359--366
J. Pavlova and
A. Fasano and
J. Janela and
A. Sequeira Numerical validation of a synthetic
cell-based model of blood coagulation 367--379
Sumaiya Iqbal and
Avdesh Mishra and
Md Tamjidul Hoque Improved prediction of accessible
surface area results in efficient energy
function application . . . . . . . . . . 380--391
Gaoshan Kou and
Yonge Feng Identify five kinds of simple
super-secondary structures with
quadratic discriminant algorithm based
on the chemical shifts . . . . . . . . . 392--398
Zeina Shreif and
Deborah A. Striegel and
Vipul Periwal The jigsaw puzzle of sequence phenotype
inference: Piecing together Shannon
entropy, importance sampling, and
Empirical Bayes . . . . . . . . . . . . 399--413
Edward W. Tekwa and
Andrew Gonzalez and
Michel Loreau Local densities connect spatial ecology
to game, multilevel selection and
inclusive fitness theories of
cooperation . . . . . . . . . . . . . . 414--425
David W. Shanafelt and
Ulf Dieckmann and
Matthias Jonas and
Oskar Franklin and
Michel Loreau and
Charles Perrings Biodiversity, productivity, and the
spatial insurance hypothesis revisited 426--435
Kehinde O. Okonjo Bohr effect of hemoglobins: Accounting
for differences in magnitude . . . . . . 436--443
Dario Differt and
Ralf Möller Insect models of illumination-invariant
skyline extraction from UV and green
channels . . . . . . . . . . . . . . . . 444--462
Irina Kareva and
Faina Berezovskaya Cancer immunoediting: a process driven
by metabolic competition as a
predator--prey-shared resource type
model . . . . . . . . . . . . . . . . . 463--472
Haoyue Fu and
Lianping Yang and
Xiangde Zhang An RNA secondary structure prediction
method based on minimum and suboptimal
free energy structures . . . . . . . . . 473--479
Wataru Nakahashi and
Hisashi Ohtsuki When is emotional contagion adaptive? 480--488
Gustavo Guerberoff and
Fernando Alvarez-Valin A stochastic microscopic model for the
dynamics of antigenic variation . . . . 489--498
Akira Endo and
Hiroshi Nishiura Transmission dynamics of vivax malaria
in the Republic of Korea: Effectiveness
of anti-malarial mass chemoprophylaxis 499--505
Xiang-Yi Li and
Stefano Giaimo and
Annette Baudisch and
Arne Traulsen Modeling evolutionary games in
populations with demographic structure 506--515
Noga Neeman and
James R. Spotila and
Michael P. O'Connor A simple, physiologically-based model of
sea turtle remigration intervals and
nesting population dynamics: Effects of
temperature . . . . . . . . . . . . . . 516--523
Xiaowei Zhao and
Qiao Ning and
Haiting Chai and
Meiyue Ai and
Zhiqiang Ma PGlcS: Prediction of protein
O-GlcNAcylation sites with multiple
features and analysis . . . . . . . . . 524--529
Matthew H. Chan and
Richard Shine and
Gregory P. Brown and
Peter S. Kim Mathematical modelling of spatial
sorting and evolution in a host-parasite
system . . . . . . . . . . . . . . . . . 530--541
Andrew Whalen and
Kevin Laland Conformity biased transmission in social
networks . . . . . . . . . . . . . . . . 542--549
Gilbert Koch and
Johannes Schropp Distributed transit compartments for
arbitrary lifespan distributions in
aging populations . . . . . . . . . . . 550--558
Xinjun Gan and
David Waxman Hard harvesting of a stochastically
changing population . . . . . . . . . . 559--568
Mark Robertson-Tessi and
Ardith El-Kareh and
Alain Goriely A model for effects of adaptive immunity
on tumor response to chemotherapy and
chemoimmunotherapy . . . . . . . . . . . 569--584
Alfonso Jiménez-Sánchez Chromosome replication status and DNA
content at any cell age in a bacterial
cell cycle . . . . . . . . . . . . . . . 585--589
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Eörs Szathmáry Editorial . . . . . . . . . . . . . . . 1--1
Eörs Szathmáry Founder of systems chemistry and
foundational theoretical biologist:
Tibor Gánti (1933--2009) . . . . . . . . 2--5
Athel Cornish-Bowden Tibor Gánti and Robert Rosen: Contrasting
approaches to the same problem . . . . . 6--10
Andrés de la Escosura and
Carlos Briones and
Kepa Ruiz-Mirazo The systems perspective at the
crossroads between chemistry and biology 11--22
James Griesemer The enduring value of Gánti's chemoton
model and life criteria: Heuristic
pursuit of exact theoretical biology . . 23--28
Vera Vasas and
Chrisantha Fernando and
András Szilágyi and
István Zachár and
Mauro Santos and
Eörs Szathmáry Primordial evolvability: Impasses and
challenges . . . . . . . . . . . . . . . 29--38
Tamás Czárán and
Balázs Könny\Hu and
Eörs Szathmáry Metabolically Coupled Replicator
Systems: Overview of an RNA-world model
concept of prebiotic evolution on
mineral surfaces . . . . . . . . . . . . 39--54
Simona Ginsburg and
Eva Jablonka The teleological transitions in
evolution: a Gántian view . . . . . . . . 55--60
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Sungrim Seirin Lee and
Tatsuo Shibata Self-organization and advective
transport in the cell polarity formation
for asymmetric cell division . . . . . . 1--14
Anonymous Pages 1--404 (7 October 2015) . . . . . 1--404
Guoqing Liu and
Yongqiang Xing and
Lu Cai Using weighted features to predict
recombination hotspots in
\bionameSaccharomyces cerevisiae . . . . 15--22
Ashish Agrahari and
C. George Priya Doss Impact of I30T and I30M substitution in
MPZ gene associated with
Dejerine--Sottas syndrome type B (DSSB):
a molecular modeling and dynamics . . . 23--33
Kornelius Kupczik and
Heiko Stark and
Roger Mundry and
Fabian T. Neininger and
Thomas Heidlauf and
Oliver Röhrle Reconstruction of muscle fascicle
architecture from iodine-enhanced
microCT images: a combined texture
mapping and streamline approach . . . . 34--43
Alastair Jamieson-Lane and
Christoph Hauert Fixation probabilities on superstars,
revisited and revised . . . . . . . . . 44--56
Avleen Randhawa and
James M. Wakeling Multidimensional models for predicting
muscle structure and fascicle pennation 57--63
Jeffrey C. Schank and
Paul E. Smaldino and
Matt L. Miller Evolution of fairness in the dictator
game by multilevel selection . . . . . . 64--73
R. B. Campbell The effect of inbreeding constraints and
offspring distribution on time to the
most recent common ancestor . . . . . . 74--80
D. White and
G. de Vries and
J. Martin and
A. Dawes Microtubule patterning in the presence
of moving motor proteins . . . . . . . . 81--90
Svetlana V. Vinogradova and
Kirill V. Zhudenkov and
Neil Benson and
Piet H. Van Der Graaf and
Oleg V. Demin and
Tatiana A. Karelina Prediction of long-term treatment
outcome in HCV following 24 day PEG-IFN
alpha-2b therapy using population
pharmacokinetic--pharmacodynamic mixture
modeling and classification analysis . . 91--98
Changchuan Yin and
Stephen S.-T. Yau An improved model for whole genome
phylogenetic analysis by Fourier
transform . . . . . . . . . . . . . . . 99--110
Alireza Baninajjaryan and
Yaghoub Tadi Beni Theoretical study of the effect of shear
deformable shell model, elastic
foundation and size dependency on the
vibration of protein microtubule . . . . 111--121
Jorge Peña and
Georg Nöldeke and
Laurent Lehmann Evolutionary dynamics of collective
action in spatially structured
populations . . . . . . . . . . . . . . 122--136
Maciej J. Da\'nko and
Jan Kozlowski and
Ralf Schaible Unraveling the non-senescence phenomenon
in Hydra . . . . . . . . . . . . . . . . 137--149
Maryam Hamzeh-Mivehroud and
Hakimeh Moghaddas-Sani and
Mahdieh Rahbar-Shahrouziasl and
Siavoush Dastmalchi Identifying key interactions stabilizing
DOF zinc finger-DNA complexes using in
silico approaches . . . . . . . . . . . 150--159
Lorenzo Pellis and
Thomas House and
Matt J. Keeling Exact and approximate moment closures
for non-Markovian network epidemics . . 160--177
Marek Ingr and
Jirí Dostál and
Tatána Majerová Enzymological description of
multitemplate PCR-Shrinking
amplification bias by optimizing the
polymerase-template ratio . . . . . . . 178--186
Reinhard Blickhan and
Emanuel Andrada and
Roy Müller and
Christian Rode and
Naomichi Ogihara Positioning the hip with respect to the
COM: Consequences for leg operation . . 187--197
Katie Sharp and
Edmund Crampin and
James Sneyd A spatial model of fluid recycling in
the airways of the lung . . . . . . . . 198--215
Osman Canko and
Ferhat Taskin and
Kamil Argin Phylogenetic tree and community
structure from a Tangled Nature model 216--222
Shibiao Wan and
Man-Wai Mak and
Sun-Yuan Kung mLASSO-Hum: a LASSO-based interpretable
human-protein subcellular localization
predictor . . . . . . . . . . . . . . . 223--234
Vladislava A. Terentyeva and
Anastasia N. Sveshnikova and
Mikhail A. Panteleev Kinetics and mechanisms of
surface-dependent coagulation factor XII
activation . . . . . . . . . . . . . . . 235--243
Angelika Manhart and
Dietmar Oelz and
Christian Schmeiser and
Nikolaos Sfakianakis An extended Filament Based Lamellipodium
Model produces various moving cell
shapes in the presence of chemotactic
signals . . . . . . . . . . . . . . . . 244--258
Stephen M. Petrie and
Jeff Butler and
Ian G. Barr and
Jodie McVernon and
Aeron C. Hurt and
James M. McCaw Quantifying relative within-host
replication fitness in influenza virus
competition experiments . . . . . . . . 259--271
Nicolas Houy The probability of undetected wild
poliovirus circulation: Can we do
better? . . . . . . . . . . . . . . . . 272--278
R. A. Thuraisingham Dense neuron system interacting with the
gravitational potential . . . . . . . . 279--283
Hisako Takigawa-Imamura and
Ritsuko Morita and
Takafumi Iwaki and
Takashi Tsuji and
Kenichi Yoshikawa Tooth germ invagination from cell--cell
interaction: Working hypothesis on
mechanical instability . . . . . . . . . 284--291
Carl Peter J. Maury Origin of life. Primordial genetics:
Information transfer in a pre-RNA world
based on self-replicating beta-sheet
amyloid conformers . . . . . . . . . . . 292--297
Takuyo Aita and
Tetsuya Yomo Evolutionary dynamics of a polymorphic
self-replicator population with a finite
population size and hyper mutation rate 298--308
Wei Pan and
Gui-Quan Sun and
Zhen Jin How demography-driven evolving networks
impact epidemic transmission between
communities . . . . . . . . . . . . . . 309--319
F. Martins and
R. Gonçalves and
J. Oliveira and
M. Cruz-Monteagudo and
J. M. Nieto-Villar and
C. Paz-y-Miño and
I. Rebelo and
E. Tejera Unravelling the relationship between
protein sequence and low-complexity
regions entropies: Interactome
implications . . . . . . . . . . . . . . 320--327
M.-R. Leung and
M. Kot Models for the spread of white pine
blister rust . . . . . . . . . . . . . . 328--336
Takayuki Ohara and
Hirokazu Fukuda and
Isao T. Tokuda An extended mathematical model for
reproducing the phase response of
\bionameArabidopsis thaliana under
various light conditions . . . . . . . . 337--344
Emily E. Riley and
Eric Lauga Small-amplitude swimmers can self-propel
faster in viscoelastic fluids . . . . . 345--355
Richard A. Kohn and
Seon-Woo Kim Using the second law of thermodynamics
for enrichment and isolation of
microorganisms to produce fuel alcohols
or hydrocarbons . . . . . . . . . . . . 356--362
Kourosh Shoele and
Qiang Zhu Drafting mechanisms between a dolphin
mother and calf . . . . . . . . . . . . 363--377
Kishore K. Bokka and
Edwin C. Jesudason and
David Warburton and
Sharon R. Lubkin Morphogenetic implications of
peristaltic fluid-tissue dynamics in the
embryonic lung . . . . . . . . . . . . . 378--385
R. P. Morse and
D. Allingham and
N. G. Stocks A phenomenological model of myelinated
nerve with a dynamic threshold . . . . . 386--396
R. P. Morse and
D. Allingham and
N. G. Stocks Stimulus-dependent refractoriness in the
Frankenhaeuser--Huxley model . . . . . . 397--404
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Jitao T. Huang and
Titi Wang and
Shanran R. Huang and
Xin Li Prediction of protein folding rates from
simplified secondary structure alphabet 1--6
Anonymous Pages 1--156 (21 October 2015) . . . . . 1--156
Mokded Rabhi and
Abdallah Atia and
Chedly Abdelly and
Abderrazak Smaoui New parameters for a better evaluation
of vegetative bioremediation, leaching,
and phytodesalination . . . . . . . . . 7--11
Abdulaziz Yousef and
Nasrollah Moghadam Charkari SFM: a novel sequence-based fusion
method for disease genes identification
and prioritization . . . . . . . . . . . 12--19
Shiguo Deng and
Jingchao Qi and
Mutua Stephen and
Lu Qiu and
Huijie Yang Network-based identification of reliable
bio-markers for cancers . . . . . . . . 20--27
Tiago Paixão and
Golnaz Badkobeh and
Nick Barton and
Do\ugan Çörü\cs and
Duc-Cuong Dang and
Tobias Friedrich and
Per Kristian Lehre and
Dirk Sudholt and
Andrew M. Sutton and
Barbora Trubenová Toward a unifying framework for
evolutionary processes . . . . . . . . . 28--43
J. M. Wentz and
V. Vainstein and
D. Oldson and
Z. Gluzman-Poltorak and
L. A. Basile and
D. Stricklin Mathematical model of radiation effects
on thrombopoiesis in rhesus macaques and
humans . . . . . . . . . . . . . . . . . 44--60
Arianna Bianchi and
Kevin J. Painter and
Jonathan A. Sherratt A mathematical model for
lymphangiogenesis in normal and diabetic
wounds . . . . . . . . . . . . . . . . . 61--86
Nao Takashina and
Akihiko Mougi Maximum sustainable yields from a
spatially-explicit harvest model . . . . 87--92
Majid Jaberi-Douraki and
Massimo Pietropaolo and
Anmar Khadra Continuum model of T-cell avidity:
Understanding autoreactive and
regulatory T-cell responses in type 1
diabetes . . . . . . . . . . . . . . . . 93--105
Carlos Alberto Martínez and
Kshitij Khare and
Mauricio A. Elzo On the Bayesness, minimaxity and
admissibility of point estimators of
allelic frequencies . . . . . . . . . . 106--115
Kazuhiro Bessho and
Yoh Iwasa and
Troy Day The evolutionary advantage of haploid
versus diploid microbes in nutrient-poor
environments . . . . . . . . . . . . . . 116--129
Soheila Shokrollahzade and
Fatemeh Sharifi and
Akbar Vaseghi and
Maryam Faridounnia and
Samad Jahandideh Protein cold adaptation: Role of
physico-chemical parameters in
adaptation of proteins to low
temperatures . . . . . . . . . . . . . . 130--137
Elad Shtilerman and
David A. Kessler and
Nadav M. Shnerb Emergence of structured communities
through evolutionary dynamics . . . . . 138--144
Alfonso Caiazzo and
Ignacio Ramis-Conde Multiscale modelling of palisade
formation in gliobastoma multiforme . . 145--156
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Perla Carlos and
Virginie Roupie and
Sébastien Holbert and
Felipe Ascencio and
Kris Huygen and
Gracia Gomez-Anduro and
Maxime Branger and
Martha Reyes-Becerril and
Carlos Angulo In silico epitope analysis of unique and
membrane associated proteins from
Mycobacterium avium subsp.
paratuberculosis for immunogenicity and
vaccine evaluation . . . . . . . . . . . 1--9
Anonymous Pages 1--152 (7 November 2015) . . . . . 1--152
Abdallah Shokry and
Per Ståhle and
Ingrid Svensson Determination of spatially dependent
diffusion parameters in bovine bone
using Kalman filter . . . . . . . . . . 10--18
Amin Mehrabian and
Younane N. Abousleiman and
Timothy B. Mapstone and
Christian A. El-Amm Dual-porosity poroviscoelasticity and
quantitative hydromechanical
characterization of the brain tissue
with experimental hydrocephalus data . . 19--32
Cameron Browne and
Hayriye Gulbudak and
Glenn Webb Modeling contact tracing in outbreaks
with application to Ebola . . . . . . . 33--49
Carlos Fernandez-Lozano and
Rubén F. Cuiñas and
José A. Seoane and
Enrique Fernández-Blanco and
Julian Dorado and
Cristian R. Munteanu Classification of signaling proteins
based on molecular star graph
descriptors using Machine Learning
models . . . . . . . . . . . . . . . . . 50--58
Mazen Alamir On probabilistic certification of
combined cancer therapies using strongly
uncertain models . . . . . . . . . . . . 59--69
Hervé Seligmann Systematic exchanges between
nucleotides: Genomic swinger repeats and
swinger transcription in human
mitochondria . . . . . . . . . . . . . . 70--77
Farman Ali and
Maqsood Hayat Classification of membrane protein types
using Voting Feature Interval in
combination with Chou's Pseudo Amino
Acid Composition . . . . . . . . . . . . 78--83
J. Escribano and
M. T. Sánchez and
J. M. García-Aznar Modeling the formation of cell-matrix
adhesions on a single $3$D matrix fiber 84--94
Kenichi W. Okamoto The dynamics of strangling among forest
trees . . . . . . . . . . . . . . . . . 95--104
S. K. Jones and
R. Laurenza and
T. L. Hedrick and
B. E. Griffith and
L. A. Miller Lift vs. drag based mechanisms for
vertical force production in the
smallest flying insects . . . . . . . . 105--120
George P. Malanson Diversity differs among three variations
of the stress gradients hypothesis in
two representations of niche space . . . 121--130
Pranay Goel Insulin resistance or hypersecretion?
The $ \beta $IG picture revisited . . . 131--139
Alexander Filippov and
Alexander Kovalev and
Yoko Matsumura and
Stanislav N. Gorb Male penile propulsion into spiraled
spermathecal ducts of female chrysomelid
beetles: a numerical simulation approach 140--146
Yoshito Hirata and
Kazuyuki Aihara Ability of intermittent androgen
suppression to selectively create a
non-trivial periodic orbit for a type of
prostate cancer patients . . . . . . . . 147--152
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Fudong Xue and
Junjie Liu and
Longfang Guo and
Lirong Zhang and
Qianzhong Li Theoretical study on the bactericidal
nature of nanopatterned surfaces . . . . 1--7
Anonymous Pages 1--174 (21 November 2015) . . . . 1--174
Ming Chen and
Meng Fan and
Rui Liu and
Xiaoyu Wang and
Xing Yuan and
Huaiping Zhu The dynamics of temperature and light on
the growth of phytoplankton . . . . . . 8--19
Helena Skutkova and
Martin Vitek and
Karel Sedlar and
Ivo Provaznik Progressive alignment of genomic signals
by multiple dynamic time warping . . . . 20--30
Khac-Minh Thai and
Duy-Phong Le and
Nguyen-Viet-Khoa Tran and
Thi-Thu-Ha Nguyen and
Thanh-Dao Tran and
Minh-Tri Le Computational assay of Zanamivir binding
affinity with original and mutant
influenza neuraminidase 9 using
molecular docking . . . . . . . . . . . 31--39
Makoto Hara and
Joung-Hun Lee and
Yoh Iwasa Cultural evolution of hinoeuma
superstition controlling human mate
choice: The role of half-believer . . . 40--49
Zhe Ju and
Jun-Zhe Cao and
Hong Gu iLM-2L: a two-level predictor for
identifying protein lysine methylation
sites and their methylation degrees by
incorporating K-gap amino acid pairs
into Chou's general PseAAC . . . . . . . 50--57
Li Chen and
Dongyi Wang An improved acquaintance immunization
strategy for complex network . . . . . . 58--65
Stephen Wirkus and
Erika T. Camacho and
Pamela A. Marshall Mathematical modeling of fungal
infection in immune compromised
individuals: The effect of back mutation
on drug treatment . . . . . . . . . . . 66--76
Morgan Craig and
Antony R. Humphries and
Fahima Nekka and
Jacques Bélair and
Jun Li and
Michael C. Mackey Neutrophil dynamics during concurrent
chemotherapy and G-CSF administration:
Mathematical modelling guides dose
optimisation to minimise neutropenia . . 77--89
Brenda Chimal-Vega and
Norma Paniagua-Castro and
Jonathan Carrillo Vazquez and
Jorge L. Rosas-Trigueros and
Absalom Zamorano-Carrillo and
Claudia G. Ben\'ìtez-Cardoza Exploring the structure and
conformational landscape of human
leptin. A molecular dynamics approach 90--101
Jia Yuan and
Bin Xue Role of structural flexibility in the
evolution of emerin . . . . . . . . . . 102--111
V. L. de Rioja and
J. Fort and
N. Isern Front propagation speeds of T7 virus
mutants . . . . . . . . . . . . . . . . 112--118
Christina Hamlet and
Lisa J. Fauci and
Eric D. Tytell The effect of intrinsic muscular
nonlinearities on the energetics of
locomotion in a computational model of
an anguilliform swimmer . . . . . . . . 119--129
Kylie J. Foster and
Stanley J. Miklavcic Toward a biophysical understanding of
the salt stress response of individual
plant cells . . . . . . . . . . . . . . 130--142
Renato Vieira dos Santos and
Fabiano L. Ribeiro and
Alexandre Souto Martinez Models for Allee effect based on
physical principles . . . . . . . . . . 143--152
Bin Liu and
Longyun Fang and
Shanyi Wang and
Xiaolong Wang and
Hongtao Li and
Kuo-Chen Chou Identification of microRNA precursor
with the degenerate K-tuple or Kmer
strategy . . . . . . . . . . . . . . . . 153--159
Paulo Amorim Modeling ant foraging: a chemotaxis
approach with pheromones and trail
formation . . . . . . . . . . . . . . . 160--173
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Marco Lugli The tradeoff between signal detection
and recognition rules auditory
sensitivity under variable background
noise conditions . . . . . . . . . . . . 1--6
Anonymous Pages 1--190 (7 December 2015) . . . . . 1--190
Yuanling Niu and
Yue Wang and
Da Zhou The phenotypic equilibrium of cancer
cells: From average-level stability to
path-wise convergence . . . . . . . . . 7--17
Bhaskar Ganguly and
Kamal Tewari and
Rashmi Singh Homology modeling, functional annotation
and comparative genomics of outer
membrane protein H of
\bionamePasteurella multocida . . . . . 18--24
Harsh Saini and
Gaurav Raicar and
Abdollah Dehzangi and
Sunil Lal and
Alok Sharma Subcellular localization for Gram
positive and Gram negative bacterial
proteins using linear interpolation
smoothing model . . . . . . . . . . . . 25--33
Jakub Rydzewski and
Wieslaw Nowak and
Giuseppe Nicosia Inferring pathological states in
cortical neuron microcircuits . . . . . 34--43
Constance Vagne and
Jacques David and
Muriel Tavaud and
Bénédicte Fontez Reciprocal sign epistasis and truncation
selection: When is recombination
favorable in a pre-breeding program with
a selfing species? . . . . . . . . . . . 44--54
S. Sunada and
A. Ide and
Y. Hoshino and
M. Okamoto A study of autorotating plant seeds . . 55--61
Jieliang Zhao and
Jianing Wu and
Shaoze Yan Erection mechanism of glossal hairs
during honeybee feeding . . . . . . . . 62--68
Shiping Gao and
Te Wu and
Suli Nie and
Long Wang Promote or hinder? The role of
punishment in the emergence of
cooperation . . . . . . . . . . . . . . 69--77
Käthe M. Dahlström and
Tiina A. Salminen $3$D model for Cancerous Inhibitor of
Protein Phosphatase 2A armadillo domain
unveils highly conserved
protein--protein interaction
characteristics . . . . . . . . . . . . 78--88
Gajendra W. Suryawanshi and
Alexander Hoffmann A multi-scale mathematical modeling
framework to investigate anti-viral
therapeutic opportunities in targeting
HIV-1 accessory proteins . . . . . . . . 89--104
Nivedita Rangarajan and
Zach Fox and
Abhyudai Singh and
Prakash Kulkarni and
Govindan Rangarajan Disorder, oscillatory dynamics and state
switching: the role of c-Myc . . . . . . 105--114
Peifeng Liang and
Jian Zu and
Juan Yin and
Hao Li and
Longfei Gao and
Fuqiang Cui and
Fuzhen Wang and
Xiaofeng Liang and
Guihua Zhuang The independent impact of newborn
hepatitis B vaccination on reducing HBV
prevalence in China, 1992--2006: a
mathematical model analysis . . . . . . 115--121
Haley D. O'Brien and
Jason Bourke Physical and computational fluid
dynamics models for the hemodynamics of
the artiodactyl carotid rete . . . . . . 122--131
Dennis Reddyhoff and
John Ward and
Dominic Williams and
Sophie Regan and
Steven Webb Timescale analysis of a mathematical
model of acetaminophen metabolism and
toxicity . . . . . . . . . . . . . . . . 132--146
Tak Fung and
Laura Villain and
Ryan A. Chisholm Analytical formulae for computing
dominance from species-abundance
distributions . . . . . . . . . . . . . 147--158
Elena Fimmel and
Simone Giannerini and
Diego Luis Gonzalez and
Lutz Strüngmann Dinucleotide circular codes and
bijective transformations . . . . . . . 159--165
Tommaso Lorenzi and
Rebecca H. Chisholm and
Laurent Desvillettes and
Barry D. Hughes Dissecting the dynamics of epigenetic
changes in phenotype-structured
populations exposed to fluctuating
environments . . . . . . . . . . . . . . 166--176
Zhilan Feng and
Andrew N. Hill and
Philip J. Smith and
John W. Glasser An elaboration of theory about
preventing outbreaks in homogeneous
populations to include heterogeneity or
preferential mixing . . . . . . . . . . 177--187
Qi Zheng The Luria--Delbrück protocol is still the
most practical . . . . . . . . . . . . . 188--190
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Jian Zu and
Bo Yuan and
Jianqiang Du Top predators induce the evolutionary
diversification of intermediate predator
species . . . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--262 (21 December 2015) . . . . 1--262
Koudai Hirao and
Atsushi J. Nagano and
Akinori Awazu Noise-plasticity correlations of gene
expression in the multicellular organism
\bionameArabidopsis thaliana . . . . . . 13--22
Antoni Guillamon and
Ernest Fontich and
Josep Sardanyés Bifurcations analysis of oscillating
hypercycles . . . . . . . . . . . . . . 23--30
Melvin Cohn Two unresolved problems facing models of
the Self--Nonself discrimination . . . . 31--38
Emmanuel Paradis Random phylogenies and the distribution
of branching times . . . . . . . . . . . 39--45
Yuan Lin and
Nicole Abaid Modeling perspectives on echolocation
strategies inspired by bats flying in
groups . . . . . . . . . . . . . . . . . 46--53
Ryszard Rudnicki and
Andrzej Tomski On a stochastic gene expression with
pre-mRNA, mRNA and protein contribution 54--67
Mansoor H. Alshehri and
Barry J. Cox and
James M. Hill Energy behaviour for DNA translocation
through graphene nanopores . . . . . . . 68--75
Cody T. Ross and
Bruce Winterhalder Sit-and-wait versus active-search
hunting: a behavioral ecological model
of optimal search mode . . . . . . . . . 76--87
Ezzeddin Kamil Mohamed Hashim and
Rosni Abdullah Rare $k$-mer DNA: Identification of
sequence motifs and prediction of CpG
island and promoter . . . . . . . . . . 88--100
Angjelina Konini and
Seyed M. Moghadas Modelling the impact of vaccination on
curtailing Haemophilus influenzae
serotype `a' . . . . . . . . . . . . . . 101--110
Ram C. Neupane and
James A. Powell Invasion speeds with active dispersers
in highly variable landscapes: Multiple
scales, homogenization, and the
migration of trees . . . . . . . . . . . 111--119
Romain Watteaux and
Roman Stocker and
John R. Taylor Sensitivity of the rate of nutrient
uptake by chemotactic bacteria to
physical and biological parameters in a
turbulent environment . . . . . . . . . 120--135
Wei-long Ding and
Shui-sheng Wu and
Nelson Max and
Fu-li Wu and
Li-feng Xu A calculation method of plant similarity
giving consideration to different plant
features . . . . . . . . . . . . . . . . 136--143
Yuriy Pichugin and
Chaitanya S. Gokhale and
Julián Garcia and
Arne Traulsen and
Paul B. Rainey Modes of migration and multilevel
selection in evolutionary multiplayer
games . . . . . . . . . . . . . . . . . 144--153
Hervé Seligmann Codon expansion and systematic
transcriptional deletions produce
tetra-, pentacoded mitochondrial
peptides . . . . . . . . . . . . . . . . 154--165
Astrid S. T. Willener and
Yves Handrich and
Lewis G. Halsey and
Siobhán Strike Effect of walking speed on the gait of
king penguins: An accelerometric
approach . . . . . . . . . . . . . . . . 166--173
Scott Greenhalgh and
Alison P. Galvani and
Jan Medlock Disease elimination and re-emergence in
differential-equation models . . . . . . 174--180
F. H. S. Costa and
M. Campos and
M. A. A. da Silva The universal growth rate behavior and
regime transition in adherent cell
colonies . . . . . . . . . . . . . . . . 181--188
Aisling J. Daly and
Jan M. Baetens and
Bernard De Baets The impact of initial evenness on
biodiversity maintenance for a
four-species in silico bacterial
community . . . . . . . . . . . . . . . 189--205
Hafiz Ahmed and
Rosane Ushirobira and
Denis Efimov On robustness of phase resetting to cell
division under entrainment . . . . . . . 206--213
Xuesong Liu and
Qiuhui Pan and
Yibin Kang and
Mingfeng He Fixation times in evolutionary games
with the Moran and Fermi processes . . . 214--220
Simon Benhamou and
Julien Collet Ultimate failure of the Lévy Foraging
Hypothesis: Two-scale searching
strategies outperform scale-free ones
even when prey are scarce and cryptic 221--227
M. Nicolás and
E. Peña and
M. Malv\`e and
M. A. Martínez Mathematical modeling of the fibrosis
process in the implantation of inferior
\bionamevena cava filters . . . . . . . 228--240
Cortland K. Griswold Additive genetic variation and
evolvability of a multivariate trait can
be increased by epistatic gene action 241--257
Thijs Janzen and
Bart Haegeman and
Rampal S. Etienne A sampling formula for ecological
communities with multiple dispersal
syndromes . . . . . . . . . . . . . . . 258--261
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Changjing Zhuge and
Xiaojuan Sun and
Yingyu Chen and
Jinzhi Lei PDCD5 functions as a regulator of p53
dynamics in the DNA damage response . . 1--10
Anonymous Pages 1--130 (7 January 2016) . . . . . 1--130
A. Kotini and
P. Anninos Alpha, delta and theta rhythms in a
neural net model. Comparison with MEG
data . . . . . . . . . . . . . . . . . . 11--14
David J. Gerberry Practical aspects of backward
bifurcation in a mathematical model for
tuberculosis . . . . . . . . . . . . . . 15--36
M. A. Al-Mamun and
D. M. Farid and
L. Ravenhil and
M. A. Hossain and
C. Fall and
R. Bass An in silico model to demonstrate the
effects of Maspin on cancer cell
dynamics . . . . . . . . . . . . . . . . 37--49
Erida Gjini and
Carina Valente and
Raquel Sá-Leão and
M. Gabriela M. Gomes How direct competition shapes
coexistence and vaccine effects in
multi-strain pathogen systems . . . . . 50--60
William Lee and
Minus van Baalen and
Vincent A. A. Jansen Siderophore production and the evolution
of investment in a public good: An
adaptive dynamics approach to kin
selection . . . . . . . . . . . . . . . 61--71
Shagufta Shafique and
Nousheen Bibi and
Sajid Rashid In silico identification of putative
bifunctional Plk1 inhibitors by
integrative virtual screening and
structural dynamics approach . . . . . . 72--84
A. Grobler and
Z. Perez Sierra and
H. J. Viljoen Modeling nanoparticle delivery of TB
drugs to granulomas . . . . . . . . . . 85--95
Junko Kusumi and
Motoshi Ichinose and
Masasuke Takefu and
Robert Piskol and
Wolfgang Stephan and
Masaru Iizuka A model of compensatory molecular
evolution involving multiple sites in
RNA molecules . . . . . . . . . . . . . 96--107
Shiqi Sun and
Yan Huang and
Qining Wang Adding adaptable toe stiffness affects
energetic efficiency and dynamic
behaviors of bipedal walking . . . . . . 108--118
Michael A. L. Hayashi and
Marisa C. Eisenberg Effects of adaptive protective behavior
on the dynamics of sexually transmitted
infections . . . . . . . . . . . . . . . 119--130
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Chu-Chu Li and
Jia-Ning Wu and
Yun-Qiang Yang and
Ren-Gao Zhu and
Shao-Ze Yan Drag reduction effects facilitated by
microridges inside the mouthparts of
honeybee workers and drones . . . . . . 1--10
Anonymous Pages 1--310 (21 January 2016) . . . . . 1--310
Koji Noshita and
Keisuke Shimizu and
Takenori Sasaki Geometric analysis and estimation of the
growth rate gradient on gastropod shells 11--19
Nicolas Houy The case for periodic OPV routine
vaccination campaigns . . . . . . . . . 20--27
G. Neofytou and
Y. N. Kyrychko and
K. B. Blyuss Time-delayed model of immune response in
plants . . . . . . . . . . . . . . . . . 28--39
Christian J. Michel and
Marco Pellegrini and
Giuseppe Pirillo Maximal dinucleotide and trinucleotide
circular codes . . . . . . . . . . . . . 40--46
J-F. Arnoldi and
M. Loreau and
B. Haegeman Resilience, reactivity and variability:
a mathematical comparison of ecological
stability measures . . . . . . . . . . . 47--59
Md. Nasrul Islam and
Sumaiya Iqbal and
Ataur R. Katebi and
Md. Tamjidul Hoque A balanced secondary structure predictor 60--71
Jorge Peña and
Georg Nöldeke Variability in group size and the
evolution of collective action . . . . . 72--82
Mauro Bologna and
Kristopher J. Chandía and
J. C. Flores A non-linear mathematical model for a
three species ecosystem: Hippos in Lake
Edward . . . . . . . . . . . . . . . . . 83--87
Hans H. Diebner and
Jörg Kirberg and
Ingo Roeder An evolutionary stability perspective on
oncogenesis control in mature T-cell
populations . . . . . . . . . . . . . . 88--100
Antonio F. Miguel Toward an optimal design principle in
symmetric and asymmetric tree flow
networks . . . . . . . . . . . . . . . . 101--109
Rafal Wcislo and
S. Shea Miller and
Witold Dzwinel PAM: Particle automata model in
simulation of \bionameFusarium
graminearum pathogen expansion . . . . . 110--122
Yoshitaka Kimori and
Kazumi Hikino and
Mikio Nishimura and
Shoji Mano Quantifying morphological features of
actin cytoskeletal filaments in plant
cells based on mathematical morphology 123--131
Angelo Sassaroli and
Jana M. Kainerstorfer and
Sergio Fantini Nonlinear extension of a hemodynamic
linear model for coherent hemodynamics
spectroscopy . . . . . . . . . . . . . . 132--145
M. Tomezak and
C. Abbadie and
E. Lartigau and
F. Cleri A biophysical model of cell evolution
after cytotoxic treatments: Damage,
repair and cell response . . . . . . . . 146--158
Gabriele Pedruzzi and
Phonindra Nath Das and
Kanury VS. Rao and
Samrat Chatterjee Understanding PGE2, LXA4 and LTB4
balance during Mycobacterium
tuberculosis infection through
mathematical model . . . . . . . . . . . 159--170
M. J. Wade and
R. W. Pattinson and
N. G. Parker and
J. Dolfing Emergent behaviour in a
chlorophenol-mineralising three-tiered
microbial `food web' . . . . . . . . . . 171--186
Kenta Ishimoto and
Jacky Cosson and
Eamonn A. Gaffney A simulation study of sperm motility
hydrodynamics near fish eggs and spheres 187--197
Christoph K. Schmitt and
Christian Wildner and
Barbara Drossel Noisy predator--prey model explains
oscillation patterns in sockeye salmon
data . . . . . . . . . . . . . . . . . . 198--205
Elena Fimmel and
Lutz Strüngmann Maximal dinucleotide comma-free codes 206--213
Grant Lythe and
Robin E. Callard and
Rollo L. Hoare and
Carmen Molina-París How many TCR clonotypes does a body
maintain? . . . . . . . . . . . . . . . 214--224
Dawei Hong and
Shushuang Man and
Joseph V. Martin A stochastic mechanism for signal
propagation in the brain: Force of rapid
random fluctuations in membrane
potentials of individual neurons . . . . 225--236
Farah Ben-Naoum and
Christophe Godin Algorithmic height compression of
unordered trees . . . . . . . . . . . . 237--252
M. Ilamathi and
R. Hemanth and
S. Nishanth and
V. Sivaramakrishnan Identification of potential
transmembrane protease serine 4
inhibitors as anti-cancer agents by
integrated computational approach . . . 253--262
Sheema Sameen and
Roberto Barbuti and
Paolo Milazzo and
Antonio Cerone and
Marzia Del Re and
Romano Danesi Mathematical modeling of drug resistance
due to KRAS mutation in colorectal
cancer . . . . . . . . . . . . . . . . . 263--273
Thomas Schmickl and
Istvan Karsai How regulation based on a common stomach
leads to economic optimization of
honeybee foraging . . . . . . . . . . . 274--286
Daniela Bertacchi and
Fabio Zucca and
Roberto Ambrosini The timing of life history events in the
presence of soft disturbances . . . . . 287--303
Bart Spronck and
John Walmsley and
Georgina Palau-Caballero and
Koen D. Reesink and
Tammo Delhaas Can significance of aortic sinus
vortices be assessed using the
assumptions in the model of Aboelkassem
et al.? . . . . . . . . . . . . . . . . 304--305
Yasser Aboelkassem and
Dragana Savic and
Stuart G. Campbell Modeling predicts a connection between
sinus vortex effects and aortic
compliance . . . . . . . . . . . . . . . 306--309
Kourosh Shoele and
Qiang Zhu Addendum to: ``Drafting mechanisms
between a dolphin mother and calf'' [J.
Theor. Biol. \bf 382 (2015) 363--377] 310--310
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Qinling Yan and
Sanyi Tang and
Sandra Gabriele and
Jianhong Wu Media coverage and hospital
notifications: Correlation analysis and
optimal media impact duration to manage
a pandemic . . . . . . . . . . . . . . . 1--13
Anonymous Pages 1--164 (7 February 2016) . . . . . 1--164
Nao Takashina and
Marissa L. Baskett Exploring the effect of the spatial
scale of fishery management . . . . . . 14--22
Nicoline Y. den Breems and
Raluca Eftimie The re-polarisation of M2 and M1
macrophages and its role on cancer
outcomes . . . . . . . . . . . . . . . . 23--39
Xiufang Chen and
Yue Wang and
Tianquan Feng and
Ming Yi and
Xingan Zhang and
Da Zhou The overshoot and phenotypic equilibrium
in characterizing cancer dynamics of
reversible phenotypic plasticity . . . . 40--49
Madhur Mangalam and
Nisarg Desai and
Mewa Singh Self-organization of laterally
asymmetrical movements as a consequence
of space-time optimization . . . . . . . 50--60
Andreas Nikolaou and
Philipp Hartmann and
Antoine Sciandra and
Beno\^\it Chachuat and
Olivier Bernard Dynamic coupling of photoacclimation and
photoinhibition in a model of microalgae
growth . . . . . . . . . . . . . . . . . 61--72
M. A. Koenders and
R. Saso A mathematical model of cell equilibrium
and joint cell formation in multiple
myeloma . . . . . . . . . . . . . . . . 73--79
Katarina Rajkovi\'c and
Du\vsica L. Mari\'c and
Neboj\vsa T. Milo\vsevi\'c and
Sanja Jeremic and
Valentina Arsi\'c Arsenijevi\'c and
Nemanja Rajkovi\'c Mathematical modeling of the neuron
morphology using two dimensional images 80--85
G. Beauchamp and
G. D. Ruxton Modeling scan and interscan durations in
antipredator vigilance . . . . . . . . . 86--96
Iaroslav Ispolatov and
Vaibhav Madhok and
Michael Doebeli Individual-based models for adaptive
diversification in high-dimensional
phenotype spaces . . . . . . . . . . . . 97--105
Maria Chaley and
Vladimir Kutyrkin Stochastic model of homogeneous coding
and latent periodicity in DNA sequences 106--116
Abhigyan Nath and
Karthikeyan Subbiah Insights into the molecular basis of
piezophilic adaptation: Extraction of
piezophilic signatures . . . . . . . . . 117--126
Mauricio A. Fuentes Theoretical considerations on maximum
running speeds for large and small
animals . . . . . . . . . . . . . . . . 127--135
Wang Jin and
Esha T. Shah and
Catherine J. Penington and
Scott W. McCue and
Lisa K. Chopin and
Matthew J. Simpson Reproducibility of scratch assays is
affected by the initial degree of
confluence: Experiments, modelling and
model selection . . . . . . . . . . . . 136--145
Aurelio A. de los Reyes V. and
Doris H. Fuertinger and
Franz Kappel and
Anna Meyring-Wösten and
Stephan Thijssen and
Peter Kotanko A physiologically based model of
vascular refilling during
ultrafiltration in hemodialysis . . . . 146--155
Áki J. Láruson and
Floyd A. Reed Stability of underdominant genetic
polymorphisms in population networks . . 156--163
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Rui Moura Coelho and
João Miranda Lemos and
Irina Alho and
Duarte Valério and
Arlindo R. Ferreira and
Lu\'ìs Costa and
Susana Vinga Dynamic modeling of bone metastasis,
microenvironment and therapy:
Integrating parathyroid hormone (PTH)
effect, anti-resorptive and anti-cancer
therapy . . . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--112 (21 February 2016) . . . . 1--112
Daniele Santoni and
Giovanni Felici and
Davide Vergni Natural vs. random protein sequences:
Discovering combinatorics properties on
amino acid words . . . . . . . . . . . . 13--20
Sanzo Miyazawa Selection maintaining protein stability
at equilibrium . . . . . . . . . . . . . 21--34
Ya-Sen Jiao and
Pu-Feng Du Predicting Golgi-resident protein types
using pseudo amino acid compositions:
Approaches with positional specific
physicochemical properties . . . . . . . 35--42
Weifeng Jin and
Fangyue Chen Topological chaos of the spatial
prisoner's dilemma game on regular
networks . . . . . . . . . . . . . . . . 43--50
Lei Zhao and
David Waxman The influence of genetic drift on the
formation and stability of polymorphisms
arising from negative
frequency-dependent selection . . . . . 51--64
Sabin Lessard and
Cintia Soares Definitions of fitness in age-structured
populations: Comparison in the haploid
case . . . . . . . . . . . . . . . . . . 65--73
John M. Murray and
Ognjen Stancevic and
Marc Lütgehetmann and
Karsten Wursthorn and
Joerg Petersen and
Maura Dandri Variability in long-term hepatitis B
virus dynamics under antiviral therapy 74--80
Erfan Khaji and
Masoumeh Karami and
Zahra Garkani-Nejad $3$D protein structure prediction using
Imperialist Competitive algorithm and
half sphere exposure prediction . . . . 81--87
Nao Takashina Simple rules for establishment of
effective marine protected areas in an
age-structured metapopulation . . . . . 88--94
Poonam K. Rathore and
V. Arathy and
Vijaylaxmi S. Attimarad and
Pramod Kumar and
Subarna Roy In-silico analysis of gymnemagenin from
\bionameGymnema sylvestre (Retz.) R.Br.
with targets related to diabetes . . . . 95--101
P. Kurian and
G. Dunston and
J. Lindesay How quantum entanglement in DNA
synchronizes double-strand breakage by
type II restriction endonucleases . . . 102--112
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Eric Tromeur and
Lars Rudolf and
Thilo Gross Impact of dispersal on the stability of
metapopulations . . . . . . . . . . . . 1--11
Anonymous Pages 1--126 (7 March 2016) . . . . . . 1--126
Wataru Nakahashi Coevolution of female ovulatory signals
and male-male competition in primates 12--22
Carmen H. S. Chan and
Lloyd P. Sanders and
Mark M. Tanaka Modelling the role of immunity in
reversion of viral antigenic sites . . . 23--34
Mostafa Bachar and
Jochen G. Raimann and
Peter Kotanko Impulsive mathematical modeling of
ascorbic acid metabolism in healthy
subjects . . . . . . . . . . . . . . . . 35--47
Philip J. G. M. Voets and
Roderick P. P. W. M. Maas Serum cardiac troponin I analysis to
determine the excessiveness of exercise
intensity: a novel equation . . . . . . 48--52
Xi Huo and
Xiaodan Sun and
Kunquan Lan and
Jianhong Wu Treatment-donation-stockpile dynamics in
Ebola convalescent blood transfusion
therapy . . . . . . . . . . . . . . . . 53--61
T. D. Frank Front waves in the early RNA world: The
Schlögl model and the logistic growth
model . . . . . . . . . . . . . . . . . 62--68
Eva Kisdi Dispersal polymorphism in stable
habitats . . . . . . . . . . . . . . . . 69--82
Jia Zhao and
Ya Shen and
Markus Haapasalo and
Zhejun Wang and
Qi Wang A $3$D numerical study of antimicrobial
persistence in heterogeneous
multi-species biofilms . . . . . . . . . 83--98
Ben Adams Household demographic determinants of
Ebola epidemic risk . . . . . . . . . . 99--106
Qiang Su Analyzing fractal property of species
abundance distribution and diversity
indexes . . . . . . . . . . . . . . . . 107--112
Qiang Zhang and
Hong Li and
Xiaoqing Zhao and
Yan Zheng and
Hu Meng and
Yun Jia and
Hui Xue and
Sulin Bo Analysis on the preference for sequence
matching between mRNA sequences and the
corresponding introns in ribosomal
protein genes . . . . . . . . . . . . . 113--121
Wim Hordijk and
Mike Steel Comment on ``Tibor Gánti and Robert
Rosen'' by Athel Cornish-Bowden . . . . 122--123
Hans Van Oosterwyck Corrigendum to: ``Oxygen as a critical
determinant of bone fracture healing ---
a multiscale model'' [J. Theor. Biol.
\bf 365 (2015) 247--264] . . . . . . . . 124--124
Felix P. Filatov and
Alexander Shargunov Corrigendum to ``Short nucleotide
sequences in herpesviral genomes
identical to the human DNA'' [J. Theor.
Biol. \bf 372 (2015) 12--21] . . . . . . 125--125
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Younes Aftabi and
Abasalt Hosseinzadeh Colagar and
Faramarz Mehrnejad An in silico approach to investigate the
source of the controversial
interpretations about the phenotypic
results of the human AhR-gene G1661A
polymorphism . . . . . . . . . . . . . . 1--15
Anonymous Pages 1--228 (21 March 2016) . . . . . . 1--228
Sebastian Boie and
Vivien Kirk and
James Sneyd and
Martin Wechselberger Effects of quasi-steady-state reduction
on biophysical models with oscillations 16--31
Andjelka Hedrih and
Milan Bani\'c The effect of friction and impact angle
on the spermatozoa-oocyte local contact
dynamics . . . . . . . . . . . . . . . . 32--42
Yunxin Huang and
Nianwan Yang and
Yun Qin and
Feng An and
Zhaohua Li and
Fanghao Wan Enhanced stability in host-parasitoid
interactions with autoparasitism and
parasitoid migration . . . . . . . . . . 43--50
Armando Aranda-Anzaldo The interphase mammalian chromosome as a
structural system based on tensegrity 51--59
R. McVinish and
P. K. Pollett and
A. Shausan Limiting the spread of disease through
altered migration patterns . . . . . . . 60--66
James Lyons and
Kuldip K. Paliwal and
Abdollah Dehzangi and
Rhys Heffernan and
Tatsuhiko Tsunoda and
Alok Sharma Protein fold recognition using HMM-HMM
alignment and dynamic programming . . . 67--74
Yuancheng Wang and
Peter H. Janssen and
Tammy A. Lynch and
Bruce van Brunt and
David Pacheco A mechanistic model of
hydrogen-methanogen dynamics in the
rumen . . . . . . . . . . . . . . . . . 75--81
Kris De Jaegher and
Britta Hoyer By-product mutualism and the ambiguous
effects of harsher environments --- a
game-theoretic model . . . . . . . . . . 82--97
Hemn Mohammadpour and
Ali Akbar Pourfathollah and
Mahin Nikougoftar Zarif and
Saeed Khalili Key role of Dkk3 protein in inhibition
of cancer cell proliferation: An in
silico identification . . . . . . . . . 98--104
Mao-Xiang Wang and
Yu-Qiang Ma and
Pik-Yin Lai Regulatory effects on the population
dynamics and wave propagation in a cell
lineage model . . . . . . . . . . . . . 105--117
Xianbing Zheng and
Jiusheng Ren Effects of the three-dimensional
residual stresses on the mechanical
properties of arterial walls . . . . . . 118--126
F. J. Burgos-Flórez and
M. E. Gavilán-Alfonso and
D. A. Garzón-Alvarado Flat bones and sutures formation in the
human cranial vault during prenatal
development and infancy: a computational
model . . . . . . . . . . . . . . . . . 127--144
Matthew H. Chan and
Kristen Hawkes and
Peter S. Kim Evolution of longevity, age at last
birth and sexual conflict with
grandmothering . . . . . . . . . . . . . 145--157
F. J. Vermolen and
E. C. M. M. Arkesteijn and
A. Gefen Modelling the immune system response to
epithelial wound infections . . . . . . 158--169
P. G. Ballard and
N. G. Bean and
J. V. Ross The probability of epidemic fade-out is
non-monotonic in transmission rate for
the Markovian SIR model with demography 170--178
Tufail Malik and
Mudassar Imran and
Raja Jayaraman Optimal control with multiple human
papillomavirus vaccines . . . . . . . . 179--193
Ekaterina S. Chernyshova and
Yulia S. Zaikina and
Galina A. Tsvetovskaya and
Dmitry I. Strokotov and
Maxim A. Yurkin and
Elena S. Serebrennikova and
Leonid Volkov and
Valeri P. Maltsev and
Andrei V. Chernyshev Influence of magnesium sulfate on
HCO$_3$ /Cl transmembrane exchange rate
in human erythrocytes . . . . . . . . . 194--202
A. Golubev Applications and implications of the
exponentially modified gamma
distribution as a model for time
variabilities related to cell
proliferation and gene expression . . . 203--217
Lei Zhao and
Toni I. Gossmann and
David Waxman A modified Wright--Fisher model that
incorporates $ N_e $: a variant of the
standard model with increased biological
realism and reduced computational
complexity . . . . . . . . . . . . . . . 218--228
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
K. Dormanns and
R. G. Brown and
T. David The role of nitric oxide in
neurovascular coupling . . . . . . . . . 1--17
Anonymous Pages 1--254 (7 April 2016) . . . . . . 1--254
Esther Ibáñez-Marcelo and
Tomás Alarcón Evolutionary escape on complex
genotype-phenotype networks . . . . . . 18--31
Edward A. Codling and
Nikolai W. F. Bode Balancing direct and indirect sources of
navigational information in a leaderless
model of collective animal movement . . 32--42
Brodie A. J. Lawson and
Mark B. Flegg A mathematical model for the induction
of the mammalian ureteric bud . . . . . 43--56
Hideo Ema and
Kouki Uchinomiya and
Yohei Morita and
Toshio Suda and
Yoh Iwasa Repopulation dynamics of single
haematopoietic stem cells in mouse
transplantation experiments: Importance
of stem cell composition in competitor
cells . . . . . . . . . . . . . . . . . 57--67
O. Malaspinas and
A. Turjman and
D. Ribeiro de Sousa and
G. Garcia-Cardena and
M. Raes and
P.-T. T. Nguyen and
Y. Zhang and
G. Courbebaisse and
C. Lelubre and
K. Zouaoui Boudjeltia and
B. Chopard A spatio-temporal model for spontaneous
thrombus formation in cerebral aneurysms 68--76
Lotte Sewalt and
Kristen Harley and
Peter van Heijster and
Sanjeeva Balasuriya Influences of Allee effects in the
spreading of malignant tumours . . . . . 77--92
Larry Bodgi and
Aurélien Canet and
Laurent Pujo-Menjouet and
Annick Lesne and
Jean-Marc Victor and
Nicolas Foray Mathematical models of radiation action
on living cells: From the target theory
to the modern approaches. A historical
and critical review . . . . . . . . . . 93--101
Pingping Sun and
Jialiang Qi and
Yizhu Zhao and
Yanxin Huang and
Guifu Yang and
Zhiqiang Ma and
Yuxin Li A novel conformational B-cell epitope
prediction method based on mimotope and
patch analysis . . . . . . . . . . . . . 102--108
Samir M. Abdel-Mageed and
Ehab I. Mohamed Comparative modeling of combined
transport of water and graded-size
molecules across the glomerular
capillary wall . . . . . . . . . . . . . 109--116
Naga Srinivas Tripuraneni and
Mohammed Afzal Azam Pharmacophore modeling, $3$D-QSAR and
docking study of $2$-phenylpyrimidine
analogues as selective PDE4B inhibitors 117--126
Mainak Patel A Simplified model of mutually
inhibitory sleep-active and wake-active
neuronal populations employing a
noise-based switching mechanism . . . . 127--136
Mike Mesterton-Gibbons and
Tom N. Sherratt How residency duration affects the
outcome of a territorial contest:
Complementary game-theoretic models . . 137--148
K. H. L. Neßler and
J. R. Henstock and
A. J. El Haj and
S. L. Waters and
J. P. Whiteley and
J. M. Osborne The influence of hydrostatic pressure on
tissue engineered bone development . . . 149--159
Yaojie Lu and
Remko A. Duursma and
Belinda E. Medlyn Optimal stomatal behaviour under
stochastic rainfall . . . . . . . . . . 160--171
Leonid Hanin and
Lyudmila Pavlova A quantitative insight into metastatic
relapse of breast cancer . . . . . . . . 172--181
Ola Hössjer and
Peder A. Tyvand A monoecious and diploid Moran model of
random mating . . . . . . . . . . . . . 182--196
Luis Soto-Ortiz and
Stacey D. Finley A cancer treatment based on synergy
between anti-angiogenic and immune cell
therapies . . . . . . . . . . . . . . . 197--211
Alessandro Rizzo and
Biagio Pedalino and
Maurizio Porfiri A network model for Ebola spreading . . 212--222
Jianhua Jia and
Zi Liu and
Xuan Xiao and
Bingxiang Liu and
Kuo-Chen Chou pSuc-Lys: Predict lysine succinylation
sites in proteins with PseAAC and
ensemble random forest approach . . . . 223--230
Fabio Dercole and
Stefan A. H. Geritz Unfolding the resident-invader dynamics
of similar strategies . . . . . . . . . 231--254
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Michael A. Andrews and
Chris T. Bauch The impacts of simultaneous disease
intervention decisions on epidemic
outcomes . . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--246 (21 April 2016) . . . . . . 1--246
Irina Kareva Escape from tumor dormancy and time to
angiogenic switch as mitigated by
tumor-induced stimulation of stroma . . 11--22
Lianping Yang and
Xiangde Zhang and
Haoyue Fu and
Chenhui Yang An estimator for local analysis of
genome based on the minimal absent word 23--30
Ignacio Rozada and
Daniel Coombs and
Viviane D. Lima Conditions for eradicating hepatitis C
in people who inject drugs: a fibrosis
aware model of hepatitis C virus
transmission . . . . . . . . . . . . . . 31--39
Howard Ramirez-Malule and
Albeiro Restrepo and
Wilson Cardona and
Stefan Junne and
Peter Neubauer and
Rigoberto Rios-Estepa Inversion of the stereochemical
configuration (3S, 5S)-clavaminic acid
into (3R, 5R)-clavulanic acid: a
computationally-assisted approach based
on experimental evidence . . . . . . . . 40--50
B. Fallqvist and
M. Kroon Constitutive modelling of composite
biopolymer networks . . . . . . . . . . 51--61
Bibaswan Dey and
G. P. Raja Sekhar Hydrodynamics and convection enhanced
macromolecular fluid transport in soft
biological tissues: Application to solid
tumor . . . . . . . . . . . . . . . . . 62--86
Zhang Cheng and
Alexander Hoffmann A stochastic spatio-temporal (SST) model
to study cell-to-cell variability in
HIV-1 infection . . . . . . . . . . . . 87--96
M. Gabriela M. Gomes and
Erida Gjini and
Joao S. Lopes and
Caetano Souto-Maior and
Carlota Rebelo A theoretical framework to identify
invariant thresholds in infectious
disease epidemiology . . . . . . . . . . 97--102
Juan Segura and
Frank M. Hilker and
Daniel Franco Adaptive threshold harvesting and the
suppression of transients . . . . . . . 103--114
Mats Gyllenberg and
Éva Kisdi and
Helene C. Weigang On the evolution of patch-type dependent
immigration . . . . . . . . . . . . . . 115--125
Mohammed Mesk and
Tewfik Mahdjoub and
Sébastien Gourbi\`ere and
Jorge E. Rabinovich and
Frédéric Menu Invasion speeds of \bionameTriatoma
dimidiata, vector of Chagas disease: An
application of orthogonal polynomials
method . . . . . . . . . . . . . . . . . 126--143
Lester Ingber Statistical mechanics of neocortical
interactions: Large-scale EEG influences
on molecular processes . . . . . . . . . 144--152
Lucia Bandiera and
Alice Pasini and
Lorenzo Pasotti and
Susanna Zucca and
Giuliano Mazzini and
Paolo Magni and
Emanuele Giordano and
Simone Furini Experimental measurements and
mathematical modeling of biological
noise arising from transcriptional and
translational regulation of basic
synthetic gene circuits . . . . . . . . 153--160
S. J. Tudge and
R. A. Watson and
M. Brede Game theoretic treatments for the
differentiation of functional roles in
the transition to multicellularity . . . 161--173
Vladislav Victorovich Khrustalev and
Eugene Victorovich Barkovsky and
Tatyana Aleksandrovna Khrustaleva Magnesium and manganese binding sites on
proteins have the same predominant motif
of secondary structure . . . . . . . . . 174--185
Xiaoqing Peng and
Jianxin Wang and
Jun Huan and
Fang-Xiang Wu Double-layer clustering method to
predict protein complexes based on
power-law distribution and protein
sublocalization . . . . . . . . . . . . 186--193
Heinrich H. Nax and
Alexandros Rigos Assortativity evolving from social
dilemmas . . . . . . . . . . . . . . . . 194--203
Simone Pigolotti and
Roberto Benzi Competition between fast- and
slow-diffusing species in
non-homogeneous environments . . . . . . 204--210
Graham M. Donovan and
Grant Lythe T cell and reticular network
co-dependence in HIV infection . . . . . 211--220
Nissim Silanikove Transcellular route as the most probable
explanation for the presence of
plasminogen in mammal's milk . . . . . . 221--226
Akiko Satake and
Motohide Seki and
Makoto Iima and
Takashi Teramoto and
Yasumasa Nishiura Florigen distribution determined by a
source--sink balance explains the
diversity of inflorescence structures in
\bionameArabidopsis . . . . . . . . . . 227--237
Patricia Rich and
Kevin J. S. Zollman Honesty through repeated interactions 238--244
Anna Fedor and
Péter Ittzés and
Eörs Szathmáry Corrigendum to: ``Parsing recursive
sentences with a connectionist model
including a neural stack and synaptic
gating'' [J. Theor. Biol. \bf 271 (2011)
100--105] . . . . . . . . . . . . . . . 245--245
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Ani D. Asatryan and
Natalia L. Komarova Evolution of genetic instability in
heterogeneous tumors . . . . . . . . . . 1--12
Anonymous Pages 1--210 (7 May 2016) . . . . . . . 1--210
Jeremy Van Cleve Cooperation, conformity, and the
coevolutionary problem of trait
associations . . . . . . . . . . . . . . 13--24
Swami Iyer and
Timothy Killingback Evolutionary dynamics of a smoothed war
of attrition game . . . . . . . . . . . 25--41
M. Trassinelli Energy cost and optimisation in
breath-hold diving . . . . . . . . . . . 42--52
Elina Numminen and
Michael Gutmann and
Mikhail Shubin and
Pekka Marttinen and
Guillaume Méric and
Willem van Schaik and
Teresa M. Coque and
Fernando Baquero and
Rob J. L. Willems and
Samuel K. Sheppard and
Edward J. Feil and
William P. Hanage and
Jukka Corander The impact of host metapopulation
structure on the population genetics of
colonizing bacteria . . . . . . . . . . 53--62
Kang Ping Chen Hydraulic resistance of a plant root to
water-uptake: a slender-body theory . . 63--74
Frédéric M. Hamelin and
Linda J. S. Allen and
Holly R. Prendeville and
M. Reza Hajimorad and
Michael J. Jeger The evolution of plant virus
transmission pathways . . . . . . . . . 75--89
Yuanling Niu and
Kevin Burrage and
Luonan Chen Modelling biochemical reaction systems
by stochastic differential equations
with reflection . . . . . . . . . . . . 90--104
James T. Murphy and
Mark P. Johnson and
Frédérique Viard A modelling approach to explore the
critical environmental parameters
influencing the growth and establishment
of the invasive seaweed \bionameUndaria
pinnatifida in Europe . . . . . . . . . 105--115
A. Yu. Morozov and
M. Banerjee and
S. V. Petrovskii Long-term transients and complex
dynamics of a stage-structured
population with time delay and the Allee
effect . . . . . . . . . . . . . . . . . 116--124
Lo\"\ic Tadrist and
Baptiste Darbois-Texier Are leaves optimally designed for
self-support? An investigation on giant
monocots . . . . . . . . . . . . . . . . 125--131
Luca Ferretti and
Benjamin Schmiegelt and
Daniel Weinreich and
Atsushi Yamauchi and
Yutaka Kobayashi and
Fumio Tajima and
Guillaume Achaz Measuring epistasis in fitness
landscapes: The correlation of fitness
effects of mutations . . . . . . . . . . 132--143
Xiaopan Zhang and
Xiong Jiao and
Jie Song and
Shan Chang Prediction of human protein--protein
interaction by a domain-based approach 144--153
Jun Nakabayashi The intracellular dynamics of hepatitis
B virus (HBV) replication with
reproduced virion ``re-cycling'' . . . . 154--162
Dorian Levy and
Heather A. Harrington and
Robert A. Van Gorder Role of seasonality on
predator--prey-subsidy population
dynamics . . . . . . . . . . . . . . . . 163--181
Montasser Ghachem The institution as a blunt instrument:
Cooperation through imperfect
observability . . . . . . . . . . . . . 182--190
Marco Archetti Cooperation among cancer cells as public
goods games on Voronoi networks . . . . 191--203
Momoko Hayamizu On the existence of infinitely many
universal tree-based networks . . . . . 204--206
Yuanling Niu and
Kevin Burrage and
Luonan Chen Corrigendum for ``Modelling biochemical
reaction systems by stochastic
differential equations with reflection'' 207--209
Changjing Zhuge and
Xiaojuan Sun and
Yingyu Chen and
Jinzhi Lei Corrigendum to ``PDCD5 interacts with
p53 and functions as a regulator of p53
dynamics in the DNA damage response''
[J. Theor. Biol., \bf 388 (2016) 1--10] 210--210
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Lindsay T. Keegan and
Jonathan Dushoff Estimating finite-population
reproductive numbers in heterogeneous
populations . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--206 (21 May 2016) . . . . . . . 1--206
Jonas Stålhand and
Gerhard A. Holzapfel Length adaptation of smooth muscle
contractile filaments in response to
sustained activation . . . . . . . . . . 13--21
N. Ali and
Z. Asghar and
O. Anwar Bég and
M. Sajid Bacterial gliding fluid dynamics on a
layer of non-Newtonian slime:
Perturbation and numerical study . . . . 22--32
Thomas Caraco and
Carrie A. Cizauskas and
Ing-Nang Wang Environmentally transmitted parasites:
Host-jumping in a heterogeneous
environment . . . . . . . . . . . . . . 33--42
Fateme Sefid and
Iraj Rasooli and
Zahra Payandeh Homology modeling of a Camelid antibody
fragment against a conserved region of
\bionameAcinetobacter baumannii biofilm
associated protein (Bap) . . . . . . . . 43--51
Yasuaki Kobayashi and
Yusuke Sawabu and
Hiroyuki Kitahata and
Mitsuhiro Denda and
Masaharu Nagayama Mathematical model for calcium-assisted
epidermal homeostasis . . . . . . . . . 52--60
Igor Pantic and
Zorica Nesic and
Jovana Paunovic Pantic and
Sanja Radojevi\'c-\vSkodri\'c and
Mila Cetkovic and
Gordana Basta Jovanovic Fractal analysis and Gray level
co-occurrence matrix method for
evaluation of reperfusion injury in
kidney medulla . . . . . . . . . . . . . 61--67
Aurora Armiento and
Marie Doumic and
Philippe Moireau and
H. Rezaei Estimation from moments measurements for
amyloid depolymerisation . . . . . . . . 68--88
Su-Chan Park and
Johannes Neidhart and
Joachim Krug Greedy adaptive walks on a correlated
fitness landscape . . . . . . . . . . . 89--102
Ning Wei and
Yoichiro Mori and
Elena G. Tolkacheva The dual effect of ephaptic coupling on
cardiac conduction with heterogeneous
expression of connexin 43 . . . . . . . 103--114
Robert Root-Bernstein and
Meredith Root-Bernstein The ribosome as a missing link in
prebiotic evolution II: Ribosomes encode
ribosomal proteins that bind to common
regions of their own mRNAs and rRNAs . . 115--127
Haim Weissmann and
Nadav M. Shnerb Predicting catastrophic shifts . . . . . 128--134
Nathaniel J. Kingsbury and
Stephanie R. Taylor and
Michael A. Henson Inhibitory and excitatory networks
balance cell coupling in the
suprachiasmatic nucleus: a modeling
approach . . . . . . . . . . . . . . . . 135--144
Zhe Ju and
Jun-Zhe Cao and
Hong Gu Predicting lysine phosphoglycerylation
with fuzzy SVM by incorporating k-spaced
amino acid pairs into Chou's general
PseAAC . . . . . . . . . . . . . . . . . 145--150
Peter Taylor Hamilton's Rule in finite populations
with synergistic interactions . . . . . 151--157
Virgile Baudrot and
Antoine Perasso and
Clémentine Fritsch and
Francis Raoul Competence of hosts and complex foraging
behavior are two cornerstones in the
dynamics of trophically transmitted
parasites . . . . . . . . . . . . . . . 158--168
Katy Gaythorpe and
Ben Adams Disease and disaster: Optimal deployment
of epidemic control facilities in a
spatially heterogeneous population with
changing behaviour . . . . . . . . . . . 169--178
Calistus N. Ngonghala and
Jemal Mohammed-Awel and
Ruijun Zhao and
Olivia Prosper Interplay between insecticide-treated
bed-nets and mosquito demography:
implications for malaria control . . . . 179--192
Josef Dolejs Single parameter of inverse proportion
between mortality and age could
determine all mortality indicators in
the first year of life . . . . . . . . . 193--198
Ali Mansouri and
Ali Fadavi and
Seyed Mohammad Mahdi Mortazavian An artificial intelligence approach for
modeling volume and fresh weight of
callus --- a case study of cumin
(\bionameCuminum cyminum L.) . . . . . . 199--205
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Shengqin Wang and
Beili Sun and
Jing Tu and
Zuhong Lu Improving the microbial community
reconstruction at the genus level by
multiple 16S rRNA regions . . . . . . . 1--8
Anonymous Pages 1--180 (7 June 2016) . . . . . . . 1--180
Ashish Goyal and
John M. Murray Dynamics of in vivo hepatitis D virus
infection . . . . . . . . . . . . . . . 9--19
David Gonzalez-Rodriguez and
Paul-Henry Courn\`ede and
Emmanuel de Langre Turgidity-dependent petiole flexibility
enables efficient water use by a tree
subjected to water stress . . . . . . . 20--31
Shibiao Wan and
Man-Wai Mak and
Sun-Yuan Kung Mem-ADSVM: a two-layer multi-label
predictor for identifying
multi-functional types of membrane
proteins . . . . . . . . . . . . . . . . 32--42
Jennifer M. Larson The evolutionary advantage of limited
network knowledge . . . . . . . . . . . 43--51
Drew Levin and
Stephanie Forrest and
Soumya Banerjee and
Candice Clay and
Judy Cannon and
Melanie Moses and
Frederick Koster A spatial model of the efficiency of T
cell search in the influenza-infected
lung . . . . . . . . . . . . . . . . . . 52--63
Anastasiya Lapytsko and
Jörg Schaber The role of time delay in adaptive
cellular negative feedback systems . . . 64--73
Andrew Leber and
Vida Abedi and
Raquel Hontecillas and
Monica Viladomiu and
Stefan Hoops and
Stanca Ciupe and
John Caughman and
Tricity Andrew and
Josep Bassaganya-Riera Bistability analyses of CD4+ T
follicular helper and regulatory cells
during Helicobacter pylori infection . . 74--84
Xiao Lin and
Gabriel Terejanu and
Sajan Shrestha and
Sourav Banerjee and
Anindya Chanda Bayesian model selection framework for
identifying growth patterns in
filamentous fungi . . . . . . . . . . . 85--95
Xiaowei Zhao and
Qiao Ning and
Meiyue Ai and
Haiting Chai and
Guifu Yang Identification of S-glutathionylation
sites in species-specific proteins by
incorporating five sequence-derived
features into the general pseudo-amino
acid composition . . . . . . . . . . . . 96--102
Catheryn W. Gray and
Adelle C. F. Coster The Akt switch model: Is location
sufficient? . . . . . . . . . . . . . . 103--111
Avdesh Mishra and
Sumaiya Iqbal and
Md Tamjidul Hoque Discriminate protein decoys from native
by using a scoring function based on
ubiquitous Phi and Psi angles computed
for all atom . . . . . . . . . . . . . . 112--121
Chuan Wang and
Xiaobao Dong and
Lei Han and
Xiao-Dong Su and
Ziding Zhang and
Jinyan Li and
Jiangning Song Identification of WD40 repeats by
secondary structure-aided
profile-profile alignment . . . . . . . 122--129
Michael A. Fishman Polymorphic Evolutionary Games . . . . . 130--135
Hsin-Hsiung Huang An ensemble distance measure of $k$-mer
and Natural Vector for the phylogenetic
analysis of multiple-segmented viruses 136--144
Jane Ivy Coons and
Joseph Rusinko A note on the path interval distance . . 145--149
P. Gramlich and
S. J. Plitzko and
L. Rudolf and
B. Drossel and
T. Gross The influence of dispersal on a
predator--prey system with two habitats 150--161
L. G. Hutchinson and
E. A. Gaffney and
P. K. Maini and
J. Wagg and
A. Phipps and
H. M. Byrne Vascular phenotype identification and
anti-angiogenic treatment
recommendation: a pseudo-multiscale
mathematical model of angiogenesis . . . 162--180
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Bjòrn Olav Hald A generative modeling approach to
connectivity --- Electrical conduction
in vascular networks . . . . . . . . . . 1--12
Anonymous Pages 1--174 (21 June 2016) . . . . . . 1--174
Mattia Frasca and
Kieran J. Sharkey Discrete-time moment closure models for
epidemic spreading in populations of
interacting individuals . . . . . . . . 13--21
Loren Haarsma and
Serita Nelesen and
Ethan VanAndel and
James Lamine and
Peter VandeHaar Simulating evolution of protein
complexes through gene duplication and
co-option . . . . . . . . . . . . . . . 22--32
Suzanne L. Robertson and
Kevin A. Caillouët A host stage-structured model of
enzootic West Nile virus transmission to
explore the effect of avian
stage-dependent exposure to vectors . . 33--42
Laure Lalande and
Laurent Bourguignon and
Pascal Maire and
Sylvain Goutelle Mathematical modeling and systems
pharmacology of tuberculosis: Isoniazid
as a case study . . . . . . . . . . . . 43--52
Théophile Lohier and
Franck Jabot and
Alexandra Weigelt and
Bernhard Schmid and
Guillaume Deffuant Predicting stochastic community dynamics
in grasslands under the assumption of
competitive symmetry . . . . . . . . . . 53--61
M. Cencini and
M. Franchino and
F. Santamaria and
G. Boffetta Centripetal focusing of gyrotactic
phytoplankton . . . . . . . . . . . . . 62--70
Mayuko Nakamaru Evolution of costly explicit memory and
cumulative culture . . . . . . . . . . . 71--83
Hervé Seligmann Swinger RNA self-hybridization and
mitochondrial non-canonical swinger
transcription, transcription
systematically exchanging nucleotides 84--91
Beatriz Carbonell-Pascual and
Eduardo Godoy and
Ana Ferrer and
Lucia Romero and
Jose M. Ferrero Comparison between Hodgkin--Huxley and
Markov formulations of cardiac ion
channels . . . . . . . . . . . . . . . . 92--102
Jason W. Olejarz and
Benjamin Allen and
Carl Veller and
Raghavendra Gadagkar and
Martin A. Nowak Evolution of worker policing . . . . . . 103--116
Andrés C. Burgos and
Daniel Polani Cooperation and antagonism in
information exchange in a growth
scenario with two species . . . . . . . 117--133
Massimo Di Giulio The lack of foundation in the mechanism
on which are based the physico-chemical
theories for the origin of the genetic
code is counterposed to the credible and
natural mechanism suggested by the
coevolution theory . . . . . . . . . . . 134--140
E. Pascal Malkemper and
Michael S. Painter and
Lukas Landler Shifted magnetic alignment in
vertebrates: Evidence for neural
lateralization? . . . . . . . . . . . . 141--147
Abbas Mikhchi and
Mahmood Honarvar and
Nasser Emam Jomeh Kashan and
Mehdi Aminafshar Assessing and comparison of different
machine learning methods in
parent-offspring trios for genotype
imputation . . . . . . . . . . . . . . . 148--158
Gil Iosilevskii Locomotion of neutrally buoyant fish
with flexible caudal fin . . . . . . . . 159--165
Kenta Ishimoto Hydrodynamic evolution of sperm
swimming: Optimal flagella by a genetic
algorithm . . . . . . . . . . . . . . . 166--174
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Lichao Zhang and
Liang Kong and
Xiaodong Han and
Jinfeng Lv Structural class prediction of protein
using novel feature extraction method
from chaos game representation of
predicted secondary structure . . . . . 1--10
Anonymous Pages 1--158 (7 July 2016) . . . . . . . 1--158
Rayapadi G. Swetha and
Madangopal Sandhya and
Sudha Ramaiah and
Anand Anbarasu Identification of CD4+ T-cell epitope
and investigation of HLA distribution
for the immunogenic proteins of
\bionameBurkholderia pseudomallei using
in silico approaches --- a key vaccine
development strategy for melioidosis . . 11--18
Stuart T. Johnston and
Joshua V. Ross and
Benjamin J. Binder and
D. L. Sean McElwain and
Parvathi Haridas and
Matthew J. Simpson Quantifying the effect of experimental
design choices for in vitro scratch
assays . . . . . . . . . . . . . . . . . 19--31
Shun Guo and
Donghui Guo and
Lifei Chen and
Qingshan Jiang A centroid-based gene selection method
for microarray data classification . . . 32--41
Enrico Mazzuca and
Andrea Aliverti and
Giuseppe Miserocchi Computational micro-scale model of
control of extravascular water and
capillary perfusion in the air blood
barrier . . . . . . . . . . . . . . . . 42--51
Sungrim Seirin Lee Positioning of polarity formation by
extracellular signaling during
asymmetric cell division . . . . . . . . 52--64
D. A. Ewing and
C. A. Cobbold and
B. V. Purse and
M. A. Nunn and
S. M. White Modelling the effect of temperature on
the seasonal population dynamics of
temperate mosquitoes . . . . . . . . . . 65--79
Alf H. Òien and
Helge Wiig Electrostatic, elastic and
hydration-dependent interactions in
dermis influencing volume exclusion and
macromolecular transport . . . . . . . . 80--91
Yang Liu and
Yong Deng and
Marko Jusup and
Zhen Wang A biologically inspired immunization
strategy for network epidemiology . . . 92--102
John T. Nardini and
Douglas A. Chapnick and
Xuedong Liu and
David M. Bortz Modeling keratinocyte wound healing
dynamics: cell--cell adhesion promotes
sustained collective migration . . . . . 103--117
Shimon Haber and
Micha\l Weisbord and
Michiaki Mishima and
Steve J. Mentzer and
Akira Tsuda Interstitial fluid flow of alveolar
primary septa after pneumonectomy . . . 118--128
Chen Jia Simplification of irreversible Markov
chains by removal of states with fast
leaving rates . . . . . . . . . . . . . 129--137
Alexander Lange Reconstruction of disease transmission
rates: Applications to measles, dengue,
and influenza . . . . . . . . . . . . . 138--153
William H. James The sex ratio of the sibs of probands
diagnosed with autism . . . . . . . . . 154--157
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Gibin G. Powathil and
Alastair J. Munro and
Mark A. J. Chaplain and
Maciej Swat Bystander effects and their implications
for clinical radiation therapy: Insights
from multiscale in silico experiments 1--14
Anonymous Pages 1--122 (21 July 2016) . . . . . . 1--122
Victor K. Kuetche Ab initio bubble-driven denaturation of
double-stranded DNA: Self-mechanical
theory . . . . . . . . . . . . . . . . . 15--29
Shu-Bo Zhang and
Qiang-Rong Tang Protein-protein interaction inference
based on semantic similarity of Gene
Ontology terms . . . . . . . . . . . . . 30--37
Takuyo Aita and
Norikazu Ichihashi and
Tetsuya Yomo Inference of fitness values and putative
appearance time points for evolvable
self-replicating molecules from time
series of occurrence frequencies in an
evolution reactor . . . . . . . . . . . 38--42
Helena L. Crowell and
Adam L. MacLean and
Michael P. H. Stumpf Feedback mechanisms control coexistence
in a stem cell model of acute myeloid
leukaemia . . . . . . . . . . . . . . . 43--53
Qi Zheng A second look at the final number of
cells in a fluctuation experiment . . . 54--63
Jennifer Paola Corredor-Gómez and
Andrés Mauricio Rueda-Ramírez and
Miguel Alejandro Gamboa-Márquez and
Carolina Torres-Rodríguez and
Carlos Julio Cortés-Rodríguez An intramembranous ossification model
for the in silico analysis of bone
tissue formation in tooth extraction
sites . . . . . . . . . . . . . . . . . 64--77
Oleksandr Ivanov and
Arjan van der Schaft and
Franz J. Weissing Steady states and stability in metabolic
networks without regulation . . . . . . 78--93
Daryl G. Clerc Nonlinear effects in evolution --- an ab
initio study: a model in which the
classical theory of evolution occurs as
a special case . . . . . . . . . . . . . 94--108
Jason Bernstein and
John Fricks Analysis of single particle diffusion
with transient binding using particle
filtering . . . . . . . . . . . . . . . 109--121
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Mohammad Akbaripour-Elahabad and
Javad Zahiri and
Reza Rafeh and
Morteza Eslami and
Mahboobeh Azari rpiCOOL: a tool for In Silico
RNA-protein interaction detection using
random forest . . . . . . . . . . . . . 1--8
Anonymous Pages 1--170 (7 August 2016) . . . . . . 1--170
David M. Schneider and
Ayana B. Martins and
Marcus A. M. de Aguiar The mutation-drift balance in spatially
structured populations . . . . . . . . . 9--17
Loris Serafino Abiogenesis as a theoretical challenge:
Some reflections . . . . . . . . . . . . 18--20
Franca Rossi and
Teresa Zotta and
Lucilla Iacumin and
Anna Reale Theoretical insight into the heat shock
response (HSR) regulation in
\bionameLactobacillus casei and
\bionameL. rhamnosus . . . . . . . . . . 21--37
Ya-Sen Jiao and
Pu-Feng Du Prediction of Golgi-resident protein
types using general form of Chou's
pseudo-amino acid compositions:
Approaches with minimal redundancy
maximal relevance feature selection . . 38--44
Huiqin Jin and
Jinzhi Lei A hybrid model of molecular regulation
and population dynamics for yeast
autophagy . . . . . . . . . . . . . . . 45--53
Ambuj Srivastava and
Prerana Gogoi and
Bhagyashree Deka and
Shrayanti Goswami and
Shankar Prasad Kanaujia In silico analysis of 5'-UTRs highlights
the prevalence of Shine--Dalgarno and
leaderless-dependent mechanisms of
translation initiation in bacteria and
archaea, respectively . . . . . . . . . 54--61
Menghua Man and
Ya Zhang and
Guilei Ma and
Karl Friston and
Shanghe Liu Quantification of degeneracy in
Hodgkin--Huxley neurons on Newman--Watts
small world network . . . . . . . . . . 62--74
Frédéric Pro\"\ia and
Alix Pernet and
Tatiana Thouroude and
Gilles Michel and
Jérémy Clotault On the characterization of flowering
curves using Gaussian mixture models . . 75--88
E. Doutel and
S. I. S. Pinto and
J. B. L. M. Campos and
J. M. Miranda Link between deviations from Murray's
Law and occurrence of low wall shear
stress regions in the left coronary
artery . . . . . . . . . . . . . . . . . 89--99
Mozafar Mohammadi and
Foroogh Nejatollahi and
Amirhossein Sakhteman and
Neda Zarei Insilico analysis of three different tag
polypeptides with dual roles in scFv
antibodies . . . . . . . . . . . . . . . 100--106
Ruben H. Roa-Ureta Size-dependent mortality rate profiles 107--116
Gaurav Raicar and
Harsh Saini and
Abdollah Dehzangi and
Sunil Lal and
Alok Sharma Improving protein fold recognition and
structural class prediction accuracies
using physicochemical properties of
amino acids . . . . . . . . . . . . . . 117--128
Maximilian O. Besenhard and
Monika Jarzabek and
Alice C. O'Farrell and
John J. Callanan and
Jochen H. M. Prehn and
Annette T. Byrne and
Heinrich J. Huber Modelling tumour cell proliferation from
vascular structure using tissue
decomposition into avascular elements 129--143
Romain Larbat and
Christophe Robin and
Cathrine Lillo and
Tormod Drengstig and
Peter Ruoff Modeling the diversion of primary carbon
flux into secondary metabolism under
variable nitrate and light/dark
conditions . . . . . . . . . . . . . . . 144--157
Lei Zhao and
Martin Lascoux and
David Waxman An informational transition in
conditioned Markov chains: Applied to
genetics and evolution . . . . . . . . . 158--170
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Víctor Serrano-Solís and
Germinal Cocho and
Marco V. José Genomic signatures in viral sequences by
in-frame and out-frame mutual
information . . . . . . . . . . . . . . 1--9
Anonymous Pages 1--218 (21 August 2016) . . . . . 1--218
Ahmed Roman and
Debanjan Dasgupta and
Michel Pleimling A theoretical approach to understand
spatial organization in complex
ecologies . . . . . . . . . . . . . . . 10--16
John H. M. Thornley and
James France Blue tongue --- a modelling examination
of fundamentals --- Seasonality and
chaos . . . . . . . . . . . . . . . . . 17--29
Farman Ali and
Maqsood Hayat Machine learning approaches for
discrimination of Extracellular Matrix
proteins using hybrid feature space . . 30--37
Pedro J. Miranda and
Sandro E. de S. Pinto and
Murilo S. Baptista and
Giuliano G. La Guardia Theoretical knock-outs on biological
networks . . . . . . . . . . . . . . . . 38--44
Pablo Araujo Granda and
Anna Gras and
Marta Ginovart and
Vincent Moulton INDISIM-Paracoccus, an individual-based
and thermodynamic model for a
denitrifying bacterium . . . . . . . . . 45--58
Weilong Ding and
Lifeng Xu and
Yang Wei and
Fuli Wu and
Defeng Zhu and
Yuping Zhang and
Nelson Max Genetic algorithm based approach to
optimize phenotypical traits of virtual
rice . . . . . . . . . . . . . . . . . . 59--67
Gang Zheng and
Wei Zhang and
Jinfeng Xu and
Ao Yuan and
Qizhai Li and
Joseph L. Gastwirth Genetic risks and genetic model
specification . . . . . . . . . . . . . 68--74
Lina Zhang and
Chengjin Zhang and
Rui Gao and
Runtao Yang and
Qing Song Using the SMOTE technique and hybrid
features to predict the types of ion
channel-targeted conotoxins . . . . . . 75--84
Kubra Karagoz and
Tuba Sevimo\uglu and
Kazim Yalcin Arga Integration of multiple biological
features yields high confidence human
protein interactome . . . . . . . . . . 85--96
Dimiter Prodanov and
Jean Delbeke A model of space-fractional-order
diffusion in the glial scar . . . . . . 97--109
Mahalakshmi Thillainayagam and
Anand Anbarasu and
Sudha Ramaiah Comparative molecular field analysis and
molecular docking studies on novel aryl
chalcone derivatives against an
important drug target cysteine protease
in \bionamePlasmodium falciparum . . . . 110--128
G. Neofytou and
Y. N. Kyrychko and
K. B. Blyuss Mathematical model of plant-virus
interactions mediated by RNA
interference . . . . . . . . . . . . . . 129--142
Kamran Kaveh and
Carl Veller and
Martin A. Nowak Games of multicellularity . . . . . . . 143--158
Yao He and
Don Kulasiri and
Sandhya Samarasinghe Modelling bidirectional modulations in
synaptic plasticity: a biochemical
pathway model to understand the
emergence of long term potentiation
(LTP) and long term depression (LTD) . . 159--177
Emile Franc Doungmo Goufo Stability and convergence analysis of a
variable order replicator-mutator
process in a moving medium . . . . . . . 178--187
Aouatef Riahi and
Abdelmonem Messaoudi and
Ridha Mrad and
Asma Fourati and
Habiba Chabouni-Bouhamed and
Maher Kharrat Molecular characterization, homology
modeling and docking studies of the
R2787H missense variation in BRCA2 gene:
Association with breast cancer . . . . . 188--196
Alex Gavryushkin and
Alexei J. Drummond The space of ultrametric phylogenetic
trees . . . . . . . . . . . . . . . . . 197--208
Mona Eskandari and
Ali Javili and
Ellen Kuhl Elastosis during airway wall remodeling
explains multiple co-existing
instability patterns . . . . . . . . . . 209--218
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Martino E. Malerba and
Kirsten Heimann and
Sean R. Connolly Improving dynamic phytoplankton
reserve-utilization models with an
indirect proxy for internal nitrogen . . 1--9
Anonymous Pages 1--398 (7 September 2016) . . . . 1--398
Kazuo Yamazaki Caterpillar mimicry by plant galls as a
visual defense against herbivores . . . 10--14
Yuting Lou and
Yu Chen Simulating the multicellular homeostasis
with a cell-based discrete receptor
dynamics model: The non-mutational
origin of cancer and aging . . . . . . . 15--29
Katharina T. Huber and
Vincent Moulton and
Taoyang Wu Transforming phylogenetic networks:
Moving beyond tree space . . . . . . . . 30--39
Seiya Nishikawa and
Atsuko Takamatsu and
Shizue Ohsawa and
Tatsushi Igaki Mathematical model for cell competition:
predator--prey interactions at the
interface between two groups of cells in
monolayer tissue . . . . . . . . . . . . 40--50
Sungrim Seirin Lee Lateral inhibition-induced pattern
formation controlled by the size and
geometry of the cell . . . . . . . . . . 51--65
Jing Yang and
Tong-Jun Zhao and
Chang-Qing Yuan and
Jing-Hui Xie and
Fang-Fang Hao A nonlinear competitive model of the
prostate tumor growth under intermittent
androgen suppression . . . . . . . . . . 66--72
Z. Ghanbari and
M. R. Housaindokht and
M. R. Bozorgmehr and
M. Izadyar The effect of glycosylation on the
transferrin structure: a molecular
dynamic simulation analysis . . . . . . 73--81
Nafiseh Sedaghat and
Mahmood Fathy and
Mohammad Hossein Modarressi and
Ali Shojaie Identifying functional cancer-specific
miRNA-mRNA interactions in testicular
germ cell tumor . . . . . . . . . . . . 82--96
Tomotaka Matsumoto and
Jun Kitano The intricate relationship between
sexually antagonistic selection and the
evolution of sex chromosome fusions . . 97--108
Manan'Iarivo Rasolonjanahary and
Bakhtier Vasiev Scaling of morphogenetic patterns in
reaction-diffusion systems . . . . . . . 109--119
Xianli Chen and
Jia Chen and
Bin Shao and
Linjie Zhao and
Haicen Yue and
Qi Ouyang Relationship between cancer mutations
and parameter sensitivity in Rb pathway 120--125
Manuela Royer-Carenzi and
Gilles Didier A comparison of ancestral state
reconstruction methods for quantitative
characters . . . . . . . . . . . . . . . 126--142
Bernd Lütkenhöner Estimation of a transient response from
steady-state responses by deconvolution
with built-in constraints . . . . . . . 143--159
Arunas L. Radzvilavicius Evolutionary dynamics of cytoplasmic
segregation and fusion: Mitochondrial
mixing facilitated the evolution of sex
at the origin of eukaryotes . . . . . . 160--168
Rebecca M. Turner and
Michael M. Walker and
Claire M. Postlethwaite Literal grid map models for animal
navigation: Assumptions and predictions 169--181
D. Muraro and
A. Larrieu and
M. Lucas and
J. Chopard and
H. Byrne and
C. Godin and
J. King A multi-scale model of the interplay
between cell signalling and hormone
transport in specifying the root
meristem of \bionameArabidopsis thaliana 182--205
Yoshinori Hayakawa and
Masashi Tachikawa and
Atsushi Mochizuki Flat leaf formation realized by
cell-division control and mutual
recessive gene regulation . . . . . . . 206--214
Anderson A. Eduardo Multiple dimensions of biodiversity and
ecosystem processes: Exploring the joint
influence of intraspecific, specific and
interspecific diversity . . . . . . . . 215--221
Tom Rosenström and
Karoline Wiesner and
Alasdair I. Houston Scalar utility theory and proportional
processing: What does it actually imply? 222--235
Petra Ehling and
Patrick Meuth and
Paul Eichinger and
Alexander M. Herrmann and
Stefan Bittner and
Matthias Pawlowski and
Susann Pankratz and
Michael Herty and
Thomas Budde and
Sven G. Meuth Human T cells in silico: Modelling their
electrophysiological behaviour in health
and disease . . . . . . . . . . . . . . 236--250
Cheng-Hong Yang and
Yu-Da Lin and
Li-Yeh Chuang tRNAfeature: An algorithm for tRNA
features to identify tRNA genes in DNA
sequences . . . . . . . . . . . . . . . 251--261
Justin Eastman and
Julian Sass and
Johnny M. Gomes and
Rodrigo Weber dos Santos and
Elizabeth M. Cherry Using delay differential equations to
induce alternans in a model of cardiac
electrophysiology . . . . . . . . . . . 262--272
Ivan Grbatini\'c and
Nebojsa Milosevi\'c Classification of adult human dentate
nucleus border neurons: Artificial
neural networks and multidimensional
approach . . . . . . . . . . . . . . . . 273--284
Prabina Kumar Meher and
Tanmaya Kumar Sahu and
A. R. Rao and
S. D. Wahi A computational approach for prediction
of donor splice sites with improved
accuracy . . . . . . . . . . . . . . . . 285--294
J. M. Cushing and
Odo Diekmann The many guises of $ R_0 $ (a didactic
note) . . . . . . . . . . . . . . . . . 295--302
Paras Gupta and
Latha Rangan and
T. Venkata Ramesh and
Mudit Gupta Comparative analysis of contextual bias
around the translation initiation sites
in plant genomes . . . . . . . . . . . . 303--311
Khaphetsi Joseph Mahasa and
Rachid Ouifki and
Amina Eladdadi and
Lisette de Pillis Mathematical model of tumor-immune
surveillance . . . . . . . . . . . . . . 312--330
Masoomeh Taghipoor and
Jaap van Milgen and
Florence Gondret A systemic approach to explore the
flexibility of energy stores at the
cellular scale: Examples from muscle
cells . . . . . . . . . . . . . . . . . 331--341
F. R. McMorris and
Robert C. Powers Some axiomatic limitations for consensus
and supertree functions on hierarchies 342--347
Simon M. Stump and
Christopher A. Klausmeier Competition and coexistence between a
syntrophic consortium and a metabolic
generalist, and its effect on
productivity . . . . . . . . . . . . . . 348--360
Tin Klanjscek and
Erik B. Muller and
Roger M. Nisbet Feedbacks and tipping points in
organismal response to oxidative stress 361--374
Mohammad H. Olyaee and
Ali Yaghoubi and
Mahdi Yaghoobi Predicting protein structural classes
based on complex networks and recurrence
analysis . . . . . . . . . . . . . . . . 375--382
B. Morsky and
C. T. Bauch Truncation selection and payoff
distributions applied to the replicator
equation . . . . . . . . . . . . . . . . 383--390
Colin J. Thompson and
Elad Shtilerman and
Lewi Stone A discrete Markov metapopulation model
for persistence and extinction of
species . . . . . . . . . . . . . . . . 391--397
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Andrew Morozov Modelling biological evolution: Linking
mathematical theories with empirical
realities . . . . . . . . . . . . . . . 1--4
Camila C. S. Caiado and
William A. Brock and
R. Alexander Bentley and
Michael J. O'Brien Fitness landscapes among many options
under social influence . . . . . . . . . 5--16
Andrew Yu. Morozov and
Oleg. A. Kuzenkov Towards developing a general framework
for modelling vertical migration in
zooplankton . . . . . . . . . . . . . . 17--28
András G. Hubai and
Ádám Kun Maximal gene number maintainable by
stochastic correction --- The second
error threshold . . . . . . . . . . . . 29--35
Ryo Yamaguchi and
Yoh Iwasa Smallness of the number of
incompatibility loci can facilitate
parapatric speciation . . . . . . . . . 36--45
Sébastien Lion Moment equations in spatial evolutionary
ecology . . . . . . . . . . . . . . . . 46--57
Rupert Mazzucco and
Ulf Dieckmann and
Johan A. J. Metz Epidemiological, evolutionary, and
economic determinants of eradication
tails . . . . . . . . . . . . . . . . . 58--65
Daniel Ritterskamp and
Daniel Bearup and
Bernd Blasius A new dimension: Evolutionary food web
dynamics in two dimensional trait space 66--81
Andrew D. Dean and
Ewan J. A. Minter and
Megan E. S. Sòrensen and
Christopher D. Lowe and
Duncan D. Cameron and
Michael A. Brockhurst and
A. Jamie Wood Host control and nutrient trading in a
photosynthetic symbiosis . . . . . . . . 82--93
Andrzej \'Swierniak and
Micha\l Krze\'slak and
Sebastian Student and
Joanna Rzeszowska-Wolny Development of a population of cancer
cells: Observation and modeling by a
Mixed Spatial Evolutionary Games
approach . . . . . . . . . . . . . . . . 94--103
A. Mund and
C. Kuttler and
J. Pérez-Velázquez and
B. A. Hense An age-dependent model to analyse the
evolutionary stability of bacterial
quorum sensing . . . . . . . . . . . . . 104--115
G. A. Kaiping and
S. J. Cox and
T. J. Sluckin Cooperation and punishment in
community-structured populations with
migration . . . . . . . . . . . . . . . 116--126
Alexander N. Gorban and
Tatiana A. Tyukina and
Elena V. Smirnova and
Lyudmila I. Pokidysheva Evolution of adaptation mechanisms:
Adaptation energy, stress, and
oscillating death . . . . . . . . . . . 127--139
Suzanne S. Sindi and
Rick Dale Culturomics as a data playground for
tests of selection: Mathematical
approaches to detecting selection in
word use . . . . . . . . . . . . . . . . 140--149
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Takanori Mizuno Suzuki and
Satoshi Chiba Dynamics of evolutionary radiation under
ecological neutrality . . . . . . . . . 1--7
Anonymous Pages 1--192 (7 October 2016) . . . . . 1--192
Yan-ping Zhang and
Wuyunqiqige and
Wei Zheng and
Shuyi Liu and
Chunguang Zhao gDNA-Prot: Predict DNA-binding proteins
by employing support vector machine and
a novel numerical characterization of
protein sequence . . . . . . . . . . . . 8--16
Darragh M. Walsh and
Philipp T. Röth and
William R. Holmes and
Kerry A. Landman and
Tobias D. Merson and
Barry D. Hughes Is cell migration or proliferation
dominant in the formation of linear
arrays of oligodendrocytes? . . . . . . 17--30
Grégory Dumont and
Jacques Henry and
Carmen Oana Tarniceriu Theoretical connections between
mathematical neuronal models
corresponding to different expressions
of noise . . . . . . . . . . . . . . . . 31--41
Xuefang Li and
Jian-Xin Xu A mathematical prognosis model for
pancreatic cancer patients receiving
immunotherapy . . . . . . . . . . . . . 42--51
L. J. Liu and
M. Schlesinger MRI contrast agent concentration and
tumor interstitial fluid pressure . . . 52--60
Hsin-Hsiung Huang and
Chenglong Yu Clustering DNA sequences using the
out-of-place measure with reduced
$n$-grams . . . . . . . . . . . . . . . 61--72
Marco Archetti and
István Scheuring Evolution of optimal Hill coefficients
in nonlinear public goods games . . . . 73--82
Jonathan A. Sherratt and
Julia J. Mackenzie How does tidal flow affect pattern
formation in mussel beds? . . . . . . . 83--92
Anup Mammen Oommen and
Neeti Somaiya and
Jisha Vijayan and
Satheesh Kumar and
Suri Venkatachalam and
Lokesh Joshi GlycoGAIT: a web database to browse
glycogenes and lectins under gastric
inflammatory diseases . . . . . . . . . 93--98
Nicole Pearcy and
Nadia Chuzhanova and
Jonathan J. Crofts Complexity and robustness in
hypernetwork models of metabolism . . . 99--104
Chunrui Xu and
Dandan Sun and
Shenghui Liu and
Yusen Zhang Protein sequence analysis by
incorporating modified chaos game and
physicochemical properties into Chou's
general pseudo amino acid composition 105--115
Linh Thi Hoai Nguyen and
Vi\d\vet Tôn T\da and
Atsushi Yagi Obstacle avoiding patterns and
cohesiveness of fish school . . . . . . 116--123
Igor Pantic and
Draga Dimitrijevic and
Dejan Nesic and
Danica Petrovic Gray level co-occurrence matrix
algorithm as pattern recognition
biosensor for oxidopamine-induced
changes in lymphocyte chromatin
architecture . . . . . . . . . . . . . . 124--128
William E. Cooper Fleeing to refuge: Escape decisions in
the race for life . . . . . . . . . . . 129--136
Shaik Mohammad Naushad and
M. Janaki Ramaiah and
Balraj Alex Stanley and
S. Prasanna Lakshmi and
J. Vishnu Priya and
Tajamul Hussain and
Salman A. Alrokayan and
Vijay Kumar Kutala In silico approaches to identify the
potential inhibitors of glutamate
carboxypeptidase II (GCPII) for
neuroprotection . . . . . . . . . . . . 137--142
Andreas F. M. Nierop and
Aimon Niklasson and
Anton Holmgren and
Lars Gelander and
Sten Rosberg and
Kerstin Albertsson-Wikland Modelling individual longitudinal human
growth from fetal to adult life --- QEPS
I . . . . . . . . . . . . . . . . . . . 143--165
Graham M. Donovan Clustered ventilation defects and
bilinear respiratory reactance in asthma 166--175
Alexandra-M. Reimers and
Arne C. Reimers The steady-state assumption in
oscillating and growing systems . . . . 176--186
Mostafa R. A. Nabawy and
William J. Crowther Optimum hovering wing planform . . . . . 187--191
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Patricia Román-Román and
Sergio Román-Román and
Juan José Serrano-Pérez and
Francisco Torres-Ruiz Modeling tumor growth in the presence of
a therapy with an effect on rate growth
and variability by means of a modified
Gompertz diffusion process . . . . . . . 1--17
Anonymous Pages 1--428 (21 October 2016) . . . . . 1--428
Nick Milne Curved bones: An adaptation to habitual
loading . . . . . . . . . . . . . . . . 18--24
Vlastimil K\vrivan and
Mark Lewis and
Barbara J. Bentz and
Sharon Bewick and
Suzanne M. Lenhart and
Andrew Liebhold A dynamical model for bark beetle
outbreaks . . . . . . . . . . . . . . . 25--37
Piotr Gwiazda and
Blazej Miasojedow and
Magdalena Rosi\'nska Bayesian inference for age-structured
population model of infectious disease
with application to varicella in Poland 38--50
Cicely K. Macnamara and
Mark A. J. Chaplain Diffusion driven oscillations in gene
regulatory networks . . . . . . . . . . 51--70
Tsuyoshi Hirashima Mathematical study on robust tissue
pattern formation in growing epididymal
tubule . . . . . . . . . . . . . . . . . 71--80
David E. Hiebeler and
Jack L. Hill Locally dispersing populations in
heterogeneous dynamic landscapes with
spatiotemporal correlations. II. Habitat
driven by voter dynamics . . . . . . . . 81--89
Motohide Seki and
Mayuko Nakamaru A model for gossip-mediated evolution of
altruism with various types of false
information by speakers and assessment
by listeners . . . . . . . . . . . . . . 90--105
Daniel Sánchez-Taltavull Optimal architecture of differentiation
cascades with asymmetric and symmetric
stem cell division . . . . . . . . . . . 106--117
Karin H. Olsson and
Henrik Gislason and
Ken Haste Andersen Differences in density-dependence drive
dual offspring size strategies in fish 118--127
Amin Oroji and
Mohd Omar and
Shantia Yarahmadian An Îto stochastic differential equations
model for the dynamics of the MCF-7
breast cancer cell line treated by
radiotherapy . . . . . . . . . . . . . . 128--137
Guo-Liang Fan and
Yan-Ling Liu and
Hui Wang Identification of thermophilic proteins
by incorporating evolutionary and acid
dissociation information into Chou's
general pseudo amino acid composition 138--142
Siddhartha Kundu Stochastic modelling suggests that an
elevated superoxide anion--hydrogen
peroxide ratio can drive extravascular
phagocyte transmigration by
lamellipodium formation . . . . . . . . 143--154
Moshe Kiflawi and
Ofri Mann and
Mark G. Meekan Heterogeneous `proportionality
constants' --- a challenge to Taylor's
Power Law for temporal fluctuations in
abundance . . . . . . . . . . . . . . . 155--160
Roberto de la Cruz and
Pilar Guerrero and
Fabian Spill and
Tomás Alarcón Stochastic multi-scale models of
competition within heterogeneous
cellular populations: Simulation methods
and mean-field analysis . . . . . . . . 161--183
Dyfed Lloyd Evans and
Shailesh Vinay Joshi Elucidating modes of activation and
herbicide resistance by sequence
assembly and molecular modelling of the
Acetolactate synthase complex in
sugarcane . . . . . . . . . . . . . . . 184--197
Angela Peace and
Monica D. Poteat and
Hao Wang Somatic Growth Dilution of a toxicant in
a predator--prey model under
stoichiometric constraints . . . . . . . 198--211
David E. Hiebeler and
Jennifer Houle and
Frank Drummond and
Peter Bilodeau and
Jeffery Merckens Locally dispersing populations in
heterogeneous dynamic landscapes with
spatiotemporal correlations. I. Block
disturbance . . . . . . . . . . . . . . 212--224
Ananthu James Role of epistasis on the fixation
probability of a non-mutator in an
adapted asexual population . . . . . . . 225--237
Tina M. Mitre and
Michael C. Mackey and
Anmar Khadra Mathematical model of galactose
regulation and metabolic consumption in
yeast . . . . . . . . . . . . . . . . . 238--258
Joseph D. Butner and
Yao-Li Chuang and
Eman Simbawa and
A. S. Al-Fhaid and
S. R. Mahmoud and
Vittorio Cristini and
Zhihui Wang A hybrid agent-based model of the
developing mammary terminal end bud . . 259--270
Thomas Koffel and
Tanguy Daufresne and
François Massol and
Christopher A. Klausmeier Geometrical envelopes: Extending
graphical contemporary niche theory to
communities and eco-evolutionary
dynamics . . . . . . . . . . . . . . . . 271--289
Vasthi Alonso Chavez and
Stephen Parnell and
Frank Van den Bosch Monitoring invasive pathogens in plant
nurseries for early-detection and to
minimise the probability of escape . . . 290--302
Jorge Calle-Espinosa and
Miguel Ponce-de-Leon and
Diego Santos-Garcia and
Francisco J. Silva and
Francisco Montero and
Juli Peretó Nature lessons: The whitefly bacterial
endosymbiont is a minimal amino acid
factory with unusual energetics . . . . 303--317
Saeid Amiri and
Ivo D. Dinov Comparison of genomic data via
statistical distribution . . . . . . . . 318--327
G. Iacobelli and
D. Madeo and
C. Mocenni Lumping evolutionary game dynamics on
networks . . . . . . . . . . . . . . . . 328--338
Sachi Yamaguchi Time required for sex change in teleost
fishes: Hormonal dynamics shaped by
selection . . . . . . . . . . . . . . . 339--348
Ross-William S. Hendron and
Michael B. Bonsall The interplay of vaccination and vector
control on small dengue networks . . . . 349--361
Dominik Schrempf and
Bui Quang Minh and
Nicola De Maio and
Arndt von Haeseler and
Carolin Kosiol Reversible polymorphism-aware
phylogenetic models and their
application to tree inference . . . . . 362--370
Krzysztof Bartoszek Phylogenetic effective sample size . . . 371--386
N. Sherborne and
K. B. Blyuss and
I. Z. Kiss Compact pairwise models for epidemics
with multiple infectious stages on
degree heterogeneous and clustered
networks . . . . . . . . . . . . . . . . 387--400
Mahnaz Rabbani and
Lindi M. Wahl The dynamics of mobile promoters:
Enhanced stability in promoter regions 401--408
Hiroshi Ito and
Akira Sasaki Evolutionary branching under
multi-dimensional evolutionary
constraints . . . . . . . . . . . . . . 409--428
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Mabelle Lin and
Benjamin Mauroy and
Joanna L. James and
Merryn H. Tawhai and
Alys R. Clark A multiscale model of placental oxygen
exchange: The effect of villous tree
structure on exchange efficiency . . . . 1--12
Anonymous Pages 1--290 (7 November 2016) . . . . . 1--290
Björn Vessman and
Philip Gerlee and
Torbjörn Lundh Estimating the probability of
coexistence in cross-feeding communities 13--21
Aslan Massahi and
Pinar Çalik Endogenous signal peptides in
recombinant protein production by
\bionamePichia pastoris: From in-silico
analysis to fermentation . . . . . . . . 22--33
Oskar Burger and
Trifon I. Missov Evolutionary theory of ageing and the
problem of correlated Gompertz
parameters . . . . . . . . . . . . . . . 34--41
James Richard Usherwood Physiological, aerodynamic and geometric
constraints of flapping account for bird
gaits, and bounding and flap-gliding
flight strategies . . . . . . . . . . . 42--52
Brian K. Taylor Validating a model for detecting
magnetic field intensity using dynamic
neural fields . . . . . . . . . . . . . 53--65
Kenji Yoshimura and
Ryo Kobayashi and
Tomohisa Ohmura and
Yoshinaga Kajimoto and
Takashi Miura A new mathematical model for pattern
formation by cranial sutures . . . . . . 66--74
Erika T. Camacho and
Claudio Punzo and
Stephen A. Wirkus Quantifying the metabolic contribution
to photoreceptor death in retinitis
pigmentosa via a mathematical model . . 75--87
M. Mocarlo Zheng and
Bin Shao and
Qi Ouyang Identifying network topologies that can
generate Turing pattern . . . . . . . . 88--96
Michael L. Palmer and
Richard A. Williams and
Derek Gatherer Rosen's $ (M, R) $ system as an
X-machine . . . . . . . . . . . . . . . 97--104
Mohammad A. Al-Mamun and
Rebecca L. Smith and
Ynte H. Schukken and
Yrjö T. Gröhn Modeling of Mycobacterium avium subsp.
paratuberculosis dynamics in a dairy
herd: An individual based approach . . . 105--117
Jonggul Lee and
Gerardo Chowell and
Eunok Jung A dynamic compartmental model for the
Middle East respiratory syndrome
outbreak in the Republic of Korea: a
retrospective analysis on control
interventions and superspreading events 118--126
Jing Wui Yeoh and
Alberto Corrias and
Martin L. Buist A mechanistic model of a PDGFR $ \alpha
$ + cell . . . . . . . . . . . . . . . . 127--136
Qinbin He and
Zhile Xia and
Bin Lin An efficient approach of attractor
calculation for large-scale Boolean gene
regulatory networks . . . . . . . . . . 137--144
Bradford P. Taylor and
Jonathan Dushoff and
Joshua S. Weitz Stochasticity and the limits to
confidence when estimating ${\cal R}_0$
of Ebola and other emerging infectious
diseases . . . . . . . . . . . . . . . . 145--154
Graeme Mitchison Conformal growth of \bionameArabidopsis
leaves . . . . . . . . . . . . . . . . . 155--166
Richard D. Wilkinson and
Apostolos Kapranas and
Ian C. W. Hardy Detecting non-binomial sex allocation
when developmental mortality operates 167--178
Jeff Gaither and
Laura Kubatko Hypothesis tests for phylogenetic
quartets, with applications to
coalescent-based species tree inference 179--186
Daniel Ritterskamp and
Daniel Bearup and
Bernd Blasius Emergence of evolutionary cycles in
size-structured food webs . . . . . . . 187--197
Karim El Soufi and
Christian J. Michel Circular code motifs in genomes of
eukaryotes . . . . . . . . . . . . . . . 198--212
Emilia Kozlowska and
Krzysztof Puszynski Application of bifurcation theory and
siRNA-based control signal to restore
the proper response of cancer cells to
DNA damage . . . . . . . . . . . . . . . 213--221
Jakub Jedrak and
Anna Ochab-Marcinek Influence of gene copy number on
self-regulated gene expression . . . . . 222--236
Steven E. Massey The neutral emergence of error minimized
genetic codes superior to the standard
genetic code . . . . . . . . . . . . . . 237--242
Alex John Quijano and
Michele L. Joyner and
Chelsea Ross and
J. Colton Watts and
Edith Seier and
Thomas C. Jones Spatio-temporal analysis of foraging
behaviors of \bionameAnelosimus
studiosus utilizing mathematical
modeling of multiple spider interaction
on a cooperative web . . . . . . . . . . 243--259
Miranda I. Teboh-Ewungkem and
Thomas Yuster Evolutionary implications for the
determination of gametocyte sex ratios
under fecundity variation for the
malaria parasite . . . . . . . . . . . . 260--273
Zhe F. Tang and
David R. McMillen Design principles for the analysis and
construction of robustly homeostatic
biological networks . . . . . . . . . . 274--289
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Ronan M. T. Fleming and
Nikos Vlassis and
Ines Thiele and
Michael A. Saunders Conditions for duality between fluxes
and concentrations in biochemical
networks . . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--172 (21 November 2016) . . . . 1--172
Manoel Figueiredo Neto and
Marxa L. Figueiredo Skeletal muscle signal peptide
optimization for enhancing propeptide or
cytokine secretion . . . . . . . . . . . 11--17
Michele Curatolo and
Luciano Teresi Modeling and simulation of fish swimming
with active muscles . . . . . . . . . . 18--26
S. Muthu Krishnan Classify vertebrate hemoglobin proteins
by incorporating the evolutionary
information into the general PseAAC with
the hybrid approach . . . . . . . . . . 27--37
Daniel Cooney and
Benjamin Allen and
Carl Veller Assortment and the evolution of
cooperation in a Moran process with
exponential fitness . . . . . . . . . . 38--46
Christopher Keane Chaos in collective health: Fractal
dynamics of social learning . . . . . . 47--59
A. D. Meyer and
D. F. Stevens and
J. C. Blackwood Predicting bat colony survival under
controls targeting multiple transmission
routes of white-nose syndrome . . . . . 60--69
Shawn A. Means and
Robert J. Smith The impact of human and vector
distributions on the spatial prevalence
of malaria in sub-Saharan Africa . . . . 70--85
Rodrick Wallace High metabolic demand in neural tissues:
Information and control theory
perspectives on the synergism between
rate and stability . . . . . . . . . . . 86--96
Misato Inaba and
Nobuyuki Takahashi and
Hisashi Ohtsuki Robustness of linkage strategy that
leads to large-scale cooperation . . . . 97--107
Ramesh Kheirabadi and
Mohammad Izadyar and
Mohammad Reza Housiandokht Computational kinetic modeling of the
selenol catalytic activity as the
glutathione peroxidase nanomimic . . . . 108--114
D. E. Moulton and
V. Sulzer and
G. Apodaca and
H. M. Byrne and
S. L. Waters Mathematical modelling of
stretch-induced membrane traffic in
bladder umbrella cells . . . . . . . . . 115--132
Hans-Rolf Gregorius Effective numbers in the partitioning of
biological diversity . . . . . . . . . . 133--147
Lei Yang and
Shiyuan Wang and
Meng Zhou and
Xiaowen Chen and
Yongchun Zuo and
Yingli Lv Characterization of BioPlex network by
topological properties . . . . . . . . . 148--154
Matan Danino and
Nadav M. Shnerb and
Sandro Azaele and
William E. Kunin and
David A. Kessler The effect of environmental
stochasticity on species richness in
neutral communities . . . . . . . . . . 155--164
Angelo B. Monteiro and
Lucas Del Bianco Faria The interplay between population
stability and food-web topology predicts
the occurrence of motifs in complex
food-webs . . . . . . . . . . . . . . . 165--171
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Stephen J. Gaunt and
Alexander L. Gaunt Possible rules for the ancestral origin
of Hox gene collinearity . . . . . . . . 1--8
Anonymous Pages 1--180 (7 December 2016) . . . . . 1--180
Antonio C. S. Marcolino and
William F. Porto and
Állan S. Pires and
Octavio L. Franco and
Sérgio A. Alencar Structural impact analysis of missense
SNPs present in the uroguanylin gene by
long-term molecular dynamics simulations 9--17
W. D. Comper and
L. M. Russo and
J. Vuchkova Are filtered plasma proteins processed
in the same way by the kidney? . . . . . 18--24
Kehinde O. Okonjo Bohr effect of avian hemoglobins:
Quantitative analyses based on the Wyman
equation . . . . . . . . . . . . . . . . 25--35
Ravi Jain and
Subash C. Sonkar and
Uma Chaudhry and
Manju Bala and
Daman Saluja In-silico Hierarchical Approach for the
Identification of Potential Universal
Vaccine Candidates (PUVCs) from
\bionameNeisseria gonorrhoeae . . . . . 36--43
Satoshi Yamashita and
Tatsuo Michiue Boundary propagation of planar cell
polarity is robust against cell packing
pattern . . . . . . . . . . . . . . . . 44--54
Tiffany Leung and
Barry D. Hughes and
Federico Frascoli and
James M. McCaw Periodic solutions in an SIRWS model
with immune boosting and cross-immunity 55--64
Biao Tang and
Yanni Xiao and
Sanyi Tang and
Jianhong Wu Modelling weekly vector control against
Dengue in the Guangdong Province of
China . . . . . . . . . . . . . . . . . 65--76
Libertad Pantoja-Hernández and
Elena Álvarez-Buylla and
Carlos F. Aguilar-Ibáñez and
Adriana Garay-Arroyo and
Alberto Soria-López and
Juan Carlos Mart\'ìnez-Garc\'ìa Retroactivity effects dependency on the
transcription factors binding mechanisms 77--106
Masoud Amiri and
Mahmood Amiri and
Soheila Nazari and
Karim Faez A new bio-inspired stimulator to
suppress hyper-synchronized neural
firing in a cortical network . . . . . . 107--118
Jean Lehmann and
Albert Libchaber and
Benjamin D. Greenbaum Fundamental amino acid mass
distributions and entropy costs in
proteomes . . . . . . . . . . . . . . . 119--124
Burton Simon and
Michael Pilosov Group-level events are catalysts in the
evolution of cooperation . . . . . . . . 125--136
Raazesh Sainudiin and
David Welch The transmission process: a
combinatorial stochastic process for the
evolution of transmission trees over
networks . . . . . . . . . . . . . . . . 137--170
Jonathan Burns and
Denys Kukushkin and
Xiao Chen and
Laura F. Landweber and
Masahico Saito and
Nata\vsa Jonoska Recurring patterns among scrambled genes
in the encrypted genome of the ciliate
\bionameOxytricha trifallax . . . . . . 171--180
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Mandana Behbahani and
Hassan Mohabatkar and
Mokhtar Nosrati Analysis and comparison of lignin
peroxidases between fungi and bacteria
using three different modes of Chou's
general pseudo amino acid composition 1--5
Anonymous Pages 1--102 (21 December 2016) . . . . 1--102
Bahareh Safarbali and
Fatemeh Hadaeghi and
Shahriar Gharibzadeh Mesoscopic model of neuronal system
deficits in Multiple Sclerosis . . . . . 6--15
Marek Ingr and
Eva Kutálková and
Josef Hrncirík and
Reinhard Lange Equilibria of oligomeric proteins under
high pressure --- a theoretical
description . . . . . . . . . . . . . . 16--26
Xia Wang and
Sanyi Tang and
Robert A. Cheke A stage structured mosquito model
incorporating effects of precipitation
and daily temperature fluctuations . . . 27--36
M. Labowsky An analysis of early-stage IL-2 capture
times in populations of T cells
diffusively interacting in a confined
environment . . . . . . . . . . . . . . 37--47
Sylvain Billiard and
Pierre Collet and
Régis Ferri\`ere and
Sylvie Méléard and
Viet Chi Tran The effect of competition and horizontal
trait inheritance on invasion, fixation,
and polymorphism . . . . . . . . . . . . 48--58
Michael H. Cortez Hydra effects in discrete-time models of
stable communities . . . . . . . . . . . 59--67
Dhrubajyoti Gogoi and
Vishwa Jyoti Baruah and
Amrita Kashyap Chaliha and
Bibhuti Bhushan Kakoti and
Diganta Sarma and
Alak Kumar Buragohain $3$D pharmacophore-based virtual
screening, docking and density
functional theory approach towards the
discovery of novel human epidermal
growth factor receptor-2 (HER2)
inhibitors . . . . . . . . . . . . . . . 68--80
Katarzyna Jesionek and
Aleksandra Slapik and
Marcin Kostur Low-density lipoprotein transport
through an arterial wall under
hypertension --- a model with time and
pressure dependent fraction of leaky
junction consistent with experiments . . 81--91
Eric Hermand and
François J. Lhuissier and
Nicolas Voituron and
Jean-Paul Richalet Ventilatory oscillations at exercise in
hypoxia: a mathematical model . . . . . 92--101
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Su Do Yi and
Seung Ki Baek and
Jung-Kyoo Choi Combination with anti-tit-for-tat
remedies problems of tit-for-tat . . . . 1--7
Anonymous Pages 1--204 (7 January 2017) . . . . . 1--204
Lo\"\ic Chaumont and
Valéry Malécot and
Richard Pymar and
Chaker Sbai Reconstructing pedigrees using
probabilistic analysis of ISSR
amplification . . . . . . . . . . . . . 8--16
Javad Salimi Sartakhti and
Mohammad Hossein Manshaei and
Mehdi Sadeghi MMP-TIMP interactions in cancer
invasion: An evolutionary
game-theoretical framework . . . . . . . 17--26
Kelvin J. Richards Viral infections of oceanic plankton
blooms . . . . . . . . . . . . . . . . . 27--35
Sunmi Lee and
Gerardo Chowell Exploring optimal control strategies in
seasonally varying flu-like epidemics 36--47
Nourridine Siewe and
Abdul-Aziz Yakubu and
Abhay R. Satoskar and
Avner Friedman Granuloma formation in leishmaniasis: a
mathematical model . . . . . . . . . . . 48--60
Abhijit Mondal and
Daniel A. Appadurai and
Nazem W. Akoum and
Frank B. Sachse and
Alonso P. Moreno Computational simulations of asymmetric
fluxes of large molecules through gap
junction channel pores . . . . . . . . . 61--73
Soyoung Kim and
Jonggul Lee and
Eunok Jung Mathematical model of transmission
dynamics and optimal control strategies
for 2009 A/H1N1 influenza in the
Republic of Korea . . . . . . . . . . . 74--85
Anupam Priyadarshi and
Sandip Mandal and
S. Lan Smith and
Hidekatsu Yamazaki Micro-scale variability enhances trophic
transfer and potentially sustains
biodiversity in plankton ecosystems . . 86--93
A. G. Dimitrov An approach to expand description of the
pump and co-transporter steady-state
current . . . . . . . . . . . . . . . . 94--99
Nina Galanter and
Dennis Silva and
Jonathan T. Rowell and
Jan Rychtár Resource competition amid overlapping
territories: The territorial raider
model applied to multi-group
interactions . . . . . . . . . . . . . . 100--106
Yang Yu and
Jie Liu and
Nuan Feng and
Bo Song and
Zeyu Zheng Combining sequence and Gene Ontology for
protein module detection in the Weighted
Network . . . . . . . . . . . . . . . . 107--112
M. E. Wosniack and
M. G. E. da Luz and
L. S. Schulman Punctuated equilibrium as an emergent
process and its modified thermodynamic
characterization . . . . . . . . . . . . 113--122
Qiang Li and
Furong Lu and
Chenxi Dai and
Minjun Fan and
Weiming Wang and
Kaifa Wang Simulating the potential role of media
coverage and infected bats in the 2014
Ebola outbreak . . . . . . . . . . . . . 123--129
Xuying Xu and
Li Ni and
Rubin Wang Synchronous transitions of up and down
states in a network model based on
stimulations . . . . . . . . . . . . . . 130--137
Changchuan Yin Identification of repeats in DNA
sequences using nucleotide distribution
uniformity . . . . . . . . . . . . . . . 138--145
Beáta Oborny and
Veronika Benedek and
Péter Englert and
Máté Gulyás and
András G. Hubai The plant in the labyrinth: Adaptive
growth and branching in heterogeneous
environments . . . . . . . . . . . . . . 146--153
Malay Banerjee and
Yasuhiro Takeuchi Maturation delay for the predators can
enhance stable coexistence for a class
of prey-predator models . . . . . . . . 154--171
Patrick De Leenheer and
Anushaya Mohapatra and
Haley A. Ohms and
David A. Lytle and
J. M. Cushing The puzzle of partial migration:
Adaptive dynamics and evolutionary game
theory perspectives . . . . . . . . . . 172--185
Deborah E. Shelton and
Martin P. Leslie and
Richard E. Michod Models of cell division initiation in
Chlamydomonas: a challenge to the
consensus view . . . . . . . . . . . . . 186--197
Pablo Mier and
Gregorio Alanis-Lobato and
Miguel A. Andrade-Navarro Protein-protein interactions can be
predicted using coiled coil co-evolution
patterns . . . . . . . . . . . . . . . . 198--203
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Jorge Hidalgo and
Samir Suweis and
Amos Maritan Species coexistence in a neutral
dynamics with environmental noise . . . 1--10
Anonymous Pages 1--86 (21 January 2017) . . . . . 1--86
Hui Lyu and
Dusan Lazár Modeling the light-induced electric
potential difference $ (\Delta \Psi) $,
the pH difference ($ \Delta $ pH) and
the proton motive force across the
thylakoid membrane in C$_3$ leaves . . . 11--23
Cécile Carr\`ere Optimization of an in vitro chemotherapy
to avoid resistant tumours . . . . . . . 24--33
Ada W. C. Yan and
Pengxing Cao and
Jane M. Heffernan and
Jodie McVernon and
Kylie M. Quinn and
Nicole L. La Gruta and
Karen L. Laurie and
James M. McCaw Modelling cross-reactivity and memory in
the cellular adaptive immune response to
influenza infection in the host . . . . 34--49
Sabrina Ellenberger and
Anke Burmester and
Stefan Schuster and
Johannes Wöstemeyer Post-translational regulation by
structural changes of
$4$-dihydromethyltrisporate
dehydrogenase, a key enzyme in sexual
and parasitic communication mediated by
the trisporic acid pheromone system, of
the fungal fusion parasite
\bionameParasitella parasitica . . . . . 50--57
Sarah Eug\`ene and
Thibault Bourgeron and
Zhou Xu Effects of initial telomere length
distribution on senescence onset and
heterogeneity . . . . . . . . . . . . . 58--65
Kazuyuki Takai Translational resistivity/conductivity
of coding sequences during exponential
growth of \bionameEscherichia coli . . . 66--71
Benjamin Watkinson-Powell and
Nina Alphey Resistance to genetic insect control:
Modelling the effects of space . . . . . 72--85
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Massimo Di Giulio Some pungent arguments against the
physico-chemical theories of the origin
of the genetic code and corroborating
the coevolution theory . . . . . . . . . 1--4
Anonymous Pages 1--268 (7 February 2017) . . . . . 1--268
Joseph Rusinko and
Matthew McPartlon Species tree estimation using Neighbor
Joining . . . . . . . . . . . . . . . . 5--7
Milad Kharratzadeh and
Marcel Montrey and
Alex Metz and
Thomas R. Shultz Specialized hybrid learners resolve
Rogers' paradox about the adaptive value
of social learning . . . . . . . . . . . 8--16
Arwen E. Nicholson and
David M. Wilkinson and
Hywel T. P. Williams and
Timothy M. Lenton Multiple states of environmental
regulation in well-mixed model
biospheres . . . . . . . . . . . . . . . 17--34
G. Vidal-Diez de Ulzurrun and
J. M. Baetens and
J. Van den Bulcke and
B. De Baets Modelling three-dimensional fungal
growth in response to environmental
stimuli . . . . . . . . . . . . . . . . 35--49
L. A. Spyrou and
M. Agoras and
K. Danas A homogenization model of the Voigt type
for skeletal muscle . . . . . . . . . . 50--61
Si-Kao Guo and
Peng-Ye Wang and
Ping Xie A model of processive movement of
dimeric kinesin . . . . . . . . . . . . 62--75
Hervé Seligmann Natural mitochondrial proteolysis
confirms transcription systematically
exchanging/deleting nucleotides,
peptides coded by expanded codons . . . 76--90
K. Kuritz and
D. Stöhr and
N. Pollak and
F. Allgöwer On the relationship between cell cycle
analysis with ergodic principles and
age-structured cell population models 91--102
Anuj Kumar and
Prashant K. Srivastava and
Yasuhiro Takeuchi Modeling the role of information and
limited optimal treatment on disease
prevalence . . . . . . . . . . . . . . . 103--119
Shigeru Kondo An updated kernel-based Turing model for
studying the mechanisms of biological
pattern formation . . . . . . . . . . . 120--127
Maryam Rahimi and
Mohammad Reza Bakhtiarizadeh and
Abdollah Mohammadi-Sangcheshmeh OOgenesis\_Pred: a sequence-based method
for predicting oogenesis proteins by six
different modes of Chou's pseudo amino
acid composition . . . . . . . . . . . . 128--136
Dominique Chu Limited by sensing --- a minimal
stochastic model of the lag-phase during
diauxic growth . . . . . . . . . . . . . 137--146
Marthe Målòy and
Frode Målòy and
Per Jakobsen and
Bjòrn Olav Brandsdal Dynamic self-organisation of
haematopoiesis and (a)symmetric cell
division . . . . . . . . . . . . . . . . 147--164
Anca R\uadulescu and
Rachel Marra A mathematical model of reward and
executive circuitry in obsessive
compulsive disorder . . . . . . . . . . 165--175
Matthijs van Veelen and
Benjamin Allen and
Moshe Hoffman and
Burton Simon and
Carl Veller Hamilton's rule . . . . . . . . . . . . 176--230
Kang-Ling Liao and
Roger D. Jones and
Patrick McCarter and
Meral Tunc-Ozdemir and
James A. Draper and
Timothy C. Elston and
David Kramer and
Alan M. Jones A shadow detector for photosynthesis
efficiency . . . . . . . . . . . . . . . 231--244
Marjorie T. Jones and
William R. Milligan and
Lee B. Kats and
Thomas L. Vandergon and
Rodney L. Honeycutt and
Robert N. Fisher and
Courtney L. Davis and
Timothy A. Lucas A discrete stage-structured model of
California newt population dynamics
during a period of drought . . . . . . . 245--253
Holger Perfahl and
Barry D. Hughes and
Tomás Alarcón and
Philip K. Maini and
Mark C. Lloyd and
Matthias Reuss and
Helen M. Byrne $3$D hybrid modelling of vascular
network formation . . . . . . . . . . . 254--268
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
József Garay and
Vill\Ho Csiszár and
Tamás F. Móri Evolutionary stability for matrix games
under time constraints . . . . . . . . . 1--12
Anonymous Pages 1--170 (21 February 2017) . . . . 1--170
Muslim Khan and
Maqsood Hayat and
Sher Afzal Khan and
Nadeem Iqbal Unb-DPC: Identify mycobacterial membrane
protein types by incorporating un-biased
dipeptide composition into Chou's
general PseAAC . . . . . . . . . . . . . 13--19
Shun Kurokawa and
Yasuo Ihara Evolution of group-wise cooperation: Is
direct reciprocity insufficient? . . . . 20--31
Masatsugu Yamada and
Masashi Iwanaga and
Kansuporn Sriyudthsak and
Masami Y. Hirai and
Fumihide Shiraishi Investigation of kinetic-order
sensitivities in metabolic reaction
networks . . . . . . . . . . . . . . . . 32--40
P. Narendra Kumar and
T. H. Swapna and
Mohamed Yahya Khan and
Jayasimha Rayalu Daddam and
Bee Hameeda Molecular dynamics and protein
interaction studies of lipopeptide
(Iturin A) on $ \alpha $- amylase of
\bionameSpodoptera litura . . . . . . . 41--47
Vasiliki Sgardeli and
Yoh Iwasa and
Harry Varvoglis and
John M. Halley A forecast for extinction debt in the
presence of speciation . . . . . . . . . 48--52
Muhammad Haseeb and
Shumaila Azam and
A. I. Bhatti and
Rizwan Azam and
Mukhtar Ullah and
Sahar Fazal On p53 revival using system oriented
drug dosage design . . . . . . . . . . . 53--57
Giovanni Marini and
Roberto Rosá and
Andrea Pugliese and
Hans Heesterbeek Exploring vector-borne infection ecology
in multi-host communities: a case study
of West Nile virus . . . . . . . . . . . 58--69
Xiulan Lai and
Avner Friedman Exosomal microRNA concentrations in
colorectal cancer: a mathematical model 70--83
Rong Li and
Dexing Zhong and
Ruiling Liu and
Hongqiang Lv and
Xinman Zhang and
Jun Liu and
Jiuqiang Han A novel method for in silico
identification of regulatory SNPs in
human genome . . . . . . . . . . . . . . 84--89
Sophie L\`ebre and
Olivier Gascuel The combinatorics of overlapping genes 90--101
A. Aydo\ugdu and
P. Frasca and
C. D'Apice and
R. Manzo and
J. M. Thornton and
B. Gachomo and
T. Wilson and
B. Cheung and
U. Tariq and
W. Saidel and
B. Piccoli Modeling birds on wires . . . . . . . . 102--112
Krishnendu Pal and
Biswajit Das and
Gautam Gangopadhyay Nonequilibrium response of a voltage
gated sodium ion channel and biophysical
characterization of dynamic hysteresis 113--124
Denise Veltman and
Thessa Laeremans and
Egle Passante and
Heinrich J. Huber Signal transduction analysis of the
NLRP3-inflammasome pathway after
cellular damage and its paracrine
regulation . . . . . . . . . . . . . . . 125--136
Shiyang Chen and
Bogdan Epureanu Regular biennial cycles in epidemics
caused by parametric resonance . . . . . 137--144
Farzaneh Maleki and
Attila Becskei An open-loop approach to calculate
noise-induced transitions . . . . . . . 145--157
Louis R. Nemzer Shannon information entropy in the
canonical genetic code . . . . . . . . . 158--170
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Min Su and
Mike Boots The impact of resource quality on the
evolution of virulence in spatially
heterogeneous environments . . . . . . . 1--7
Anonymous Pages 1--208 (7 March 2017) . . . . . . 1--208
Sarah E. Hook and
James France and
Jan Dijkstra Further assessment of the protozoal
contribution to the nutrition of the
ruminant animal . . . . . . . . . . . . 8--15
Xia Wang and
Gregory Mink and
Daniel Lin and
Xinyu Song and
Libin Rong Influence of raltegravir intensification
on viral load and $2$-LTR dynamics in
HIV patients on suppressive
antiretroviral therapy . . . . . . . . . 16--27
Troy Vargason and
Daniel P. Howsmon and
Stepan Melnyk and
S. Jill James and
Juergen Hahn Mathematical modeling of the methionine
cycle and transsulfuration pathway in
individuals with autism spectrum
disorder . . . . . . . . . . . . . . . . 28--37
Marzo Forment and
Guillermo Rodrigo Molecular noise can minimize the
collective sensitivity of a clonal
heterogeneous cell population . . . . . 38--44
Hirofumi Takesue Partner selection and emergence of the
merit-based equity norm . . . . . . . . 45--51
Yi-Shan Wang and
Jonathan R. Potts Partial differential equation techniques
for analysing animal movement: a
comparison of different methods . . . . 52--67
Matteo Smerlak and
Ahmed Youssef Limiting fitness distributions in
evolutionary dynamics . . . . . . . . . 68--80
Ya-Sen Jiao and
Pu-Feng Du Predicting protein submitochondrial
locations by incorporating the
positional-specific physicochemical
properties into Chou's general
pseudo-amino acid compositions . . . . . 81--87
Dennis J. Yoon and
Kevin Y. Chen and
André M. Lopes and
April A. Pan and
Joseph Shiloach and
Anne B. Mason and
Daniel T. Kamei Mathematical modeling of mutant
transferrin-CRM107 molecular conjugates
for cancer therapy . . . . . . . . . . . 88--98
Louise Viger and
Fabrice Denis and
Clément Draghi and
Thibault Ménard and
Christophe Letellier Spatial avascular growth of tumor in a
homogeneous environment . . . . . . . . 99--112
Alla P. Toropova and
Andrey A. Toropov Nano-QSAR in cell biology: Model of cell
viability as a mathematical function of
available eclectic data . . . . . . . . 113--118
A. Fallah and
M. T. Ahmadian and
K. Firozbakhsh and
M. M. Aghdam Micromechanical modeling of
rate-dependent behavior of Connective
tissues . . . . . . . . . . . . . . . . 119--128
Kalle Parvinen and
Hisashi Ohtsuki and
Joe Yuichiro Wakano The effect of fecundity derivatives on
the condition of evolutionary branching
in spatial models . . . . . . . . . . . 129--143
Alexander A. Tulub and
Vassily E. Stefanov Hidden symmetries of DNA molecule . . . 144--148
Erica J. Graham and
James F. Selgrade A model of ovulatory regulation
examining the effects of
insulin-mediated testosterone production
on ovulatory function . . . . . . . . . 149--160
Yi Jing and
Xia Wang and
Sanyi Tang and
Jianhong Wu Data informed analysis of 2014 dengue
fever outbreak in Guangzhou: Impact of
multiple environmental factors and
vector control . . . . . . . . . . . . . 161--179
Andrei E. Tarkhov and
Leonid I. Menshikov and
Peter O. Fedichev Strehler--Mildvan correlation is a
degenerate manifold of Gompertz fit . . 180--189
Sheanna Steingass and
Markus Horning Individual-based energetic model
suggests bottom up mechanisms for the
impact of coastal hypoxia on Pacific
harbor seal (\booktitlePhoca vitulina
richardii) foraging behavior . . . . . . 190--198
Vlastimil K\vrivan and
Ross Cressman Interaction times change evolutionary
outcomes: Two-player matrix games . . . 199--207
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Qian Xu and
Yi Xiong and
Hao Dai and
Kotni Meena Kumari and
Qin Xu and
Hong-Yu Ou and
Dong-Qing Wei PDC-SGB: Prediction of effective drug
combinations using a stochastic gradient
boosting algorithm . . . . . . . . . . . 1--7
Anonymous Pages 1--142 (21 March 2017) . . . . . . 1--142
Carlos Alberto Martínez and
Kshitij Khare and
Arunava Banerjee and
Mauricio A. Elzo Joint genome-wide prediction in several
populations accounting for randomness of
genotypes: a hierarchical Bayes
approach. I: Multivariate Gaussian
priors for marker effects and derivation
of the joint probability mass function
of genotypes . . . . . . . . . . . . . . 8--19
Tamas David-Barrett and
Robin I. M. Dunbar Fertility, kinship and the evolution of
mass ideologies . . . . . . . . . . . . 20--27
Partha Sharathi Dutta and
Bob W. Kooi and
Ulrike Feudel The impact of a predator on the outcome
of competition in the three-trophic food
web . . . . . . . . . . . . . . . . . . 28--42
Mostafa Sabzekar and
Mahmoud Naghibzadeh and
Javad Sadri Efficient dynamic programming algorithm
with prior knowledge for protein $ \beta
$-strand alignment . . . . . . . . . . . 43--50
D. Hala In silico predicted reproductive
endocrine transcriptional regulatory
networks during zebrafish (\bionameDanio
rerio) development . . . . . . . . . . . 51--60
Lawrence S. Schulman Bacterial resistance to antibodies: a
model evolutionary study . . . . . . . . 61--67
Ken-ichi Hironaka and
Yoshihiro Morishita Adaptive significance of critical weight
for metamorphosis in holometabolous
insects . . . . . . . . . . . . . . . . 68--83
Felipe A. Veloso On the developmental self-regulatory
dynamics and evolution of individuated
multicellular organisms . . . . . . . . 84--99
Christopher Bryant and
Mareike Fischer and
Simone Linz and
Charles Semple On the quirks of maximum parsimony and
likelihood on phylogenetic networks . . 100--108
J. Max Wyse and
Ian C. W. Hardy and
Lisa Yon and
Mike Mesterton-Gibbons The impact of competition on elephant
musth strategies: a game-theoretic model 109--130
Carlos Alberto Martínez and
Kshitij Khare and
Arunava Banerjee and
Mauricio A. Elzo Joint genome-wide prediction in several
populations accounting for randomness of
genotypes: a hierarchical Bayes
approach. II: Multivariate spike and
slab priors for marker effects and
derivation of approximate Bayes and
fractional Bayes factors for the
complete family of models . . . . . . . 131--141
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Emma Lejeune and
Christian Linder Quantifying the relationship between
cell division angle and morphogenesis
through computational modeling . . . . . 1--7
Anonymous Pages 1--138 (7 April 2017) . . . . . . 1--138
David E. Hiebeler and
Andrew Audibert and
Emma Strubell and
Isaac J. Michaud An epidemiological model of Internet
worms with hierarchical dispersal and
spatial clustering of hosts . . . . . . 8--15
Marc D. Ryser and
Kevin A. Murgas Bone remodeling as a spatial
evolutionary game . . . . . . . . . . . 16--26
Yuval R. Zelnik and
Hannes Uecker and
Ulrike Feudel and
Ehud Meron Desertification by front propagation? 27--35
Lloyd A. C. Chapman and
Jonathan P. Whiteley and
Helen M. Byrne and
Sarah L. Waters and
Rebecca J. Shipley Mathematical modelling of cell layer
growth in a hollow fibre bioreactor . . 36--56
Ace R. North and
H. Charles J. Godfray The dynamics of disease in a
metapopulation: The role of dispersal
range . . . . . . . . . . . . . . . . . 57--65
B. Huard and
A. Bridgewater and
M. Angelova Mathematical investigation of
diabetically impaired ultradian
oscillations in the glucose-insulin
regulation . . . . . . . . . . . . . . . 66--76
Priyadarshini P. Pai and
Tirtharaj Dash and
Sukanta Mondal Sequence-based discrimination of
protein-RNA interacting residues using a
probabilistic approach . . . . . . . . . 77--83
Yushuang Li and
Yanfen Lv and
Xiaonan Li and
Wenli Xiao and
Chun Li Sequence comparison and essential gene
identification with new inter-nucleotide
distance sequences . . . . . . . . . . . 84--93
Ján Elias Positive effect of Mdm2 on p53
expression explains excitability of p53
in response to DNA damage . . . . . . . 94--104
Lei Wang and
Zhu-Hong You and
Shi-Xiong Xia and
Feng Liu and
Xing Chen and
Xin Yan and
Yong Zhou Advancing the prediction accuracy of
protein--protein interactions by
utilizing evolutionary information from
position-specific scoring matrix and
ensemble classifier . . . . . . . . . . 105--110
Mansour Poorebrahim and
Solmaz Sadeghi and
Raziyeh Ghorbani and
Matin Asghari and
Mohammad Foad Abazari and
Hourieh Kalhor and
Hamzeh Rahimi In silico enhancement of the stability
and activity of keratinocyte growth
factor . . . . . . . . . . . . . . . . . 111--121
Pedro L. Valencia and
Carolina Astudillo-Castro and
Diego Gajardo and
Sebastián Flores Application of the median method to
estimate the kinetic constants of the
substrate uncompetitive inhibition
equation . . . . . . . . . . . . . . . . 122--128
Celine Scornavacca and
Joan Carles Pons Mayol and
Gabriel Cardona Fast algorithm for the reconciliation of
gene trees and LGT networks . . . . . . 129--137
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Marco Ajelli and
Maria Litvinova Estimating contact patterns relevant to
the spread of infectious diseases in
Russia . . . . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--394 (21 April 2017) . . . . . . 1--394
Alfonso Jiménez-Sánchez Bacterial cell cycle classification.
Application to DNA synthesis and DNA
content at any cell age . . . . . . . . 8--12
Mickaël Teixeira Alves and
Frank M. Hilker Hunting cooperation and Allee effects in
predators . . . . . . . . . . . . . . . 13--22
Riccardo Vesipa and
Luca Ridolfi Impact of seasonal forcing on reactive
ecological systems . . . . . . . . . . . 23--35
Thomas F. Hansen On the definition and measurement of
fitness in finite populations . . . . . 36--43
Diego López Alonso and
Isabel M. Ortiz-Rodríguez Offspring mortality was a determinant
factor in the evolution of paternal
investment in humans: An evolutionary
game approach . . . . . . . . . . . . . 44--51
Petteri Karisto and
Éva Kisdi Evolution of dispersal under variable
connectivity . . . . . . . . . . . . . . 52--65
Sungchan Kim and
M. A. Masud and
Giphil Cho and
Il Hyo Jung Analysis of a vector-bias effect in the
spread of malaria between two different
incidence areas . . . . . . . . . . . . 66--76
Harshana Rajakaruna and
Mark Lewis Temperature cycles affect colonization
potential of calanoid copepods . . . . . 77--89
Oren Rimer and
Gil Ariel Kinetic order-disorder transitions in a
pause-and-go swarming model with memory 90--99
Yvonne Richter and
Pedro G. Lind and
Gunnar Seemann and
Philipp Maass Anatomical and spiral wave reentry in a
simplified model for atrial
electrophysiology . . . . . . . . . . . 100--107
Ali Mohseni and
Shahriar Gharibzadeh and
Fatemeh Bakouie The role of driver nodes in managing
epileptic seizures: Application of
Kuramoto model . . . . . . . . . . . . . 108--115
Don Kulasiri and
Jingyi Liang and
Yao He and
Sandhya Samarasinghe Global sensitivity analysis of a model
related to memory formation in synapses:
Model reduction based on epistemic
parameter uncertainties and related
issues . . . . . . . . . . . . . . . . . 116--136
José A. Capitán and
Sara Cuenda and
David Alonso Stochastic competitive exclusion leads
to a cascade of species extinctions . . 137--151
Jinyou Yang and
Yuji Shimogonya and
Takuji Ishikawa Mixing and pumping functions of the
intestine of zebrafish larvae . . . . . 152--158
Omri Tal and
Tat Dat Tran and
Jacobus Portegies From typical sequences to typical
genotypes . . . . . . . . . . . . . . . 159--183
J. Mark Rowland and
Clifford R. Qualls and
Bruno A. Buzatto A model for conditional male
trimorphisms . . . . . . . . . . . . . . 184--192
Állan S. Pires and
William F. Porto and
Pryscilla O. Castro and
Octavio L. Franco and
Sérgio A. Alencar Theoretical structural characterization
of lymphoguanylin: a potential candidate
for the development of drugs to treat
gastrointestinal disorders . . . . . . . 193--200
Kenta Suzuki and
Yuji Yamauchi and
Takehito Yoshida Interplay between microbial trait
dynamics and population dynamics
revealed by the combination of
laboratory experiment and computational
approaches . . . . . . . . . . . . . . . 201--210
A. Stéphanou and
A. C. Lesart and
J. Deverch\`ere and
A. Juhem and
A. Popov and
F. Est\`eve How tumour-induced vascular changes
alter angiogenesis: Insights from a
computational model . . . . . . . . . . 211--226
Ercan E. Kuruo\uglu and
Peter F. Arndt The information capacity of the genetic
code: Is the natural code optimal? . . . 227--237
Guillaume Bassil and
Manuel Zarzoso and
Sami F. Noujaim Allometric scaling of electrical
excitation and propagation in the
mammalian heart . . . . . . . . . . . . 238--242
Gaku Oya and
Hisashi Ohtsuki Stable polymorphism of cooperators and
punishers in a public goods game . . . . 243--253
Katia Pane and
Lorenzo Durante and
Orlando Crescenzi and
Valeria Cafaro and
Elio Pizzo and
Mario Varcamonti and
Anna Zanfardino and
Viviana Izzo and
Alberto Di Donato and
Eugenio Notomista Antimicrobial potency of cationic
antimicrobial peptides can be predicted
from their amino acid composition:
Application to the detection of
``cryptic'' antimicrobial peptides . . . 254--265
Masayori Inouye and
Yojiro Ishida and
Keiko Inouye Designing of a single gene encoding four
functional proteins . . . . . . . . . . 266--268
Hitomi I. Sano and
Tamami Toki and
Yasuhiro Naito and
Masaru Tomita Developmental changes in the balance of
glycolytic ATP production and oxidative
phosphorylation in ventricular cells: a
simulation study . . . . . . . . . . . . 269--277
Mircea T. Sofonea and
Samuel Alizon and
Yannis Michalakis Exposing the diversity of multiple
infection patterns . . . . . . . . . . . 278--289
Pierre Magal and
Zhengyang Zhang Competition for light in forest
population dynamics: From computer
simulator to mathematical model . . . . 290--304
Ali Mehri Non-extensive distribution of human eye
photoreceptors . . . . . . . . . . . . . 305--309
Arnaud Dragicevic and
Vincent Boulanger and
Max Bruciamacchie and
Sandrine Chauchard and
Jean-Luc Dupouey and
Anne Stenger Network connectivity value . . . . . . . 310--322
Andrew E. F. Burgess and
Tommaso Lorenzi and
Piet\`a G. Schofield and
Stephen F. Hubbard and
Mark A. J. Chaplain Examining the role of individual
movement in promoting coexistence in a
spatially explicit prisoner's dilemma 323--332
Simon L. Goede and
Bastiaan E. de Galan and
Melvin Khee Shing Leow Personalized glucose-insulin model based
on signal analysis . . . . . . . . . . . 333--342
George P. Malanson Interactions and constraints in model
species response to environmental
heteroscedasticity . . . . . . . . . . . 343--349
I. A. Kuznetsov and
A. V. Kuznetsov Utilization of the bootstrap method for
determining confidence intervals of
parameters for a model of MAP1B protein
transport in axons . . . . . . . . . . . 350--361
Hassan Shafiey and
Toni I. Gossmann and
David Waxman Evolutionary control: Targeted change of
allele frequencies in natural
populations using externally directed
evolution . . . . . . . . . . . . . . . 362--374
Jose A. Cuesta and
Susanna Manrubia Enumerating secondary structures and
structural moieties for circular RNAs 375--382
James Sneyd and
Shawn Means and
Di Zhu and
John Rugis and
Jong Hak Won and
David I. Yule Modeling calcium waves in an
anatomically accurate three-dimensional
parotid acinar cell . . . . . . . . . . 383--393
Ada W. C. Yan and
Pengxing Cao and
Jane M. Heffernan and
Jodie McVernon and
Kylie M. Quinn and
Nicole L. La Gruta and
Karen L. Laurie and
James M. McCaw Corrigendum to ``Modelling
cross-reactivity and memory in the
cellular adaptive immune response to
influenza infection in the host'' [
J.Theor. Biol. \bf 413 (2017) 34--49] 394--394
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
W. Scott Persons and
Philip J. Currie The functional origin of dinosaur
bipedalism: Cumulative evidence from
bipedally inclined reptiles and
disinclined mammals . . . . . . . . . . 1--7
Anonymous Pages 1--324 (7 May 2017) . . . . . . . 1--324
Shi-Chang Wang and
Jie-Ru Yu and
Shun Kurokawa and
Yi Tao Imitation dynamics with time delay . . . 8--11
Xiu-Deng Zheng and
Cong Li and
Jie-Ru Yu and
Shi-Chang Wang and
Song-Jia Fan and
Bo-Yu Zhang and
Yi Tao A simple rule of direct reciprocity
leads to the stable coexistence of
cooperation and defection in the
Prisoner's Dilemma game . . . . . . . . 12--17
Bing Wang and
Yuexing Han and
Gouhei Tanaka Interplay between epidemic spread and
information propagation on
metapopulation networks . . . . . . . . 18--25
F. Débarre Fidelity of parent-offspring
transmission and the evolution of social
behavior in structured populations . . . 26--35
Joseba Dalmau Convergence of a Moran model to Eigen's
quasispecies model . . . . . . . . . . . 36--40
Jacob Hochard and
David Finnoff Cross-jurisdictional management of a
trophy-hunted species . . . . . . . . . 41--52
Takeshi Nishimura and
Akira Okada and
Yasuhiro Shirata Evolution of fairness and coalition
formation in three-person ultimatum
games . . . . . . . . . . . . . . . . . 53--67
Elizabeth C. Lee and
Michael R. Kelly and
Brad M. Ochocki and
Segun M. Akinwumi and
Karen E. S. Hamre and
Joseph H. Tien and
Marisa C. Eisenberg Model distinguishability and inference
robustness in mechanisms of cholera
transmission and loss of immunity . . . 68--81
Raluca Eftimie and
Haneen Hamam Modelling and investigation of the CD4+
T cells --- Macrophages paradox in
melanoma immunotherapies . . . . . . . . 82--104
Fyodor A. Syomin and
Andrey K. Tsaturyan A simple model of cardiac muscle for
multiscale simulation: Passive
mechanics, crossbridge kinetics and
calcium regulation . . . . . . . . . . . 105--116
Lena-Maria Holtz and
Dieter Wolf-Gladrow and
Silke Thoms Stable carbon isotope signals in
particulate organic and inorganic carbon
of coccolithophores --- a numerical
model study for \bionameEmiliania
huxleyi . . . . . . . . . . . . . . . . 117--127
Chunyan Zhang and
Yuying Zhu and
Zengqiang Chen and
Jianlei Zhang Punishment in the form of shared cost
promotes altruism in the cooperative
dilemma games . . . . . . . . . . . . . 128--134
Lei Zhao and
Dong Mi and
Yeqing Sun A novel multitarget model of
radiation-induced cell killing based on
the Gaussian distribution . . . . . . . 135--143
Benjamin D. Kaehler Full reconstruction of non-stationary
strand-symmetric models on rooted
phylogenies . . . . . . . . . . . . . . 144--151
Miljko V. Sataric and
Dalibor L. Sekulic and
Slobodan Zdravkovic and
Nebojsa M. Ralevic A biophysical model of how $ \alpha
$-tubulin carboxy-terminal tails tune
kinesin-1 processivity along microtubule 152--157
Kris De Jaegher By-product mutualism with evolving
common enemies . . . . . . . . . . . . . 158--173
Mike Steel and
Christoph Leuenberger The optimal rate for resolving a
near-polytomy in a phylogeny . . . . . . 174--179
Masoumeh Karami and
Chiya Jalali and
Sako Mirzaie Combined virtual screening, MMPBSA,
molecular docking and dynamics studies
against deadly anthrax: An in silico
effort to inhibit Bacillus anthracis
nucleoside hydrolase . . . . . . . . . . 180--189
Jonathan R. Potts and
Sergei V. Petrovskii Fortune favours the brave: Movement
responses shape demographic dynamics in
strongly competing populations . . . . . 190--199
Alberto Nakauma and
G. Sander van Doorn Reconstructing the genotype-to-fitness
map for the bacterial chemotaxis network
and its emergent behavioural phenotypes 200--212
Ross D. Booton and
Yoh Iwasa and
James A. R. Marshall and
Dylan Z. Childs Stress-mediated Allee effects can cause
the sudden collapse of honey bee
colonies . . . . . . . . . . . . . . . . 213--219
Joëlle De Caluwé and
José Romário Fernandes de Melo and
Alen Tosenberger and
Christian Hermans and
Nathalie Verbruggen and
Jean-Christophe Leloup and
Didier Gonze Modeling the photoperiodic entrainment
of the plant circadian clock . . . . . . 220--231
Peter Ashcroft and
Cassandra E. R. Smith and
Matthew Garrod and
Tobias Galla Effects of population growth on the
success of invading mutants . . . . . . 232--240
Lulan Shen and
Robert A. Van Gorder Predator--prey-subsidy population
dynamics on stepping-stone domains . . . 241--258
Ezhilarasi Krishnamoorthy and
Sameer Hassan and
Luke Elizabeth Hanna and
Indira Padmalayam and
Rama Rajaram and
Vijay Viswanathan Homology modeling of \bionameHomo
sapiens lipoic acid synthase: Substrate
docking and insights on its binding mode 259--266
Wolfgang Halter and
Jan Maximilian Montenbruck and
Zoltan A. Tuza and
Frank Allgöwer A resource dependent protein synthesis
model for evaluating synthetic circuits 267--278
Krzysztof Argasinski and
Ryszard Rudnicki Nest site lottery revisited: towards a
mechanistic model of population growth
suppressed by the availability of nest
sites . . . . . . . . . . . . . . . . . 279--289
Sharon Bewick and
Phillip P. A. Staniczenko and
Bingtuan Li and
David K. Karig and
William F. Fagan Invasion speeds in microbial systems
with toxin production and quorum sensing 290--303
Jonathan Warrell and
Musa Mhlanga Stability and structural properties of
gene regulation networks with
coregulation rules . . . . . . . . . . . 304--317
Tomer Handelman and
Benny Chor Cases in which ancestral maximum
likelihood will be confusingly
misleading . . . . . . . . . . . . . . . 318--323
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Wisam Ibrahim and
Mohammad Saniee Abadeh Extracting features from protein
sequences to improve deep extreme
learning machine for protein fold
recognition . . . . . . . . . . . . . . 1--15
Anonymous Pages 1--202 (21 May 2017) . . . . . . . 1--202
Shun Kurokawa The extended reciprocity: Strong belief
outperforms persistence . . . . . . . . 16--27
L. D. Valdez and
G. J. Sibona and
L. A. Diaz and
M. S. Contigiani and
C. A. Condat Effects of rainfall on \bionameCulex
mosquito population dynamics . . . . . . 28--38
Nina Shin and
Taewoo Kwag and
Sangwook Park and
Yon Hui Kim Effects of operational decisions on the
diffusion of epidemic disease: a system
dynamics modeling of the MERS-CoV
outbreak in South Korea . . . . . . . . 39--50
Manuel Pájaro and
Antonio A. Alonso and
Irene Otero-Muras and
Carlos Vázquez Stochastic modeling and numerical
simulation of gene regulatory networks
with protein bursting . . . . . . . . . 51--70
Xue Feng and
Yanling Zhang and
Long Wang Evolution of stinginess and generosity
in finite populations . . . . . . . . . 71--80
Ryo Yamaguchi and
Yoh Iwasa A tipping point in parapatric speciation 81--92
Yusuke Ikegawa and
Chihiro Himuro Limited mobility of target pests
crucially lowers controllability when
sterile insect releases are
spatiotemporally biased . . . . . . . . 93--100
Mohammad Tehrani and
Alireza S. Sarvestani Force-driven growth of intercellular
junctions . . . . . . . . . . . . . . . 101--111
Lester Caudill and
Barry Lawson A unified inter-host and in-host model
of antibiotic resistance and infection
spread in a hospital ward . . . . . . . 112--126
Kota Sawada and
Sachi Yamaguchi and
Yoh Iwasa Be a good loser: a theoretical model for
subordinate decision-making on
bi-directional sex change in haremic
fishes . . . . . . . . . . . . . . . . . 127--135
Shota Shibasaki and
Yuka Shirokawa and
Masakazu Shimada Cooperation induces other cooperation:
Fruiting bodies promote the evolution of
macrocysts in \bionameDictyostelium
discoideum . . . . . . . . . . . . . . . 136--145
Wendell P. Barreto and
Flavia M. D. Marquitti and
Marcus A. M. de Aguiar A genetic approach to the
rock-paper-scissors game . . . . . . . . 146--152
Kris V. Parag and
Oliver G. Pybus Optimal point process filtering and
estimation of the coalescent process . . 153--167
Shimon Haber and
Micha\l Weisbord and
Steven J. Mentzer and
Akira Tsuda Alveolar septal patterning during
compensatory lung growth: Part II the
effect of parenchymal pressure gradients 168--178
Pietro Mascheroni and
Daniela Boso and
Luigi Preziosi and
Bernhard A. Schrefler Evaluating the influence of mechanical
stress on anticancer treatments through
a multiphase porous media model . . . . 179--188
Jillian J. Jordan and
David G. Rand Third-party punishment as a costly
signal of high continuation
probabilities in repeated games . . . . 189--202
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Oleksii M. Matsiaka and
Catherine J. Penington and
Ruth E. Baker and
Matthew J. Simpson Continuum approximations for
lattice-free multi-species models of
collective cell migration . . . . . . . 1--11
Anonymous Pages 1--90 (7 June 2017) . . . . . . . 1--90
Vladimir Mityushev Optimal and stable random pattern
formations . . . . . . . . . . . . . . . 12--17
Bader Al-Anzi and
Sherif Gerges and
Noah Olsman and
Christopher Ormerod and
Georgios Piliouras and
John Ormerod and
Kai Zinn Modeling and analysis of modular
structure in diverse biological networks 18--30
Li Xu and
Jin Wang Quantifying the potential and flux
landscapes of multi-locus evolution . . 31--49
Frazer Meacham and
Thomas Getty Deadbeats or losers: Discretionary male
parental investment can make females
less choosy . . . . . . . . . . . . . . 50--58
S. Sahmani and
M. M. Aghdam Size-dependent axial instability of
microtubules surrounded by cytoplasm of
a living cell based on nonlocal strain
gradient elasticity theory . . . . . . . 59--71
Mohsen B. Mesgaran and
Juliette Bouhours and
Mark A. Lewis and
Roger D. Cousens How to be a good neighbour: Facilitation
and competition between two co-flowering
species . . . . . . . . . . . . . . . . 72--83
Cangzhi Jia and
Yun Zuo S-SulfPred: a sensitive predictor to
capture S-sulfenylation sites based on a
resampling one-sided selection
undersampling-synthetic minority
oversampling technique . . . . . . . . . 84--89
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Magnus Bordewich and
Simone Linz and
Charles Semple Lost in space? Generalising subtree
prune and regraft to spaces of
phylogenetic networks . . . . . . . . . 1--12
Anonymous Pages 1--70 (21 June 2017) . . . . . . . 1--70
Parvathi Haridas and
Catherine J. Penington and
Jacqui A. McGovern and
D. L. Sean McElwain and
Matthew J. Simpson Quantifying rates of cell migration and
cell proliferation in co-culture barrier
assays reveals how skin and melanoma
cells interact during melanoma spreading
and invasion . . . . . . . . . . . . . . 13--25
Robert J. Clegg and
Jan-Ulrich Kreft Reducing discrepancies between $3$D and
$2$D simulations due to cell packing
density . . . . . . . . . . . . . . . . 26--30
Stuart Serdoz and
Attila Egri-Nagy and
Jeremy Sumner and
Barbara R. Holland and
Peter D. Jarvis and
Mark M. Tanaka and
Andrew R. Francis Maximum likelihood estimates of pairwise
rearrangement distances . . . . . . . . 31--40
Ashish Goyal and
John M. Murray Roadmap to control HBV and HDV epidemics
in China . . . . . . . . . . . . . . . . 41--52
András Szilágyi and
Gergely Boza and
István Scheuring Analysis of stability to cheaters in
models of antibiotic degrading microbial
communities . . . . . . . . . . . . . . 53--62
Sijia Wu and
Jiuqiang Han and
Xinman Zhang and
Dexing Zhong and
Ruiling Liu A computational model for predicting
integrase catalytic domain of retrovirus 63--70
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Akira Sasaki and
Akiko N. Mizuno Partitioning light spectra: Adaptive
stratification of phytobenthic
communities in Antarctic lakes . . . . . 1--10
Anonymous Pages 1--110 (7 July 2017) . . . . . . . 1--110
Chris Guiver and
David Packman and
Stuart Townley A necessary condition for dispersal
driven growth of populations with
discrete patch dynamics . . . . . . . . 11--25
Virginie Raybaud and
Sylvie Tambutté and
Christine Ferrier-Pag\`es and
Stéphanie Reynaud and
Alexander A. Venn and
Éric Tambutté and
Paul Nival and
Denis Allemand Computing the carbonate chemistry of the
coral calcifying medium and its response
to ocean acidification . . . . . . . . . 26--36
Christopher E. Miles and
James P. Keener Bidirectionality from cargo thermal
fluctuations in motor-mediated transport 37--48
Pooja Tripathi and
Paras N. Pandey A novel alignment-free method to
classify protein folding types by
combining spectral graph clustering with
Chou's pseudo amino acid composition . . 49--54
Marc Sturrock and
Shiyu Li and
Vahid Shahrezaei The influence of nuclear
compartmentalisation on stochastic
dynamics of self-repressing gene
expression . . . . . . . . . . . . . . . 55--72
Fengqin Zhang and
Jianquan Li and
Jia Li Epidemic characteristics of two classic
SIS models with disease-induced death 73--83
Nicholas J. Ose and
Paul R. Ohmann The selfish herd: Noise effects in Local
Crowded Horizon and Voronoi models . . . 84--90
Sergei Petrovskii and
Yadigar Sekerci and
Ezio Venturino Regime shifts and ecological
catastrophes in a model of
plankton-oxygen dynamics under the
climate change . . . . . . . . . . . . . 91--109
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
R. De Vita and
R. Grange and
P. Nardinocchi and
L. Teresi Mathematical model for isometric and
isotonic muscle contractions . . . . . . 1--10
Anonymous Pages 1--112 (21 July 2017) . . . . . . 1--112
Tuomas Nurmi and
Kalle Parvinen and
Vesa Selonen The evolution of site-selection strategy
during dispersal . . . . . . . . . . . . 11--22
Akane Hara and
Yoh Iwasa When is allergen immunotherapy
effective? . . . . . . . . . . . . . . . 23--42
Jie Zhang and
Angela G. Fleischman and
Dominik Wodarz and
Natalia L. Komarova Determining the role of inflammation in
the selection of JAK2 mutant cells in
myeloproliferative neoplasms . . . . . . 43--52
Paul A. Roberts and
Eamonn A. Gaffney and
Philip J. Luthert and
Alexander J. E. Foss and
Helen M. Byrne Mathematical models of retinitis
pigmentosa: The oxygen toxicity
hypothesis . . . . . . . . . . . . . . . 53--71
Peng Du and
Gregory O'Grady and
Leo K. Cheng A theoretical analysis of anatomical and
functional intestinal slow wave re-entry 72--79
Ze-Gang Wei and
Shao-Wu Zhang DBH: a de Bruijn graph-based heuristic
method for clustering large-scale 16S
rRNA sequences into OTUs . . . . . . . . 80--87
Christopher D. Powell and
Secundino López and
André Dumas and
Dominique P. Bureau and
Sarah E. Hook and
James France Mathematical descriptions of
indeterminate growth . . . . . . . . . . 88--96
Abdollah Dehzangi and
Yosvany López and
Sunil Pranit Lal and
Ghazaleh Taherzadeh and
Jacob Michaelson and
Abdul Sattar and
Tatsuhiko Tsunoda and
Alok Sharma PSSM-Suc: Accurately predicting
succinylation using position specific
scoring matrix into bigram for feature
extraction . . . . . . . . . . . . . . . 97--102
A. C. Szatmary and
R. Nossal Determining whether observed eukaryotic
cell migration indicates chemotactic
responsiveness or random chemokinetic
motion . . . . . . . . . . . . . . . . . 103--112
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
P. Xenitidis and
I. Seimenis and
S. Kakolyris and
A. Adamopoulos Evaluation of artificial time series
microarray data for dynamic gene
regulatory network inference . . . . . . 1--16
Anonymous Pages 1--180 (7 August 2017) . . . . . . 1--180
Stefan Landmann and
Nicolas Preuss and
Ulrich Behn Self-tolerance and autoimmunity in a
minimal model of the idiotypic network 17--39
Michaela Hamm and
Barbara Drossel Habitat heterogeneity hypothesis and
edge effects in model metacommunities 40--48
N. Almeira and
S. Risau-Gusman Role of transcriptional bursts in
cellular oscillations . . . . . . . . . 49--56
Juan Camilo Ramírez and
James A. R. Marshall Can natural selection encode Bayesian
priors? . . . . . . . . . . . . . . . . 57--66
Omer Edhan and
Ziv Hellman and
Dana Sherill-Rofe Sex with no regrets: How sexual
reproduction uses a no regret learning
algorithm for evolutionary advantage . . 67--81
Mainak Patel and
Aaditya Rangan Role of the \bionamelocus coeruleus in
the emergence of power law wake bouts in
a model of the brainstem sleep-wake
system through early infancy . . . . . . 82--95
William F. Porto and
Állan S. Pires and
Octavio L. Franco Antimicrobial activity predictors
benchmarking analysis using shuffled and
designed synthetic peptides . . . . . . 96--103
Ricardo Martínez-García and
Corina E. Tarnita Seasonality can induce coexistence of
multiple bet-hedging strategies in
\bionameDictyostelium discoideum via
storage effect . . . . . . . . . . . . . 104--116
Raouf El Cheikh and
Samuel Bernard and
Nader El Khatib A multiscale modelling approach for the
regulation of the cell cycle by the
circadian clock . . . . . . . . . . . . 117--125
Shanxin Zhang and
Zhiping Zhou and
Xinmeng Chen and
Yong Hu and
Lindong Yang pDHS-SVM: a prediction method for plant
DNase I hypersensitive sites based on
support vector machine . . . . . . . . . 126--133
Nasrollah Rezaei-Ghaleh and
Davood Bakhtiari and
Armin Rashidi Reverse allostasis in biological
systems: Minimal conditions and
implications . . . . . . . . . . . . . . 134--139
Helene C. Weigang Coevolution of patch-type dependent
emigration and patch-type dependent
immigration . . . . . . . . . . . . . . 140--151
Ariel Ram\'ìrez-Torres and
Reinaldo Rodr\'ìguez-Ramos and
Federico J. Sabina and
Catherine Garc\'ìa-Reimbert and
Raimondo Penta and
José Merodio and
Raúl Guinovart-D\'ìaz and
Julián Bravo-Castillero and
Aura Conci and
Luigi Preziosi The role of malignant tissue on the
thermal distribution of cancerous breast 152--161
V. R. Chechetkin and
V. V. Lobzin Large-scale chromosome folding versus
genomic DNA sequences: a discrete double
Fourier transform technique . . . . . . 162--179
Kenta Suzuki and
Yuji Yamauchi and
Takehito Yoshida Corrigendum to ``Interplay between
microbial trait dynamics and population
dynamics revealed by the combination of
laboratory experiment and computational
approaches'' [Journal of Theoretical
Biology \bf 419 (2017) 201--210] . . . . 180--180
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Markus Schmidt and
Arne Kutzner and
Klaus Heese A novel specialized single-linkage
clustering algorithm for taxonomically
ordered data . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--90 (1 August 2017) . . . . . . 1--90
Ashim K. Chakravarty, FNASc. Thermodynamic stability of biomolecules
and evolution . . . . . . . . . . . . . 8--9
Hui Liu and
Dawei Hu and
Chen Dong and
Yuming Fu and
Guanghui Liu and
Youcai Qin and
Yi Sun and
Dianlei Liu and
Lei Li and
Hong Liu Low-dose ionizing radiation limitations
to seed germination: Results from a
model linking physiological
characteristics and
developmental-dynamics simulation
strategy . . . . . . . . . . . . . . . . 10--16
Yukitaka Ishimoto and
Kaoru Sugimura A mechanical model for diversified
insect wing margin shapes . . . . . . . 17--27
A. B. M. Shamim Ul Hasan and
Hiroyuki Kurata Mathematical comparison of memory
functions between mutual activation and
repression networks in a stochastic
environment . . . . . . . . . . . . . . 28--40
Lily He and
Yongkun Li and
Rong Lucy He and
Stephen S.-T. Yau A novel alignment-free vector method to
cluster protein sequences . . . . . . . 41--52
Geoff Wild and
Judith Korb Evolution of delayed dispersal and
subsequent emergence of helping, with
implications for cooperative breeding 53--64
Yuma Sakai and
Takenori Takada The analysis of an effect of seed
propagation on defense strategy against
pathogen transmission within clonal
plant population using lattice model . . 65--76
Ion Bica and
Thomas Hillen and
Kevin J. Painter Aggregation of biological particles
under radial directional guidance . . . 77--89
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Sze-chuan Suen and
Jeremy D. Goldhaber-Fiebert and
Margaret L. Brandeau Risk stratification in compartmental
epidemic models: Where to draw the line? 1--17
Anonymous Pages 1--168 (7 September 2017) . . . . 1--168
Katharina Brinck and
Henrik Jeldtoft Jensen The evolution of ecosystem ascendency in
a complex systems based model . . . . . 18--25
Candace Jones and
Brad Pearce and
Ingrid Barrera and
Amanda Mummert Fetal programming and eating disorder
risk . . . . . . . . . . . . . . . . . . 26--33
Andrew S. Tupper and
Paul G. Higgs Error thresholds for RNA replication in
the presence of both point mutations and
premature termination errors . . . . . . 34--42
Simon Garnier and
Daniel J. C. Kronauer The adaptive significance of phasic
colony cycles in army ants . . . . . . . 43--47
Serafino Teseo and
Francesco Delloro Reduced foraging investment as an
adaptation to patchy food sources: a
phasic army ant simulation . . . . . . . 48--55
Koichiro Uriu and
Hajime Tei Feedback loops interlocked at
competitive binding sites amplify and
facilitate genetic oscillations . . . . 56--64
Jeremy P. D'Silva and
Marisa C. Eisenberg Modeling spatial invasion of Ebola in
West Africa . . . . . . . . . . . . . . 65--75
Joung-Hun Lee and
Marko Jusup and
Yoh Iwasa Games of corruption in preventing the
overuse of common-pool resources . . . . 76--86
H. A. Castro-Abril and
J. M. Guevara and
M. A. Moncayo and
S. J. Shefelbine and
L. A. Barrera and
D. A. Garzón-Alvarado Cellular scale model of growth plate: An
in silico model of chondrocyte
hypertrophy . . . . . . . . . . . . . . 87--97
Arndt Telschow and
Florian Grziwotz and
Philip Crain and
Takeshi Miki and
James W. Mains and
George Sugihara and
Stephen L. Dobson and
Chih-hao Hsieh Infections of \bionameWolbachia may
destabilize mosquito population dynamics 98--105
David Rudrauf and
Daniel Bennequin and
Isabela Granic and
Gregory Landini and
Karl Friston and
Kenneth Williford A mathematical model of embodied
consciousness . . . . . . . . . . . . . 106--131
E. J. Müller and
S. J. van Albada and
J. W. Kim and
P. A. Robinson Unified neural field theory of brain
dynamics underlying oscillations in
Parkinson's disease and generalized
epilepsies . . . . . . . . . . . . . . . 132--146
Lingling Li and
Tianhai Tian and
Xinan Zhang The impact of radiation on the
development of lung cancer . . . . . . . 147--152
J. C. Helps and
N. D. Paveley and
F. van den Bosch Identifying circumstances under which
high insecticide dose increases or
decreases resistance selection . . . . . 153--167
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Hayley C. Warsinske and
Robert M. DiFazio and
Jennifer J. Linderman and
JoAnne L. Flynn and
Denise E. Kirschner Identifying mechanisms driving formation
of granuloma-associated fibrosis during
Mycobacterium tuberculosis infection . . 1--17
Anonymous Pages 1--266 (21 September 2017) . . . . 1--266
Diana White and
Stéphane Honoré and
Florence Hubert Exploring the effect of end-binding
proteins and microtubule targeting
chemotherapy drugs on microtubule
dynamic instability . . . . . . . . . . 18--34
Krzysztof Bartoszek and
Sylvain Glémin and
Ingemar Kaj and
Martin Lascoux Using the Ornstein--Uhlenbeck process to
model the evolution of interacting
populations . . . . . . . . . . . . . . 35--45
Roberto Andrea Abbiati and
Petra Cagnardi and
Giuliano Ravasio and
Roberto Villa and
Davide Manca A physiologically based model for
tramadol pharmacokinetics in horses . . 46--51
M. Gámez and
I. López and
C. Rodríguez and
Z. Varga and
J. Garay Ecological monitoring in a discrete-time
prey-predator model . . . . . . . . . . 52--60
D. Peurichard and
F. Delebecque and
A. Lorsignol and
C. Barreau and
J. Rouquette and
X. Descombes and
L. Casteilla and
P. Degond Simple mechanical cues could explain
adipose tissue morphology . . . . . . . 61--81
Jan Eric Sträng and
Rainer Schuler and
Michael Kühl and
Hans A. Kestler Switch-like behavior enables Wnt11
concentration specific response during
dorso-ventral axis formation in
\bionameXenopus laevis . . . . . . . . . 82--94
Daiki Sasaki and
Hitomi Nakajima and
Yoshimi Yamaguchi and
Ryuji Yokokawa and
Shin-Ichiro Ei and
Takashi Miura Mathematical modeling for meshwork
formation of endothelial cells in fibrin
gels . . . . . . . . . . . . . . . . . . 95--104
Karan Pattni and
Mark Broom and
Jan Rychtár Evolutionary dynamics and the evolution
of multiplayer cooperation in a
subdivided population . . . . . . . . . 105--115
Ehsan Saghapour and
Mohammadreza Sehhati Prediction of metastasis in advanced
colorectal carcinomas using CGH data . . 116--123
Olga A. Nev and
Oleg A. Nev and
Hugo A. van den Berg Optimal management of nutrient reserves
in microorganisms under time-varying
environmental conditions . . . . . . . . 124--141
Ibrahim Cimentepe and
Haluk O. Bingol Parent oriented teacher selection causes
language diversity . . . . . . . . . . . 142--148
Marc Garbey and
Stefano Casarin and
Scott A. Berceli Vascular Adaptation: Pattern Formation
and Cross Validation between an Agent
Based Model and a Dynamical System . . . 149--163
Sòren Toxvaerd The role of the peptides at the origin
of life . . . . . . . . . . . . . . . . 164--169
Matthew H. Holden and
Eve McDonald-Madden High prices for rare species can drive
large populations extinct: the
anthropogenic Allee effect revisited . . 170--180
Umberto Lucia and
Giulia Grisolia and
Antonio Ponzetto and
Francesca Silvagno An engineering thermodynamic approach to
select the electromagnetic wave
effective on cell growth . . . . . . . . 181--189
Jienian Yang and
David E. Axelrod and
Natalia L. Komarova Determining the control networks
regulating stem cell lineages in colonic
crypts . . . . . . . . . . . . . . . . . 190--203
Ali Abroudi and
Sandhya Samarasinghe and
Don Kulasiri A comprehensive complex systems approach
to the study and analysis of mammalian
cell cycle control system in the
presence of DNA damage stress . . . . . 204--228
Sourav Kumar Sasmal and
Yueping Dong and
Yasuhiro Takeuchi Mathematical modeling on T-cell mediated
adaptive immunity in primary dengue
infections . . . . . . . . . . . . . . . 229--240
Chung Yin (Joey) Leung and
Joshua S. Weitz Modeling the synergistic elimination of
bacteria by phage and the innate immune
system . . . . . . . . . . . . . . . . . 241--252
Olivier Gallinato and
Thierry Colin and
Olivier Saut and
Clair Poignard Tumor growth model of ductal carcinoma:
from in situ phase to stroma invasion 253--266
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Alexander É. Filippov and
Jonas O. Wolff and
Michael Seiter and
Stanislav N. Gorb Numerical simulation of colloidal
self-assembly of super-hydrophobic
arachnid cerotegument structures . . . . 1--8
Anonymous Pages 1--282 (7 October 2017) . . . . . 1--282
Yu-Ting Wen and
Hai-Jun Lei and
Zhu-Hong You and
Bai-Ying Lei and
Xing Chen and
Li-Ping Li Prediction of protein--protein
interactions by label propagation with
protein evolutionary and chemical
information derived from heterogeneous
network . . . . . . . . . . . . . . . . 9--20
J. David Van Dyken Noise slows the rate of
Michaelis--Menten reactions . . . . . . 21--31
Hendrik B. Tiedemann and
Elida Schneltzer and
Johannes Beckers and
Gerhard K. H. Przemeck and
Martin Hrabe de Angelis Modeling coexistence of oscillation and
Delta/Notch-mediated lateral inhibition
in pancreas development and neurogenesis 32--44
Annette Cazaubiel and
Alessandra F. Lütz and
Jeferson J. Arenzon Collective strategies and cyclic
dominance in asymmetric predator--prey
spatial games . . . . . . . . . . . . . 45--52
Jonathan Fiorentino and
Andrea De Martino Independent channels for miRNA
biosynthesis ensure efficient static and
dynamic control in the regulation of the
early stages of myogenesis . . . . . . . 53--63
Hassan Shafiey and
David Waxman Exact results for the probability and
stochastic dynamics of fixation in the
Wright--Fisher model . . . . . . . . . . 64--77
Christine Mayer and
Thomas F. Hansen Evolvability and robustness: a paradox
restored . . . . . . . . . . . . . . . . 78--85
József Garay and
Vill\Ho Csiszár and
Tamás F. Móri Survival phenotype, selfish individual
versus Darwinian phenotype . . . . . . . 86--91
Martin P. Leslie and
Deborah E. Shelton and
Richard E. Michod Generation time and fitness tradeoffs
during the evolution of multicellularity 92--102
Zsolt Bertalan and
Stefano Zapperi and
Caterina A. M. La Porta Modeling mechanical control of spindle
orientation of intestinal crypt stem
cells . . . . . . . . . . . . . . . . . 103--108
Jason Laurie and
Amit K. Chattopadhyay and
Darren R. Flower Protein lipograms . . . . . . . . . . . 109--116
Pengxing Cao and
Nectarios Klonis and
Sophie Zaloumis and
David S. Khoury and
Deborah Cromer and
Miles P. Davenport and
Leann Tilley and
Julie A. Simpson and
James M. McCaw A mechanistic model quantifies
artemisinin-induced parasite growth
retardation in blood-stage
\bionamePlasmodium falciparum infection 117--127
Matthew P. Edgington and
Luke S. Alphey Conditions for success of engineered
underdominance gene drive systems . . . 128--140
Christian F. Schmutz and
Trey D. Hatton and
Michael P. Blomfield and
Benjamin D. Chandler and
Trent C. Benedick and
Marc D. H. Hansen A cellular automaton based on plasma
membrane turnover accurately
recapitulates cell mechanics during
epithelial scattering . . . . . . . . . 141--156
Chase Cockrell and
Gary An Sepsis reconsidered: Identifying novel
metrics for behavioral landscape
characterization with a high-performance
computing implementation of an
agent-based model . . . . . . . . . . . 157--168
Álvaro G. López and
Kelly C. Iarosz and
Antonio M. Batista and
Jesús M. Seoane and
Ricardo L. Viana and
Miguel A. F. Sanjuán The dose-dense principle in chemotherapy 169--176
R. Arthur and
A. Nicholson An entropic model of Gaia . . . . . . . 177--184
J. David Van Dyken Propagation and control of gene
expression noise with non-linear
translation kinetics . . . . . . . . . . 185--194
Sargon A. Gabriel and
Yan Ding and
Yuqing Feng Quantifying the influence of oscillatory
flow disturbances on blood flow . . . . 195--206
Kristina Wicke and
Mareike Fischer Comparing the rankings obtained from two
biodiversity indices: the Fair
Proportion Index and the Shapley Value 207--214
Seung Ki Baek and
Su Do Yi and
Hyeong-Chai Jeong Duality between cooperation and
defection in the presence of tit-for-tat
in replicator dynamics . . . . . . . . . 215--220
Christian Cherubini and
Simonetta Filippi and
Alessio Gizzi and
Ricardo Ruiz-Baier A note on stress-driven anisotropic
diffusion and its role in active
deformable media . . . . . . . . . . . . 221--228
Valentin Thouzeau and
Michel Raymond Emergence and maintenance of menopause
in humans: a game theory model . . . . . 229--236
Shai Pilosof and
Gili Greenbaum and
Boris R. Krasnov and
Yuval R. Zelnik Asymmetric disease dynamics in multihost
interconnected networks . . . . . . . . 237--244
Chin F. Ng and
Hermann B. Frieboes Model of vascular desmoplastic
multispecies tumor growth . . . . . . . 245--282
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Hanna Schenk and
Arne Traulsen and
Chaitanya S. Gokhale Chaotic provinces in the kingdom of the
Red Queen . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--96 (27 October 2017) . . . . . 1--96
R. Rockenfeller and
M. Günther Hill equation and Hatze's muscle
activation dynamics complement each
other: enhanced pharmacological and
physiological interpretability of
modelled activity-pCa curves . . . . . . 11--24
Tomotaka Matsumoto and
Kohta Yoshida and
Jun Kitano Contribution of gene flow to the
evolution of recombination suppression
in sex chromosomes . . . . . . . . . . . 25--31
Jiri Vohradsky Lambda phage genetic switch as a system
with critical behaviour . . . . . . . . 32--38
Ronny Straube Operating regimes of covalent
modification cycles at high enzyme
concentrations . . . . . . . . . . . . . 39--48
Ross Cunning and
Erik B. Muller and
Ruth D. Gates and
Roger M. Nisbet A dynamic bioenergetic model for
coral-\bionameSymbiodinium symbioses and
coral bleaching as an alternate stable
state . . . . . . . . . . . . . . . . . 49--62
Marisa C. Eisenberg and
Harsh V. Jain A confidence building exercise in data
and identifiability: Modeling cancer
chemotherapy as a case study . . . . . . 63--78
Daniel J. M. Crouch Statistical aspects of evolution under
natural selection, with implications for
the advantage of sexual reproduction . . 79--86
Liane Gabora and
Mike Steel Autocatalytic networks in cognition and
the origin of culture . . . . . . . . . 87--95
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Yao-ban Chan and
Vincent Ranwez and
Céline Scornavacca Inferring incomplete lineage sorting,
duplications, transfers and losses with
reconciliations . . . . . . . . . . . . 1--13
Anonymous Pages 1--168 (7 November 2017) . . . . . 1--168
Massimo Di Giulio The aminoacyl-tRNA synthetases had only
a marginal role in the origin of the
organization of the genetic code:
Evidence in favor of the coevolution
theory . . . . . . . . . . . . . . . . . 14--24
Francisco Serrano-Alcalde and
José Manuel García-Aznar and
María José Gómez-Benito The role of nuclear mechanics in cell
deformation under creeping flows . . . . 25--32
Johannes W. R. Martini A measure to quantify the degree of
cooperativity in overall titration
curves . . . . . . . . . . . . . . . . . 33--37
James P. Grover Sink or swim? Vertical movement and
nutrient storage in phytoplankton . . . 38--48
Xiong Jiao and
Shoba Ranganathan Prediction of interface residue based on
the features of residue interaction
network . . . . . . . . . . . . . . . . 49--54
B. Polizzi and
O. Bernard and
M. Ribot A time-space model for the growth of
microalgae biofilms for biofuel
production . . . . . . . . . . . . . . . 55--79
Jing-Xuan Zhai and
Tian-Jie Cao and
Ji-Yong An and
Yong-Tao Bian Highly accurate prediction of protein
self-interactions by incorporating the
average block and PSSM information into
the general PseAAC . . . . . . . . . . . 80--86
Lorenzo Mari and
Manuela Ciddio and
Renato Casagrandi and
Javier Perez-Saez and
Enrico Bertuzzo and
Andrea Rinaldo and
Susanne H. Sokolow and
Giulio A. De Leo and
Marino Gatto Heterogeneity in schistosomiasis
transmission dynamics . . . . . . . . . 87--99
Xiaona Sheng and
Yihong Qiu and
Ying Zhou and
Wensheng Zhu Joint parameter estimation in the QTL
mapping of ordinal traits . . . . . . . 100--108
Henry R. Allen and
Mariya Ptashnyk Mathematical modelling and analysis of
the brassinosteroid and gibberellin
signalling pathways and their
interactions . . . . . . . . . . . . . . 109--131
Ram P. Sigdel and
Madhur Anand and
Chris T. Bauch Competition between injunctive social
norms and conservation priorities gives
rise to complex dynamics in a model of
forest growth and opinion dynamics . . . 132--140
Paula Sanz-Leon and
P. A. Robinson Multistability in the corticothalamic
system . . . . . . . . . . . . . . . . . 141--156
Qian Yang and
Tim Rogers and
Jonathan H. P. Dawes Demographic noise slows down cycles of
dominance . . . . . . . . . . . . . . . 157--168
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Bingxiang Xu and
Hao Ge and
Zhihua Zhang An efficient and assumption-free method
to approximate protein level
distribution in the two-states gene
expression model . . . . . . . . . . . . 1--7
Anonymous Pages 1--106 (21 November 2017) . . . . 1--106
Blerta Shtylla Mathematical modeling of spatiotemporal
protein localization patterns in
\bionameC. crescentus bacteria: a
mechanism for asymmetric FtsZ ring
positioning . . . . . . . . . . . . . . 8--20
Sanzo Miyazawa Selection originating from protein
stability/foldability: Relationships
between protein folding free energy,
sequence ensemble, and fitness . . . . . 21--38
Simão Laranjeira and
Mkael Symmonds and
Jacqueline Palace and
Stephen J. Payne and
Piotr Orlowski A mathematical model of cellular
swelling in Neuromyelitis optica . . . . 39--48
Shi-Lei Xue and
Shao-Zhen Lin and
Bo Li and
Xi-Qiao Feng A nonlinear poroelastic theory of solid
tumors with glycosaminoglycan swelling 49--56
Zhijun Qiu and
Bo Zhou and
Jiangfeng Yuan Protein-protein interaction site
predictions with minimum covariance
determinant and Mahalanobis distance . . 57--63
Tadeas Priklopil and
Krishnendu Chatterjee and
Martin Nowak Optional interactions and suspicious
behaviour facilitates trustful
cooperation in prisoners dilemma . . . . 64--72
N. Hafizah Mokhtar and
Aizat Abas and
N. A. Razak and
Muhammad Najib Abdul Hamid and
Soon Lay Teong Effect of different stent configurations
using Lattice Boltzmann method and
particles image velocimetry on artery
bifurcation aneurysm problem . . . . . . 73--84
Kavita Jain and
Ananthu James Fixation probability of a nonmutator in
a large population of asexual mutators 85--93
Daniel Koch and
Robert S. Eisinger and
Alexander Gebharter A causal Bayesian network model of
disease progression mechanisms in
chronic myeloid leukemia . . . . . . . . 94--105
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Athel Cornish-Bowden Lynn Margulis and the origin of the
eukaryotes . . . . . . . . . . . . . . . 1--1
William F. Martin Physiology, anaerobes, and the origin of
mitosing cells 50 years on . . . . . . . 2--10
W. Ford Doolittle Darwinizing Gaia . . . . . . . . . . . . 11--19
Purificación López-García and
Laura Eme and
David Moreira Symbiosis in eukaryotic evolution . . . 20--33
Maureen A. O'Malley From endosymbiosis to holobionts:
Evaluating a conceptual legacy . . . . . 34--41
Wylie Stroberg and
Santiago Schnell On the origin of non-membrane-bound
organelles, and their physiological
function . . . . . . . . . . . . . . . . 42--49
John F. Allen The CoRR hypothesis for genes in
organelles . . . . . . . . . . . . . . . 50--57
Nick Lane Serial endosymbiosis or singular event
at the origin of eukaryotes? . . . . . . 58--67
Athel Cornish-Bowden and
María Luz Cárdenas Life before LUCA . . . . . . . . . . . . 68--74
Patrick J. Keeling and
John P. McCutcheon Endosymbiosis: The feeling is not mutual 75--79
Antonio Lazcano and
Juli Peretó On the origin of mitosing cells: a
historical appraisal of Lynn Margulis
endosymbiotic theory . . . . . . . . . . 80--87
Ajith Harish and
Charles G. Kurland Mitochondria are not captive bacteria 88--98
Duur K. Aanen and
Paul Eggleton Symbiogenesis: Beyond the endosymbiosis
theory? . . . . . . . . . . . . . . . . 99--103
Naoki Sato Revisiting the theoretical basis of the
endosymbiotic origin of plastids in the
original context of Lynn Margulis on the
origin of mitosing, eukaryotic cells . . 104--113
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Mario Cañón and
Hernando Diaz and
Andrés Olarte Mathematical model for the spread of
drug resistance in \bionamePlasmodium
falciparum parasite considering
transmission conditions . . . . . . . . 1--11
Anonymous Pages 1--264 (21 December 2017) . . . . 1--264
Sharon Bewick and
Guoqing Wang and
Hannah Younes and
Bingtuan Li and
William F. Fagan Invasion dynamics of competing species
with stage-structure . . . . . . . . . . 12--21
Wim Hordijk Autocatalytic confusion clarified . . . 22--28
Jan Toman and
Jaroslav Flegr Stability-based sorting: The forgotten
process behind (not only) biological
evolution . . . . . . . . . . . . . . . 29--41
Thejaswini Venkatesh and
Shaharabhanu A. Hussain and
Padmanaban S. Suresh A tale of three RNAs in mitochondria:
tRNA, tRNA derived fragments and
mitomiRs . . . . . . . . . . . . . . . . 42--49
Bing Hu and
Xiaoqiang Zou and
Yu Guo and
Zhejia Yang and
Feng Shi and
Wangyuan Dong Control of absence epilepsy seizures in
specific relay nuclei of thalamus . . . 50--61
Solenne Deveraux and
Rachele Allena and
Denis Aubry A numerical model suggests the interplay
between nuclear plasticity and stiffness
during a perfusion assay . . . . . . . . 62--77
Li You and
Joel S. Brown and
Frank Thuijsman and
Jessica J. Cunningham and
Robert A. Gatenby and
Jingsong Zhang and
Kate\vrina Sta\vnková Spatial vs. non-spatial eco-evolutionary
dynamics in a tumor growth model . . . . 78--97
G. M. Donovan Inter-airway structural heterogeneity
interacts with dynamic heterogeneity to
determine lung function and flow
patterns in both asthmatic and control
simulated lungs . . . . . . . . . . . . 98--105
Kyle Q. Lepage and
Sujith Vijayan The relationship between coherence and
the phase-locking value . . . . . . . . 106--109
Tsuyoshi Hirashima and
Miho Hoshuyama and
Taiji Adachi In vitro tubulogenesis of Madin--Darby
canine kidney (MDCK) spheroids occurs
depending on constituent cell number and
scaffold gel concentration . . . . . . . 110--115
Muslim Khan and
Maqsood Hayat and
Sher Afzal Khan and
Saeed Ahmad and
Nadeem Iqbal Bi-PSSM: Position specific scoring
matrix based intelligent computational
model for identification of
mycobacterial membrane proteins . . . . 116--124
Tatiana A. Kovalenko and
Mikhail A. Panteleev and
Anastasia N. Sveshnikova Substrate delivery mechanism and the
role of membrane curvature in factor X
activation by extrinsic tenase . . . . . 125--133
Xi Chen and
Yan-Mei Kang and
Yu-Xuan Fu Switches in a genetic regulatory system
under multiplicative non-Gaussian noise 134--144
Maurizio Porfiri and
Manuel Ruiz Marín Symbolic dynamics of animal interaction 145--156
Gaël Beaunée and
Elisabeta Vergu and
Alain Joly and
Pauline Ezanno Controlling bovine paratuberculosis at a
regional scale: Towards a decision
modelling tool . . . . . . . . . . . . . 157--183
Jason M. Graham and
Albert B. Kao and
Dylana A. Wilhelm and
Simon Garnier Optimal construction of army ant living
bridges . . . . . . . . . . . . . . . . 184--198
Vladislav Victorovich Khrustalev and
Marina Anatolyevna Ermalovich and
Judith M. Hübschen and
Tatyana Aleksandrovna Khrustaleva Transcription-associated mutational
pressure in the Parvovirus B19 genome:
Reactivated genomes contribute to the
variability of viral populations . . . . 199--207
E. Siva Sankari and
D. Manimegalai Predicting membrane protein types using
various decision tree classifiers based
on various modes of general PseAAC for
imbalanced datasets . . . . . . . . . . 208--217
R. Dybowski and
O. Restif and
D. J. Price and
P. Mastroeni Inferring within-host bottleneck size: a
Bayesian approach . . . . . . . . . . . 218--228
Swakkhar Shatabda and
Sanjay Saha and
Alok Sharma and
Abdollah Dehzangi iPHLoc-ES: Identification of
bacteriophage protein locations using
evolutionary and structural features . . 229--237
T. Reeves and
H. Ohtsuki and
S. Fukui Asymmetric public goods game cooperation
through pest control . . . . . . . . . . 238--247
Ilan N. Rubin and
Michael Doebeli Rethinking the evolution of
specialization: a model for the
evolution of phenotypic heterogeneity 248--264
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Laila D. Kazimierski and
Marcelo N. Kuperman and
Horacio S. Wio and
Guillermo Abramson Waves of seed propagation induced by
delayed animal dispersion . . . . . . . 1--7
Anonymous Pages 1--134 (7 January 2018) . . . . . 1--134
N. López-Marín and
R. Mulet In silico modelling of apoptosis induced
by photodynamic therapy . . . . . . . . 8--17
Yongxiao Yang and
Xinqi Gong A new probability method to understand
protein--protein interface formation
mechanism at amino acid level . . . . . 18--25
Julien Flaig and
Nicolas Houy and
Philippe Michel Canonical modeling of anticipatory
vaccination behavior and long term
epidemic recurrence . . . . . . . . . . 26--38
F. Hoffman and
D. Gavaghan and
J. Osborne and
I. P. Barrett and
T. You and
H. Ghadially and
R. Sainson and
R. W. Wilkinson and
H. M. Byrne A mathematical model of
antibody-dependent cellular cytotoxicity
(ADCC) . . . . . . . . . . . . . . . . . 39--50
Thomas Caraco and
Wendy C. Turner Pathogen transmission at
stage-structured infectious patches:
Killers and vaccinators . . . . . . . . 51--63
E. Siero Nonlocal grazing in patterned ecosystems 64--71
Rodrick Wallace New statistical models of nonergodic
cognitive systems and their pathologies 72--78
J.-F. Arnoldi and
A. Bideault and
M. Loreau and
B. Haegeman How ecosystems recover from pulse
perturbations: a theory of short- to
long-term responses . . . . . . . . . . 79--92
Michael P. O'Connor and
Sean O'Donnell Implications of iterative communication
for biological system performance . . . 93--104
M. H. Korayem and
Z. Mahmoodi and
M. Mohammadi $3$D investigation of dynamic behavior
and sensitivity analysis of the
parameters of spherical biological
particles in the first phase of
AFM-based manipulations with the
consideration of humidity effect . . . . 105--119
H. Cho and
D. Levy Modeling the chemotherapy-induced
selection of drug-resistant traits
during tumor growth . . . . . . . . . . 120--134
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Xuesong Liu and
Qiuhui Pan and
Mingfeng He Promotion of cooperation in evolutionary
game dynamics with local information . . 1--8
Anonymous Pages 1--318 (21 January 2018) . . . . . 1--318
Ronesh Sharma and
Maitsetseg Bayarjargal and
Tatsuhiko Tsunoda and
Ashwini Patil and
Alok Sharma MoRFPred-plus: Computational
Identification of MoRFs in Protein
Sequences using Physicochemical
Properties and HMM profiles . . . . . . 9--16
Inkyung Ahn and
Seongman Heo and
Seunghyun Ji and
Kyung Hyun Kim and
Taehwan Kim and
Eun Joo Lee and
Jooyoung Park and
Keehoon Sung Investigation of nonlinear
epidemiological models for analyzing and
controlling the MERS outbreak in Korea 17--28
Victor Pozzobon and
Patrick Perre Han's model parameters for microalgae
grown under intermittent illumination:
Determined using particle swarm
optimization . . . . . . . . . . . . . . 29--35
Junli Liu and
Zhenguo Bai and
Tailei Zhang A periodic two-patch SIS model with time
delay and transport-related infection 36--44
Longgui Liu and
Mao Sun The added mass forces in insect flapping
wings . . . . . . . . . . . . . . . . . 45--50
Nuno R. Nené and
Ville Mustonen and
Christopher J. R. Illingworth Evaluating genetic drift in time-series
evolutionary analysis . . . . . . . . . 51--57
Soibam Shyamchand Singh and
Dineshchandra Haobijam and
Md. Zubbair Malik and
Romana Ishrat and
R. K. Brojen Singh Fractal rules in brain networks:
Signatures of self-organization . . . . 58--66
Carlos Alberto Martínez and
Kshitij Khare and
Syed Rahman and
Mauricio A. Elzo Modeling correlated marker effects in
genome-wide prediction via Gaussian
concentration graph models . . . . . . . 67--78
Mayuko Nakamaru and
Hayato Shimura and
Yoko Kitakaji and
Susumu Ohnuma The effect of sanctions on the evolution
of cooperation in linear division of
labor . . . . . . . . . . . . . . . . . 79--91
Alexis D. Synodinos and
Britta Tietjen and
Dirk Lohmann and
Florian Jeltsch The impact of inter-annual rainfall
variability on African savannas changes
with mean rainfall . . . . . . . . . . . 92--100
Iulian Ilies and
Rifat Sipahi and
Günther K. H. Zupanc Growth of adult spinal cord in
knifefish: Development and
parametrization of a distributed model 101--114
Simone Cenci and
Ana Montero-Castaño and
Serguei Saavedra Estimating the effect of the
reorganization of interactions on the
adaptability of species to changing
environments . . . . . . . . . . . . . . 115--125
Emilene Pliego Pliego and
Jorge Velázquez-Castro and
Markus P. Eichhorn and
Andrés Fraguela Collar Increased efficiency in the second-hand
tire trade provides opportunity for
dengue control . . . . . . . . . . . . . 126--136
Marcelino Fuentes Biological novelty in the anthropocene 137--140
Tatsuya Hayashi and
Tetsuji Tokihiro and
Hiroki Kurihara and
Fumimasa Nomura and
Kenji Yasuda Integrate and fire model with refractory
period for synchronization of two
cardiomyocytes . . . . . . . . . . . . . 141--148
A. Jalilvand and
B. Akbari and
F. Zare Mirakabad S-FLN: a sequence-based hierarchical
approach for functional linkage network
construction . . . . . . . . . . . . . . 149--162
Noble. J. Malunguza and
Senelani D. Hove-Musekwa and
Zindoga Mukandavire Projecting the impact of anal
intercourse on HIV transmission among
heterosexuals in high HIV prevalence
settings. . . . . . . . . . . . . . . . 163--178
Farida Chamchod Modeling the spread of capripoxvirus
among livestock and optimal vaccination
strategies . . . . . . . . . . . . . . . 179--186
Atsushi Hashimoto and
Atsuki Nagao and
Satoru Okuda Topological graph description of
multicellular dynamics based on vertex
model . . . . . . . . . . . . . . . . . 187--201
Jiayu Wu and
Hong Yuan and
Longyuan Li and
Kunjie Fan and
Shanguang Qian and
Bing Li Viscoelastic shear lag model to predict
the micromechanical behavior of tendon
under dynamic tensile loading . . . . . 202--213
Yukio Yasui and
Jin Yoshimura Bet-hedging against male-caused
reproductive failures may explain
ubiquitous cuckoldry in female birds . . 214--221
Mike Steel and
Stuart Kauffman A note on random catalytic branching
processes . . . . . . . . . . . . . . . 222--224
Kevin J. Painter and
William Ho and
Denis J. Headon A chemotaxis model of feather primordia
pattern formation during avian
development . . . . . . . . . . . . . . 225--238
Shengli Zhang and
Xin Duan Prediction of protein subcellular
localization with oversampling approach
and Chou's general PseAAC . . . . . . . 239--250
Alexander P. Browning and
Scott W. McCue and
Rachelle N. Binny and
Michael J. Plank and
Esha T. Shah and
Matthew J. Simpson Inferring parameters for a lattice-free
model of cell migration and
proliferation using experimental data 251--260
Casey O. Diekman and
Amitabha Bose Reentrainment of the circadian pacemaker
during jet lag: East-west asymmetry and
the effects of north-south travel . . . 261--285
O. Angulo and
O. Gandrillon and
F. Crauste Investigating the role of the
experimental protocol in
phenylhydrazine-induced anemia on mice
recovery . . . . . . . . . . . . . . . . 286--298
Matthijs van Veelen Fisher's fundamental theorem of natural
selection, dynamic sufficiency, and the
necessity of higher moments . . . . . . 299--304
Ashish Kumar Agrahari and
Amit Kumar and
Siva R. and
Hatem Zayed and
George Priya Doss C. Substitution impact of highly conserved
arginine residue at position 75 in GJB1
gene in association with X-linked
Charcot--Marie-tooth disease: a
computational study . . . . . . . . . . 305--317
Anonymous Editorial Board . . . . . . . . . . . . ifc--ifc
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Paul David Williams and
Stephanie Jill Kamel The evolution of pathogen virulence:
Effects of transitions between host
types . . . . . . . . . . . . . . . . . 1--8
Anonymous Pages 1--174 (7 February 2018) . . . . . 1--174
M. Jabed A. Choudhury and
Philip M. J. Trevelyan and
Graeme P. Boswell A mathematical model of nutrient
influence on fungal competition . . . . 9--20
Dan E. Ganz and
Briana Sexton-Stallone and
Emily L. Brackett and
Neil S. Forbes Tissue transport affects how treatment
scheduling increases the efficacy of
chemotherapeutic drugs . . . . . . . . . 21--33
Dan Wu and
Richard C. Boucher and
Brian Button and
Timothy Elston and
Ching-Long Lin An integrated mathematical epithelial
cell model for airway surface liquid
regulation by mechanical forces . . . . 34--45
Ernesto Estrada and
Grant J. Ross Centralities in simplicial complexes.
Applications to protein interaction
networks . . . . . . . . . . . . . . . . 46--60
Genki Ichinose and
Naoki Masuda Zero-determinant strategies in finitely
repeated games . . . . . . . . . . . . . 61--77
Mrinmay Kumar Mallik An attempt to understand glioma stem
cell biology through centrality analysis
of a protein interaction network . . . . 78--91
Pouria Dasmeh Multi-step regulation of transcription
kinetics explains the non-linear
relation between RNA polymerase II
density and mRNA expression in dosage
compensation . . . . . . . . . . . . . . 92--95
Ivan Grbatini\'c and
Nebojsa Milosevi\'c and
Bojana Krstonosi\'c The neuromorphological caudate-putaminal
clustering of neostriate interneurons:
Kohonen self-organizing maps and
supervised artificial neural networks
with multivariate analysis . . . . . . . 96--115
Wei Liu and
Yaolin Jiang Bifurcation of a delayed Gause
predator--prey model with
Michaelis--Menten type harvesting . . . 116--132
Sorinel A. Oprisan and
Tristan Aft and
Mona Buhusi and
Catalin V. Buhusi Scalar timing in memory: a temporal map
in the hippocampus . . . . . . . . . . . 133--142
Maria Beatriz Walter Costa and
Christian Höner zu Siederdissen and
Dan Tulpan and
Peter F. Stadler and
Katja Nowick Temporal ordering of substitutions in
RNA evolution: Uncovering the structural
evolution of the Human Accelerated
Region 1 . . . . . . . . . . . . . . . . 143--150
Mike Steel and
Vahab Pourfaraj and
Abhishek Chaudhary and
Arne Mooers Evolutionary isolation and phylogenetic
diversity loss under random extinction
events . . . . . . . . . . . . . . . . . 151--155
Vitor H. Sanches and
Dhyan V. H. Kuraoka and
Pedro R. Almeida and
Carla Goldman A phenomenological analysis of
eco-evolutionary coupling under dilution 156--164
Pierre Pelcé Competition of energy between active
transport and vesicle fusion at the
origin of intracellular gradient fields 165--173
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Michael J. Chen and
Jonathan P. Whiteley and
Colin P. Please and
Andrea Schwab and
Franziska Ehlicke and
Sarah L. Waters and
Helen M. Byrne Inducing chondrogenesis in
MSC/chondrocyte co-cultures using
exogenous TGF-$ \beta $: a mathematical
model . . . . . . . . . . . . . . . . . 1--13
Anonymous Pages 1--232 (14 February 2018) . . . . 1--232
Mohsin Yousuf Lone and
Sivakumar Prasanth Kumar and
Mohd Athar and
Prakash Chandra Jha Exploration of Mycobacterium
tuberculosis structural proteome: An
in-silico approach . . . . . . . . . . . 14--23
D. Melchionda and
E. Pastacaldi and
C. Perri and
M. Banerjee and
E. Venturino Social behavior-induced multistability
in minimal competitive ecosystems . . . 24--38
Mohit P. Dalwadi and
Marco Garavaglia and
Joseph P. Webb and
John R. King and
Nigel P. Minton Applying asymptotic methods to synthetic
biology: Modelling the reaction kinetics
of the mevalonate pathway . . . . . . . 39--49
S. Dini and
B. J. Binder and
J. E. F. Green Understanding interactions between
populations: Individual based modelling
and quantification using pair
correlation functions . . . . . . . . . 50--64
Xue Feng and
Bin Wu and
Long Wang Voluntary vaccination dilemma with
evolving psychological perceptions . . . 65--75
Igal Berenshtein and
Claire B. Paris and
Hezi Gildor and
Erick Fredj and
Yael Amitai and
Omri Lapidot and
Moshe Kiflawi Auto-correlated directional swimming can
enhance settlement success and
connectivity in fish larvae . . . . . . 76--85
Anna Konstorum and
John S. Lowengrub Activation of the HGF/c-Met axis in the
tumor microenvironment: a multispecies
model . . . . . . . . . . . . . . . . . 86--99
Wenfeng Feng and
Richard M. Bailey Unifying relationships between
complexity and stability in mutualistic
ecological communities . . . . . . . . . 100--126
Can Chen and
Chentong Li and
Yanmei Kang Modelling the effects of cutting off
infected branches and replanting on
fire-blight transmission using Filippov
systems . . . . . . . . . . . . . . . . 127--140
Xiaoxia Liu and
Zhihao Yang and
Ziwei Zhou and
Yuanyuan Sun and
Hongfei Lin and
Jian Wang and
Bo Xu The impact of protein interaction
networks' characteristics on
computational complex detection methods 141--151
Sha Gong and
Yanli Wang and
Zhen Wang and
Yujie Wang and
Wenbing Zhang Genetic regulation mechanism of the yjdF
riboswitch . . . . . . . . . . . . . . . 152--159
Tanja Stadler and
Stavroula Skylaki and
Konstantinos D. Kokkaliaris and
Timm Schroeder On the statistical analysis of single
cell lineage trees . . . . . . . . . . . 160--165
Juraj Bergman and
Dominik Schrempf and
Carolin Kosiol and
Claus Vogl Inference in population genetics using
forward and backward, discrete and
continuous time processes . . . . . . . 166--180
Christine Bürli and
Helmut Harbrecht and
Peter Odermatt and
Somphou Sayasone and
Nakul Chitnis Mathematical analysis of the
transmission dynamics of the liver
fluke, \bionameOpisthorchis viverrini 181--194
Martin Grunnill An exploration of the role of
asymptomatic infections in the
epidemiology of dengue viruses through
susceptible, asymptomatic, infected and
recovered (SAIR) models . . . . . . . . 195--204
Mercedes Lombarte and
Maela Lupo and
L. Fina Brenda and
German Campetelli and
A. R. Buzalaf Marilia and
Marta Basualdo and
Alfredo Rigalli In vivo measurement of the rate constant
of liver handling of glucose and glucose
uptake by insulin-dependent tissues,
using a mathematical model for glucose
homeostasis in diabetic rats . . . . . . 205--215
Shuixian Yan and
Yu Zhang and
Junling Ma and
Sanling Yuan An edge-based SIR model for sexually
transmitted diseases on the contact
network . . . . . . . . . . . . . . . . 216--225
John H. M. Thornley and
James France Exploration of bimodal kinetics in
marker digesta outflows using
compartmental models . . . . . . . . . . 226--231
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Mugen Huang and
Jiaowan Luo and
Linchao Hu and
Bo Zheng and
Jianshe Yu Assessing the efficiency of
\bionameWolbachia driven \bionameAedes
mosquito suppression by delay
differential equations . . . . . . . . . 1--11
Anonymous Pages 1--132 (7 March 2018) . . . . . . 1--132
Wataru Nakahashi and
Hisashi Ohtsuki Evolution of emotional contagion in
group-living animals . . . . . . . . . . 12--20
Kazuhiro Maeda and
Hiroyuki Kurata Long negative feedback loop enhances
period tunability of biological
oscillators . . . . . . . . . . . . . . 21--31
Lei Zhou and
Aming Li and
Long Wang Coevolution of nonlinear group
interactions and strategies in
well-mixed and structured populations 32--41
Tomás A. Revilla and
Vlastimil K\vrivan Competition, trait-mediated
facilitation, and the structure of
plant-pollinator communities . . . . . . 42--57
Charlotte Ferris and
Alex Best The evolution of host defence to
parasitism in fluctuating environments. 58--65
Andrés J. Cortés On how role versatility boosts an STI 66--69
M. S. Ghuchani Comment on: An engineering thermodynamic
approach to select the electromagnetic
wave effective on cell growth . . . . . 70--70
Adrien Fauré and
Shizuo Kaji A circuit-preserving mapping from
multilevel to Boolean dynamics . . . . . 71--79
Aiko Kawasumi-Kita and
Daisuke Ohtsuka and
Yoshihiro Morishita Morphometric staging of organ
development based on cross sectional
images . . . . . . . . . . . . . . . . . 80--87
Yanir Damti and
Ilan Gronau and
Shlomo Moran and
Irad Yavneh Comparing evolutionary distances via
adaptive distance functions . . . . . . 88--99
Di Hu and
Cai-Hua Xiong and
Ming-Jin Liu Exploring the existence of better hands
for manipulation than the human hand
based on hand proportions . . . . . . . 100--111
Mayuko Iwamoto and
Daishin Ueyama Basis of self-organized proportion
regulation resulting from local contacts 112--120
Madhurima Nath and
Yihui Ren and
Yasamin Khorramzadeh and
Stephen Eubank Determining whether a class of random
graphs is consistent with an observed
contact network . . . . . . . . . . . . 121--132
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Lichao Zhang and
Liang Kong iRSpot-ADPM: Identify recombination
spots by incorporating the associated
dinucleotide product model into Chou's
pseudo components . . . . . . . . . . . 1--8
Anonymous Pages 1--92 (14 March 2018) . . . . . . 1--92
Ludek Berec and
Veronika Bernhauerová and
Barbara Boldin Evolution of mate-finding Allee effect
in prey . . . . . . . . . . . . . . . . 9--18
Peng-Bi Cui and
Lei Gao and
Wei Wang Epidemic spreading dynamics with drug
resistance and heterogeneous contacts 19--27
Martina Devi and
Esther Chingbiaknem and
R. H. Duncan Lyngdoh A molecular mechanics study on GA codon
box translation . . . . . . . . . . . . 28--43
Sumit Tarafder and
Md. Toukir Ahmed and
Sumaiya Iqbal and
Md Tamjidul Hoque and
M. Sohel Rahman RBSURFpred: Modeling protein accessible
surface area in real and binary space
using regularized and optimized
regression . . . . . . . . . . . . . . . 44--57
Atsushi Yamauchi and
Minus van Baalen and
Maurice W. Sabelis Spatial patterns generated by
simultaneous cooperation and
exploitation favour the evolution of
altruism . . . . . . . . . . . . . . . . 58--67
Mainak Patel and
Badal Joshi Deterministic stability regimes and
noise-induced quasistable behavior in a
pair of reciprocally inhibitory neurons 68--83
Matan Danino and
Nadav M. Shnerb Fixation and absorption in a fluctuating
environment . . . . . . . . . . . . . . 84--92
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Seyed Peyman Shariatpanahi and
Seyed Pooya Shariatpanahi and
Keivan Madjidzadeh and
Moustapha Hassan and
Manuchehr Abedi-Valugerdi Mathematical modeling of tumor-induced
immunosuppression by myeloid-derived
suppressor cells: Implications for
therapeutic targeting strategies . . . . 1--10
Anonymous Pages 1--158 (7 April 2018) . . . . . . 1--158
Muhammad Arif and
Maqsood Hayat and
Zahoor Jan iMem-2LSAAC: a two-level model for
discrimination of membrane proteins and
their types by extending the notion of
SAAC into Chou's pseudo amino acid
composition . . . . . . . . . . . . . . 11--21
Uduak Z. George and
Sharon R. Lubkin Tissue geometry may govern lung
branching mode selection . . . . . . . . 22--30
Vrishti M. Phadumdeo and
Seth H. Weinberg Heart rate variability alters cardiac
repolarization and electromechanical
dynamics . . . . . . . . . . . . . . . . 31--43
L. J. Bridge and
J. Mead and
E. Frattini and
I. Winfield and
G. Ladds Modelling and simulation of biased
agonism dynamics at a G protein-coupled
receptor . . . . . . . . . . . . . . . . 44--65
Christoph G. Jäger and
Dietrich Borchardt Longitudinal patterns and response
lengths of algae in riverine ecosystems:
a model analysis emphasising
benthic-pelagic interactions . . . . . . 66--78
L. Dinh and
G. Chowell and
R. Rothenberg Growth scaling for the early dynamics of
HIV/AIDS epidemics in Brazil and the
influence of socio-demographic factors 79--86
Ozgur Aydogmus Discovering the effect of nonlocal
payoff calculation on the stabilty of
ESS: Spatial patterns of Hawk--Dove game
in metapopulations . . . . . . . . . . . 87--97
Saritha Kodikara and
Haydar Demirhan and
Lewi Stone Inferring about the extinction of a
species using certain and uncertain
sightings . . . . . . . . . . . . . . . 98--109
Olcay Akman and
Timothy D. Comar and
Daniel Hrozencik Model selection for integrated pest
management with stochasticity . . . . . 110--122
Donal A. Hickey and
G. Brian Golding The advantage of recombination when
selection is acting at many genetic Loci 123--128
Lucas Deecke and
Hana M. Dobrovolny Intermittent treatment of severe
influenza . . . . . . . . . . . . . . . 129--138
Tejas Joshi and
Bret D. Elderd and
Karen C. Abbott No appendix necessary: Fecal transplants
and antibiotics can resolve
\bionameClostridium difficile infection 139--148
Qi Su and
Aming Li and
Long Wang Evolution of cooperation with
interactive identity and diversity . . . 149--157
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Dominique Chu Performance limits and trade-offs in
entropy-driven biochemical computers . . 1--9
Anonymous Pages 1--176 (14 April 2018) . . . . . . 1--176
Massimo Di Giulio On Earth, there would be a number of
fundamental kinds of primary cells ---
cellular domains --- greater than or
equal to four . . . . . . . . . . . . . 10--17
Akira R. Kinjo Cooperative ``folding transition'' in
the sequence space facilitates
function-driven evolution of protein
families . . . . . . . . . . . . . . . . 18--27
Don Yu and
Neal Madras and
Huaiping Zhu Temperature-driven population abundance
model for \bionameCulex pipiens and
\bionameCulex restuans (\bionameDiptera:
Culicidae) . . . . . . . . . . . . . . . 28--38
Adam K. Zienkiewicz and
Fabrizio Ladu and
David A. W. Barton and
Maurizio Porfiri and
Mario Di Bernardo Data-driven modelling of social forces
and collective behaviour in zebrafish 39--51
Jacob Peedicayil and
Dennis R. Grayson An epigenetic basis for an omnigenic
model of psychiatric disorders . . . . . 52--55
Eleanor Brush and
Åke Brännström and
Ulf Dieckmann Indirect reciprocity with negative
assortment and limited information can
promote cooperation . . . . . . . . . . 56--65
Jochen Kursawe and
Ruth E. Baker and
Alexander G. Fletcher Approximate Bayesian computation reveals
the importance of repeated measurements
for parameterising cell-based models of
growing tissues . . . . . . . . . . . . 66--81
Ting-Ting Zheng and
Lin-Fei Nie Modelling the transmission dynamics of
two-strain Dengue in the presence
awareness and vector control . . . . . . 82--91
Orr Levy and
Isak Nethanël Gath Effects of mating patterns on
genealogical trees: Assessment of the
high carrier rate of Familial
Mediterranean Fever in rural Israeli
districts . . . . . . . . . . . . . . . 92--99
Soyoung Kim and
Aurelio A. de los Reyes and
Eunok Jung Mathematical model and intervention
strategies for mitigating tuberculosis
in the Philippines . . . . . . . . . . . 100--112
Jong Hyuk Byun and
Il Hyo Jung Mathematical modeling of antibody drug
conjugates with the target and tubulin
dynamics to predict AUC . . . . . . . . 113--124
Jiangning Song and
Fuyi Li and
Kazuhiro Takemoto and
Gholamreza Haffari and
Tatsuya Akutsu and
Kuo-Chen Chou and
Geoffrey I. Webb PREvaIL, an integrative approach for
inferring catalytic residues using
sequence, structural, and network
features in a machine-learning framework 125--137
Md. Raihan Uddin and
Alok Sharma and
Dewan Md Farid and
Md. Mahmudur Rahman and
Abdollah Dehzangi and
Swakkhar Shatabda EvoStruct-Sub: An accurate Gram-positive
protein subcellular localization
predictor using evolutionary and
structural features . . . . . . . . . . 138--146
Tatjana Thiel and
Barbara Drossel Impact of stochastic migration on
species diversity in meta-food webs
consisting of several patches . . . . . 147--156
Frances Pool and
Richard Currie and
Peter K. Sweby and
José Domingo Salazar and
Marcus J. Tindall A mathematical model of the mevalonate
cholesterol biosynthesis pathway . . . . 157--176
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Sami Lehtinen Understanding the Venus flytrap through
mathematical modelling . . . . . . . . . 1--10
Anonymous Pages 1--124 (7 May 2018) . . . . . . . 1--124
Arijit Pal and
Amiya Ranjan Bhowmick and
Farhana Yeasmin and
Sabyasachi Bhattacharya Evolution of model specific relative
growth rate: Its genesis and performance
over Fisher's growth rates . . . . . . . 11--27
Guirong Liu and
Zhimei Liu and
Zhen Jin Dynamics analysis of epidemic and
information spreading in overlay
networks . . . . . . . . . . . . . . . . 28--37
Corey Melnick and
Massoud Kaviany Thermal actuation in TRPV1: Role of
embedded lipids and intracellular
domains . . . . . . . . . . . . . . . . 38--49
Tuomas Nurmi and
Kalle Parvinen and
Vesa Selonen Joint evolution of dispersal propensity
and site selection in structured
metapopulation models . . . . . . . . . 50--72
Abhigyan Nath and
S. Karthikeyan Enhanced prediction of recombination
hotspots using input features extracted
by class specific autoencoders . . . . . 73--82
Jan Werner and
Nikolaos Sfakianakis and
Alan D. Rendall and
Eva Maria Griebeler Energy intake functions and energy
budgets of ectotherms and endotherms
derived from their ontogenetic growth in
body mass and timing of sexual
maturation . . . . . . . . . . . . . . . 83--92
Leif Zinn-Björkman and
Frederick R. Adler Modeling factors that regulate cell
cooperativity in the zebrafish posterior
lateral line primordium . . . . . . . . 93--99
L. A. Crompton and
L. L. McKnight and
C. K. Reynolds and
J. A. N. Mills and
J. L. Ellis and
M. D. Hanigan and
J. Dijkstra and
B. J. Bequette and
A. Bannink and
J. France An isotope dilution model for
partitioning of phenylalanine and
tyrosine uptake by the liver of
lactating dairy cows . . . . . . . . . . 100--107
D. Pond and
A. T. McBride and
L. M. Davids and
B. D. Reddy and
G. Limbert Microstructurally-based constitutive
modelling of the skin --- Linking
intrinsic ageing to microstructural
parameters . . . . . . . . . . . . . . . 108--123
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Umberto Lucia and
Thomas S. Deisboeck The importance of ion fluxes for cancer
proliferation and metastasis: a
thermodynamic analysis . . . . . . . . . 1--8
Anonymous Pages 1--186 (14 May 2018) . . . . . . . 1--186
Abhinandan Khan and
Goutam Saha and
Rajat Kumar Pal An approach for reduction of false
predictions in reverse engineering of
gene regulatory networks . . . . . . . . 9--30
Philip J. G. M. Voets Central line-associated bloodstream
infections and catheter dwell-time: a
theoretical foundation for a rule of
thumb . . . . . . . . . . . . . . . . . 31--32
Marissa Renardy and
Alexandra Jilkine and
Leili Shahriyari and
Ching-Shan Chou Control of cell fraction and population
recovery during tissue regeneration in
stem cell lineages . . . . . . . . . . . 33--50
Wang Jin and
Scott W. McCue and
Matthew J. Simpson Extended logistic growth model for
heterogeneous populations . . . . . . . 51--61
S. Muthu Krishnan Using Chou's general PseAAC to analyze
the evolutionary relationship of
receptor associated proteins (RAP) with
various folding patterns of protein
domains . . . . . . . . . . . . . . . . 62--74
José Antonio Carrillo and
Annachiara Colombi and
Marco Scianna Adhesion and volume constraints via
nonlocal interactions determine cell
organisation and migration profiles . . 75--91
Mohammad Farhan Khan and
Sarah Spurgeon and
Tobias von der Haar Origins of robustness in translational
control via eukaryotic translation
initiation factor (eIF) 2 . . . . . . . 92--102
Fernando Antoneli and
Martin Golubitsky and
Ian Stewart Homeostasis in a feed forward loop gene
regulatory motif . . . . . . . . . . . . 103--109
Nicolas Loeuille and
Céline Hauzy Multidimensionality of plant defenses
and herbivore niches: Implications for
eco-evolutionary dynamics . . . . . . . 110--119
Ross D. Booton and
Ryo Yamaguchi and
James A. R. Marshall and
Dylan Z. Childs and
Yoh Iwasa Interactions between immunotoxicants and
parasite stress: Implications for host
health . . . . . . . . . . . . . . . . . 120--127
Jordi Roca-Lacostena and
Jesús Fernández-Sánchez Embeddability of Kimura 3ST Markov
matrices . . . . . . . . . . . . . . . . 128--135
Zhen-Xing Feng and
Qian-Zhong Li and
Jian-Jun Meng Recognition of the long range
enhancer-promoter interactions by
further adding DNA structure properties
and transcription factor binding motifs
in human cell lines . . . . . . . . . . 136--150
Rifat Sipahi and
Günther K. H. Zupanc Stochastic cellular automata model of
neurosphere growth: Roles of
proliferative potential, contact
inhibition, cell death, and phagocytosis 151--165
Karen E. Wood and
Natalia L. Komarova Cooperation-based branching as a
mechanism of evolutionary speciation . . 166--186
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Kenta Ishimoto and
Hermes Gadêlha and
Eamonn A. Gaffney and
David J. Smith and
Jackson Kirkman-Brown Human sperm swimming in a high viscosity
mucus analogue . . . . . . . . . . . . . 1--10
Anonymous Pages 1--260 (7 June 2018) . . . . . . . 1--260
E. H. Colombo and
C. Anteneodo Nonlinear population dynamics in a
bounded habitat . . . . . . . . . . . . 11--18
Frederick Chen Voluntary vaccinations and vaccine
shortages: a theoretical analysis . . . 19--32
Simon Maccracken Stump and
Evan Curtis Johnson and
Zepeng Sun and
Christopher A. Klausmeier How spatial structure and neighbor
uncertainty promote mutualists and
weaken black queen effects . . . . . . . 33--60
Chuanyan Wu and
Rui Gao and
Yang De Marinis and
Yusen Zhang A novel model for protein sequence
similarity analysis based on spectral
radius . . . . . . . . . . . . . . . . . 61--70
Nicolas Houy and
François Le Grand Administration of temozolomide:
Comparison of conventional and
metronomic chemotherapy regimens . . . . 71--78
Ryan Nikin-Beers and
Julie C. Blackwood and
Lauren M. Childs and
Stanca M. Ciupe Unraveling within-host signatures of
dengue infection at the population level 79--86
Ruth Bowness and
Mark A. J. Chaplain and
Gibin G. Powathil and
Stephen H. Gillespie Modelling the effects of bacterial cell
state and spatial location on
tuberculosis treatment: Insights from a
hybrid multiscale cellular automaton
model . . . . . . . . . . . . . . . . . 87--100
Jinyou Yang and
Yuji Shimogonya and
Takuji Ishikawa What causes the spatial heterogeneity of
bacterial flora in the intestine of
zebrafish larvae? . . . . . . . . . . . 101--109
Abhishek Kumar Tiwari and
Rakesh Kumar and
Dharmendra Tripathi and
Subham Badhyal In silico modeling of bone adaptation to
rest-inserted loading: Strain energy
density versus fluid flow as stimulus 110--127
Hemachander Subramanian and
Robert A. Gatenby Evolutionary advantage of directional
symmetry breaking in self-replicating
polymers . . . . . . . . . . . . . . . . 128--136
Heather M. Lindberg and
Kurt A. McKean and
T. Caraco and
Ing-Nang Wang Within-host dynamics and random duration
of pathogen infection: Implications for
between-host transmission . . . . . . . 137--148
Elena Piretto and
Marcello Delitala and
Mario Ferraro Combination therapies and intra-tumoral
competition: Insights from mathematical
modeling . . . . . . . . . . . . . . . . 149--159
Andrew Francis and
Vincent Moulton Identifiability of tree-child
phylogenetic networks under a
probabilistic recombination-mutation
model of evolution . . . . . . . . . . . 160--167
Samuel R. J. Hoare and
Nicolas Pierre and
Arturo Gonzalez Moya and
Brad Larson Kinetic operational models of agonism
for G-protein-coupled receptors . . . . 168--204
Daniel John Cleather The patella: a mechanical determinant of
coordination during vertical jumping . . 205--211
Yantao Luo and
Long Zhang and
Zhidong Teng and
Donald L. DeAngelis A parasitism-mutualism-predation model
consisting of crows, cuckoos and cats
with stage-structure and maturation
delays on crows and cuckoos . . . . . . 212--228
Weiping Ding and
Sen Liu and
Shibo Li and
Duobiao Ge and
Fenfen Li and
Dayong Gao Simulation of blood and oxygen
distributions in a hepatic lobule with
sinusoids obstructed by cancer cells . . 229--237
D. Calvetti and
G. Capo Rangel and
L. Gerardo Giorda and
E. Somersalo A computational model integrating brain
electrophysiology and metabolism
highlights the key role of extracellular
potassium and oxygen . . . . . . . . . . 238--258
J. M. López and
J. Herrero and
D. Puigjaner and
G. Fortuny Corrigendum to ``A $3$D
electro-mechanical continuum model for
simulating skeletal muscle
contraction'', J. Theor. Biol. 335
(2013) 108--118 . . . . . . . . . . . . 259--259
Alfonso Jiménez-Sánchez Corrigendum to ``Bacterial cell cycle
classification. Application to DNA
synthesis and DNA content at any cell
age'' [Journal of Theoretical Biology
\bf 419 (2017) 8--12] . . . . . . . . . 260--260
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Trong Hieu Nguyen and
Timothée Brochier and
Pierre Auger and
Viet Duoc Trinh and
Patrice Brehmer Competition or cooperation in
transboundary fish stocks management:
Insight from a dynamical model . . . . . 1--11
Anonymous Pages 1--200 (14 June 2018) . . . . . . 1--200
Alfonso Ruiz-Herrera and
Pedro J. Torres Effects of diffusion on total biomass in
simple metacommunities . . . . . . . . . 12--24
Philip B. Greenspoon and
Sydney Banton and
Nicole Mideo Immune system handling time may alter
the outcome of competition between
pathogens and the immune system . . . . 25--31
Gerald Soslau Circular RNA (circRNA) was an important
bridge in the switch from the RNA world
to the DNA world . . . . . . . . . . . . 32--40
Tanja Stadler and
Alexandra Gavryushkina and
Rachel C. M. Warnock and
Alexei J. Drummond and
Tracy A. Heath The fossilized birth-death model for the
analysis of stratigraphic range data
under different speciation modes . . . . 41--55
James Moore and
Hasan Ahmed and
Rustom Antia High dimensional random walks can appear
low dimensional: Application to
influenza H3N2 evolution . . . . . . . . 56--64
Min Li and
Wenkai Li and
Fang-Xiang Wu and
Yi Pan and
Jianxin Wang Identifying essential proteins based on
sub-network partition and prioritization
by integrating subcellular localization
information . . . . . . . . . . . . . . 65--73
Danilo G. Muniz and
Glauco Machado Mate sampling influences the intensity
of sexual selection and the evolution of
costly sexual ornaments . . . . . . . . 74--83
C. De La Fuente Canto and
D. I. Kalogiros and
M. Ptashnyk and
T. S. George and
R. Waugh and
A. G. Bengough and
J. Russell and
L. X. Dupuy Morphological and genetic
characterisation of the root system
architecture of selected barley
recombinant chromosome substitution
lines using an integrated phenotyping
approach . . . . . . . . . . . . . . . . 84--97
F. Fatehi Chenar and
Y. N. Kyrychko and
K. B. Blyuss Mathematical model of immune response to
hepatitis B . . . . . . . . . . . . . . 98--110
Masashi Kameyama and
Sousuke Takeuchi and
Shinya Ishii Steady-state relationship between
average glucose, HbA1c and RBC lifespan 111--117
Yue Zhang and
Qing-Chuan Zheng Exploring the interactions of EGFR with
phosphorylated Mig6 by molecular
dynamics simulations and MM-PBSA
calculations . . . . . . . . . . . . . . 118--125
Lorenzo Mari and
Renato Casagrandi and
Andrea Rinaldo and
Marino Gatto Epidemicity thresholds for water-borne
and water-related diseases . . . . . . . 126--138
Reza Rezazadegan and
Chris Barrett and
Christian Reidys Multiplicity of phenotypes and RNA
evolution . . . . . . . . . . . . . . . 139--146
Juan Mei and
Ji Zhao Analysis and prediction of presynaptic
and postsynaptic neurotoxins by Chou's
general pseudo amino acid composition
and motif features . . . . . . . . . . . 147--153
Charline Smadi and
Hél\`ene Leman and
Violaine Llaurens Looking for the right mate in diploid
species: How does genetic dominance
affect the spatial differentiation of a
sexual trait? . . . . . . . . . . . . . 154--170
Qinbin He and
Zhile Xia and
Bin Lin P\_UNSAT approach of attractor
calculation for Boolean gene regulatory
networks . . . . . . . . . . . . . . . . 171--177
Sébastien Lion From the Price equation to the selection
gradient in class-structured
populations: a quasi-equilibrium route 178--189
Joel R. Peck and
David Waxman What is adaptation and how should it be
measured? . . . . . . . . . . . . . . . 190--198
Stefan Landmann and
Nicolas Preuss and
Ulrich Behn Corrigendum to `Self-tolerance and
autoimmunity in a minimal model of the
idiotypic network' [Journal of
Theoretical Biology \bf 426 (2017)
17--39] . . . . . . . . . . . . . . . . 199--199
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Clement Aldebert and
Bob W. Kooi and
David Nerini and
Jean-Christophe Poggiale Is structural sensitivity a problem of
oversimplified biological models?
Insights from nested Dynamic Energy
Budget models . . . . . . . . . . . . . 1--8
Anonymous Pages 1--156 (7 July 2018) . . . . . . . 1--156
Gottfried Sachs and
Henri Weimerskirch Flight of frigatebirds inside clouds ---
energy gain, stability and control . . . 9--16
Peter C. Jentsch and
Madhur Anand and
Chris T. Bauch Spatial correlation as an early warning
signal of regime shifts in a multiplex
disease-behaviour network . . . . . . . 17--25
Ouassim Bara and
Michel Fliess and
Cédric Join and
Judy Day and
Seddik M. Djouadi Toward a model-free feedback control
synthesis for treating acute
inflammation . . . . . . . . . . . . . . 26--37
Louis T. Curtis and
Victor H. van Berkel and
Hermann B. Frieboes Pharmacokinetic/pharmacodynamic modeling
of combination-chemotherapy for lung
cancer . . . . . . . . . . . . . . . . . 38--52
Yazhi Li and
Xianning Liu A sex-structured model with birth pulse
and release strategy for the spread of
\bionameWolbachia in mosquito population 53--65
Gouhei Tanaka and
Elisa Domínguez-Hüttinger and
Panayiotis Christodoulides and
Kazuyuki Aihara and
Reiko J. Tanaka Bifurcation analysis of a mathematical
model of atopic dermatitis to determine
patient-specific effects of treatments
on dynamic phenotypes . . . . . . . . . 66--79
Kosaku Kitagawa and
Shinji Nakaoka and
Yusuke Asai and
Koichi Watashi and
Shingo Iwami A PDE multiscale model of hepatitis C
virus infection can be transformed to a
system of ODEs . . . . . . . . . . . . . 80--85
Dominik Wodarz Effect of cellular de-differentiation on
the dynamics and evolution of tissue and
tumor cells in mathematical models with
feedback regulation . . . . . . . . . . 86--93
Behzad Mehrafrooz and
Amir Shamloo Mechanical differences between ATP and
ADP actin states: a molecular dynamics
study . . . . . . . . . . . . . . . . . 94--103
Junnosuke Horita and
Yoh Iwasa and
Yuuya Tachiki Evolutionary bistability of life history
decision in male masu salmon . . . . . . 104--111
Ágnes Móréh and
Anett Endrédi and
Ferenc Jordán Additivity of pairwise perturbations in
food webs: Topological effects . . . . . 112--121
Alexander Tam and
J. Edward F. Green and
Sanjeeva Balasuriya and
Ee Lin Tek and
Jennifer M. Gardner and
Joanna F. Sundstrom and
Vladimir Jiranek and
Benjamin J. Binder Nutrient-limited growth with non-linear
cell diffusion as a mechanism for floral
pattern formation in yeast biofilms . . 122--141
Ping Xie A model of DNA unwinding dynamics by the
RecBCD complex and its regulation by Chi
recognition . . . . . . . . . . . . . . 142--156
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Juping Zhang and
Chan Yang and
Zhen Jin and
Jia Li Dynamics analysis of SIR epidemic model
with correlation coefficients and
clustering coefficient in networks . . . 1--13
Anonymous Pages 1--124 (14 July 2018) . . . . . . 1--124
Shahrukh Husain and
Vijay Kumar and
Md. Imtaiyaz Hassan Phosphorylation-induced changes in the
energetic frustration in human Tank
binding kinase 1 . . . . . . . . . . . . 14--22
Luke Tait and
Kyle Wedgwood and
Krasimira Tsaneva-Atanasova and
Jon T. Brown and
Marc Goodfellow Control of clustered action potential
firing in a mathematical model of
entorhinal cortex stellate cells . . . . 23--34
Andrew L. Krause and
Lawrence Kurowski and
Kamran Yawar and
Robert A. Van Gorder Stochastic epidemic metapopulation
models on networks: SIS dynamics and
control strategies . . . . . . . . . . . 35--52
Amira Kebir and
Nina H. Fefferman and
Slimane Ben Miled A general structured model of a
hermaphrodite population . . . . . . . . 53--59
Feng Huang and
Xiaojie Chen and
Long Wang Evolution of cooperation in a
hierarchical society with corruption
control . . . . . . . . . . . . . . . . 60--72
L. J. Cooper and
B. Zeller-Plumhoff and
G. F. Clough and
B. Ganapathisubramani and
T. Roose Using high resolution X-ray computed
tomography to create an image based
model of a lymph node . . . . . . . . . 73--82
Maya Gussmann and
Carsten Kirkeby and
Kaare Græsbòll and
Michael Farre and
Tariq Halasa A strain-, cow-, and herd-specific
bio-economic simulation model of
intramammary infections in dairy cattle
herds . . . . . . . . . . . . . . . . . 83--93
Yohsuke Murase and
Seung Ki Baek Seven rules to avoid the tragedy of the
commons . . . . . . . . . . . . . . . . 94--102
Walid Djema and
Catherine Bonnet and
Frédéric Mazenc and
Jean Clairambault and
Emilia Fridman and
Pierre Hirsch and
François Delhommeau Control in dormancy or eradication of
cancer stem cells: Mathematical modeling
and stability issues . . . . . . . . . . 103--123
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
N. Terranova and
E. M. Tosca and
E. Borella and
E. Pesenti and
M. Rocchetti and
P. Magni Modeling tumor growth inhibition and
toxicity outcome after administration of
anticancer agents in xenograft mice: a
Dynamic Energy Budget (DEB) approach . . 1--14
Anonymous Pages 1--104 (7 August 2018) . . . . . . 1--104
Cangzhi Jia and
Qing Yang and
Quan Zou NucPosPred: Predicting species-specific
genomic nucleosome positioning via four
different modes of general PseKNC . . . 15--21
Takashi Nagatani and
Genki Ichinose and
Kei-ichi Tainaka Metapopulation model for
rock-paper-scissors game: Mutation
affects paradoxical impacts . . . . . . 22--29
Chuliang Song and
Rudolf P. Rohr and
Serguei Saavedra A guideline to study the feasibility
domain of multi-trophic and changing
ecological communities . . . . . . . . . 30--36
Aaron R. Casha and
Liberato Camilleri and
Marilyn Gauci and
Ruben Gatt and
David Sladden and
Stanley Chetcuti and
Joseph N. Grima A mathematical model for pressure-based
organs behaving as biological pressure
vessels . . . . . . . . . . . . . . . . 37--42
Prateek Verma and
Anjan K. Nandi and
Supratim Sengupta Bribery games on interdependent complex
networks . . . . . . . . . . . . . . . . 43--52
Muyi Guo and
Yan Cai and
Xinke Yao and
Zhiyong Li Mathematical modeling of atherosclerotic
plaque destabilization: Role of
neovascularization and intraplaque
hemorrhage . . . . . . . . . . . . . . . 53--65
Takashi Nagatani and
Genki Ichinose and
Kei-ichi Tainaka Epidemics of random walkers in
metapopulation model for complete,
cycle, and star graphs . . . . . . . . . 66--75
Eva Janousková and
Ludek Berec Host-pathogen dynamics under sterilizing
pathogens and fecundity-longevity
trade-off in hosts . . . . . . . . . . . 76--85
Wenying Qiu and
Shan Li and
Xiaowen Cui and
Zhaomin Yu and
Minghui Wang and
Junwei Du and
Yanjun Peng and
Bin Yu Predicting protein submitochondrial
locations by incorporating the
pseudo-position specific scoring matrix
into the general Chou's pseudo-amino
acid composition . . . . . . . . . . . . 86--103
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Anum Munir and
Shumaila Azam and
Sahar Fazal and
A. I. Bhatti Evaluation of the whole body
physiologically based pharmacokinetic
(WB-PBPK) modeling of drugs . . . . . . 1--9
Anonymous Pages 1--122 (14 August 2018) . . . . . 1--122
Travis Monk Martingales and the fixation probability
of high-dimensional evolutionary graphs 10--18
Ragna M. Eide and
Andrew L. Krause and
Nabil T. Fadai and
Robert A. Van Gorder predator--prey-subsidy population
dynamics on stepping-stone domains with
dispersal delays . . . . . . . . . . . . 19--34
Patil Sneha and
Pritam Kumar Panda and
Fatemeh Rahimi Gharemirshamlu and
Kourosh Bamdad and
Seetharaman Balaji Structural discordance in HIV-1 Vpu from
brain isolate alarms amyloid fibril
forming behavior- a computational
perspective . . . . . . . . . . . . . . 35--45
Hayato Shimura and
Mayuko Nakamaru Large group size promotes the evolution
of cooperation in the mutual-aid game 46--56
ZhuoHua Shen and
Justin Seipel Effective leg stiffness of animal
running and the co-optimization of
energetic cost and stability . . . . . . 57--66
Bing Hu and
Qianqian Shi and
Yu Guo and
Xiyezi Diao and
Heng Guo and
Jinsong Zhang and
Liang Yu and
Hao Dai and
Luonan Chen The oscillatory boundary conditions of
different frequency bands in Parkinson's
disease . . . . . . . . . . . . . . . . 67--79
Daihai He and
Xueying Wang and
Daozhou Gao and
Jin Wang Modeling the 2016--2017 Yemen cholera
outbreak with the impact of limited
medical resources . . . . . . . . . . . 80--85
Maxim B. Kuznetsov and
Andrey V. Kolobov Transient alleviation of tumor hypoxia
during first days of antiangiogenic
therapy as a result of therapy-induced
alterations in nutrient supply and tumor
metabolism --- Analysis by mathematical
modeling . . . . . . . . . . . . . . . . 86--100
Tommaso Lorenzi and
Chandrasekhar Venkataraman and
Alexander Lorz and
Mark A. J. Chaplain The role of spatial variations of
abiotic factors in mediating intratumour
phenotypic heterogeneity . . . . . . . . 101--110
Valmir C. Barbosa Information-theoretic signatures of
biodiversity in the barcoding gene . . . 111--116
Sòren Toxvaerd The start of the Abiogenesis:
Preservation of homochirality in
proteins as a necessary and sufficient
condition for the establishment of the
metabolism . . . . . . . . . . . . . . . 117--121
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
M. Fazli Sabooh and
Nadeem Iqbal and
Mukhtaj Khan and
Muslim Khan and
H. F. Maqbool Identifying $5$-methylcytosine sites in
RNA sequence using composite encoding
feature into Chou's PseKNC . . . . . . . 1--9
Anonymous Pages 1--84 (7 September 2018) . . . . . 1--84
Z. Schuss and
K. Tor and
D. Holcman Do cells sense time by number of
divisions? . . . . . . . . . . . . . . . 10--16
Jian Zhou and
Guanghui Lin Will forest size structure follow the $
- 2 $ power-law distribution under ideal
demographic equilibrium state? . . . . . 17--21
M. Saifur Rahman and
Swakkhar Shatabda and
Sanjay Saha and
M. Kaykobad and
M. Sohel Rahman DPP-PseAAC: a DNA-binding protein
prediction model using Chou's general
PseAAC . . . . . . . . . . . . . . . . . 22--34
Bérénice Grec and
Bertrand Maury and
Nicolas Meunier and
Laurent Navoret A $1$D model of leukocyte adhesion
coupling bond dynamics with blood
velocity . . . . . . . . . . . . . . . . 35--46
Tong Chen and
Zhenghong Wu and
Le Wang Disseminators or silencers: The effect
of information diffusion intensity on
cooperation in public goods game . . . . 47--55
Kerri-Ann Norton and
Kideok Jin and
Aleksander S. Popel Modeling triple-negative breast cancer
heterogeneity: Effects of stromal
macrophages, fibroblasts and tumor
vasculature . . . . . . . . . . . . . . 56--68
Robert A. Laird Sequential interactions-in which one
player plays first and another
responds-promote cooperation in
evolutionary-dynamical simulations of
single-shot Prisoner's Dilemma and
Snowdrift games . . . . . . . . . . . . 69--80
Jacob Peedicayil and
Dennis R. Grayson Some implications of an epigenetic-based
omnigenic model of psychiatric disorders 81--84
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Juddy H. Arias and
Jesus Gómez-Gardeñes and
Sandro Meloni and
Ernesto Estrada Epidemics on plants: Modeling long-range
dispersal on spatially embedded networks 1--13
Anonymous Pages 1--156 (14 September 2018) . . . . 1--156
Edwin Barrios and
Sunmi Lee and
Olga Vasilieva Assessing the effects of daily commuting
in two-patch dengue dynamics: a case
study of Cali, Colombia . . . . . . . . 14--39
A. Alvarez Modeling the odor-landscape resulting
from the pumping behavior of bivalve
clams in the presence of predators . . . 40--47
Paulo Cabrita Resin flow in conifers . . . . . . . . . 48--57
Majid Masso All-atom four-body knowledge-based
statistical potential to distinguish
native tertiary RNA structures from
nonnative folds . . . . . . . . . . . . 58--67
Andrey A. Grinevich and
Ludmila V. Yakushevich The influence of the DNA torque on the
dynamics of transcription bubbles in
plasmid PTTQ18 . . . . . . . . . . . . . 68--77
A. Ashyani and
O. RabieiMotlagh and
H. M. Mohammadinejad A mathematical approach to effects of
CTLs on cancer virotherapy in the second
injection of virus . . . . . . . . . . . 78--87
Nao Takashina and
Buntarou Kusumoto and
Maria Beger and
Suren Rathnayake and
Hugh P. Possingham Spatially explicit approach to
estimation of total population abundance
in field surveys . . . . . . . . . . . . 88--95
A. J. Cooper and
T. Déirdre Hollingsworth The impact of seasonality on the
dynamics and control of \bionameAscaris
lumbricoides infections . . . . . . . . 96--107
M. Susree and
Mikhail A. Panteleev and
M. Anand Coated platelets introduce significant
delay in onset of peak thrombin
production: Theoretical predictions . . 108--116
Golnaz Baghdadi and
Farzad Towhidkhah and
Reza Rostami A mathematical model to mimic the shape
of event related
desynchronization/synchronization . . . 117--124
Johannes Scheiblauer and
Stefan Scheiner and
Martin Joksch and
Barbara Kavsek Fermentation of \bionameSaccharomyces
cerevisiae --- Combining kinetic
modeling and optimization techniques
points out avenues to effective process
design . . . . . . . . . . . . . . . . . 125--135
Sachi Yamaguchi and
Yoh Iwasa Why is bidirectional sex change rare? 136--145
Sachi Yamaguchi and
Yoh Iwasa Temperature-dependent sex determination,
realized by hormonal dynamics with
enzymatic reactions sensitive to ambient
temperature . . . . . . . . . . . . . . 146--155
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Shi Zhao and
Yijun Lou and
Alice P. Y. Chiu and
Daihai He Modelling the skip-and-resurgence of
Japanese encephalitis epidemics in Hong
Kong . . . . . . . . . . . . . . . . . . 1--10
Anonymous Pages 1--424 (7 October 2018) . . . . . 1--424
F. Deeba and
Paula Sanz-Leon and
P. A. Robinson Dependence of absence seizure dynamics
on physiological parameter evolution . . 11--21
Yunyun Liang and
Shengli Zhang Identify Gram-negative bacterial
secreted protein types by incorporating
different modes of PSSM into Chou's
general PseAAC via Kullback--Leibler
divergence . . . . . . . . . . . . . . . 22--29
Yuriria Cortes-Poza and
Pablo Padilla-Longoria and
Elena Alvarez-Buylla Spatial dynamics of floral organ
formation . . . . . . . . . . . . . . . 30--40
Adrianne Jenner and
Chae-Ok Yun and
Arum Yoon and
Peter S. Kim and
Adelle C. F. Coster Modelling heterogeneity in viral-tumour
dynamics: The effects of
gene-attenuation on viral
characteristics . . . . . . . . . . . . 41--52
Yuhang Fan and
Yandong Xiao and
Babak Momeni and
Yang-Yu Liu Horizontal gene transfer can help
maintain the equilibrium of microbial
communities . . . . . . . . . . . . . . 53--59
Irina V. Khalo and
Anastasiya I. Konokhova and
Darya Y. Orlova and
Konstantin V. Trusov and
Maxim A. Yurkin and
Eva Bartova and
Stanislav Kozubek and
Valeri P. Maltsev and
Andrei V. Chernyshev Nuclear apoptotic volume decrease in
individual cells: Confocal microscopy
imaging and kinetic modeling . . . . . . 60--69
Da Zhou and
Shanjun Mao and
Jing Cheng and
Kaiyi Chen and
Xiaofang Cao and
Jie Hu A Bayesian statistical analysis of
stochastic phenotypic plasticity model
of cancer cells . . . . . . . . . . . . 70--79
Ashrafur Rahman and
Daniel Munther and
Aamir Fazil and
Ben Smith and
Jianhong Wu With-in host dynamics of \bionameL.
monocytogenes and thresholds for
distinct infection scenarios . . . . . . 80--90
J. Hettich and
J. C. M. Gebhardt Transcription factor target site search
and gene regulation in a background of
unspecific binding sites . . . . . . . . 91--101
Guillaume Dechristé and
Jérôme Fehrenbach and
Elena Griseti and
Valérie Lobjois and
Clair Poignard Viscoelastic modeling of the fusion of
multicellular tumor spheroids in growth
phase . . . . . . . . . . . . . . . . . 102--109
Roberto Cazzolla Gatti and
Brian Fath and
Wim Hordijk and
Stuart Kauffman and
Robert Ulanowicz Niche emergence as an autocatalytic
process in the evolution of ecosystems 110--117
Qiao-Qiao He and
Tian-Jiao Feng and
Yi Tao and
Boyu Zhang and
Ting Ji Asymmetric evolutionary game dynamics
based on individuals' own volition . . . 118--125
Annika Aurbach and
Baptiste Schmid and
Felix Liechti and
Ndaona Chokani and
Reza Abhari Complex behaviour in complex terrain ---
Modelling bird migration in a high
resolution wind field across mountainous
terrain to simulate observed patterns 126--138
Ernesto Contreras-Torres Predicting structural classes of
proteins by incorporating their global
and local physicochemical and
conformational properties into general
Chou's PseAAC . . . . . . . . . . . . . 139--145
Henintsoa O. Minoarivelo and
Cang Hui Alternative assembly processes from
trait-mediated co-evolution in
mutualistic communities . . . . . . . . 146--153
Brandon H. Schlomann Stationary moments, diffusion limits,
and extinction times for logistic growth
with random catastrophes . . . . . . . . 154--163
Yi Wang and
Junling Ma and
Jinde Cao and
Li Li Edge-based epidemic spreading in
degree-correlated complex networks . . . 164--181
Ruben van Drongelen and
Tania Vazquez-Faci and
Teun A. P. M. Huijben and
Maurijn van der Zee and
Timon Idema Mechanics of epithelial tissue formation 182--189
Kalle Parvinen and
Hisashi Ohtsuki and
Joe Yuichiro Wakano Spatial heterogeneity and evolution of
fecundity-affecting traits . . . . . . . 190--204
Andrew R. Tilman and
Simon Levin and
James R. Watson Revenue-sharing clubs provide economic
insurance and incentives for
sustainability in common-pool resource
systems . . . . . . . . . . . . . . . . 205--214
Dominic L. Maderazo and
Jennifer A. Flegg and
Melanie R. Neeland and
Michael J. de Veer and
Mark B. Flegg Physiological factors leading to a
successful vaccination: a computational
approach . . . . . . . . . . . . . . . . 215--230
Bryce Morsky and
Dervis Can Vural Cheater-altruist synergy in public goods
games . . . . . . . . . . . . . . . . . 231--239
Robert Rockenfeller and
Michael Günther Inter-filament spacing mediates calcium
binding to troponin: a simple
geometric-mechanistic model explains the
shift of force-length maxima with muscle
activation . . . . . . . . . . . . . . . 240--252
Sara Hamis and
Perumal Nithiarasu and
Gibin G. Powathil What does not kill a tumour may make it
stronger: In silico insights into
chemotherapeutic drug resistance . . . . 253--267
Victor J. Barranca and
Xiuqi George Zhu A computational study of the role of
spatial receptive field structure in
processing natural and non-natural
scenes . . . . . . . . . . . . . . . . . 268--277
Simon Maccracken Stump and
Evan Curtis Johnson and
Christopher A. Klausmeier How leaking and overproducing resources
affect the evolutionary robustness of
cooperative cross-feeding . . . . . . . 278--291
D. Horvath and
B. Brutovsky A new conceptual framework for the
therapy by optimized multidimensional
pulses of therapeutic activity. The case
of multiple myeloma model . . . . . . . 292--309
Isabella Marinelli and
Theodore Vo and
Luca Gerardo-Giorda and
Richard Bertram Transitions between bursting modes in
the integrated oscillator model for
pancreatic $ \beta $-cells . . . . . . . 310--319
Jonggul Lee and
Bo Youl Choi and
Eunok Jung Metapopulation model using commuting
flow for national spread of the 2009
H1N1 influenza virus in the Republic of
Korea . . . . . . . . . . . . . . . . . 320--329
A. H. Karimi and
H. R. Mirdamadi and
S. Ziaei-Rad Mathematical modeling of dynamic
behavior of fluid bilayer membranes
under the effect of density asymmetry 330--344
Kalenia M. Márquez-Flórez and
James R. Monaghan and
Sandra J. Shefelbine and
Angélica Ramirez-Martínez and
Diego A. Garzón-Alvarado A computational model for the joint
onset and development . . . . . . . . . 345--356
Adnane Ez-zizi and
John M. McNamara and
Gaurav Malhotra and
Alasdair I. Houston Optimal gut size of small birds and its
dependence on environmental and
physiological parameters . . . . . . . . 357--366
Toshinori Namba and
Tatsuo Shibata Propagation of regulatory fluctuations
induces coordinated switching of
flagellar motors in chemotaxis signaling
pathway of single bacteria . . . . . . . 367--375
Keith Paarporn and
Ceyhun Eksin and
Joshua S. Weitz Information sharing for a coordination
game in fluctuating environments . . . . 376--385
Maria Rita Fumagalli and
Stefano Zapperi and
Caterina A. M. La Porta Impact of the cross-talk between
circular and messenger RNAs on cell
regulation . . . . . . . . . . . . . . . 386--395
Surabhi Pandey and
Seema Nanda and
Amit Vutha and
Ram Naresh Modeling the impact of biolarvicides on
malaria transmission . . . . . . . . . . 396--409
Christopher T. Richards and
Laura B. Porro A novel kinematics analysis method using
quaternion interpolation --- a case
study in frog jumping . . . . . . . . . 410--424
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Weiyang Chen and
Bo Liao and
Weiwei Li Use of image texture analysis to find
DNA sequence similarities . . . . . . . 1--6
Anonymous Pages 1--370 (14 October 2018) . . . . . 1--370
Isamu Okada and
Tatsuya Sasaki and
Yutaka Nakai A solution for private assessment in
indirect reciprocity using solitary
observation . . . . . . . . . . . . . . 7--15
Valery Peng and
Natalka Suchowerska and
Ana Dos Santos Esteves and
Linda Rogers and
Elizabeth Claridge Mackonis and
Joanne Toohey and
David R. McKenzie Models for the bystander effect in
gradient radiation fields: Range and
signalling type . . . . . . . . . . . . 16--25
Wei Liu and
Liangyu Ma and
Byeungwoo Jeon and
Ling Chen and
Bolun Chen A Network Hierarchy-Based method for
functional module detection in
protein--protein interaction networks 26--38
Yusuke Ito and
Alexandra Tauzin and
Azaria Remion and
Keisuke Ejima and
Fabrizio Mammano and
Shingo Iwami Dynamics of HIV-1 coinfection in
different susceptible target cell
populations during cell-free infection 39--46
Joe Pharaon and
Chris T. Bauch The influence of social behaviour on
competition between virulent pathogen
strains . . . . . . . . . . . . . . . . 47--53
Adam L. Cronin An agent-based model of nest-site
selection in a mass-recruiting ant . . . 54--63
Micha\l Theuer and
Ludek Berec Impacts of infection avoidance for
populations affected by sexually
transmitted infections . . . . . . . . . 64--74
Qianqian Zhang and
Biao Tang and
Sanyi Tang Vaccination threshold size and backward
bifurcation of SIR model with
state-dependent pulse control . . . . . 75--85
Debdas Paul and
Nicole Radde The role of stochastic sequestration
dynamics for intrinsic noise filtering
in signaling network motifs . . . . . . 86--96
Kohji Sato Why does hyperglycinemia exhibit so
grave brain anomalies and so severe
neurological symptoms? . . . . . . . . . 97--100
Daniel J. Cleather An important role of the biarticular
hamstrings is to exert internal/external
rotation moments on the tibia during
vertical jumping . . . . . . . . . . . . 101--108
Amy Veprauskas and
Azmy S. Ackleh and
Tingting Tang Examining the effect of reoccurring
disturbances on population persistence
with application to marine mammals . . . 109--117
Nakul Chitnis and
Allan Schapira and
Christian Schindler and
Melissa A. Penny and
Thomas A. Smith Mathematical analysis to prioritise
strategies for malaria elimination . . . 118--130
Jimmy Ka Ho Chiu and
Tharam S. Dillon and
Yi-Ping Phoebe Chen Large-scale frequent stem pattern mining
in RNA families . . . . . . . . . . . . 131--139
Wei Song and
Huaping Liu and
Jiajia Wang and
Yan Kong and
Xia Yin and
Weidong Zang MATHT: a web server for comprehensive
transcriptome data analysis . . . . . . 140--146
Marco Tutone and
Alessia Virz\`\i and
Anna Maria Almerico Reverse screening on indicaxanthin from
\bionameOpuntia ficus-indica as natural
chemoactive and chemopreventive agent 147--160
Jelle Bruineberg and
Erik Rietveld and
Thomas Parr and
Leendert van Maanen and
Karl J. Friston Free-energy minimization in joint
agent-environment systems: a niche
construction perspective . . . . . . . . 161--178
D. Hala and
J. A. Cullen and
B. Hernout and
I. Ivanov In silico predicted transcriptional
regulatory control of steroidogenesis in
spawning female fathead minnows
(\bionamePimephales promelas) . . . . . 179--190
Péter Bayer and
Joel S. Brown and
Katerina Stanková A two-phenotype model of immune evasion
by cancer cells . . . . . . . . . . . . 191--204
Shahid Akbar and
Maqsood Hayat iMethyl-STTNC: Identification of
N$^6$-methyladenosine sites by extending
the idea of SAAC into Chou's PseAAC to
formulate RNA sequences . . . . . . . . 205--211
Hojjat Bazzazi and
Yu Zhang and
Mohammad Jafarnejad and
Aleksander S. Popel Computational modeling of synergistic
interaction between $ \alpha $V$ \beta
$3 integrin and VEGFR2 in endothelial
cells: Implications for the mechanism of
action of angiogenesis-modulating
integrin-binding peptides . . . . . . . 212--221
Kerstin Bunte and
David J. Smith and
Michael J. Chappell and
Zaki K. Hassan-Smith and
Jeremy W. Tomlinson and
Wiebke Arlt and
Peter Ti\vno Learning pharmacokinetic models for in
vivo glucocorticoid activation . . . . . 222--231
Vlastimil K\vrivan and
Theodore E. Galanthay and
Ross Cressman Beyond replicator dynamics: From
frequency to density dependent models of
evolutionary games . . . . . . . . . . . 232--248
Jeffrey West and
Yongqian Ma and
Paul K. Newton Capitalizing on competition: An
evolutionary model of competitive
release in metastatic castration
resistant prostate cancer treatment . . 249--260
Cesar Vargas-Garcia and
Ryan Zurakowski and
Abhyudai Singh Synaptic transmission may provide an
evolutionary benefit to HIV through
modulation of latency . . . . . . . . . 261--268
Ashish Goyal and
Ranjit Chauhan The dynamics of integration, viral
suppression and cell--cell transmission
in the development of occult Hepatitis B
virus infection . . . . . . . . . . . . 269--280
Miguel A. Valderrama-Gómez and
Rebecca E. Parales and
Michael A. Savageau Phenotype-centric modeling for
elucidation of biological design
principles . . . . . . . . . . . . . . . 281--292
Guo Shan and
Hong Chuan-shan and
Sun Ming-zhu and
Zhao Xin Meshwork pattern transformed from
branching pattern in spherical shell
domain . . . . . . . . . . . . . . . . . 293--302
P. D. N. Srinivasu and
D. K. K. Vamsi and
V. S. Ananth Additional food supplements as a tool
for biological conservation of
predator--prey systems involving type
III functional response: a qualitative
and quantitative investigation . . . . . 303--318
E. Siva Sankari and
D. Manimegalai Predicting membrane protein types by
incorporating a novel feature set into
Chou's general PseAAC . . . . . . . . . 319--328
Roman M. Link and
Bernhard Schuldt and
Brendan Choat and
Steven Jansen and
Alexander R. Cobb Maximum-likelihood estimation of xylem
vessel length distributions . . . . . . 329--341
Jing Chen and
John C. Beier and
Robert Stephen Cantrell and
Chris Cosner and
Douglas O. Fuller and
Yongtao Guan and
Guoyan Zhang and
Shigui Ruan Modeling the importation and local
transmission of vector-borne diseases in
Florida: The case of Zika outbreak in
2016 . . . . . . . . . . . . . . . . . . 342--356
Cody Ross and
Luis Pacheco-Cobos and
Bruce Winterhalder A general model of forager search:
Adaptive encounter-conditional
heuristics outperform Lévy flights in the
search for patchily distributed prey . . 357--369
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Doran Khamis and
Claire El Mouden and
Klodeta Kura and
Michael B. Bonsall Ecological effects on underdominance
threshold drives for vector control . . 1--15
Anonymous Pages 1--314 (7 November 2018) . . . . . 1--314
Elena C. Lascano and
Juan I. Felice and
Sandra Wray and
Sara Kosta and
Pierre C. Dauby and
Edmundo I. Cabrera-Fischer and
Jorge A. Negroni Experimental assessment of a
myocyte-based multiscale model of
cardiac contractile dysfunction . . . . 16--28
Margarita Stritzler and
Carolina Berini and
Cintia Jozefkowicz and
Gabriela Soto and
Nicolás Ayub Understanding the
intracellular-to-extracellular
localization switch of
polyhydroxybutyrate polymerase in
\bionamepseudomonas backgrounds as a
microevolutionary process . . . . . . . 29--33
Kun Tian and
Xin Zhao and
Stephen S.-T. Yau Convex hull analysis of evolutionary and
phylogenetic relationships between
biological groups . . . . . . . . . . . 34--40
Juan Mei and
Yi Fu and
Ji Zhao Analysis and prediction of ion channel
inhibitors by using feature selection
and Chou's general pseudo amino acid
composition . . . . . . . . . . . . . . 41--48
Martin Bouda and
Craig Brodersen and
James Saiers Whole root system water conductance
responds to both axial and radial traits
and network topology over natural range
of trait variation . . . . . . . . . . . 49--61
Gilberto González-Parra and
Hana M. Dobrovolny Modeling of fusion inhibitor treatment
of RSV in African green monkeys . . . . 62--73
Andrei Korobeinikov Immune response and within-host viral
evolution: Immune response can
accelerate evolution . . . . . . . . . . 74--83
Yanbo Teng and
Yanjun Ding and
Mingming Zhang and
Xinren Chen and
Xizi Wang and
Hang Yu and
Chonghui Liu and
Hongchao Lv and
Ruijie Zhang Genome-wide haplotype association study
identifies risk genes for non-small cell
lung cancer . . . . . . . . . . . . . . 84--90
Kazuto Doi and
Mayuko Nakamaru The coevolution of transitive inference
and memory capacity in the hawk-dove
game . . . . . . . . . . . . . . . . . . 91--107
Sofia H. Piltz and
Lauri Harhanen and
Mason A. Porter and
Philip K. Maini Inferring parameters of prey switching
in a 1 predator-2 prey plankton system
with a linear preference tradeoff . . . 108--122
Michael G. Watson and
Helen M. Byrne and
Charlie Macaskill and
Mary R. Myerscough A two-phase model of early fibrous cap
formation in atherosclerosis . . . . . . 123--136
Michael Günther and
Daniel F. B. Haeufle and
Syn Schmitt The basic mechanical structure of the
skeletal muscle machinery: One model for
linking microscopic and macroscopic
scales . . . . . . . . . . . . . . . . . 137--167
Taryn M. Kay and
Paul R. Ohmann Effects of random motion in traveling
and grazing herds . . . . . . . . . . . 168--174
Alan Grafen The left hand side of the Fundamental
Theorem of Natural Selection . . . . . . 175--189
Carlos Martínez and
Francis Mairet and
Olivier Bernard Theory of turbid microalgae cultures . . 190--200
Samuel R. Fleischer and
Casey P. terHorst and
Jing Li Pick your trade-offs wisely:
predator--prey eco-evo dynamics are
qualitatively different under different
trade-offs . . . . . . . . . . . . . . . 201--212
Rei Kadota and
Kazuma Sugita and
Kenko Uchida and
Hitoshi Yamada and
Masashi Yamashita and
Hidenori Kimura A mathematical model of type 1 diabetes
involving leptin effects on glucose
metabolism . . . . . . . . . . . . . . . 213--223
C. V. Haridas and
Brigitte Tenhumberg Modeling effects of ecological factors
on evolution of polygenic pesticide
resistance . . . . . . . . . . . . . . . 224--232
Mariia Dvoriashyna and
Alexander J. E. Foss and
Eamonn A. Gaffney and
Oliver E. Jensen and
Rodolfo Repetto Osmotic and electroosmotic fluid
transport across the retinal pigment
epithelium: a mathematical model . . . . 233--248
Yong Liu and
Jingan Chen and
Jieying Qian and
Hao Lin and
Ning Sun and
Zunnan Huang Evolutionary analysis and structural
characterization of \bionameAquilaria
sinensis sesquiterpene synthase in
agarwood formation: a computational
study . . . . . . . . . . . . . . . . . 249--260
Dóra Lakatos and
Ellák Somfai and
El\Hod Méhes and
András Czirók Soluble VEGFR1 signaling guides vascular
patterns into dense branching
morphologies . . . . . . . . . . . . . . 261--278
Hal Whitehead and
John K. B. Ford Consequences of culturally-driven
ecological specialization: Killer whales
and beyond . . . . . . . . . . . . . . . 279--294
David A. Baum The origin and early evolution of life
in chemical composition space . . . . . 295--304
Dieter Vanderelst and
Herbert Peremans Modeling bat prey capture in
echolocating bats: The feasibility of
reactive pursuit . . . . . . . . . . . . 305--314
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Adrian M. Davies and
Alan G. Holt Why antioxidant therapies have failed in
clinical trials . . . . . . . . . . . . 1--5
Anonymous Pages 1--270 (14 November 2018) . . . . 1--270
Zhe Ju and
Shi-Yun Wang Prediction of S-sulfenylation sites
using mRMR feature selection and fuzzy
support vector machine algorithm . . . . 6--13
Aishwarya Kakade and
Baby Kumari and
Pankaj Singh Dholaniya Feature selection using logistic
regression in case-control DNA
methylation data of Parkinson's disease:
a comparative study . . . . . . . . . . 14--18
Manuel Adrian Acuña-Zegarra and
Daniel Olmos-Liceaga and
Jorge X. Velasco-Hernández The role of animal grazing in the spread
of Chagas disease . . . . . . . . . . . 19--28
Abhishikha Srivastava and
Ravindra Kumar and
Manish Kumar BlaPred: Predicting and classifying $
\beta $-lactamase using a $3$-tier
prediction system via Chou's general
PseAAC . . . . . . . . . . . . . . . . . 29--36
Marina Voinson and
Alexandra Alvergne and
Sylvain Billiard and
Charline Smadi Stochastic dynamics of an epidemic with
recurrent spillovers from an endemic
reservoir . . . . . . . . . . . . . . . 37--50
Nosaka Michiko and
Budi Setyawan and
Syunya Sunaba-Mitsumasu Enzymatic reaction sites on a plane
formed with four exon-junctions . . . . 51--56
Fabio A. C. C. Chalub and
Max O. Souza Fitness potentials and qualitative
properties of the Wright--Fisher
dynamics . . . . . . . . . . . . . . . . 57--65
Leah R. Band and
Simon P. Preston Parameter inference to motivate
asymptotic model reduction: An analysis
of the gibberellin biosynthesis pathway 66--78
Paul Smolen and
Douglas A. Baxter and
John H. Byrne Paradoxical LTP maintenance with
inhibition of protein synthesis and the
proteasome suggests a novel protein
synthesis requirement for early LTP
reversal . . . . . . . . . . . . . . . . 79--87
Manu Aggarwal and
M. Y. Hussaini and
Leonardo De La Fuente and
Fernando Navarrete and
N. G. Cogan A framework for model analysis across
multiple experiment regimes:
Investigating effects of zinc on
\bionameXylella fastidiosa as a case
study . . . . . . . . . . . . . . . . . 88--100
Emmanouil Lempidakis and
Rory P. Wilson and
Adrian Luckman and
Richard S. Metcalfe What can knowledge of the energy
landscape tell us about animal movement
trajectories and space use? A case study
with humans . . . . . . . . . . . . . . 101--111
Tirthabir Biswas and
Suhas Rao and
Vikas Bhandawat A simple extension of inverted pendulum
template to explain features of slow
walking . . . . . . . . . . . . . . . . 112--123
S. Basu and
S. Sutradhar and
R. Paul Substrate stiffness and mechanical
stress due to intercellular
cooperativity guides tissue structure 124--136
Takayuki Ohara and
Timothy J. Hearn and
Alex A. R. Webb and
Akiko Satake Gene regulatory network models in
response to sugars in the plant
circadian system . . . . . . . . . . . . 137--151
Joseph P. McKenna and
Richard Bertram Fast-slow analysis of the Integrated
Oscillator Model for pancreatic $ \beta
$-cells . . . . . . . . . . . . . . . . 152--162
Shengli Zhang and
Yunyun Liang Predicting apoptosis protein subcellular
localization by integrating auto-cross
correlation and PSSM into Chou's PseAAC 163--169
Jason Olejarz and
Kamran Kaveh and
Carl Veller and
Martin A. Nowak Selection for synchronized cell division
in simple multicellular organisms . . . 170--179
Yi Fu and
Zhiguo Chen and
Jun Sun Random drift particle swarm optimisation
algorithm for highly flexible
protein-ligand docking . . . . . . . . . 180--189
Lo\"\ic Marrec and
Anne-Florence Bitbol Quantifying the impact of a periodic
presence of antimicrobial on resistance
evolution in a homogeneous microbial
population of fixed size . . . . . . . . 190--198
David W. Shanafelt and
Jean Clobert and
Eli P. Fenichel and
Michael E. Hochberg and
Ann Kinzig and
Michel Loreau and
Pablo A. Marquet and
Charles Perrings Species dispersal and biodiversity in
human-dominated metacommunities . . . . 199--210
Jorge Peña and
Georg Nöldeke Group size effects in social evolution 211--220
G. Bocharov and
A. Meyerhans and
N. Bessonov and
S. Trofimchuk and
V. Volpert Interplay between reaction and diffusion
processes in governing the dynamics of
virus infections . . . . . . . . . . . . 221--236
Hanna ten Brink and
André M. de Roos Large-amplitude consumer-resource cycles
allow for the evolution of ontogenetic
niche shifts in consumer life history 237--248
Arwen E. Nicholson and
David M. Wilkinson and
Hywel T. P. Williams and
Timothy M. Lenton Alternative mechanisms for Gaia . . . . 249--257
Sargon A. Gabriel and
Yan Ding and
Yuqing Feng Modelling the period-average transport
of species within pulsatile blood flow 258--269
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
G. Nicolis and
S. C. Nicolis Feedbacks, nonlinearities and
nonequilibria: a thermodynamic
perspective . . . . . . . . . . . . . . 1--9
Anonymous Pages 1--206 (7 December 2018) . . . . . 1--206
Xiaoli Wang and
Guohong Zhang Vegetation pattern formation in seminal
systems due to internal competition
reaction between plants . . . . . . . . 10--14
Abdelhafid Zenati and
Messaoud Chakir and
Mohamed Tadjine Global stability analysis and optimal
control therapy of blood cell production
process (hematopoiesis) in acute myeloid
leukemia . . . . . . . . . . . . . . . . 15--30
Jill Gallaher and
Kamila Larripa and
Marissa Renardy and
Blerta Shtylla and
Nessy Tania and
Diana White and
Karen Wood and
Li Zhu and
Chaitali Passey and
Michael Robbins and
Natalie Bezman and
Suresh Shelat and
Hearn Jay Cho and
Helen Moore Methods for determining key components
in a mathematical model for tumor-immune
dynamics in multiple myeloma . . . . . . 31--46
Jieun Choi and
Yong-Jung Kim predator--prey equations with constant
harvesting and planting . . . . . . . . 47--57
Marcin Molski Theoretical modeling of pre and
postnatal growth . . . . . . . . . . . . 58--67
Lo\"\ic Prosnier and
Vincent Médoc and
Nicolas Loeuille Parasitism effects on coexistence and
stability within simple trophic modules 68--77
Allanah Kenny and
Michael J. Plank and
Tim David Macro scale modelling of cortical
spreading depression and the role of
astrocytic gap junctions . . . . . . . . 78--91
Xiang Cheng and
Xuan Xiao and
Kuo-Chen Chou pLoc\_bal-mGneg: Predict subcellular
localization of Gram-negative bacterial
proteins by quasi-balancing training
dataset and general PseAAC . . . . . . . 92--102
Takashi Nagatani and
Kei-ichi Tainaka and
Genki Ichinose Metapopulation model of
rock-scissors-paper game with
subpopulation-specific victory rates
stabilized by heterogeneity . . . . . . 103--110
Leon Glass and
Roderick Edwards Hybrid models of genetic networks:
Mathematical challenges and biological
relevance . . . . . . . . . . . . . . . 111--118
Gina Polo and
Marcelo B. Labruna and
Fernando Ferreira Basic reproduction number for the
Brazilian Spotted Fever . . . . . . . . 119--124
Yun Xia and
Zhang Cheng and
Shaobing Wang and
Di Guan and
Feng Liu Modeling the crosstalk between the
circadian clock and ROS in Neurospora
crassa . . . . . . . . . . . . . . . . . 125--132
T. Michel and
J. Fehrenbach and
V. Lobjois and
J. Laurent and
A. Gomes and
T. Colin and
C. Poignard Mathematical modeling of the
proliferation gradient in multicellular
tumor spheroids . . . . . . . . . . . . 133--147
Jason T. George and
Herbert Levine Stochastic modeling of tumor progression
and immune evasion . . . . . . . . . . . 148--155
J. M. Deutsch Computational mechanisms in genetic
regulation by RNA . . . . . . . . . . . 156--168
Mubashir Hassan and
Muhammad Athar Abbasi and
Aziz-ur-Rehman and
Sabahat Zahra Siddiqui and
Ghulam Hussain and
Syed Adnan Ali Shah and
Muhammad Shahid and
Sung-Yum Seo Exploration of synthetic multifunctional
amides as new therapeutic agents for
Alzheimer's disease through enzyme
inhibition, chemoinformatic properties,
molecular docking and dynamic simulation
insights . . . . . . . . . . . . . . . . 169--183
Hartmut Klein and
Linnea Hesse and
Matthias Boljen and
Tim Kampowski and
Irina Butschek and
Thomas Speck and
Olga Speck Finite element modelling of complex
movements during self-sealing of ring
incisions in leaves of
\bionameDelosperma cooperi . . . . . . . 184--206
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Ana Guerra and
Jorge Belinha and
Renato Natal Jorge Modelling skin wound healing
angiogenesis: a review . . . . . . . . . 1--17
Anonymous Pages 1--170 (14 December 2018) . . . . 1--170
Cheng Ly and
Seth H. Weinberg Analysis of heterogeneous cardiac
pacemaker tissue models and traveling
wave dynamics . . . . . . . . . . . . . 18--35
Jordan C. Rozum and
Réka Albert Self-sustaining positive feedback loops
in discrete and continuous systems . . . 36--44
Angelo Facchiano and
Massimo Di Giulio The genetic code is not an optimal code
in a model taking into account both the
biosynthetic relationships between amino
acids and their physicochemical
properties . . . . . . . . . . . . . . . 45--51
Ryan Scott and
Brian MacPherson and
Robin Gras A comparison of stable and fluctuating
resources with respect to evolutionary
adaptation and life-history traits using
individual-based modeling and machine
learning . . . . . . . . . . . . . . . . 52--66
Jessica J. Cunningham and
Joel S. Brown and
Robert A. Gatenby and
Katerina Stanková Optimal control to develop therapeutic
strategies for metastatic castrate
resistant prostate cancer . . . . . . . 67--78
Adrien Baudier and
François Fages and
Sylvain Soliman Graphical requirements for
multistationarity in reaction networks
and their verification in BioModels . . 79--89
Dinesh B. Ekanayake and
Amy J. Ekanayake and
Jason Hunt and
Catherine L. Miller-Hunt Modeling reproduction of whitetail deer
and its applications . . . . . . . . . . 90--102
Panchaksaram Muthukumaran and
Muniyan Rajiniraja MIA-QSAR based model for bioactivity
prediction of flavonoid derivatives as
acetylcholinesterase inhibitors . . . . 103--110
Anum Munir and
Shahid Hussain and
Erum Dilshad Silver nanoparticles conjugated with
Neurotrophin 3 upregulate myelin gene
transcription pathway . . . . . . . . . 111--118
Ali Karimnezhad and
Fahimeh Moradi Allelic frequency estimation in presence
of uncertain priors . . . . . . . . . . 119--129
Lorenzo Farina and
Paola Paci A feature-based integrated scoring
scheme for cell cycle-regulated genes
prioritization . . . . . . . . . . . . . 130--141
Dayang Wang and
Chaobo He and
Chengqing Wu and
Yongshan Zhang Mechanical behaviors of tension and
relaxation of tongue and soft palate:
Experimental and analytical modeling . . 142--153
R. Ernesto Blanco and
Washington W. Jones and
Nicolás Benech The seismic wave motion camouflage of
large carnivorous dinosaurs . . . . . . 154--161
Rana Adnan Tahir and
Hao Wu and
Muhammad Ahmad Rizwan and
Tassadaq Hussain Jafar and
Shahzad Saleem and
Sheikh Arslan Sehgal Immunoinformatics and molecular docking
studies reveal potential epitope-based
peptide vaccine against DENV-NS3 protein 162--170
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Sudipta Tung and
M. Rajamani and
Amitabh Joshi and
Sutirth Dey Complex interaction of resource
availability, life-history and
demography determines the dynamics and
stability of stage-structured
populations . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--274 (7 January 2019) . . . . . 1--274
Carlos Hernandez-Suarez and
Paula Medone and
Carlos Castillo-Chavez and
Jorge Rabinovich Building matrix population models when
individuals are non-identifiable . . . . 13--17
Kris De Jaegher Harsh environments: Multi-player
cooperation with excludability and
congestion . . . . . . . . . . . . . . . 18--36
Evans K. Afenya and
Rachid Ouifki and
Suneel D. Mundle Mathematical modeling of bone marrow ---
peripheral blood dynamics in the disease
state based on current emerging
paradigms, part II . . . . . . . . . . . 37--55
Daniel Wechsler and
Jordi Bascompte Thresholds in the resilience of modular
social networks to invasion by defectors 56--63
Sheikh Adilina and
Dewan Md Farid and
Swakkhar Shatabda Effective DNA binding protein prediction
by using key features via Chou's general
PseAAC . . . . . . . . . . . . . . . . . 64--78
Xuesong Liu and
Qiuhui Pan and
Mingfeng He Stochastic dynamics in the fitness-based
process which can be on behalf of the
standard Moran, local and Wright--Fisher
processes . . . . . . . . . . . . . . . 79--87
Laura Lema-Perez and
Jose Garcia-Tirado and
Carlos Builes-Montaño and
Hernan Alvarez Phenomenological-Based model of human
stomach and its role in glucose
metabolism . . . . . . . . . . . . . . . 88--100
Ivan Ramirez-Zuniga and
Jonathan E. Rubin and
David Swigon and
Gilles Clermont Mathematical modeling of energy
consumption in the acute inflammatory
response . . . . . . . . . . . . . . . . 101--114
J. David Van Dyken and
Bo Zhang Carrying capacity of a
spatially-structured population:
Disentangling the effects of dispersal,
growth parameters, habitat heterogeneity
and habitat clustering . . . . . . . . . 115--124
Yuko Hamaguchi and
Takayuki Yamaguchi and
Hiroshi Nishiura Estimating the annual risk of
tuberculosis infection in Japan from
interferon-gamma release assay data . . 125--133
Mariana Rocha and
Roger Springett Electron transfer between cytochrome c
and the binuclear center of cytochrome
oxidase . . . . . . . . . . . . . . . . 134--141
Massimo Di Giulio The universal ancestor, the deeper nodes
of the tree of life, and the fundamental
types of primary cells (cellular
domains) . . . . . . . . . . . . . . . . 142--143
Ignacio A. Rodriguez-Brenes and
Natalia L. Komarova and
Dominik Wodarz The role of telomere shortening in
carcinogenesis: a hybrid
stochastic-deterministic approach . . . 144--152
Vasileios Basios and
Chris G. Antonopoulos Hyperchaos and labyrinth chaos:
Revisiting Thomas-Rössler systems . . . . 153--159
Daipeng Chen and
Yanni Xiao and
Sanyi Tang Air quality index induced nonsmooth
system for respiratory infection . . . . 160--169
Joan Fornés and
J. Tomás Lázaro and
Tomás Alarcón and
Santiago F. Elena and
Josep Sardanyés Viral replication modes in single-peak
fitness landscapes: a dynamical systems
analysis . . . . . . . . . . . . . . . . 170--183
M. Ferdousi and
T. Babaie Janvier and
P. A. Robinson Nonlinear harmonic generation in the
corticothalamic system . . . . . . . . . 184--194
Jianhua Jia and
Xiaoyan Li and
Wangren Qiu and
Xuan Xiao and
Kuo-Chen Chou iPPI-PseAAC(CGR): Identify
protein--protein interactions by
incorporating chaos game representation
into PseAAC . . . . . . . . . . . . . . 195--203
Clarence C. King and
Amelia Ann Brown and
Irmak Sargin and
K. M. Bratlie and
S. P. Beckman Modeling of reaction--diffusion
transport into a core-shell geometry . . 204--208
Juan Zhang and
Zhen Jin and
Yuan Yuan Assessing the spread of foot and mouth
disease in mainland China by dynamical
switching model . . . . . . . . . . . . 209--219
J. Solowiej-Wedderburn and
D. J. Smith and
S. S. Lopes and
T. D. Montenegro-Johnson Wall stress enhanced exocytosis of
extracellular vesicles as a possible
mechanism of left-right
symmetry-breaking in vertebrate
development . . . . . . . . . . . . . . 220--226
S. T. Johnston and
K. J. Painter The impact of short- and long-range
perception on population movements . . . 227--242
D. Calvetti and
J. Prezioso and
E. Somersalo Estimating hemodynamic stimulus and
blood vessel compliance from cerebral
blood flow data . . . . . . . . . . . . 243--261
Ross Cressman and
Vlastimil K\vrivan Bimatrix games that include interaction
times alter the evolutionary outcome:
The Owner--Intruder game . . . . . . . . 262--273
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Kohei Tamura and
Hiroki Takikawa Modelling the emergence of an
egalitarian society in the n-player game
framework . . . . . . . . . . . . . . . 1--7
Anonymous Pages 1--290 (14 January 2019) . . . . . 1--290
Yoann Bourhis and
Timothy R. Gottwald and
Francisco J. Lopez-Ruiz and
Sujin Patarapuwadol and
Frank van den Bosch Sampling for disease absence-deriving
informed monitoring from epidemic traits 8--16
Nicolae Moise and
Avner Friedman Rheumatoid arthritis --- a mathematical
model . . . . . . . . . . . . . . . . . 17--33
Nicolas Houy and
François Le Grand Optimizing immune cell therapies with
artificial intelligence . . . . . . . . 34--40
Wentian Li and
Dimitrios Thanos and
Astero Provata Quantifying local randomness in human
DNA and RNA sequences using Erdös motifs 41--50
Lidong Wang and
Ruijun Zhang and
Yashuang Mu Fu-SulfPred: Identification of Protein
S-sulfenylation Sites by Fusing Forests
via Chou's General PseAAC . . . . . . . 51--58
Fahad Al Basir and
Arnab Banerjee and
Santanu Ray Role of farming awareness in crop pest
management --- a mathematical model . . 59--67
Cheng-Hong Yang and
Huai-Shuo Yang and
Li-Yeh Chuang PBMDR: a particle swarm
optimization-based multifactor
dimensionality reduction for the
detection of multilocus interactions . . 68--75
Mina Karami and
Begoña Calvo and
Hassan Zohoor and
Keikhosrow Firoozbakhsh and
Jorge Grasa Assessing the role of Ca$^{2+}$ in
skeletal muscle fatigue using a
multi-scale continuum model . . . . . . 76--83
Peter S. Kim and
John S. McQueen and
Kristen Hawkes Why does women's fertility end in
mid-life? Grandmothering and age at last
birth . . . . . . . . . . . . . . . . . 84--91
Guodong Chen and
Man Cao and
Jialin Yu and
Xinyun Guo and
Shaoping Shi Prediction and functional analysis of
prokaryote lysine acetylation site by
incorporating six types of features into
Chou's general PseAAC . . . . . . . . . 92--101
Michael A. Boemo and
Helen M. Byrne Mathematical modelling of a
hypoxia-regulated oncolytic virus
delivered by tumour-associated
macrophages . . . . . . . . . . . . . . 102--116
Clément Draghi and
Fabrice Denis and
Alain Tolédano and
Christophe Letellier Parameter identification of a model for
prostate cancer treated by intermittent
therapy . . . . . . . . . . . . . . . . 117--132
Christopher D. Powell and
Secundino López and
James France Elementary functions modified for
seasonal effects to describe growth in
freshwater fish . . . . . . . . . . . . 133--144
John C. Mason and
Markus W. Covert An energetic reformulation of kinetic
rate laws enables scalable parameter
estimation for biochemical networks . . 145--156
Babak Pourziaei and
Gregory M. Lewis and
Huaxiong Huang and
John E. Lewis Spatiotemporal model for depth
perception in electric sensing . . . . . 157--169
Nao Takashina and
Buntarou Kusumoto and
Yasuhiro Kubota and
Evan P. Economo A geometric approach to scaling
individual distributions to
macroecological patterns . . . . . . . . 170--188
Daniah Tahir and
Sylvain Glémin and
Martin Lascoux and
Ingemar Kaj Modeling a trait-dependent
diversification process coupled with
molecular evolution on a random species
tree . . . . . . . . . . . . . . . . . . 189--203
M. C. Köhnke and
H. Malchow Wave pinning in competition-diffusion
models in variable environments . . . . 204--214
Lydia M. Bilinsky and
David J. Thomas and
Jeffrey W. Fisher Using mathematical modeling to infer the
valence state of arsenicals in tissues:
a PBPK model for dimethylarsinic acid
(DMA V) and dimethylarsinous acid (DMA
III) in mice . . . . . . . . . . . . . . 215--229
Lei Wang and
Xin Yan and
Meng-Lin Liu and
Ke-Jian Song and
Xiao-Fei Sun and
Wen-Wen Pan Prediction of RNA-protein interactions
by combining deep convolutional neural
network with feature selection ensemble
method . . . . . . . . . . . . . . . . . 230--238
Janet Dyson and
Frank Le Foll and
Pierre Magal and
Ahmed Noussair and
Jennifer Pasquier Direct and indirect P-glycoprotein
transfers in MCF7 breast cancer cells 239--253
Subhashree Rout and
Rajani Kanta Mahapatra In silico analysis of \bionamePlasmodium
falciparum CDPK5 protein through
molecular modeling, docking and dynamics 254--267
Yuanshi Wang and
Hong Wu Global dynamics of
parasitism-competition systems with one
host and multiple parasites . . . . . . 268--275
Claude Gérard and
Didier Gonze and
Albert Goldbeter Revisiting a skeleton model for the
mammalian cell cycle: From bistability
to Cdk oscillations and cellular
heterogeneity . . . . . . . . . . . . . 276--290
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Saori Nojo and
Yasuo Ihara The effect of sexual selection on
phenotypic diversification among human
populations: a simulation study . . . . 1--11
Anonymous Pages 1--582 (7 February 2019) . . . . . 1--582
Rani Anupama and
Sajitha Lulu and
Rout Madhusmita and
Sundararajan Vino and
Amitava Mukherjee and
Subramanian Babu Insights into the interaction of key
biofilm proteins in Pseudomonas
aeruginosa PAO1 with TiO 2 nanoparticle:
An in silico analysis . . . . . . . . . 12--25
Elizabeth F. Fussell and
Andrew L. Krause and
Robert A. Van Gorder Hybrid approach to modeling spatial
dynamics of systems with generalist
predators . . . . . . . . . . . . . . . 26--47
Shyr-Shea Chang and
Marcus Roper Microvascular networks with uniform flow 48--64
Hayriye Gulbudak and
Joshua S. Weitz Heterogeneous viral strategies promote
coexistence in virus-microbe systems . . 65--84
Sandrine Pavoine An ordination approach to explore
similarities among communities . . . . . 85--96
Mia Åstrand and
Julia Cuellar and
Jukka Hytönen and
Tiina A. Salminen Predicting the ligand-binding properties
of \bionameBorrelia burgdorferi s.s. Bmp
proteins in light of the conserved
features of related \bionameBorrelia
proteins . . . . . . . . . . . . . . . . 97--108
Ryan Viertel and
Alla Borisyuk A Computational model of the mammalian
external tufted cell . . . . . . . . . . 109--121
Zhongpu Xu and
Kezan Li and
Mengfeng Sun and
Xinchu Fu Interaction between epidemic spread and
collective behavior in scale-free
networks with community structure . . . 122--133
Ket Hing Chong and
Sandhya Samarasinghe and
Don Kulasiri and
Jie Zheng Mathematical modelling of core
regulatory mechanism in p53 protein that
activates apoptotic switch . . . . . . . 134--147
Robert W. Gregg and
Saumendra N. Sarkar and
Jason E. Shoemaker Mathematical modeling of the cGAS
pathway reveals robustness of DNA
sensing to TREX1 feedback . . . . . . . 148--157
Z. P. Adams and
J. Ehlting and
R. Edwards The regulatory role of shikimate in
plant phenylalanine metabolism . . . . . 158--170
Ross Corkrey and
Cameron Macdonald and
Tom McMeekin The Biokinetic Spectrum for Temperature
and optimal Darwinian fitness . . . . . 171--183
Loukas Zagkos and
Mark Mc Auley and
Jason Roberts and
Nikos I. Kavallaris Mathematical models of DNA methylation
dynamics: Implications for health and
ageing . . . . . . . . . . . . . . . . . 184--193
Lingzi Wang and
Stephen J. Cornell and
Michael P. Speed The evolution of variance in sequential
defences . . . . . . . . . . . . . . . . 194--209
Tamsin E. Lee and
Melissa A. Penny Identifying key factors of the
transmission dynamics of drug-resistant
malaria . . . . . . . . . . . . . . . . 210--220
Yi Pan and
Shiyuan Wang and
Qi Zhang and
Qianzi Lu and
Dongqing Su and
Yongchun Zuo and
Lei Yang Analysis and prediction of animal toxins
by various Chou's pseudo components and
reduced amino acid compositions . . . . 221--229
Yinan Shen and
Jijun Tang and
Fei Guo Identification of protein subcellular
localization via integrating
evolutionary and physicochemical
information into Chou's general PseAAC 230--239
Weidong Li and
Qingniao Zhou and
Yong Gao and
Yonghua Jiang and
Yuanjie Huang and
Zengnan Mo and
Yiming Zou and
Yanling Hu eQTL analysis from co-localization of
2739 GWAS loci detects associated genes
across 14 human cancers . . . . . . . . 240--246
Linchao Hu and
Mugen Huang and
Moxun Tang and
Jianshe Yu and
Bo Zheng \bionameWolbachia spread dynamics in
multi-regimes of environmental
conditions . . . . . . . . . . . . . . . 247--258
Madalena Chaves and
Diego A. Oyarzún and
Jean-Luc Gouzé Analysis of a genetic-metabolic
oscillator with piecewise linear models 259--269
Arnaud Z. Dragicevic Comparing forest governance models
against invasive biological threats . . 270--282
Ainhoa Calleja-Rodriguez and
Zitong Li and
Henrik R. Hallingbäck and
Mikko J. Sillanpää and
Harry X. Wu and
Sara Abrahamsson and
Maria Rosario Garc\'ìa-Gil Analysis of phenotypic- and Estimated
Breeding Values (EBV) to dissect the
genetic architecture of complex traits
in a Scots pine three-generation
pedigree design . . . . . . . . . . . . 283--292
Naoki Sato and
Kaoru Sato Statistical analysis of word usage in
biological publications since 1965:
Historical delineation highlighting an
emergence of function-oriented
discourses in contemporary molecular and
cellular biology . . . . . . . . . . . . 293--303
Zsuzsanna Vig-Milkovics and
István Zachar and
Ádám Kun and
András Szilágyi and
Eörs Szathmáry Moderate sex between protocells can
balance between a decrease in assortment
load and an increase in parasite spread 304--310
Benjamin J. Walker and
Richard J. Wheeler and
Kenta Ishimoto and
Eamonn A. Gaffney Boundary behaviours of
\bionameLeishmania mexicana: a
hydrodynamic simulation study . . . . . 311--320
N. J. López-Alamilla and
M. W. Jack and
K. J. Challis Analysing single-molecule trajectories
to reconstruct free-energy landscapes of
cyclic motor proteins . . . . . . . . . 321--328
Baoguang Tian and
Xue Wu and
Cheng Chen and
Wenying Qiu and
Qin Ma and
Bin Yu Predicting protein--protein interactions
by fusing various Chou's pseudo
components and using wavelet denoising
approach . . . . . . . . . . . . . . . . 329--346
Christoph Hauert and
Camille Saade and
Alex McAvoy Asymmetric evolutionary games with
environmental feedback . . . . . . . . . 347--360
Te Wu and
Feng Fu and
Long Wang Phenotype affinity mediated interactions
can facilitate the evolution of
cooperation . . . . . . . . . . . . . . 361--369
V. Belitsky and
G. M. Schütz RNA Polymerase interactions and
elongation rate . . . . . . . . . . . . 370--380
Dmitry Gromov and
Ingo Bulla and
Ethan O. Romero-Severson Systematic evaluation of the
population-level effects of alternative
treatment strategies on the basic
reproduction number . . . . . . . . . . 381--390
Silvia Zaoli and
Andrea Giometto and
Jonathan Giezendanner and
Amos Maritan and
Andrea Rinaldo On the probabilistic nature of the
species-area relation . . . . . . . . . 391--407
Mirjam Laager and
Monique Léchenne and
Kemdongarti Naissengar and
Rolande Mindekem and
Assandi Oussiguere and
Jakob Zinsstag and
Nakul Chitnis A metapopulation model of dog rabies
transmission in N'Djamena, Chad . . . . 408--417
Rachata Muneepeerakul and
Enrico Bertuzzo and
Andrea Rinaldo and
Ignacio Rodriguez-Iturbe Evolving biodiversity patterns in
changing river networks . . . . . . . . 418--424
Takashi Nagatani and
Genki Ichinose and
Kei-ichi Tainaka Metapopulation dynamics in the
rock-paper-scissors game with mutation:
Effects of time-varying migration paths 425--431
Changjing Zhuge and
Michael C. Mackey and
Jinzhi Lei Origins of oscillation patterns in
cyclical thrombocytopenia . . . . . . . 432--445
A. M. Portillo and
E. Varela and
J. A. García-Velasco Mathematical model to study the aging of
the human follicle according to the
telomerase activity . . . . . . . . . . 446--454
Ali Mai and
Guowei Sun and
Fengqin Zhang and
Lin Wang The joint impacts of dispersal delay and
dispersal patterns on the stability of
predator--prey metacommunities . . . . . 455--465
Nicholas J. Beeton and
Scott Carver and
Lawrence K. Forbes A model for the treatment of
environmentally transmitted sarcoptic
mange in bare-nosed wombats
(\bionameVombatus ursinus) . . . . . . . 466--474
Michael A. Fishman Animal conflicts in diploid populations
with sexual reproduction . . . . . . . . 475--478
Naoya Hatanaka and
Takao Seki and
Jun-ichiro Inoue and
Atsushi Tero and
Takashi Suzuki Critical roles of I$ \kappa $B$ \alpha $
and RelA phosphorylation in transitional
oscillation in NF-$ \kappa $B signaling
module . . . . . . . . . . . . . . . . . 479--489
Xiulan Lai and
Avner Friedman Mathematical modeling in scheduling
cancer treatment with combination of
VEGF inhibitor and chemotherapy drugs 490--498
Yasser Aboelkassem and
Zdravko Virag A hybrid Windkessel--Womersley model for
blood flow in arteries . . . . . . . . . 499--513
John J. Tyson and
Teeraphan Laomettachit and
Pavel Kraikivski Modeling the dynamic behavior of
biochemical regulatory networks . . . . 514--527
Yu-Xiang Yao and
Zhi-Tong Bing and
Liang Huang and
Zi-Gang Huang and
Ying-Cheng Lai A network approach to quantifying
radiotherapy effect on cancer:
Radiosensitive gene group centrality . . 528--536
Frédéric Pro\"\ia and
Fabien Panloup and
Chiraz Trabelsi and
Jérémy Clotault Probabilistic reconstruction of
genealogies for polyploid plant species 537--551
Simon Labarthe and
Bastien Polizzi and
Thuy Phan and
Thierry Goudon and
Magali Ribot and
Beatrice Laroche A mathematical model to investigate the
key drivers of the biogeography of the
colon microbiota . . . . . . . . . . . . 552--581
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Wenpin Hou and
Peiying Ruan and
Wai-Ki Ching and
Tatsuya Akutsu On the number of driver nodes for
controlling a Boolean network when the
targets are restricted to attractors . . 1--11
Anonymous Pages 1--166 (21 February 2019) . . . . 1--166
Jie Jiang and
Anglu Shen and
Hao Wang and
Sanling Yuan Regulation of phosphate uptake kinetics
in the bloom-forming dinoflagellates
\bionameProrocentrum donghaiense with
emphasis on two-stage dynamic process 12--21
Weike Zhou and
Yanni Xiao and
Jane M. Heffernan A two-thresholds policy to interrupt
transmission of West Nile Virus to birds 22--46
Yaser Daanial Khan and
Mehreen Jamil and
Waqar Hussain and
Nouman Rasool and
Sher Afzal Khan and
Kuo-Chen Chou pSSbond-PseAAC: Prediction of disulfide
bonding sites by integration of PseAAC
and statistical moments . . . . . . . . 47--55
Joëlle De Caluwé and
Alen Tosenberger and
Didier Gonze and
Genevi\`eve Dupont Signalling-modulated gene regulatory
networks in early mammalian development 56--66
Adrien Richard Positive and negative cycles in Boolean
networks . . . . . . . . . . . . . . . . 67--76
Chuanze Kang and
Yanhao Huo and
Lihui Xin and
Baoguang Tian and
Bin Yu Feature selection and tumor
classification for microarray data using
relaxed Lasso and generalized
multi-class support vector machine . . . 77--91
Osman Doluca G4Catchall: a G-quadruplex prediction
approach considering atypical features 92--98
Jamal Ahmad and
Maqsood Hayat MFSC: Multi-voting based feature
selection for classification of Golgi
proteins by adopting the general form of
Chou's PseAAC components . . . . . . . . 99--109
Szymon Wasik and
Natalia Szostak and
Mateusz Kudla and
Micha\l Wachowiak and
Krzysztof Krawiec and
Jacek Blazewicz Detecting life signatures with RNA
sequence similarity measures . . . . . . 110--120
Steven A. Frank Evolutionary design of regulatory
control. I. A robust control theory
analysis of tradeoffs . . . . . . . . . 121--137
Ying Chen and
John S. Lowengrub Tumor growth and calcification in
evolving microenvironmental geometries 138--154
Isao T. Tokuda and
Ozgur E. Akman and
James C. W. Locke Reducing the complexity of mathematical
models for the plant circadian clock by
distributed delays . . . . . . . . . . . 155--166
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Farshid Rayhan and
Sajid Ahmed and
Dewan Md Farid and
Abdollah Dehzangi and
Swakkhar Shatabda CFSBoost: Cumulative feature subspace
boosting for drug-target interaction
prediction . . . . . . . . . . . . . . . 1--8
Anonymous Pages 1--182 (7 March 2019) . . . . . . 1--182
Akane Hara and
Yoh Iwasa Coupled dynamics of intestinal
microbiome and immune system --- a
mathematical study . . . . . . . . . . . 9--20
Pawe\l Blazej and
Ma\lgorzata Wnetrzak and
Dorota Mackiewicz and
Przemyslaw Gagat and
Pawe\l Mackiewicz Many alternative and theoretical genetic
codes are more robust to amino acid
replacements than the standard genetic
code . . . . . . . . . . . . . . . . . . 21--32
Kandasamy Saravanan and
Poomani Kumaradhas Acylguanidine-BACE1 complex: Insights of
intermolecular interactions and dynamics 33--49
Indrajit Ghosh and
Pankaj Kumar Tiwari and
Joydev Chattopadhyay Effect of active case finding on dengue
control: Implications from a
mathematical model . . . . . . . . . . . 50--62
Avirup Ghosh and
Hong Yan Hydrogen bond analysis of the EGFR-ErbB3
heterodimer related to non-small cell
lung cancer and drug resistance . . . . 63--71
Mojeeb Al-Rahman El-Nor Osman and
Jinhui Li Analysis of a vector-bias malaria
transmission model with application to
Mexico, Sudan and Democratic Republic of
the Congo . . . . . . . . . . . . . . . 72--84
Weam Alharbi and
Sergei Petrovskii Effect of complex landscape geometry on
the invasive species spread: Invasion
with stepping stones . . . . . . . . . . 85--97
Natália Martínková and
Pavel Skrabánek and
Jiri Pikula Modelling invasive pathogen load from
non-destructive sampling data . . . . . 98--103
Xiaoyan Xu and
Jianing Wu and
Kai Wang and
Yunqiang Yang and
Shaoze Yan Locking of the operculum in a water
snail: Theoretical modeling and
applications for mechanical sealing . . 104--111
Sailen Barik How universal is the transcription
regulatory moonlighting role of fructose
1,6-bisphosphate aldolase? . . . . . . . 112--114
Ben Ashby and
Ryosuke Iritani and
Alex Best and
Andy White and
Mike Boots Understanding the role of
eco-evolutionary feedbacks in
host-parasite coevolution . . . . . . . 115--125
Massimo Di Giulio A qualitative criterion for identifying
the root of the tree of life . . . . . . 126--131
J. C. Dallon and
Cécile Leduc and
Sandrine Etienne-Manneville and
Stéphanie Portet Stochastic modeling reveals how motor
protein and filament properties affect
intermediate filament transport . . . . 132--148
Longgui Liu and
Mao Sun Dynamic flight stability of hovering
mosquitoes . . . . . . . . . . . . . . . 149--158
John Ellis and
Natalia Petrovskaya and
Sergei Petrovskii Effect of density-dependent individual
movement on emerging spatial population
distribution: Brownian motion vs Levy
flights . . . . . . . . . . . . . . . . 159--178
Marisa C. Eisenberg and
Harsh V. Jain Corrigendum to ``A confidence building
exercise in data and identifiability:
Modeling cancer chemotherapy as a case
study'' [Journal of Theoretical Biology
\bf 431 (2017) 63--78] . . . . . . . . . 179--179
Mark Robertson-Tessi and
Ardith El-Kareh and
Alain Goriely Corrigendum to ``A mathematical model of
tumor-immune interactions'' [Journal of
Theoretical Biology \bf 294 (2012)
56--73] . . . . . . . . . . . . . . . . 180--180
Mark Robertson-Tessi and
Ardith El-Kareh and
Alain Goriely Corrigendum to ``A model for effects of
adaptive immunity on tumor response to
chemotherapy and chemoimmunotherapy''
[Journal of Theoretical Biology \bf 380
(2015) 569--584] . . . . . . . . . . . . 181--181
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Muhammad Tahir and
Hilal Tayara and
Kil To Chong iRNA-PseKNC(2methyl): Identify RNA
2'-O-methylation sites by convolution
neural network and Chou's pseudo
components . . . . . . . . . . . . . . . 1--6
Anonymous Pages 1--134 (21 March 2019) . . . . . . 1--134
Masashi Shiraishi and
Rito Takeuchi and
Hiroyuki Nakagawa and
Shin I. Nishimura and
Akinori Awazu and
Hiraku Nishimori Diverse stochasticity leads a colony of
ants to optimal foraging . . . . . . . . 7--16
Xian-jia Wang and
Cui-ling Gu and
Ji Quan Evolutionary game dynamics of the
Wright--Fisher process with different
selection intensities . . . . . . . . . 17--26
Nita H. Shah and
Nehal Shukla and
Moksha H. Satia and
Foram A. Thakkar Optimal control of HCV transmission
under liquoring . . . . . . . . . . . . 27--33
Sahil Jain and
Manoj Baranwal Computational analysis in designing T
cell epitopes enriched peptides of Ebola
glycoprotein exhibiting strong binding
interaction with HLA molecules . . . . . 34--44
Fatemeh Taheriyan and
Mohammad Teshnehlab and
Shahriar Gharibzadeh Presenting a Neuroid model of wind-up
based on dynamic synapse . . . . . . . . 45--50
Sophie J. Rhodes and
Gwenan M. Knight and
Denise E. Kirschner and
Richard G. White and
Thomas G. Evans Dose finding for new vaccines: The role
for immunostimulation/immunodynamic
modelling . . . . . . . . . . . . . . . 51--55
Keita Iida and
Nobuaki Obata and
Yoshitaka Kimura Quantifying heterogeneity of stochastic
gene expression . . . . . . . . . . . . 56--62
Zepeng Sun and
Thomas Koffel and
Simon M. Stump and
Ghjuvan M. Grimaud and
Christopher A. Klausmeier Microbial cross-feeding promotes
multiple stable states and species
coexistence, but also susceptibility to
cheaters . . . . . . . . . . . . . . . . 63--77
Ana Martinci\'c Spoljari\'c and
Ivica Rubelj and
Miljenko Huzak Mathematical model and computer
simulations of telomere loss . . . . . . 78--89
Johnny T. Ottesen and
Rasmus K. Pedersen and
Zamra Sajid and
Johanne Gudmand-Hoeyer and
Katrine O. Bangsgaard and
Vibe Skov and
Lasse Kjær and
Trine A. Knudsen and
Niels Pallisgaard and
Hans C. Hasselbalch and
Morten Andersen Bridging blood cancers and inflammation:
The reduced Cancitis model . . . . . . . 90--108
Johnny Thew and
Pamela Burrage and
Natalie Medlicott and
Dann Mallet Modelling optimal delivery of bFGF to
chronic wounds using ODEs . . . . . . . 109--116
Shrish Kumar Pandey and
Saveg Yadav and
Yugal Goel and
Mithlesh Kumar Temre and
Vinay Kumar Singh and
Sukh Mahendra Singh Molecular docking of anti-inflammatory
drug diclofenac with metabolic targets:
Potential applications in cancer
therapeutics . . . . . . . . . . . . . . 117--125
Marcelle Kaufman and
Christophe Soulé On the multistationarity of chemical
reaction networks . . . . . . . . . . . 126--133
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Scott O. Rogers Evolution of the genetic code based on
conservative changes of codons, amino
acids, and aminoacyl tRNA synthetases 1--10
Anonymous Pages 1--144 (7 April 2019) . . . . . . 1--144
Chathranee Jayathilake and
Philip K. Maini and
Harriet W. Hopf and
D. L. Sean McElwain and
Helen M. Byrne and
Mark B. Flegg and
Jennifer A. Flegg A mathematical model of the use of
supplemental oxygen to combat surgical
site infection . . . . . . . . . . . . . 11--23
Lubna Pinky and
Gilberto González-Parra and
Hana M. Dobrovolny Superinfection and cell regeneration can
lead to chronic viral coinfections . . . 24--38
Wassim Abou-Jaoudé and
Pedro T. Monteiro On logical bifurcation diagrams . . . . 39--63
Bryce Morsky and
Chris T. Bauch The impact of truncation selection and
diffusion on cooperation in spatial
games . . . . . . . . . . . . . . . . . 64--83
Arran Hodgkinson and
Laurent Le Cam and
Dumitru Trucu and
Ovidiu R\uadulescu Spatio-Genetic and phenotypic modelling
elucidates resistance and
re-sensitisation to treatment in
heterogeneous melanoma . . . . . . . . . 84--105
Elena Braverman and
Ilia Ilmer On the interplay of harvesting and
various diffusion strategies for
spatially heterogeneous populations . . 106--118
Jin Xu and
Junghyo Jo Broad cross-reactivity of the T-cell
repertoire achieves specific and
sufficiently rapid target searching . . 119--127
Cortland K. Griswold An ancestral process with selection in
an ecological community . . . . . . . . 128--144
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Yixing Guo and
Ying Zhou A modified association test for rare and
common variants based on affected
sib-pair design . . . . . . . . . . . . 1--6
Anonymous Pages 1--174 (21 April 2019) . . . . . . 1--174
Suling Bo and
Hong Li and
Qiang Zhang and
Zhanyuan Lu and
Tonglaga Bao and
Xiaoqing Zhao Potential relations between post-spliced
introns and mature mRNAs in the
\bionameCaenorhabditis elegans genome 7--14
Stefan Bornholdt and
Stuart Kauffman Ensembles, dynamics, and cell types:
Revisiting the statistical mechanics
perspective on cellular regulation . . . 15--22
Ivan Colorado Cervantes and
Vittorio Sansalone and
Luciano Teresi The heart function as a motor-brake
system . . . . . . . . . . . . . . . . . 23--30
Gabriel S. Zamudio and
Francisco Prosdocimi and
Sávio Torres de Farias and
Marco V. José A neutral evolution test derived from a
theoretical amino acid substitution
model . . . . . . . . . . . . . . . . . 31--38
Xiaowei Zhao and
Ye Zhang and
Qiao Ning and
Hongrui Zhang and
Jinchao Ji and
Minghao Yin Identifying N$^6$-methyladenosine sites
using extreme gradient boosting system
optimized by particle swarm optimizer 39--47
Juliano Morimoto Foraging decisions as multi-armed bandit
problems: Applying reinforcement
learning algorithms to foraging data . . 48--56
Hossein Hassani and
Mohammad Reza Yeganegi and
Emmanuel Sirimal Silva and
Fatemeh Ghodsi Risk management, signal processing and
econometrics: a new tool for forecasting
the risk of disease outbreaks . . . . . 57--62
Rinaldo B. Schinazi Can evolution paths be explained by
chance alone? . . . . . . . . . . . . . 63--65
Méline Wery and
Olivier Dameron and
Jacques Nicolas and
Elisabeth Remy and
Anne Siegel Formalizing and enriching phenotype
signatures using Boolean networks . . . 66--79
David Waxman and
Pierre Nouvellet Sub- or supercritical transmissibilities
in a finite disease outbreak: Symmetry
in outbreak properties of a disease
conditioned on extinction . . . . . . . 80--86
Karen Larson and
Loukas Zagkos and
Mark Mc Auley and
Jason Roberts and
Nikos I. Kavallaris and
Anastasios Matzavinos Data-driven selection and parameter
estimation for DNA methylation
mathematical models . . . . . . . . . . 87--99
Günther K. H. Zupanc and
Frederick B. Zupanc and
Rifat Sipahi Stochastic cellular automata model of
tumorous neurosphere growth: Roles of
developmental maturity and cell death 100--110
Joan Ponce and
Yiqiang Zheng and
Guang Lin and
Zhilan Feng Assessing the effects of modeling the
spectrum of clinical symptoms on the
dynamics and control of Ebola . . . . . 111--122
Jacques Demongeot and
Hana Hasgui and
Michel Thellier Memory in plants: Boolean modeling of
the learning and store/recall memory
functions in response to environmental
stimuli . . . . . . . . . . . . . . . . 123--133
Junko Kusumi and
Motoshi Ichinose and
Masaru Iizuka Effects of gene duplication, epistasis,
recombination and gene conversion on the
fixation time of compensatory mutations 134--141
Jin Tao and
Xiaoqing Liu and
Siqian Yang and
Chaohui Bao and
Pingan He and
Qi Dai An efficient genomic signature ranking
method for genomic island prediction
from a single genome . . . . . . . . . . 142--149
Diana Schepens and
Ross P. Carlson and
Jeff Heys and
Ashley E. Beck and
Tomás Gedeon Role of resource allocation and
transport in emergence of cross-feeding
in microbial consortia . . . . . . . . . 150--163
Mayumi Seto and
Yoh Iwasa Population dynamics of chemotrophs in
anaerobic conditions where the metabolic
energy acquisition per redox reaction is
limited . . . . . . . . . . . . . . . . 164--173
Asterios Pantokratoras Comment on the paper ``Peristaltic
transport of multilayered power-law
fluids with distinct viscosities: a
mathematical model for intestinal flows,
S. K. Pandey, M. K. Chaube, Dharmendra
Tripathi, Journal of Theoretical Biology
\bf 278 (2011) 11--19'' . . . . . . . . 174--174
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Waqar Hussain and
Yaser Daanial Khan and
Nouman Rasool and
Sher Afzal Khan and
Kuo-Chen Chou SPrenylC-PseAAC: a sequence-based model
developed via Chou's $5$-steps rule and
general PseAAC for identifying
S-prenylation sites in proteins . . . . 1--11
Anonymous Pages 1--92 (7 May 2019) . . . . . . . . 1--92
Miki Hamada and
Fugo Takasu Equilibrium properties of the spatial
SIS model as a point pattern dynamics
--- How is infection distributed over
space? . . . . . . . . . . . . . . . . . 12--26
Cicely K. Macnamara and
Elaine I. Mitchell and
Mark A. J. Chaplain Spatial-Stochastic modelling of
synthetic gene regulatory networks . . . 27--44
Christopher E. Overton and
Mark Broom and
Christoforos Hadjichrysanthou and
Kieran J. Sharkey Methods for approximating stochastic
evolutionary dynamics on graphs . . . . 45--59
Aike Beckmann and
C-Elisa Schaum and
Inga Hense Phytoplankton adaptation in ecosystem
models . . . . . . . . . . . . . . . . . 60--71
Steven A. Frank Evolutionary design of regulatory
control. II. Robust error-correcting
feedback increases genetic and
phenotypic variability . . . . . . . . . 72--81
Marta Alonso-Hearn and
Gesham Magombedze and
Naiara Abendaño and
Mariana Landin and
Ramon A. Juste Deciphering the virulence of
Mycobacterium avium subsp.
paratuberculosis isolates in animal
macrophages using mathematical models 82--91
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Marissa Renardy and
Denise E. Kirschner Evaluating vaccination strategies for
tuberculosis in endemic and non-endemic
settings . . . . . . . . . . . . . . . . 1--11
Anonymous Pages 1--202 (21 May 2019) . . . . . . . 1--202
Rui Dilão and
Bárbara Mota The transcriptional regulation of PER
protein in \bionameDrosophila . . . . . 12--17
Panchaksaram Muthukumaran and
Muniyan Rajiniraja Aug--MIA--QSAR based strategy in
bioactivity prediction of a series of
flavonoid derivatives as HIV-1
inhibitors . . . . . . . . . . . . . . . 18--24
Zhongyan Li and
Fugang Yan and
Qingqing Miao and
Yang Meng and
Li Wen and
Qianhu Jiang and
Peng Zhou Self-binding peptides:
Binding-upon-folding versus
folding-upon-binding . . . . . . . . . . 25--34
Tapan Kumar Kar and
Debprasad Pal and
Bapan Ghosh Managing yield and resilience in a
harvested tri-trophic food chain model 35--46
Grace E. Mahlbacher and
Kara C. Reihmer and
Hermann B. Frieboes Mathematical modeling of tumor-immune
cell interactions . . . . . . . . . . . 47--60
Swarnendu Banerjee and
Ram Rup Sarkar and
Joydev Chattopadhyay Effect of copper contamination on
zooplankton epidemics . . . . . . . . . 61--74
Hugh Trenchard Cell pelotons: a model of early
evolutionary cell sorting, with
application to slime mold
\bionameDictyostelium discoideum . . . . 75--95
Ezio Venturino and
Simona Collino and
Luca Ferreri and
Luigi Bertolotti and
Sergio Rosati and
Mario Giacobini An effective management strategy for the
control of two lentiviruses in goat
breedings . . . . . . . . . . . . . . . 96--106
Kazuki Kuga and
Jun Tanimoto and
Marko Jusup To vaccinate or not to vaccinate: a
comprehensive study of
vaccination-subsidizing policies with
multi-agent simulations and mean-field
modeling . . . . . . . . . . . . . . . . 107--126
D. Peurichard and
M. Ousset and
J. Paupert and
B. Aymard and
A. Lorsignol and
L. Casteilla and
P. Degond Extra-cellular matrix rigidity may
dictate the fate of injury outcome . . . 127--136
Oleg A. Zhukov and
Tatiana A. Kazakova and
Georgy V. Maksimov and
Alexey R. Brazhe Cost of auditory sharpness: Model-Based
estimate of energy use by auditory
brainstem ``octopus'' neurons . . . . . 137--147
Jacek Jaworski and
Jason H. T. Bates Sources of breathing pattern variability
in the respiratory feedback control loop 148--162
Ashish Kumar Agrahari and
George Priya C. Doss and
R. Siva and
R. Magesh and
Hatem Zayed Molecular insights of the G2019S
substitution in LRRK2 kinase domain
associated with Parkinson's disease: a
molecular dynamics simulation approach 163--171
Kento Koyama and
Hiroki Abe and
Shuso Kawamura and
Shige Koseki Calculating stochastic inactivation of
individual cells in a bacterial
population using variability in
individual cell inactivation time and
initial cell number . . . . . . . . . . 172--179
Strelnikov Kuzma Energy-information coupling during
integrative cognitive processes . . . . 180--186
Anne Bisson and
Céline Casenave and
Simon Boudsocq and
Tanguy Daufresne Maximization of fertility transfers from
rangeland to cropland: The contribution
of control theory . . . . . . . . . . . 187--200
Victor Pozzobon and
Patrick Perre Corrigendum to ``Han's model parameters
for microalgae grown under intermittent
illumination: Determined using particle
swarm optimization'' [Journal of
Theoretical Biology \bf 437 (2018)
29--35] . . . . . . . . . . . . . . . . 201--201
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Bing Hu and
Xiyezi Diao and
Liqing Zong and
Jingsong Zhang and
Liang Yu and
Hao Dai and
Luonan Chen The onset mechanism of Parkinson's beta
oscillations: a theoretical analysis . . 1--16
Anonymous Pages 1--120 (7 June 2019) . . . . . . . 1--120
Kohji Sato Why is glycine cleavage system
segmentally expressed in radial glia? 17--19
Nan Zhang and
Pengcheng Zhao and
Yuguo Li Increased infection severity in
downstream cities in infectious disease
transmission and tourists surveillance
analysis . . . . . . . . . . . . . . . . 20--29
Jesse A. Sharp and
Alexander P. Browning and
Tarunendu Mapder and
Kevin Burrage and
Matthew J. Simpson Optimal control of acute myeloid
leukaemia . . . . . . . . . . . . . . . 30--42
Qiao Ning and
Zhiqiang Ma and
Xiaowei Zhao dForml(KNN)-PseAAC: Detecting
formylation sites from protein sequences
using $K$-nearest neighbor algorithm via
Chou's $5$-step rule and pseudo
components . . . . . . . . . . . . . . . 43--49
Sourav Kumar Sasmal and
Yasuhiro Takeuchi and
Shinji Nakaoka T-Cell mediated adaptive immunity and
antibody-dependent enhancement in
secondary dengue infection . . . . . . . 50--63
Barbara Schmidt and
Dalia Alansary and
Ivan Bogeski and
Barbara A. Niemeyer and
Heiko Rieger Reaction-diffusion model for STIM-ORAI
interaction: The role of ROS and
mutations . . . . . . . . . . . . . . . 64--75
Masoumeh Zareh and
Mohammad Hossein Manshaei and
Mehdi Adibi and
Mohammad Ali Montazeri Neurons and astrocytes interaction in
neuronal network: a game-theoretic
approach . . . . . . . . . . . . . . . . 76--89
Huan Du and
Thi-Bich-Thuy Tran and
Patrick Perré A $3$-variable PDE model for predicting
fungal growth derived from microscopic
mechanisms . . . . . . . . . . . . . . . 90--100
Radoslaw W. Piast Shannon's information, Bernal's
biopoiesis and Bernoulli distribution as
pillars for building a definition of
life . . . . . . . . . . . . . . . . . . 101--107
Aniruddha Deka and
Samit Bhattacharyya Game dynamic model of optimal budget
allocation under individual vaccination
choice . . . . . . . . . . . . . . . . . 108--118
S. K. Pandey and
M. K. Chaube and
Dharmendra Tripathi Corrigendum to ``Peristaltic transport
of multilayered power-law fluids with
distinct viscosities: a mathematical
model for intestinal flows'' [Journal of
Theoretical Biology \bf 278 (2011)
11--19] . . . . . . . . . . . . . . . . 119--119
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Hyojung Lee and
Hiroshi Nishiura Sexual transmission and the probability
of an end of the Ebola virus disease
epidemic . . . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--124 (21 June 2019) . . . . . . 1--124
Wataru Nakahashi Cultural skill and language: How
structuration affects cultural evolution 13--21
Benjamin R. Liu and
Mark Kot Accelerating invasions and the
asymptotics of fat-tailed dispersal . . 22--41
Robinson F. Alvarez and
José A. M. Barbuto and
Roberto Venegeroles A nonlinear mathematical model of
cell-mediated immune response for tumor
phenotypic heterogeneity . . . . . . . . 42--50
Shota Shibasaki The evolutionary game of interspecific
mutualism in the multi-species model . . 51--58
Rakesh Kumar and
Abhishek Kumar Tiwari and
Dharmendra Tripathi and
Nikhil Vivek Shrivas and
Fahad Nizam Canalicular fluid flow induced by
loading waveforms: a comparative
analysis . . . . . . . . . . . . . . . . 59--73
Fuhua Lu and
Maoshu Zhu and
Ying Lin and
Hongbin Zhong and
Lei Cai and
Lin He and
Kuo-Chen Chou The preliminary efficacy evaluation of
the CTLA-$4$-Ig treatment against
\bionameLupus nephritis through
in-silico analyses . . . . . . . . . . . 74--81
Shannon Dee Algar and
Thomas Stemler and
Michael Small The active selfish herd . . . . . . . . 82--90
Nicolas Bajeux and
Frédéric Grognard and
Ludovic Mailleret Influence of the components of propagule
pressure, Allee effects, and
stochasticity on the time to establish
introduced populations . . . . . . . . . 91--107
Jacques Demongeot and
Hervé Seligmann Theoretical minimal RNA rings
recapitulate the order of the genetic
code's codon-amino acid assignments . . 108--116
Günther K. H. Zupanc and
Stephanie M. Amaro and
Dávid Lehotzky and
Frederick B. Zupanc and
Nicholas Y. Leung Glia-mediated modulation of
extracellular potassium concentration
determines the sexually dimorphic output
frequency of a model brainstem
oscillator . . . . . . . . . . . . . . . 117--124
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Yuko Hamaguchi and
Hiroshi Nishiura Estimate of the annual risk of
tuberculosis infection in a general
population of Japan . . . . . . . . . . 1--3
Anonymous Pages 1--124 (7 July 2019) . . . . . . . 1--124
Tao Deng Configuration of DNA polyhedra of
truncated tetrahedron, cuboctahedron,
truncated octahedron . . . . . . . . . . 4--10
Allanah Kenny and
Michael J. Plank and
Tim David The effects of cerebral curvature on
cortical spreading depression . . . . . 11--26
Rui-Juan Niu and
Qing-Chuan Zheng and
Hong-Xing Zhang Molecular dynamics simulations study of
influence of Tyr422Ala mutation on
transcriptional enhancer activation
domain 4 (TEAD4) and transcription
co-activators complexes . . . . . . . . 27--35
Amanda M. Saunders and
Daniel Ashlock and
Steffen P. Graether Testing the rogue taxa hypothesis for
clustering instability . . . . . . . . . 36--45
Laura Menini and
Corrado Possieri and
Antonio Tornamb\`e Boolean network analysis through the
joint use of linear algebra and
algebraic geometry . . . . . . . . . . . 46--53
Yao-ban Chan and
Charles Robin Reconciliation of a gene network and
species tree . . . . . . . . . . . . . . 54--66
Yutaka Kobayashi and
Joe Yuichiro Wakano and
Hisashi Ohtsuki Evolution of cumulative culture for
niche construction . . . . . . . . . . . 67--76
Sabin Lessard and
Warren J. Ewens The left-hand side of the Fundamental
Theorem of Natural Selection: a reply 77--83
Tatsuaki Tsuruyama Non-equilibrium thermodynamics of
biological signal transduction predicts
conservation of entropy production rate 84--87
Laureano Castro and
Miguel Ángel Castro-Nogueira and
Miguel Ángel Toro Assessor teaching and the development of
the capacity to innovate and to imitate 88--94
Bo Zheng and
Xiaoping Liu and
Moxun Tang and
Zhiyong Xi and
Jianshe Yu Use of age-stage structural models to
seek optimal \bionameWolbachia-infected
male mosquito releases for
mosquito-borne disease control . . . . . 95--109
Ankur Gupta and
Phonindra Nath Das and
Rania Bouzeyen and
Sonali Porey Karmakar and
Ramandeep Singh and
Nandadulal Bairagi and
Samrat Chatterjee Restoration of cytosolic calcium
inhibits Mycobacterium tuberculosis
intracellular growth: Theoretical
evidence and experimental observation 110--123
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Ahmad Hassan Butt and
Nouman Rasool and
Yaser Daanial Khan Prediction of antioxidant proteins by
incorporating statistical moments based
features into Chou's PseAAC . . . . . . 1--8
Anonymous Pages 1--94 (21 July 2019) . . . . . . . 1--94
Lingzi Wang and
Graeme D. Ruxton and
Stephen J. Cornell and
Michael P. Speed and
Mark Broom A theory for investment across defences
triggered at different stages of a
predator--prey encounter . . . . . . . . 9--19
Luis U. Aguilera and
Jesús Rodríguez-González Modeling the effect of tat inhibitors on
HIV latency . . . . . . . . . . . . . . 20--27
A. Alvarez Secondary dispersal of seagrass seeds in
complex microtopographies . . . . . . . 28--37
Wei Zhao and
Guang-Ping Li and
Jun Wang and
Yuan-Ke Zhou and
Yang Gao and
Pu-Feng Du Predicting protein sub-Golgi locations
by combining functional domain
enrichment scores with pseudo-amino acid
compositions . . . . . . . . . . . . . . 38--43
Xiaolu Bai and
Xiaolin Chen Rational design, conformational analysis
and membrane-penetrating dynamics study
of Bac2A-derived antimicrobial peptides
against gram-positive clinical strains
isolated from pyemia . . . . . . . . . . 44--51
Qasim Ali and
Riccardo Dainese and
Marija Cvijovic Adaptive damage retention mechanism
enables healthier yeast population . . . 52--66
Silvia Trichilo and
Stefan Scheiner and
Mark Forwood and
David M. L. Cooper and
Peter Pivonka Computational model of the dual action
of PTH --- Application to a rat model of
osteoporosis . . . . . . . . . . . . . . 67--79
Krisztina Szalisznyó and
David N. Silverstein and
János Tóth Neural dynamics in co-morbid
schizophrenia and OCD: a computational
approach . . . . . . . . . . . . . . . . 80--94
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Chengguan Tan and
Yuanshi Wang and
Hong Wu Population abundance of a two-patch
chemostat system with asymmetric
diffusion . . . . . . . . . . . . . . . 1--13
Anonymous Pages 1--102 (7 August 2019) . . . . . . 1--102
Jose A. Carrillo and
Hideki Murakawa and
Makoto Sato and
Hideru Togashi and
Olena Trush A population dynamics model of
cell--cell adhesion incorporating
population pressure and density
saturation . . . . . . . . . . . . . . . 14--24
Zhan Chen The formation of the Thickveins (Tkv)
gradient in \bionameDrosophila wing
discs: a theoretical study . . . . . . . 25--41
Denis Thieffry and
Marcelle Kaufman Prologue to the special issue of JTB
dedicated to the memory of René Thomas
(1928--2017): a journey through
biological circuits, logical puzzles and
complex dynamics . . . . . . . . . . . . 42--47
Sòren Toxvaerd A Prerequisite for Life . . . . . . . . 48--51
Jirí C. Moravec and
Stephen Marsland and
Murray P. Cox Warfare induces post-marital residence
change . . . . . . . . . . . . . . . . . 52--62
Amit Kumar Roy and
Fahad Al Basir and
Priti Kumar Roy A vivid cytokines interaction model on
psoriasis with the effect of impulse
biologic (TNF-$ \alpha $ inhibitor)
therapy . . . . . . . . . . . . . . . . 63--77
Caterina Vitale and
Alex Best The paradox of tolerance: Parasite
extinction due to the evolution of host
defence . . . . . . . . . . . . . . . . 78--87
Andrei R. Akhmetzhanov and
Jong Wook Kim and
Ryan Sullivan and
Robert A. Beckman and
Pablo Tamayo and
Chen-Hsiang Yeang Modelling bistable tumour population
dynamics to design effective treatment
strategies . . . . . . . . . . . . . . . 88--102
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
I. Johanna Stamper and
Xujing Wang Integrated multiscale mathematical
modeling of insulin secretion reveals
the role of islet network integrity for
proper oscillatory glucose-dose response 1--24
Anonymous Pages 1-72 (21 August 2019) . . . . . . 1--72
Ian Sorrell and
Rebecca J Shipley and
Sophie Regan and
Iain Gardner and
Michael P. Storm and
Marianne Ellis and
John Ward and
Dominic Williams and
Pratibha Mistry and
José Domingo Salazar and
Andrew Scott and
Steven Webb Mathematical modelling of a liver hollow
fibre bioreactor . . . . . . . . . . . . 25--33
Winston Garira and
Dephney Mathebula A coupled multiscale model to guide
malaria control and elimination . . . . 34--59
Anna Stopka and
Marcelo Boareto A stochastic model of adult neurogenesis
coupling cell cycle progression and
differentiation . . . . . . . . . . . . 60--72
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
H. Allen Orr Measures of the efficiency of natural
selection during gene substitution . . . 1--4
Anonymous Pages 1-108 (7 September 2019) . . . . . 1--108
Diana M. Hendrickx and
Steven Abrams and
Niel Hens The impact of behavioral interventions
on co-infection dynamics: An exploration
of the effects of home isolation . . . . 5--18
Zhonghui Ou Approximate nutrient flux and
concentration solutions of the
Nye--Tinker--Barber model by the
perturbation expansion method . . . . . 19--29
Saurabh Kumar Sharma and
Soibam Shyamchand Singh and
Dineshchandra Haobijam and
Md. Zubbair Malik and
R. K. Brojen Singh Organization in complex brain networks:
Energy distributions and phase shift . . 30--35
Xianjia Wang and
Shaojie Lv The public goods game with shared
punishment cost in well-mixed and
structured populations . . . . . . . . . 36--43
Daniel T. Reed and
Colin R. Tosh Diversity loss is predicted to increase
extinction risk of specialist animals by
constraining their ability to expand
niche . . . . . . . . . . . . . . . . . 44--50
Yuanshi Wang Pollination-mutualisms in a two-patch
system with dispersal . . . . . . . . . 51--61
John Alexander Edgar L-ascorbic acid and the evolution of
multicellular eukaryotes . . . . . . . . 62--73
Shing Hei Ho and
Daihai He and
Raluca Eftimie Mathematical models of transmission
dynamics and vaccine strategies in Hong
Kong during the 2017--2018 winter
influenza season . . . . . . . . . . . . 74--94
Timothy C. Reluga and
Rachel A. Smith and
David P. Hughes Dynamic and game theory of infectious
disease stigmas . . . . . . . . . . . . 95--107
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Federica Conti and
Robert A. Van Gorder The role of network structure and time
delay in a metapopulation Wilson--Cowan
model . . . . . . . . . . . . . . . . . 1--13
Anonymous Pages 1--126 (21 September 2019) . . . . 1--126
T. A. Lynch and
Y. Wang and
B. van Brunt and
D. Pacheco and
P. H. Janssen Modelling thermodynamic feedback on the
metabolism of hydrogenotrophic
methanogens . . . . . . . . . . . . . . 14--23
Hiroki Yokoi and
Kei-ichi Tainaka and
Kazunori Sato Metapopulation model for a prey-predator
system: Nonlinear migration due to the
finite capacities of patches . . . . . . 24--35
Dongmei Fan and
Guo-Ping Jiang and
Yu-Rong Song and
Yin-Wei Li and
Guanrong Chen Novel epidemic models on PSO-based
networks . . . . . . . . . . . . . . . . 36--43
Sarah E. Marzen Novelty detection improves performance
of reinforcement learners in
fluctuating, partially observable
environments . . . . . . . . . . . . . . 44--50
Mainak Patel Analysis of feedforward mechanisms of
multiwhisker receptive field generation
in a model of the rat barrel cortex . . 51--62
Azumi Mamiya and
Genki Ichinose Strategies that enforce linear payoff
relationships under observation errors
in Repeated Prisoner's Dilemma game . . 63--76
Yang Yu and
Zeyu Zheng Protein complex identification based on
weighted PPI network with multi-source
information . . . . . . . . . . . . . . 77--83
Timothy W. Russell and
Matthew J. Russell and
Francisco Úbeda and
Vincent A. A. Jansen Stable cycling in quasi-linkage
equilibrium: Fluctuating dynamics under
gene conversion and selection . . . . . 84--95
Atsushi Yamauchi and
Takahiro Yamagishi and
Ross Booton and
Arndt Telschow and
Gaku Kudo Theory of coevolution of cytoplasmic
male-sterility, nuclear restorer and
selfing . . . . . . . . . . . . . . . . 96--107
Daniel J. Nicholson Is the cell really a machine? . . . . . 108--126
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Janani Srree Murallidharan and
Stephen J. Payne Thrombus growth modelling and stenosis
prediction in the cerebral
microvasculature . . . . . . . . . . . . 1--13
Anonymous Pages 1--168 (7 October 2019) . . . . . 1--168
Darka Labavi\'c and
Mohamed Tahar Ladjimi and
Quentin Thommen and
Benjamin Pfeuty Scaling laws of cell-fate responses to
transient stress . . . . . . . . . . . . 14--25
G. Capo Rangel and
J. Prezioso and
L. Gerardo-Giorda and
E. Somersalo and
D. Calvetti Brain energetics plays a key role in the
coordination of electrophysiology,
metabolism and hemodynamics: Evidence
from an integrated computational model 26--39
Hideo Ezoe Adaptive partner recruitment can help
maintain an intra-guild diversity in
mutualistic systems . . . . . . . . . . 40--47
Ayako Nakanishi and
Yoshito Hirata Practically scheduling hormone therapy
for prostate cancer using a mathematical
model . . . . . . . . . . . . . . . . . 48--57
Anyesha Sarkar and
Brian M. Kobylkevich and
David M. Graham and
Mark A. Messerli Electromigration of cell surface
macromolecules in DC electric fields
during cell polarization and
galvanotaxis . . . . . . . . . . . . . . 58--73
Grzegorz Dudziuk and
Weronika Wronowska and
Anna Gambin and
Zuzanna Szyma\'nska and
Miko\laj Rybi\'nski Biologically sound formal model of Hsp70
heat induction . . . . . . . . . . . . . 74--101
Joshua Veasy and
Yi Ming Lai and
Stephen Coombes and
Rüdiger Thul Complex patterns of subcellular cardiac
alternans . . . . . . . . . . . . . . . 102--114
Emmanuel J. Dansu and
Hiromi Seno A model for epidemic dynamics in a
community with visitor subpopulation . . 115--127
Allison R. Hrycik and
Paris D. Collingsworth and
Timothy M. Sesterhenn and
Daisuke Goto and
Tomas O. Höök Movement rule selection through
eco-genetic modeling: Application to
diurnal vertical movement . . . . . . . 128--138
Abhishek Senapati and
Tridip Sardar and
Krishnendra Sankar Ganguly and
Krishna Sankar Ganguly and
Asis Kumar Chattopadhyay and
Joydev Chattopadhyay Impact of adult mosquito control on
dengue prevalence in a multi-patch
setting: a case study in Kolkata
(2014--2015) . . . . . . . . . . . . . . 139--152
Sherry Chu and
Mehran Kardar and
David R. Nelson and
Daniel A. Beller Evolution in range expansions with
competition at rough boundaries . . . . 153--160
Wilfried Konrad and
Rena Schott and
Anita Roth-Nebelsick A model for extracellular freezing based
on observations on \bionameEquisetum
hyemale . . . . . . . . . . . . . . . . 161--168
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Sami O. Lehtinen and
Stefan A. H. Geritz Cyclic prey evolution with cannibalistic
predators . . . . . . . . . . . . . . . 1--13
Anonymous Pages 1--106 (21 October 2019) . . . . . 1--106
Matthew P. Edgington and
Luke S. Alphey Modeling the mutation and reversal of
engineered underdominance gene drives 14--21
Salma Zaman and
Mahwish Gul Magnetohydrodynamic bioconvective flow
of Williamson nanofluid containing
gyrotactic microorganisms subjected to
thermal radiation and Newtonian
conditions . . . . . . . . . . . . . . . 22--28
Akane Hara and
Shoya Iwanami and
Yusuke Ito and
Tomoyuki Miura and
Shinji Nakaoka and
Shingo Iwami Revealing uninfected and infected target
cell dynamics from peripheral blood data
in highly and less pathogenic
simian/human immunodeficiency virus
infected \bionameRhesus macaque . . . . 29--36
Abhigyan Nath and
Gopal Krishna Sahu Exploiting ensemble learning to improve
prediction of phospholipidosis inducing
potential . . . . . . . . . . . . . . . 37--47
Hugh Z. Ford and
Helen M. Byrne and
Mary R. Myerscough A lipid-structured model for macrophage
populations in atherosclerotic plaques 48--63
Anna Vanselow and
Sebastian Wieczorek and
Ulrike Feudel When very slow is too fast --- collapse
of a predator--prey system . . . . . . . 64--72
Federica Bubba and
Camille Pouchol and
Nathalie Ferrand and
Guillaume Vidal and
Luis Almeida and
Beno\^ìt Perthame and
Mich\`ele Sabbah A chemotaxis-based explanation of
spheroid formation in $3$D cultures of
breast cancer cells . . . . . . . . . . 73--80
Lingling Li and
Tianhai Tian and
Xinan Zhang Stochastic modelling of multistage
carcinogenesis and progression of human
lung cancer . . . . . . . . . . . . . . 81--89
Shimon Haber and
Zeev Holtzman and
Steven J. Mentzer and
Akira Tsuda Why do myofibroblasts preferentially
accumulate on the convex surface of the
remodeling lung after pneumonectomy? . . 90--96
Soyoung Kim and
Eunok Jung Prioritization of vaccine strategy using
an age-dependent mathematical model for
2009 A/H1N1 influenza in the Republic of
Korea . . . . . . . . . . . . . . . . . 97--105
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Koichi Ito and
Michael Doebeli The joint evolution of cooperation and
competition . . . . . . . . . . . . . . 1--12
Anonymous Pages 1--284 (7 November 2019) . . . . . 1--284
Shun Kurokawa Three-player repeated games with an
opt-out option . . . . . . . . . . . . . 13--22
Terry Kenakin G-Protein/Receptor inhibitors as
blockers of receptor signaling . . . . . 23--33
Jawahar Khetan and
Dipak Barua Analysis of Fn14-NF-$ \kappa $B
signaling response dynamics using a
mechanistic model . . . . . . . . . . . 34--42
FR Macfarlane and
MAJ Chaplain and
T. Lorenzi A stochastic individual-based model to
explore the role of spatial interactions
and antigen recognition in the immune
response against solid tumours . . . . . 43--55
Rui Qu and
Shu-Shen Liu and
Ze-Jun Wang and
Fu Chen A novel method based on similarity and
triangulation for predicting the
toxicities of various binary mixtures 56--64
Christopher K. Syed and
Robert H. Lee Slow and fast grouping of cargo
velocities in axonal transport due to
single versus multi-motor transport . . 65--70
Md. Nazmul Hassan and
Lale Asik and
Jackson Kulik and
K. R. Long and
Angela Peace Environmental seasonality on
predator-prey systems under nutrient and
toxicant constraints . . . . . . . . . . 71--80
Riccardo Muolo and
Malbor Asllani and
Duccio Fanelli and
Philip K. Maini and
Timoteo Carletti Patterns of non-normality in networked
systems . . . . . . . . . . . . . . . . 81--91
Chu W. Kwang-Hua Temperature-dependent viscosity
dominated transport control through AQP1
water channel . . . . . . . . . . . . . 92--98
Massimo Di Giulio A comparison between two models for
understanding the origin of the tRNA
molecule . . . . . . . . . . . . . . . . 99--103
Chengyuan Wu and
Shiquan Ren and
Jie Wu and
Kelin Xia Magnus representation of genome
sequences . . . . . . . . . . . . . . . 104--111
Vlastimil Krivan and
Tomás A. Revilla Plant coexistence mediated by adaptive
foraging preferences of exploiters or
mutualists . . . . . . . . . . . . . . . 112--128
Adrianne L. Jenner and
Peter S. Kim and
Federico Frascoli Oncolytic virotherapy for tumours
following a Gompertz growth law . . . . 129--140
Gaoshi Li and
Min Li and
Wei Peng and
Yaohang Li and
Yi Pan and
Jianxin Wang A novel extended Pareto Optimality
Consensus model for predicting essential
proteins . . . . . . . . . . . . . . . . 141--149
Henk J. van Lingen and
James G. Fadel and
Luis E. Moraes and
André Bannink and
Jan Dijkstra Bayesian mechanistic modeling of
thermodynamically controlled volatile
fatty acid, hydrogen and methane
production in the bovine rumen . . . . . 150--165
Rui Cai and
Ziying He and
Yancai Liu and
Jinqiao Duan and
Jürgen Kurths and
Xiaofan Li Effects of Lévy noise on the
Fitzhugh--Nagumo model: a perspective on
the maximal likely trajectories . . . . 166--174
Leonardo M. Santana and
Shridar Ganesan and
Gyan Bhanot A Quasi Birth-and-Death model for tumor
recurrence . . . . . . . . . . . . . . . 175--191
Mezouaghi Abdelheq and
Omar Belhamiti and
Leila Bouzid and
Deccy Y. Trejos and
Jose C. Valverde A predictive spatio-temporal model for
bovine Babesiosis epidemic transmission 192--204
Andrew D. Dean and
Malcolm J. Horsburgh and
Bakhti Vasiev Toxin-mediated competition in weakly
motile bacteria . . . . . . . . . . . . 205--217
Ren-Chao Zou and
Shu-Feng Xiao and
Zhi-Tian Shi and
Yang Ke and
Hao-Ran Tang and
Tian-Gen Wu and
Zhi-Tang Guo and
Fan Ni and
Wen-Xing Li and
Lin Wang Identification of metabolism-associated
pathways and genes involved in male and
female liver cancer patients . . . . . . 218--228
M. Chowkwale and
G. J. Mahler and
P. Huang and
B. T. Murray A multiscale in silico model of
endothelial to mesenchymal
transformation in a tumor
microenvironment . . . . . . . . . . . . 229--240
Marie Doumic and
Klemens Fellner and
Mathieu Mezache and
Human Rezaei A bi-monomeric, nonlinear
Becker--Döring-type system to capture
oscillatory aggregation kinetics in
prion dynamics . . . . . . . . . . . . . 241--261
Kris V. Parag On signalling and estimation limits for
molecular birth-processes . . . . . . . 262--273
Zhaopeng Zhang and
Jishou Ruan and
Jianzhao Gao and
Fang-Xiang Wu Predicting essential proteins from
protein-protein interactions using order
statistics . . . . . . . . . . . . . . . 274--283
Anonymous Editorial Board . . . . . . . . . . . . ii--ii
Anonymous Have we come to the end of theoretical
and mathematical biology? . . . . . . . 1--2
Anonymous Overview . . . . . . . . . . . . . . . . 3--5
Anonymous Professor Philip K. Maini FRS: a very
small selection of his research
contributions . . . . . . . . . . . . . 6--9
Michael Pan and
Peter J. Gawthrop and
Kenneth Tran and
Joseph Cursons and
Edmund J. Crampin A thermodynamic framework for modelling
membrane transporters . . . . . . . . . 10--23
Meghan A. Burke Maini's many contributions to
mathematical enzyme kinetics: a review 24--27
Justin Eilertsen and
Wylie Stroberg and
Santiago Schnell Characteristic, completion or matching
timescales? An analysis of temporary
boundaries in enzyme kinetics . . . . . 28--43
Karen M. Page Oscillations in well-mixed,
deterministic feedback systems: Beyond
ring oscillators . . . . . . . . . . . . 44--53
Andrew Dhawan and
Adrian L. Harris and
Francesca M. Buffa and
Jacob G. Scott Endogenous miRNA sponges mediate the
generation of oscillatory dynamics for a
non-coding RNA network . . . . . . . . . 54--60
Ruth E. Baker and
Andrew Parker and
Matthew J. Simpson A free boundary model of epithelial
dynamics . . . . . . . . . . . . . . . . 61--74
Murray P. J. and
Carrieri F. A. and
Dale J. K. Cell cycle regulation of oscillations
yields coupling of growth and form in a
computational model of the presomitic
mesoderm . . . . . . . . . . . . . . . . 75--83
Linus J. Schumacher Neural crest migration with continuous
cell states . . . . . . . . . . . . . . 84--90
Enrico Gavagnin and
Matthew J. Ford and
Richard L. Mort and
Tim Rogers and
Christian A. Yates The invasion speed of cell migration
models with realistic cell cycle time
distributions . . . . . . . . . . . . . 91--99
Nils B. Becker and
Matthias Günther and
Congxin Li and
Adrien Jolly and
Thomas Höfer Stem cell homeostasis by integral
feedback through the niche . . . . . . . 100--109
Noemi Picco and
Thomas E. Woolley Time to change your mind? Modelling
transient properties of cortex formation
highlights the importance of evolving
cell division strategies . . . . . . . . 110--118
D. Cusseddu and
L. Edelstein-Keshet and
J. A. Mackenzie and
S. Portet and
A. Madzvamuse A coupled bulk-surface model for cell
polarisation . . . . . . . . . . . . . . 119--135
Faustino Sánchez-Garduño and
Andrew L. Krause and
Jorge A. Castillo and
Pablo Padilla Turing--Hopf patterns on growing
domains: the torus and the sphere . . . 136--150
Jamie J. R. Bennett and
Jonathan A. Sherratt Long-distance seed dispersal affects the
resilience of banded vegetation patterns
in semi-deserts . . . . . . . . . . . . 151--161
Kevin J. Painter Mathematical models for chemotaxis and
their applications in self-organisation
phenomena . . . . . . . . . . . . . . . 162--182
Adjani Gama Dessavre and
Emma Southall and
Michael J. Tildesley and
Louise Dyson The problem of detrending when analysing
potential indicators of disease
elimination . . . . . . . . . . . . . . 183--193
Ashley B. Pitcher and
Annick Borquez and
Britt Skaathun and
Natasha K. Martin Mathematical modeling of hepatitis $c$
virus (HCV) prevention among people who
inject drugs: a review of the literature
and insights for elimination strategies 194--201
Gideon A. Ngwa and
Miranda I. Teboh-Ewungkem and
Yves Dumont and
Rachid Ouifki and
Jacek Banasiak On a three-stage structured model for
the dynamics of malaria transmission
with human treatment, adult vector
demographics and one aquatic stage . . . 202--222
Jasmina Panovska-Griffiths and
Luca Grieco and
Edwin van Leeuwen and
Marc Baguelin and
Richard Pebody and
Martin Utley Are we prepared for the next influenza
pandemic? Lessons from modelling
different preparedness policies against
four pandemic scenarios . . . . . . . . 223--232
Diana Barac and
Michael D. Multerer and
Dagmar Iber Global optimization using Gaussian
processes to estimate biological
parameters from image data . . . . . . . 233--248
Anonymous 7 December 2019 . . . . . . . . . . . . ??
Anonymous Editorial Board . . . . . . . . . . . . Article 110010
Anonymous Publisher's Note . . . . . . . . . . . . Article 109988
Romain Chaput and
John E. Majoris and
Peter M. Buston and
Claire B. Paris Hydrodynamic and biological constraints
on group cohesion in plankton . . . . . Article 109987
Yang He and
Suyan Tian and
Pu Tian Fundamental asymmetry of insertions and
deletions in genomes size evolution . . Article 109983
Loredana G. Marcu and
David Marcu The role of hypofractionated
radiotherapy in the management of head
and neck cancer --- a modelling approach Article 109998
Oleksii M. Matsiaka and
Ruth E. Baker and
Matthew J. Simpson Continuum descriptions of spatial
spreading for heterogeneous cell
populations: Theory and experiment . . . Article 109997
Amir Hossein Amiri Mehra and
Iman Zamani and
Zohreh Abbasi and
Asier Ibeas Observer-based adaptive PI sliding mode
control of developed uncertain SEIAR
influenza epidemic model considering
dynamic population . . . . . . . . . . . Article 109984
Adam Rhodes and
Thomas Hillen A mathematical model for the
immune-mediated theory of metastasis . . Article 109999
Manuela Royer-Carenzi and
Gilles Didier Testing for correlation between traits
under directional evolution . . . . . . Article 109982
Laura Sánchez-Gómez and
Agustín Guerrero-Hernández and
Moisés Santillán Polymerization of sarcoplasmic-reticulum
calcium-binding proteins might explain
observed reticulum kinetics-on-demand
behavior . . . . . . . . . . . . . . . . Article 109986
M. V. Sheraton and
V. R. Melnikov and
P. M. A. Sloot Prediction and quantification of
bacterial biofilm detachment using
Glazier--Graner--Hogeweg method based
model simulations . . . . . . . . . . . Article 109994
Niccolo Anceschi and
Jorge Hidalgo and
Carlos A. Plata and
Tommaso Bellini and
Amos Maritan and
Samir Suweis Neutral and niche forces as drivers of
species selection . . . . . . . . . . . Article 109969
Anonymous 21 December 2019 . . . . . . . . . . . . ??
Anonymous Editorial Board . . . . . . . . . . . . Article 110023
Mark Broom and
Ross Cressman and
Vlastimil Krivan Revisiting the ``fallacy of averages''
in ecology: Expected gain per unit time
equals expected gain divided by expected
time . . . . . . . . . . . . . . . . . . Article 109993
Wendy K. Caldwell and
Benjamin Freedman and
Luke Settles and
Michael M. Thomas and
Erika T. Camacho and
Stephen Wirkus The Vicodin abuse problem: a
mathematical approach . . . . . . . . . Article 110003
Michael G. Cortes and
Jonathan Krog and
Gábor Balázsi Optimality of the spontaneous prophage
induction rate . . . . . . . . . . . . . Article 110005
Adam L. Cronin Fussy groups thwart the collective
burden of choice: a theoretical study of
house-hunting ants . . . . . . . . . . . Article 110000
Mohammadreza Dorvash and
Mohammad Farahmandnia and
Pouria Mosaddeghi and
Mitra Farahmandnejad and
Hosein Saber and
Mohammadhossein Khorraminejad-Shirazi and
Amir Azadi and
Iman Tavassoly Dynamic modeling of signal transduction
by mTOR complexes in cancer . . . . . . Article 109992
Thierry Fredrich and
Michael Welter and
Heiko Rieger Dynamic vessel adaptation in synthetic
arteriovenous networks . . . . . . . . . Article 109989
Sami O. Lehtinen and
Stefan A. H. Geritz Coevolution of cannibalistic predators
and timid prey: evolutionary cycling and
branching . . . . . . . . . . . . . . . Article 110001
Sophie R. Meakin and
Matt J. Keeling Correlations between stochastic endemic
infection in multiple interacting
subpopulations . . . . . . . . . . . . . Article 109991
Gonzalo Oteo-García and
José Angel Oteo Evolutionary distances corrected for
purifying selection and ancestral
polymorphisms . . . . . . . . . . . . . Article 110004
Marija Rosandi\'c and
Ines Vlahovi\'c and
Vladimir Paar Novel look at DNA and life-Symmetry as
evolutionary forcing . . . . . . . . . . Article 109985
Yuting Wei and
Yaosen Lin and
Bin Wu Vaccination dilemma on an evolving
social network . . . . . . . . . . . . . Article 109978
Michael Günther and
Daniel F. B. Haeufle and
Syn Schmitt Corrigendum to ``The basic mechanical
structure of the skeletal muscle
machinery: One model for linking
microscopic and macroscopic scales''
[Journal of Theoretical Biology \bf 456
(2018) 137--167] . . . . . . . . . . . . Article 110143
Yuting Wei and
Yaosen Lin and
Bin Wu Corrigendum to ``Vaccination dilemma on
an evolving social network'' [Journal of
Theoretical Biology \bf 483 (2019)
109978] . . . . . . . . . . . . . . . . Article 110154
Tanja Stadler and
Stavroula Skylaki and
Konstantinos D. Kokkaliaris and
Timm Schroeder Erratum to ``On the statistical analysis
of single cell lineage trees'' [J.
Theor. Biol. \bf 439 (2018) 160--165] Article 110424
Clarence C. King and
Amelia Ann Brown and
Irmak Sargin and
K. M. Bratlie and
S. P. Beckman Corrigendum to: Modeling of
reaction--diffusion transport into a
core-shell geometry . . . . . . . . . . Article 110439
Brandon H. Schlomann Corrigendum to ``Stationary moments,
diffusion limits, and extinction times
for logistic growth with random
catastrophes'' [J. Theor. Biol. \bf 454
(2018) 154--163] . . . . . . . . . . . . Article 110595
William C. Jordan-Cooley and
Romuald N. Lipcius and
Leah B. Shaw and
Jian Shen and
Junping Shi Corrigendum to ``Bistability in a
differential equation model of oyster
reef height and sediment accumulation''
[J. Theor. Biol. \bf 289 (2011) 1--11] ??
Lawrence S. Schulman Corrigendum to ``Bacterial resistance to
antibodies: a model evolutionary study''
[J. Theor. Biol. \bf 417 (2017) 61--67] ??
Sébastien Lion Corrigendum to ``From the Price equation
to the selection gradient in
class-structured populations: a
quasi-equilibrium route'' [J. Theor.
Biol. \bf 447 (2018) 178--189] . . . . . ??