PLOS Computational Biology

2005 - 2025

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Volume 6, issue 12, 2010

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

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

Tilo Schwalger, Karin Fisch, Jan Benda and Benjamin Lindner

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

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

Volume 6, issue 11, 2010

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

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

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

Yoshihisa Kubota and M Neal Waxham

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

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

Volume 6, issue 10, 2010

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

Dimitris Iliopoulos, Arend Hintze and Christoph Adami

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

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

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

Klaas Enno Stephan, Anthony Randal McIntosh and Claus C Hilgetag

Bistability in Apoptosis by Receptor Clustering pp. 1-9

Kenneth L Ho and Heather A Harrington

Volume 6, issue 9, 2010

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

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

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

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

Ten Simple Rules for Editing Wikipedia pp. 1-3

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

Volume 6, issue 8, 2010

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

David R Wozny, Ulrik R Beierholm and Ladan Shams

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

Robert Legenstein, Niko Wilbert and Laurenz Wiskott

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

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

Volume 6, issue 7, 2010

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

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

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

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

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

Jonathan Platkiewicz and Romain Brette

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

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

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

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

Volume 6, issue 6, 2010

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

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

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

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

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

Yan Gai, Brent Doiron and John Rinzel

Optimal Drug Synergy in Antimicrobial Treatments pp. 1-9

Joseph Peter Torella, Remy Chait and Roy Kishony

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

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

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

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

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

Mark Reimers

Assimilating Seizure Dynamics pp. 1-12

Ghanim Ullah and Steven J Schiff

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

Simon DeDeo, David C Krakauer and Jessica C Flack

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

Volume 6, issue 4, 2010

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

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

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

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

Dirk Helbing, Attila Szolnoki, Matjaž Perc and György Szabó

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

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

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

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

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

Volume 6, issue 3, 2010

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

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

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

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

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

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

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

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

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

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

Thomas House and Matt J Keeling

Volume 6, issue 2, 2010

Spatial Simulations of Myxobacterial Development pp. 1-13

Antony B Holmes, Sara Kalvala and David E Whitworth

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

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

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

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

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

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

Ingo Bojak and David T J Liley

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

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

Tal Peleg, Nir Yosef, Eytan Ruppin and Roded Sharan

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

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

Anna Dvorkin, Henry Szechtman and Ilan Golani