PLOS Computational Biology

2005 - 2022

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Volume 6, issue 12, 2010

Rhythmic Dynamics and Synchronization via Dimensionality Reduction: Application to Human Gait pp. 1-11

Jie Zhang, Kai Zhang, Jianfeng Feng and Michael Small

Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations pp. 1-13

Benjamin A Logsdon and Jason Mezey

Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW pp. 1-13

Faruck Morcos, Santanu Chatterjee, Christopher L McClendon, Paul R Brenner, Roberto López-Rendón, John Zintsmaster, Maria Ercsey-Ravasz, Christopher R Sweet, Matthew P Jacobson, Jeffrey W Peng and Jesús A Izaguirre

Sequence-Based Prediction for Vaccine Strain Selection and Identification of Antigenic Variability in Foot-and-Mouth Disease Virus pp. 1-13

Richard Reeve, Belinda Blignaut, Jan J Esterhuysen, Pamela Opperman, Louise Matthews, Elizabeth E Fry, Tjaart A P de Beer, Jacques Theron, Elizabeth Rieder, Wilna Vosloo, Hester G O'Neill, Daniel T Haydon and Francois F Maree

Determinants of Heterogeneity, Excitation and Conduction in the Sinoatrial Node: A Model Study pp. 1-13

Ronit V Oren and Colleen E Clancy

A Scalable Approach for Discovering Conserved Active Subnetworks across Species pp. 1-18

Raamesh Deshpande, Shikha Sharma, Catherine M Verfaillie, Wei-Shou Hu and Chad L Myers

Structure Learning in Human Sequential Decision-Making pp. 1-12

Daniel E Acuña and Paul Schrater

Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs pp. 1-12

William H Majoros and Uwe Ohler

Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway pp. 1-8

Andreja Jovic, Bryan Howell, Michelle Cote, Susan M Wade, Khamir Mehta, Atsushi Miyawaki, Richard R Neubig, Jennifer J Linderman and Shuichi Takayama

How Noisy Adaptation of Neurons Shapes Interspike Interval Histograms and Correlations pp. 1-25

Tilo Schwalger, Karin Fisch, Jan Benda and Benjamin Lindner

Axial and Radial Forces of Cross-Bridges Depend on Lattice Spacing pp. 1-10

C David Williams, Michael Regnier and Thomas L Daniel

Little Italy: An Agent-Based Approach to the Estimation of Contact Patterns- Fitting Predicted Matrices to Serological Data pp. 1-10

Fabrizio Iozzi, Francesco Trusiano, Matteo Chinazzi, Francesco Billari, Emilio Zagheni, Stefano Merler, Marco Ajelli, Emanuele Del Fava and Piero Manfredi

Volume 6, issue 11, 2010

On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1 pp. 1-12

Chun Wu and Joan-Emma Shea

Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification pp. 1-8

Cristina Marino Buslje, Elin Teppa, Tomas Di Doménico, José María Delfino and Morten Nielsen

Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data pp. 1-14

Matthieu Wyart, David Botstein and Ned S Wingreen

Compensation for Changing Motor Uncertainty pp. 1-14

Todd E Hudson, Hadley Tassinari and Michael S Landy

Modelling Vesicular Release at Hippocampal Synapses pp. 1-17

Suhita Nadkarni, Thomas M Bartol, Terrence J Sejnowski and Herbert Levine

Environments that Induce Synthetic Microbial Ecosystems pp. 1-17

Niels Klitgord and Daniel Segrè

A New Method to Reconstruct Recombination Events at a Genomic Scale pp. 1-13

Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and The Genographic Consortium

Genome-Wide Association between Branch Point Properties and Alternative Splicing pp. 1-13

André Corvelo, Martina Hallegger, Christopher W J Smith and Eduardo Eyras

Monte Carlo Analysis of Neck Linker Extension in Kinesin Molecular Motors pp. 1-11

Matthew L Kutys, John Fricks and William O Hancock

Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes pp. 1-11

Ulrich D Kadolsky and Becca Asquith

Analysis of Stochastic Strategies in Bacterial Competence: A Master Equation Approach pp. 1-11

Sandra H Dandach and Mustafa Khammash

A New Integrated Variable Based on Thermometry, Actimetry and Body Position (TAP) to Evaluate Circadian System Status in Humans pp. 1-11

Elisabet Ortiz-Tudela, Antonio Martinez-Nicolas, Manuel Campos, María Ángeles Rol and Juan Antonio Madrid

Untangling the Interplay between Epidemic Spread and Transmission Network Dynamics pp. 1-9

Christel Kamp

Pattern Recognition Software and Techniques for Biological Image Analysis pp. 1-10

Lior Shamir, John D Delaney, Nikita Orlov, D Mark Eckley and Ilya G Goldberg

Lobe Specific Ca2+-Calmodulin Nano-Domain in Neuronal Spines: A Single Molecule Level Analysis pp. 1-21

Yoshihisa Kubota and M Neal Waxham

PLoS Computational Biology Conference Postcards from ISMB 2010 pp. 1-4

Guilhem Chalancon, Mickey Kosloff, Hatice Ulku Osmanbeyoglu and Saras Saraswathi

Volume 6, issue 10, 2010

Bistability in Apoptosis by Receptor Clustering pp. 1-9

Kenneth L Ho and Heather A Harrington

A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes pp. 1-12

Gaurav Bhatia, Vikas Bansal, Olivier Harismendy, Nicholas J Schork, Eric J Topol, Kelly Frazer and Vineet Bafna

Biosensor Approach to Psychopathology Classification pp. 1-12

Misha Koshelev, Terry Lohrenz, Marina Vannucci and P Read Montague

Inherent High Correlation of Individual Motility Enhances Population Dispersal in a Heterotrophic, Planktonic Protist pp. 1-10

Susanne Menden-Deuer

Critical Dynamics in the Evolution of Stochastic Strategies for the Iterated Prisoner's Dilemma pp. 1-8

Dimitris Iliopoulos, Arend Hintze and Christoph Adami

Individualization as Driving Force of Clustering Phenomena in Humans pp. 1-8

Michael Mäs, Andreas Flache and Dirk Helbing

Non-Centered Spike-Triggered Covariance Analysis Reveals Neurotrophin-3 as a Developmental Regulator of Receptive Field Properties of ON-OFF Retinal Ganglion Cells pp. 1-16

Donald R Cantrell, Jianhua Cang, John B Troy and Xiaorong Liu

In Memoriam: Rolf Kötter (1961–2010) pp. 1-3

Klaas Enno Stephan, Anthony Randal McIntosh and Claus C Hilgetag

Volume 6, issue 9, 2010

Instantaneous Non-Linear Processing by Pulse-Coupled Threshold Units pp. 1-10

Moritz Helias, Moritz Deger, Stefan Rotter and Markus Diesmann

Wide-Field Motion Integration in Fly VS Cells: Insights from an Inverse Approach pp. 1-10

Benjamin Torben-Nielsen and Klaus M Stiefel

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions pp. 1-12

Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble and Christina Leslie

Differences in Nutrient Requirements Imply a Non-Linear Emergence of Leaders in Animal Groups pp. 1-9

Cédric Sueur, Jean-Louis Deneubourg, Odile Petit and Iain D Couzin

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G pp. 1-9

Suryani Lukman, Barry J Grant, Alemayehu A Gorfe, Guy H Grant and J Andrew McCammon

Ten Simple Rules for Editing Wikipedia pp. 1-3

Darren W Logan, Massimo Sandal, Paul P Gardner, Magnus Manske and Alex Bateman

Forcing Versus Feedback: Epidemic Malaria and Monsoon Rains in Northwest India pp. 1-13

Karina Laneri, Anindya Bhadra, Edward L Ionides, Menno Bouma, Ramesh C Dhiman, Rajpal S Yadav and Mercedes Pascual

Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells pp. 1-11

Amrita X Sarkar and Eric A Sobie

Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach pp. 1-11

Liesbet Geris, Anita A C Reed, Jos Vander Sloten, A Hamish R W Simpson and Hans Van Oosterwyck

Evolution and Optimality of Similar Neural Mechanisms for Perception and Action during Search pp. 1-11

Sheng Zhang and Miguel P Eckstein

Rescuing Loading Induced Bone Formation at Senescence pp. 1-16

Sundar Srinivasan, Brandon J Ausk, Jitendra Prasad, Dewayne Threet, Steven D Bain, Thomas S Richardson and Ted S Gross

A Dynamic Neural Field Model of Mesoscopic Cortical Activity Captured with Voltage-Sensitive Dye Imaging pp. 1-14

Valentin Markounikau, Christian Igel, Amiram Grinvald and Dirk Jancke

Finding the “Dark Matter” in Human and Yeast Protein Network Prediction and Modelling pp. 1-14

Juan A G Ranea, Ian Morilla, Jon G Lees, Adam J Reid, Corin Yeats, Andrew B Clegg, Francisca Sanchez-Jimenez and Christine Orengo

Volume 6, issue 8, 2010

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors pp. 1-21

Thomas C Whisenant, David T Ho, Ryan W Benz, Jeffrey S Rogers, Robyn M Kaake, Elizabeth A Gordon, Lan Huang, Pierre Baldi and Lee Bardwell

Correlation of Influenza Virus Excess Mortality with Antigenic Variation: Application to Rapid Estimation of Influenza Mortality Burden pp. 1-10

Aiping Wu, Yousong Peng, Xiangjun Du, Yuelong Shu and Taijiao Jiang

Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data pp. 1-10

Kakajan Komurov, Michael A White and Prahlad T Ram

A Mechanistic View of the Role of E3 in Sumoylation pp. 1-10

Melda Tozluoğlu, Ezgi Karaca, Ruth Nussinov and Türkan Haliloğlu

Stochastic Ion Channel Gating in Dendritic Neurons: Morphology Dependence and Probabilistic Synaptic Activation of Dendritic Spikes pp. 1-18

Robert C Cannon, Cian O'Donnell and Matthew F Nolan

Dendritic Spikes Amplify the Synaptic Signal to Enhance Detection of Motion in a Simulation of the Direction-Selective Ganglion Cell pp. 1-24

Michael J Schachter, Nicholas Oesch, Robert G Smith and W Rowland Taylor

Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling pp. 1-12

Katarzyna A Rejniak, Shizhen E Wang, Nicole S Bryce, Hang Chang, Bahram Parvin, Jerome Jourquin, Lourdes Estrada, Joe W Gray, Carlos L Arteaga, Alissa M Weaver, Vito Quaranta and Alexander R A Anderson

CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences pp. 1-17

Wayne Delport, Konrad Scheffler, Gordon Botha, Mike B Gravenor, Spencer V Muse and Sergei L Kosakovsky Pond

Reinforcement Learning on Slow Features of High-Dimensional Input Streams pp. 1-13

Robert Legenstein, Niko Wilbert and Laurenz Wiskott

A Model for a Correlated Random Walk Based on the Ordered Extension of Pseudopodia pp. 1-11

Peter J M Van Haastert

Quantitative Test of the Barrier Nucleosome Model for Statistical Positioning of Nucleosomes Up- and Downstream of Transcription Start Sites pp. 1-11

Wolfram Möbius and Ulrich Gerland

Probability Matching as a Computational Strategy Used in Perception pp. 1-7

David R Wozny, Ulrik R Beierholm and Ladan Shams

Modeling and Dynamics of the Inward-Facing State of a Na+/Cl− Dependent Neurotransmitter Transporter Homologue pp. 1-14

Saher Afshan Shaikh and Emad Tajkhorshid

Nonlinear Gap Junctions Enable Long-Distance Propagation of Pulsating Calcium Waves in Astrocyte Networks pp. 1-14

Mati Goldberg, Maurizio De Pittà, Vladislav Volman, Hugues Berry and Eshel Ben-Jacob

Continuous Attractors with Morphed/Correlated Maps pp. 1-19

Sandro Romani and Misha Tsodyks

Volume 6, issue 7, 2010

Avalanches in a Stochastic Model of Spiking Neurons pp. 1-13

Marc Benayoun, Jack D Cowan, Wim van Drongelen and Edward Wallace

Do Humans Optimally Exploit Redundancy to Control Step Variability in Walking? pp. 1-15

Jonathan B Dingwell, Joby John and Joseph P Cusumano

Risk-Sensitive Optimal Feedback Control Accounts for Sensorimotor Behavior under Uncertainty pp. 1-15

Arne Nagengast, Daniel A Braun and Daniel M Wolpert

The Construction and Use of Log-Odds Substitution Scores for Multiple Sequence Alignment pp. 1-17

Stephen F Altschul, John C Wootton, Elena Zaslavsky and Yi-Kuo Yu

A Threshold Equation for Action Potential Initiation pp. 1-16

Jonathan Platkiewicz and Romain Brette

A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature pp. 1-19

Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg and Ulf Leser

Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis pp. 1-19

Yonghua Wang, Yan Li, Zhi Ma, Wei Yang and Chunzhi Ai

More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology pp. 1-19

Wing-Cheong Wong, Sebastian Maurer-Stroh and Frank Eisenhaber

Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye pp. 1-14

David E Larson, Ruth I Johnson, Maciej Swat, Julia B Cordero, James A Glazier and Ross L Cagan

Organization of Cellular Receptors into a Nanoscale Junction during HIV-1 Adhesion pp. 1-14

Terrence M Dobrowsky, Brian R Daniels, Robert F Siliciano, Sean X Sun and Denis Wirtz

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins pp. 1-10

Hilal Kazan, Debashish Ray, Esther T Chan, Timothy R Hughes and Quaid Morris

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein pp. 1-12

Michael C Prentiss, David J Wales and Peter G Wolynes

Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human pp. 1-12

James R Wagner, Bing Ge, Dmitry Pokholok, Kevin L Gunderson, Tomi Pastinen and Mathieu Blanchette

Large-Scale Analysis of Network Bistability for Human Cancers pp. 1-12

Tetsuya Shiraishi, Shinako Matsuyama and Hiroaki Kitano

Volume 6, issue 6, 2010

2010 ISCB Overton Prize Awarded to Steven E. Brenner pp. 1-2

Morrison McKay Bj and Clare Sansom

Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor Exploits Competition between L-Arginine Ligands and Resident Arginine Residues pp. 1-12

Rebecca Strawn, Milan Melichercik, Michael Green, Thomas Stockner, Jannette Carey and Rüdiger Ettrich

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology pp. 1-12

Timothy R Lezon and Ivet Bahar

Multiscale Coarse-Graining of the Protein Energy Landscape pp. 1-12

Ronald D Hills, Lanyuan Lu and Gregory A Voth

Optimal Drug Synergy in Antimicrobial Treatments pp. 1-9

Joseph Peter Torella, Remy Chait and Roy Kishony

Nonlinearity of Mechanochemical Motions in Motor Proteins pp. 1-9

Yuichi Togashi, Toshio Yanagida and Alexander S Mikhailov

Protein–Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks pp. 1-8

Javier De Las Rivas and Celia Fontanillo

Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails pp. 1-8

Peter M Kasson, Erik Lindahl and Vijay S Pande

Transat—A Method for Detecting the Conserved Helices of Functional RNA Structures, Including Transient, Pseudo-Knotted and Alternative Structures pp. 1-22

Nicholas J P Wiebe and Irmtraud M Meyer

The Roots of Bioinformatics pp. 1-7

David B Searls

Combinatorial Gene Regulation Using Auto-Regulation pp. 1-13

Rutger Hermsen, Bas Ursem and Pieter Rein ten Wolde

Fast- or Slow-inactivated State Preference of Na+ Channel Inhibitors: A Simulation and Experimental Study pp. 1-13

Robert Karoly, Nora Lenkey, Andras O Juhasz, E Sylvester Vizi and Arpad Mike

Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses pp. 1-13

Andres Kriete, William J Bosl and Glenn Booker

Plato's Cave Algorithm: Inferring Functional Signaling Networks from Early Gene Expression Shadows pp. 1-13

Yishai Shimoni, Marc Y Fink, Soon-gang Choi and Stuart C Sealfon

Slope-Based Stochastic Resonance: How Noise Enables Phasic Neurons to Encode Slow Signals pp. 1-15

Yan Gai, Brent Doiron and John Rinzel

Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families pp. 1-11

Kyle Ellrott, Lukasz Jaroszewski, Weizhong Li, John C Wooley and Adam Godzik

The 20S Proteasome Splicing Activity Discovered by SpliceMet pp. 1-11

Juliane Liepe, Michele Mishto, Kathrin Textoris-Taube, Katharina Janek, Christin Keller, Petra Henklein, Peter Michael Kloetzel and Alexey Zaikin

Volume 6, issue 5, 2010

Analysis and Computational Dissection of Molecular Signature Multiplicity pp. 1-9

Alexander Statnikov and Constantin F Aliferis

Game Theory of Social Distancing in Response to an Epidemic pp. 1-9

Timothy C Reluga

Assimilating Seizure Dynamics pp. 1-12

Ghanim Ullah and Steven J Schiff

A Differentiation-Based Phylogeny of Cancer Subtypes pp. 1-14

Markus Riester, Camille Stephan-Otto Attolini, Robert J Downey, Samuel Singer and Franziska Michor

Making Informed Choices about Microarray Data Analysis pp. 1-7

Mark Reimers

Inductive Game Theory and the Dynamics of Animal Conflict pp. 1-16

Simon DeDeo, David C Krakauer and Jessica C Flack

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies pp. 1-11

Oliver Stegle, Leopold Parts, Richard Durbin and John Winn

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation pp. 1-11

Jochen S Hub, Marcus B Kubitzki and Bert L de Groot

Chemotactic Response and Adaptation Dynamics in Escherichia coli pp. 1-11

Diana Clausznitzer, Olga Oleksiuk, Linda Løvdok, Victor Sourjik and Robert G Endres

Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks pp. 1-11

Karine Audouze, Agnieszka Sierakowska Juncker, Francisco J S S A Roque, Konrad Krysiak-Baltyn, Nils Weinhold, Olivier Taboureau, Thomas Skøt Jensen and Søren Brunak

Mathematical Modelling of DNA Replication Reveals a Trade-off between Coherence of Origin Activation and Robustness against Rereplication pp. 1-13

Anneke Brümmer, Carlos Salazar, Vittoria Zinzalla, Lilia Alberghina and Thomas Höfer

What Do I Want from the Publisher of the Future? pp. 1-3

Philip E Bourne

Influence of Low-Level Stimulus Features, Task Dependent Factors, and Spatial Biases on Overt Visual Attention pp. 1-20

Sepp Kollmorgen, Nora Nortmann, Sylvia Schröder and Peter König

Volume 6, issue 4, 2010

Quantifying Aggregated Uncertainty in Plasmodium falciparum Malaria Prevalence and Populations at Risk via Efficient Space-Time Geostatistical Joint Simulation pp. 1-12

Peter W Gething, Anand P Patil and Simon I Hay

Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data pp. 1-12

Eric Samorodnitsky and B Franklin Pugh

Coordinate Dependence of Variability Analysis pp. 1-16

Dagmar Sternad, Se-Woong Park, Hermann Müller and Neville Hogan

Simulating Microdosimetry in a Virtual Hepatic Lobule pp. 1-16

John Wambaugh and Imran Shah

How Informative Are Spatial CA3 Representations Established by the Dentate Gyrus? pp. 1-16

Erika Cerasti and Alessandro Treves

Dynamics and Control of Diseases in Networks with Community Structure pp. 1-11

Marcel Salathé and James H Jones

Predicting Odor Pleasantness with an Electronic Nose pp. 1-11

Rafi Haddad, Abebe Medhanie, Yehudah Roth, David Harel and Noam Sobel

A Critical Quantity for Noise Attenuation in Feedback Systems pp. 1-17

Liming Wang, Jack Xin and Qing Nie

Signatures of Arithmetic Simplicity in Metabolic Network Architecture pp. 1-13

William J Riehl, Paul L Krapivsky, Sidney Redner and Daniel Segrè

New Insights into the Genetic Control of Gene Expression using a Bayesian Multi-tissue Approach pp. 1-13

Enrico Petretto, Leonardo Bottolo, Sarah R Langley, Matthias Heinig, Chris McDermott-Roe, Rizwan Sarwar, Michal Pravenec, Norbert Hübner, Timothy J Aitman, Stuart A Cook and Sylvia Richardson

Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets pp. 1-13

Manikandan Narayanan, Adrian Vetta, Eric E Schadt and Jun Zhu

Learning “graph-mer” Motifs that Predict Gene Expression Trajectories in Development pp. 1-13

Xuejing Li, Casandra Panea, Chris H Wiggins, Valerie Reinke and Christina Leslie

Flow-Based Cytometric Analysis of Cell Cycle via Simulated Cell Populations pp. 1-10

M Rowan Brown, Huw D Summers, Paul Rees, Paul J Smith, Sally C Chappell and Rachel J Errington

A Reaction-Diffusion Model of Human Brain Development pp. 1-10

Julien Lefèvre and Jean-François Mangin

Independent Component Analysis in Spiking Neurons pp. 1-10

Cristina Savin, Prashant Joshi and Jochen Triesch

Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study pp. 1-10

Jussi Aittoniemi, Heidi de Wet, Frances M Ashcroft and Mark S P Sansom

Global Entrainment of Transcriptional Systems to Periodic Inputs pp. 1-26

Giovanni Russo, Mario di Bernardo and Eduardo D Sontag

Neighbor-Dependent Ramachandran Probability Distributions of Amino Acids Developed from a Hierarchical Dirichlet Process Model pp. 1-21

Daniel Ting, Guoli Wang, Maxim Shapovalov, Rajib Mitra, Michael I Jordan and Roland L Dunbrack

Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions pp. 1-9

Dirk Helbing, Attila Szolnoki, Matjaž Perc and György Szabó

Polyglutamine Induced Misfolding of Huntingtin Exon1 is Modulated by the Flanking Sequences pp. 1-9

Vinal V Lakhani, Feng Ding and Nikolay V Dokholyan

A Stevedore's Protein Knot pp. 1-6

Daniel Bölinger, Joanna I Sułkowska, Hsiao-Ping Hsu, Leonid A Mirny, Mehran Kardar, José N Onuchic and Peter Virnau

The Origins of Time-Delay in Template Biopolymerization Processes pp. 1-15

Luis Mier-y-Terán-Romero, Mary Silber and Vassily Hatzimanikatis

Volume 6, issue 3, 2010

Within- and Cross-Modal Distance Information Disambiguate Visual Size-Change Perception pp. 1-10

Peter W Battaglia, Massimiliano Di Luca, Marc O Ernst, Paul R Schrater, Tonja Machulla and Daniel Kersten

Detailed Simulations of Cell Biology with Smoldyn 2.1 pp. 1-10

Steven S Andrews, Nathan J Addy, Roger Brent and Adam P Arkin

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm pp. 1-18

Sean R McGuffee and Adrian H Elcock

Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation pp. 1-9

Carey D Nadell, Kevin R Foster and João B Xavier

The Impact of Contact Tracing in Clustered Populations pp. 1-9

Thomas House and Matt J Keeling

Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods pp. 1-15

Christelle Reynès, Hélène Host, Anne-Claude Camproux, Guillaume Laconde, Florence Leroux, Anne Mazars, Benoit Deprez, Robin Fahraeus, Bruno O Villoutreix and Olivier Sperandio

Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector pp. 1-15

Sergi Bermúdez i Badia, Ulysses Bernardet and Paul F M J Verschure

Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement pp. 1-15

Laurence Calzone, Laurent Tournier, Simon Fourquet, Denis Thieffry, Boris Zhivotovsky, Emmanuel Barillot and Andrei Zinovyev

Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance pp. 1-15

Bernie J Daigle, Alicia Deng, Tracey McLaughlin, Samuel W Cushman, Margaret C Cam, Gerald Reaven, Philip S Tsao and Russ B Altman

Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction pp. 1-22

Hiroyuki Kuwahara, Chris J Myers and Michael S Samoilov

Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation pp. 1-25

Julian M L Budd, Krisztina Kovács, Alex S Ferecskó, Péter Buzás, Ulf T Eysel and Zoltán F Kisvárday

Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils pp. 1-12

Chun Wu, Michael T Bowers and Joan-Emma Shea

Parameter Estimation and Model Selection in Computational Biology pp. 1-17

Gabriele Lillacci and Mustafa Khammash

Investigating Homology between Proteins using Energetic Profiles pp. 1-17

James O Wrabl and Vincent J Hilser

Systematic Planning of Genome-Scale Experiments in Poorly Studied Species pp. 1-13

Yuanfang Guan, Maitreya Dunham, Amy Caudy and Olga Troyanskaya

Slower Visuomotor Corrections with Unchanged Latency are Consistent with Optimal Adaptation to Increased Endogenous Noise in the Elderly pp. 1-13

Michael Sherback, Francisco J Valero-Cuevas and Raffaello D'Andrea

Estimating the Stochastic Bifurcation Structure of Cellular Networks pp. 1-11

Carl Song, Hilary Phenix, Vida Abedi, Matthew Scott, Brian P Ingalls, Mads Kærn and Theodore J Perkins

Estimating the Stoichiometry of HIV Neutralization pp. 1-11

Carsten Magnus and Roland R Regoes

Comparing Families of Dynamic Causal Models pp. 1-14

Will D Penny, Klaas E Stephan, Jean Daunizeau, Maria J Rosa, Karl J Friston, Thomas M Schofield and Alex P Leff

Volume 6, issue 2, 2010

A Review of 2009 for PLoS Computational Biology pp. 1-2

Rosemary Dickin, Cecy Marden, Catherine Nancarrow and Philip E Bourne

Predicted Functions of MdmX in Fine-Tuning the Response of p53 to DNA Damage pp. 1-18

Sohyoung Kim, Mirit I Aladjem, Geoffrey B McFadden and Kurt W Kohn

Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus pp. 1-12

Florence Thuderoz, Maria-Ana Simonet, Olivier Hansen, Nicolas Pasqual, Aurélie Dariz, Thierry Pascal Baum, Vivien Hierle, Jacques Demongeot, Patrice Noël Marche and Evelyne Jouvin-Marche

Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture pp. 1-12

Ju Han, Hang Chang, Orsi Giricz, Genee Y Lee, Frederick L Baehner, Joe W Gray, Mina J Bissell, Paraic A Kenny and Bahram Parvin

A Bayesian Approach to Quantifying the Effects of Mass Poultry Vaccination upon the Spatial and Temporal Dynamics of H5N1 in Northern Vietnam pp. 1-9

Patrick G T Walker, Simon Cauchemez, Raphaëlle Métras, Do Huu Dung, Dirk Pfeiffer and Azra C Ghani

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species pp. 1-10

Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan and Eytan Ruppin

Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable α-Lytic Protease pp. 1-14

Neema L Salimi, Bosco Ho and David A Agard

Spatial Simulations of Myxobacterial Development pp. 1-13

Antony B Holmes, Sara Kalvala and David E Whitworth

A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II pp. 1-15

Shirley Pepke, Tamara Kinzer-Ursem, Stefan Mihalas and Mary B Kennedy

Identifying the Rules of Engagement Enabling Leukocyte Rolling, Activation, and Adhesion pp. 1-15

Jonathan Tang and C Anthony Hunt

Explicit Kinetic Heterogeneity: Mathematical Models for Interpretation of Deuterium Labeling of Heterogeneous Cell Populations pp. 1-11

Vitaly V Ganusov, José A M Borghans and Rob J De Boer

Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks pp. 1-11

Sashi Marella and Bard Ermentrout

Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells pp. 1-11

Murat Cirit, Matej Krajcovic, Colin K Choi, Erik S Welf, Alan F Horwitz and Jason M Haugh

Volume 6, issue 1, 2010

A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules pp. 1-10

Wei Zhang, Jun Zhu, Eric E Schadt and Jun S Liu

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments pp. 1-18

Lukas Burger and Erik van Nimwegen

How Synchronization Protects from Noise pp. 1-9

Nicolas Tabareau, Jean-Jacques Slotine and Quang-Cuong Pham

Associating Genes and Protein Complexes with Disease via Network Propagation pp. 1-9

Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi and Roded Sharan

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains pp. 1-9

Isabella Daidone, Hannes Neuweiler, Sören Doose, Markus Sauer and Jeremy C Smith

A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network pp. 1-15

Lufang Zhou, Miguel A Aon, Tabish Almas, Sonia Cortassa, Raimond L Winslow and Brian O'Rourke

Axonal Velocity Distributions in Neural Field Equations pp. 1-25

Ingo Bojak and David T J Liley

Network-Free Inference of Knockout Effects in Yeast pp. 1-8

Tal Peleg, Nir Yosef, Eytan Ruppin and Roded Sharan

FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model pp. 1-8

Dennis L Chao, M Elizabeth Halloran, Valerie J Obenchain and Ira M Longini

Knots: Attractive Places with High Path Tortuosity in Mouse Open Field Exploration pp. 1-12

Anna Dvorkin, Henry Szechtman and Ilan Golani

SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models pp. 1-13

Aroop Sircar and Jeffrey J Gray

Protein Interaction Networks—More Than Mere Modules pp. 1-13

Stefan Pinkert, Jörg Schultz and Jörg Reichardt

Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics pp. 1-16

Jason N Bazil, Gregery T Buzzard and Ann E Rundell

A Neurophysiologically Plausible Population Code Model for Feature Integration Explains Visual Crowding pp. 1-11

Ronald van den Berg, Jos B T M Roerdink and Frans W Cornelissen

Quantitative Modeling of GRK-Mediated β2AR Regulation pp. 1-14

Sharat J Vayttaden, Jacqueline Friedman, Tuan M Tran, Thomas C Rich, Carmen W Dessauer and Richard B Clark