PLOS Computational Biology

2005 - 2025

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Volume 6, issue 12, 2010

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

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

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

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

Volume 6, issue 11, 2010

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

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

Environments that Induce Synthetic Microbial Ecosystems pp. 1-17

Niels Klitgord and Daniel Segrè

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

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

Volume 6, issue 10, 2010

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

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

Dimitris Iliopoulos, Arend Hintze and Christoph Adami

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

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

Susanne Menden-Deuer

Volume 6, issue 9, 2010

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

Ten Simple Rules for Editing Wikipedia pp. 1-3

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

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

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

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

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

Volume 6, issue 8, 2010

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

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

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

Robert Legenstein, Niko Wilbert and Laurenz Wiskott

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

David R Wozny, Ulrik R Beierholm and Ladan Shams

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

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

Jonathan Platkiewicz and Romain Brette

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

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

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

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

Volume 6, issue 6, 2010

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

Optimal Drug Synergy in Antimicrobial Treatments pp. 1-9

Joseph Peter Torella, Remy Chait and Roy Kishony

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

Yan Gai, Brent Doiron and John Rinzel

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

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

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

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

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

Mark Reimers

Assimilating Seizure Dynamics pp. 1-12

Ghanim Ullah and Steven J Schiff

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

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

Simon DeDeo, David C Krakauer and Jessica C Flack

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

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

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

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

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

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

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

Thomas House and Matt J Keeling

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

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

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

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

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

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

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

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

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

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

Volume 6, issue 1, 2010

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 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

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

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

Tal Peleg, Nir Yosef, Eytan Ruppin and Roded Sharan