PLOS Computational Biology

2005 - 2025

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Volume 5, issue 12, 2009

Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases pp. 1-16

Kai Wang, Manikandan Narayanan, Hua Zhong, Martin Tompa, Eric E Schadt and Jun Zhu

Hyperbolic Planforms in Relation to Visual Edges and Textures Perception pp. 1-16

Pascal Chossat and Olivier Faugeras

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies pp. 1-13

Alexandra M Schnoes, Shoshana D Brown, Igor Dodevski and Patricia C Babbitt

Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation pp. 1-7

Jorge M Pacheco, Flávio Pinheiro and Francisco C Santos

Calculating Evolutionary Dynamics in Structured Populations pp. 1-7

Charles G Nathanson, Corina E Tarnita and Martin A Nowak

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data pp. 1-11

Alexander Mitsos, Ioannis N Melas, Paraskeuas Siminelakis, Aikaterini D Chairakaki, Julio Saez-Rodriguez and Leonidas G Alexopoulos

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks pp. 1-11

João F Matias Rodrigues and Andreas Wagner

Model of Transcriptional Activation by MarA in Escherichia coli pp. 1-11

Michael E Wall, David A Markowitz, Judah L Rosner and Robert G Martin

Inferring Binding Energies from Selected Binding Sites pp. 1-8

Yue Zhao, David Granas and Gary D Stormo

Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task pp. 1-9

Ian H Stevenson, Hugo L Fernandes, Iris Vilares, Kunlin Wei and Konrad P Körding

Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation pp. 1-19

Brian J Schmidt, Jason A Papin and Michael B Lawrence

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure pp. 1-18

John A Capra, Roman A Laskowski, Janet M Thornton, Mona Singh and Thomas A Funkhouser

Volume 5, issue 11, 2009

Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model pp. 1-12

Samuel Bandara, Johannes P Schlöder, Roland Eils, Hans Georg Bock and Tobias Meyer

A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen pp. 1-12

Omer Dushek, Raibatak Das and Daniel Coombs

Discovery of Regulatory Elements is Improved by a Discriminatory Approach pp. 1-8

Eivind Valen, Albin Sandelin, Ole Winther and Anders Krogh

Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators pp. 1-16

Eric A Zilli, Motoharu Yoshida, Babak Tahvildari, Lisa M Giocomo and Michael E Hasselmo

A Novel Extended Granger Causal Model Approach Demonstrates Brain Hemispheric Differences during Face Recognition Learning pp. 1-13

Tian Ge, Keith M Kendrick and Jianfeng Feng

Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST2 Model pp. 1-13

Srivas Chennu, Patrick Craston, Brad Wyble and Howard Bowman

Volume 5, issue 10, 2009

Grasping Objects with Environmentally Induced Position Uncertainty pp. 1-11

Vassilios N Christopoulos and Paul R Schrater

Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES pp. 1-13

Hsiao-Mei Lu and Jie Liang

Getting Started in Gene Expression Microarray Analysis pp. 1-4

Donna K Slonim and Itai Yanai

Gene Circuit Analysis of the Terminal Gap Gene huckebein pp. 1-16

Maksat Ashyraliyev, Ken Siggens, Hilde Janssens, Joke Blom, Michael Akam and Johannes Jaeger

The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation pp. 1-10

Jin Liu and Ruth Nussinov

‘Glocal’ Robustness Analysis and Model Discrimination for Circadian Oscillators pp. 1-10

Marc Hafner, Heinz Koeppl, Martin Hasler and Andreas Wagner

Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots pp. 1-15

Mateusz Sikora, Joanna I Sułkowska and Marek Cieplak

Towards a Mathematical Theory of Cortical Micro-circuits pp. 1-26

Dileep George and Jeff Hawkins

Volume 5, issue 9, 2009

A Structured Model of Video Reproduces Primary Visual Cortical Organisation pp. 1-16

Pietro Berkes, Richard E Turner and Maneesh Sahani

Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields pp. 1-16

Balázs Ujfalussy, Tamás Kiss and Péter Érdi

Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions? pp. 1-6

Stefano Allesina and Mercedes Pascual

Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning pp. 1-12

Samuel A Danziger, Roberta Baronio, Lydia Ho, Linda Hall, Kirsty Salmon, G Wesley Hatfield, Peter Kaiser and Richard H Lathrop

A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels pp. 1-9

Steven H Wu, Michael A Black, Robyn A North, Kelly R Atkinson and Allen G Rodrigo

Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein pp. 1-15

Jennifer L Lahti, Adam P Silverman and Jennifer R Cochran

Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification pp. 1-15

Stephen A Stanhope, Srikumar Sengupta, Johan den Boon, Paul Ahlquist and Michael A Newton

Volume 5, issue 8, 2009

FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies pp. 1-12

Oliver C Redfern, Benoît H Dessailly, Timothy J Dallman, Ian Sillitoe and Christine A Orengo

A Self-Organizing Algorithm for Modeling Protein Loops pp. 1-11

Pu Liu, Fangqiang Zhu, Dmitrii N Rassokhin and Dimitris K Agrafiotis

Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens pp. 1-17

Leighton Pritchard, Hui Liu, Clare Booth, Emma Douglas, Patrice François, Jacques Schrenzel, Peter E Hedley, Paul R J Birch and Ian K Toth

Nash Equilibria in Multi-Agent Motor Interactions pp. 1-8

Daniel A Braun, Pedro A Ortega and Daniel M Wolpert

Qualia: The Geometry of Integrated Information pp. 1-24

David Balduzzi and Giulio Tononi

Geometric De-noising of Protein-Protein Interaction Networks pp. 1-10

Oleksii Kuchaiev, Marija Rašajski, Desmond J Higham and Nataša Pržulj

Computation of Conformational Coupling in Allosteric Proteins pp. 1-10

Brian A Kidd, David Baker and Wendy E Thomas

Volume 5, issue 7, 2009

Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels pp. 1-9

Guido Gigante, Maurizio Mattia, Jochen Braun and Paolo Del Giudice

Semantic Similarity in Biomedical Ontologies pp. 1-12

Catia Pesquita, Daniel Faria, André O Falcão, Phillip Lord and Francisco M Couto

Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs pp. 1-10

Flávio Codeço Coelho and Claudia T Codeço

Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors pp. 1-10

Andrew J Olaharski, Nina Gonzaludo, Hans Bitter, David Goldstein, Stephan Kirchner, Hirdesh Uppal and Kyle Kolaja

Volume 5, issue 6, 2009

Taking the Lag out of Jet Lag through Model-Based Schedule Design pp. 1-14

Dennis A Dean , II, Daniel B Forger and Elizabeth B Klerman

Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences pp. 1-14

Zhang Zhang and Jeffrey P Townsend

Volume 5, issue 5, 2009

A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family pp. 1-16

Gregory D Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler and Tanja Kortemme

Functional Brain Networks Develop from a “Local to Distributed” Organization pp. 1-14

Damien A Fair, Alexander L Cohen, Jonathan D Power, Nico U F Dosenbach, Jessica A Church, Francis M Miezin, Bradley L Schlaggar and Steven E Petersen

Volume 5, issue 4, 2009

Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons pp. 1-12

Cheng Ly and Brent Doiron

Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis pp. 1-14

Gitanjali Yadav, Rajesh S Gokhale and Debasisa Mohanty

Natural Image Coding in V1: How Much Use Is Orientation Selectivity? pp. 1-16

Jan Eichhorn, Fabian Sinz and Matthias Bethge

Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology pp. 1-4

B J Morrison McKay and Clare Sansom

Polymorphism Data Can Reveal the Origin of Species Abundance Statistics pp. 1-6

Yosef E Maruvka and Nadav M Shnerb

Volume 5, issue 3, 2009

Broadband Criticality of Human Brain Network Synchronization pp. 1-13

Manfred G Kitzbichler, Marie L Smith, Søren R Christensen and Ed Bullmore

Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments pp. 1-13

Oscar Westesson and Ian Holmes

“I Look in Your Eyes, Honey”: Internal Face Features Induce Spatial Frequency Preference for Human Face Processing pp. 1-13

Matthias S Keil

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics pp. 1-10

Barry J Grant, Alemayehu A Gorfe and J Andrew McCammon

Accurate Prediction of Peptide Binding Sites on Protein Surfaces pp. 1-10

Evangelia Petsalaki, Alexander Stark, Eduardo García-Urdiales and Robert B Russell

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis pp. 1-12

Matthew A Hibbs, Chad L Myers, Curtis Huttenhower, David C Hess, Kai Li, Amy A Caudy and Olga G Troyanskaya

A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis pp. 1-12

Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A Cruikshank, Dennis Shasha, Gloria M Coruzzi and Rodrigo A Gutiérrez

Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation pp. 1-15

Emili Balaguer-Ballester, Nicholas R Clark, Martin Coath, Katrin Krumbholz and Susan L Denham

Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy pp. 1-15

Arash Bahrami, Amir H Assadi, John L Markley and Hamid R Eghbalnia

Volume 5, issue 2, 2009

Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing pp. 1-10

John M Higgins, David T Eddington, Sangeeta N Bhatia and L Mahadevan

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins pp. 1-14

Michael D Daily and Jeffrey J Gray

The Temporal Winner-Take-All Readout pp. 1-13

Maoz Shamir

Volume 5, issue 1, 2009

Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks pp. 1-12

Adel Dayarian, Madalena Chaves, Eduardo D Sontag and Anirvan M Sengupta

Evolutionary Sequence Modeling for Discovery of Peptide Hormones pp. 1-12

Kemal Sonmez, Naunihal T Zaveri, Ilan A Kerman, Sharon Burke, Charles R Neal, Xinmin Xie, Stanley J Watson and Lawrence Toll

Action Potential Initiation in the Hodgkin-Huxley Model pp. 1-7

Lucy J Colwell and Michael P Brenner

Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties pp. 1-15

Wenxu Tong, Ying Wei, Leonel F Murga, Mary Jo Ondrechen and Ronald J Williams