PLOS Computational Biology

2005 - 2025

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Volume 7, issue 12, 2011

Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers pp. 1-15

Andrew T Kwon, Alice Yi Chou, David J Arenillas and Wyeth W Wasserman

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes pp. 1-10

Amin R Mazloom, Ruth Dannenfelser, Neil R Clark, Arsen V Grigoryan, Kathryn M Linder, Timothy J Cardozo, Julia C Bond, Aislyn D W Boran, Ravi Iyengar, Anna Malovannaya, Rainer B Lanz and Avi Ma'ayan

Genetic Co-Occurrence Network across Sequenced Microbes pp. 1-9

Pan-Jun Kim and Nathan D Price

Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons pp. 1-25

Dejan Pecevski, Lars Buesing and Wolfgang Maass

Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry pp. 1-11

Pranesh Padmanabhan and Narendra M Dixit

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model pp. 1-11

Edward B Baskerville, Andy P Dobson, Trevor Bedford, Stefano Allesina, T Michael Anderson and Mercedes Pascual

Radial and Spiral Stream Formation in Proteus mirabilis Colonies pp. 1-11

Chuan Xue, Elena O Budrene and Hans G Othmer

Chemotaxis when Bacteria Remember: Drift versus Diffusion pp. 1-8

Sakuntala Chatterjee, Rava Azeredo da Silveira and Yariv Kafri

Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome pp. 1-16

Ismail Adeniran, Mark J McPate, Harry J Witchel, Jules C Hancox and Henggui Zhang

Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains pp. 1-14

Ashok Litwin-Kumar, Anne-Marie M Oswald, Nathaniel N Urban and Brent Doiron

Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps) pp. 1-13

Zhichao Liu, Qiang Shi, Don Ding, Reagan Kelly, Hong Fang and Weida Tong

Volume 7, issue 11, 2011

Optimizing Experimental Design for Comparing Models of Brain Function pp. 1-18

Jean Daunizeau, Kerstin Preuschoff, Karl Friston and Klaas Stephan

Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons pp. 1-22

Lars Buesing, Johannes Bill, Bernhard Nessler and Wolfgang Maass

The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations pp. 1-9

Joshua H Goldwyn and Eric Shea-Brown

Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits pp. 1-9

Rutger Hermsen, David W Erickson and Terence Hwa

How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes pp. 1-8

E P Raposo, F Bartumeus, M G E da Luz, P J Ribeiro-Neto, T A Souza and G M Viswanathan

High Degree of Heterogeneity in Alzheimer's Disease Progression Patterns pp. 1-6

Natalia L Komarova and Craig J Thalhauser

Trade-Offs and Constraints in Allosteric Sensing pp. 1-13

Bruno MC Martins and Peter S Swain

Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy pp. 1-14

Seyed Yahya Anvar, Allan Tucker, Veronica Vinciotti, Andrea Venema, Gert-Jan B van Ommen, Silvere M van der Maarel, Vered Raz and Peter A C ‘t Hoen

Volume 7, issue 10, 2011

Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models pp. 1-9

Jeffrey D Fitzgerald, Ryan J Rowekamp, Lawrence C Sincich and Tatyana O Sharpee

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis pp. 1-15

Anna Divoli, Eneida A Mendonça, James A Evans and Andrey Rzhetsky

Brain Rhythms Reveal a Hierarchical Network Organization pp. 1-15

G Karl Steinke and Roberto F Galán

Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer pp. 1-10

Anup Dewanji, Jihyoun Jeon, Rafael Meza and E Georg Luebeck

Coupled Information Diffusion–Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs pp. 1-10

François Rebaudo and Olivier Dangles

The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers pp. 1-10

Sean A Rands

Accelerated Profile HMM Searches pp. 1-16

Sean R Eddy

The Dynamics of Supply and Demand in mRNA Translation pp. 1-16

Chris A Brackley, M Carmen Romano and Marco Thiel

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability pp. 1-16

Kirsten H ten Tusscher and Paulien Hogeweg

Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks pp. 1-16

Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West and Lingchong You

Receptive Field Inference with Localized Priors pp. 1-16

Mijung Park and Jonathan W Pillow

Metabolic Regulation in Progression to Autoimmune Diabetes pp. 1-16

Marko Sysi-Aho, Andrey Ermolov, Peddinti V Gopalacharyulu, Abhishek Tripathi, Tuulikki Seppänen-Laakso, Johanna Maukonen, Ismo Mattila, Suvi T Ruohonen, Laura Vähätalo, Laxman Yetukuri, Taina Härkönen, Erno Lindfors, Janne Nikkilä, Jorma Ilonen, Olli Simell, Maria Saarela, Mikael Knip, Samuel Kaski, Eriika Savontaus and Matej Orešič

Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics pp. 1-14

Jyh-Ying Peng, Chung-Chih Lin, Yen-Jen Chen, Lung-Sen Kao, Young-Chau Liu, Chung-Chien Chou, Yi-Hung Huang, Fang-Rong Chang, Yang-Chang Wu, Yuh-Show Tsai and Chun-Nan Hsu

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity pp. 1-14

Hyun Joo, Archana G Chavan, Ryan Day, Kristin P Lennox, Paul Sukhanov, David B Dahl, Marina Vannucci and Jerry Tsai

Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex pp. 1-13

Anurag Sethi, Byron Goldstein and S Gnanakaran

Integrated Information Increases with Fitness in the Evolution of Animats pp. 1-13

Jeffrey A Edlund, Nicolas Chaumont, Arend Hintze, Christof Koch, Giulio Tononi and Christoph Adami

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation pp. 1-7

César Augusto F de Oliveira, Barry J Grant, Michelle Zhou and J Andrew McCammon

Formation of Regulatory Modules by Local Sequence Duplication pp. 1-12

Armita Nourmohammad and Michael Lässig

Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects pp. 1-12

Max Berniker and Konrad P Kording

Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response pp. 1-12

Yaakov Maman, Ran Nir-Paz and Yoram Louzoun

Three People Can Synchronize as Coupled Oscillators during Sports Activities pp. 1-8

Keiko Yokoyama and Yuji Yamamoto

Volume 7, issue 9, 2011

Ten Simple Rules for Getting Help from Online Scientific Communities pp. 1-3

Giovanni M Dall'Olio, Jacopo Marino, Michael Schubert, Kevin L Keys, Melanie I Stefan, Colin S Gillespie, Pierre Poulain, Khader Shameer, Robert Sugar, Brandon M Invergo, Lars J Jensen, Jaume Bertranpetit and Hafid Laayouni

A Combined Experimental and Mathematical Approach for Molecular-based Optimization of Irinotecan Circadian Delivery pp. 1-12

Annabelle Ballesta, Sandrine Dulong, Chadi Abbara, Boris Cohen, Alper Okyar, Jean Clairambault and Francis Levi

Neuromotor Noise, Error Tolerance and Velocity-Dependent Costs in Skilled Performance pp. 1-15

Dagmar Sternad, Masaki O Abe, Xiaogang Hu and Hermann Müller

Network-Based Prediction and Analysis of HIV Dependency Factors pp. 1-15

T M Murali, Matthew D Dyer, David Badger, Brett M Tyler and Michael G Katze

Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions pp. 1-11

Adi Shklarsh, Gil Ariel, Elad Schneidman and Eshel Ben-Jacob

Volume 7, issue 8, 2011

Understanding Auditory Spectro-Temporal Receptive Fields and Their Changes with Input Statistics by Efficient Coding Principles pp. 1-16

Lingyun Zhao and Li Zhaoping

Volume 7, issue 7, 2011

A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells pp. 1-13

Tian Hong, Jianhua Xing, Liwu Li and John J Tyson

Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties pp. 1-18

Etay Hay, Sean Hill, Felix Schürmann, Henry Markram and Idan Segev

Volume 7, issue 6, 2011

Neurobiologically Realistic Determinants of Self-Organized Criticality in Networks of Spiking Neurons pp. 1-14

Mikail Rubinov, Olaf Sporns, Jean-Philippe Thivierge and Michael Breakspear

The Binding of Learning to Action in Motor Adaptation pp. 1-14

Luis Nicolas Gonzalez Castro, Craig Bryant Monsen and Maurice A Smith

International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011 pp. 1-4

Justin Mullins and Morrison McKay Bj

Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics pp. 1-13

Erik M Volz, Joel C Miller, Alison Galvani and Lauren Ancel Meyers

How Haptic Size Sensations Improve Distance Perception pp. 1-13

Peter W Battaglia, Daniel Kersten and Paul R Schrater

Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram pp. 1-8

Bratislav Mišić, Vasily A Vakorin, Nataša Kovačević, Tomáš Paus and Anthony R McIntosh

Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth pp. 1-22

Richard Kennaway, Enrico Coen, Amelia Green and Andrew Bangham

Volume 7, issue 5, 2011

Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases pp. 1-6

Frank Emmert-Streib and Galina V Glazko

Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making pp. 1-19

Emili Balaguer-Ballester, Christopher C Lapish, Jeremy K Seamans and Daniel Durstewitz

Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability pp. 1-14

Alistair N Boettiger, Peter L Ralph and Steven N Evans

How Structure Determines Correlations in Neuronal Networks pp. 1-14

Volker Pernice, Benjamin Staude, Stefano Cardanobile and Stefan Rotter

Spatial Learning and Action Planning in a Prefrontal Cortical Network Model pp. 1-21

Louis-Emmanuel Martinet, Denis Sheynikhovich, Karim Benchenane and Angelo Arleo

A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein pp. 1-11

Daniel-Adriano Silva, Gregory R Bowman, Alejandro Sosa-Peinado and Xuhui Huang

Volume 7, issue 4, 2011

A Third Measure-Metastable State in the Dynamics of Spontaneous Shape Change in Healthy Human's White Cells pp. 1-8

Karen A Selz

A Stochastic Model of Latently Infected Cell Reactivation and Viral Blip Generation in Treated HIV Patients pp. 1-15

Jessica M Conway and Daniel Coombs

Minimum Information About a Simulation Experiment (MIASE) pp. 1-4

Dagmar Waltemath, Richard Adams, Daniel A Beard, Frank T Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T Cooling, Jonathan Cooper, Edmund J Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter Hunter, Edda Klipp, Camille Laibe, Andrew K Miller, Ion Moraru, David Nickerson, Poul Nielsen, Macha Nikolski, Sven Sahle, Herbert M Sauro, Henning Schmidt, Jacky L Snoep, Dominic Tolle, Olaf Wolkenhauer and Nicolas Le Novère

Volume 7, issue 3, 2011

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli pp. 1-20

Melody K Morris, Julio Saez-Rodriguez, David C Clarke, Peter K Sorger and Douglas A Lauffenburger

Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells pp. 1-12

Rachel Cavill, Atanas Kamburov, James K Ellis, Toby J Athersuch, Marcus S C Blagrove, Ralf Herwig, Timothy M D Ebbels and Hector C Keun

Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding pp. 1-13

Dana Bar-On, Esther Nachliel, Menachem Gutman and Uri Ashery

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations pp. 1-14

Lars Skjaerven, Barry Grant, Arturo Muga, Knut Teigen, J Andrew McCammon, Nathalie Reuter and Aurora Martinez

Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts pp. 1-9

Luis Rocha, Fredrik Liljeros and Petter Holme

Volume 7, issue 2, 2011

De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference pp. 1-13

Jens Keilwagen, Jan Grau, Ivan A Paponov, Stefan Posch, Marc Strickert and Ivo Grosse

Automatic Design of Digital Synthetic Gene Circuits pp. 1-13

Mario A Marchisio and Jörg Stelling

First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics pp. 1-14

José M Ponciano and Marcos A Capistrán

ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature pp. 1-3

Richard H Lathrop, Burkhard Rost, Membership Iscb, Executive Committee Iscb, Board of Directors Iscb and Public Affairs Committee Iscb

Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives pp. 1-11

T Déirdre Hollingsworth, Don Klinkenberg, Hans Heesterbeek and Roy M Anderson

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations pp. 1-11

Chikako Ragan, Michael Zuker and Mark A Ragan

Application of Biomarkers in Cancer Risk Management: Evaluation from Stochastic Clonal Evolutionary and Dynamic System Optimization Points of View pp. 1-7

Xiaohong Li, Patricia L Blount, Thomas L Vaughan and Brian J Reid

Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics pp. 1-12

Amber M Smith, Frederick R Adler, Julie L McAuley, Ryan N Gutenkunst, Ruy M Ribeiro, Jonathan A McCullers and Alan S Perelson

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation pp. 1-18

David M Holloway, Francisco J P Lopes, Luciano da Fontoura Costa, Bruno A N Travençolo, Nina Golyandina, Konstantin Usevich and Alexander V Spirov

A Mathematical Framework for Protein Structure Comparison pp. 1-10

Wei Liu, Anuj Srivastava and Jinfeng Zhang

Transition from Persistent to Anti-Persistent Correlations in Postural Sway Indicates Velocity-Based Control pp. 1-10

Didier Delignières, Kjerstin Torre and Pierre-Louis Bernard

Power-Law Input-Output Transfer Functions Explain the Contrast-Response and Tuning Properties of Neurons in Visual Cortex pp. 1-21

Erez Persi, David Hansel, Lionel Nowak, Pascal Barone and Carl van Vreeswijk

Volume 7, issue 1, 2011

A Novel Approach to Pharmacodynamic Assessment of Antimicrobial Agents: New Insights to Dosing Regimen Design pp. 1-8

Vincent H Tam and Michael Nikolaou

Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding pp. 1-8

Iain Melvin, Jason Weston, William Stafford Noble and Christina Leslie

From Spiking Neuron Models to Linear-Nonlinear Models pp. 1-16

Srdjan Ostojic and Nicolas Brunel

A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System pp. 1-16

Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M Blom, Benjamin Leong, Sunil Sethi, Bow Ho, Jeak Ling Ding and P S Thiagarajan

Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings pp. 1-14

Elise Payzan-LeNestour and Peter Bossaerts

Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia pp. 1-2

Philip E Bourne

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data pp. 1-13

Thomas J Sharpton, Samantha J Riesenfeld, Steven W Kembel, Joshua Ladau, James P O'Dwyer, Jessica L Green, Jonathan A Eisen and Katherine S Pollard

Is My Network Module Preserved and Reproducible? pp. 1-29

Peter Langfelder, Rui Luo, Michael C Oldham and Steve Horvath

Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays pp. 1-15

Hao Chen, Haipeng Xing and Nancy R Zhang

Practical Measures of Integrated Information for Time-Series Data pp. 1-18

Adam B Barrett and Anil K Seth

Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks pp. 1-10

Daniel M Cornforth, Timothy C Reluga, Eunha Shim, Chris T Bauch, Alison P Galvani and Lauren Ancel Meyers