PLOS Computational Biology

2005 - 2025

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Volume 5, issue 12, 2009

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

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

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

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

Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics pp. 1-10

Gustavo Deco, Daniel Martí, Anders Ledberg, Ramon Reig and Maria V Sanchez Vives

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

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

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

A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton pp. 1-16

Raibatak Das, Christopher W Cairo and Daniel Coombs

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

Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation pp. 1-13

Arno Onken, Steffen Grünewälder, Matthias H J Munk and Klaus Obermayer

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

Eivind Valen, Albin Sandelin, Ole Winther and Anders Krogh

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

Volume 5, issue 10, 2009

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

Dileep George and Jeff Hawkins

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

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

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

Mateusz Sikora, Joanna I Sułkowska and Marek Cieplak

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

Volume 5, issue 9, 2009

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

Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities pp. 1-12

Rui-Ru Ji, Heshani de Silva, Yisheng Jin, Robert E Bruccoleri, Jian Cao, Aiqing He, Wenjun Huang, Paul S Kayne, Isaac M Neuhaus, Karl-Heinz Ott, Becky Penhallow, Mark I Cockett, Michael G Neubauer, Nathan O Siemers and Petra Ross-Macdonald

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

Stefano Allesina and Mercedes Pascual

Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns pp. 1-6

Deborah A Striegel and Monica K Hurdal

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

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

Volume 5, issue 8, 2009

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

Evolutionary Triplet Models of Structured RNA pp. 1-20

Robert K Bradley and Ian Holmes

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

David Balduzzi and Giulio Tononi

Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data pp. 1-9

Joost Van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau and Joost Schymkowitz

Detection of Functional Modes in Protein Dynamics pp. 1-13

Jochen S Hub and Bert L de Groot

Investigating CTL Mediated Killing with a 3D Cellular Automaton pp. 1-12

Frederik Graw and Roland R Regoes

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 Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization pp. 1-10

Steven Lemm, Klaus-Robert Müller and Gabriel Curio

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

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

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

Volume 5, issue 7, 2009

Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation pp. 1-10

Daniel Geberth and Marc-Thorsten Hütt

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

Semantic Similarity in Biomedical Ontologies pp. 1-12

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

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

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

Volume 5, issue 6, 2009

The Effect of Ongoing Exposure Dynamics in Dose Response Relationships pp. 1-12

Josep M Pujol, Joseph E Eisenberg, Charles N Haas and James S Koopman

Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening pp. 1-11

Nobuyoshi Nagamine, Takayuki Shirakawa, Yusuke Minato, Kentaro Torii, Hiroki Kobayashi, Masaya Imoto and Yasubumi Sakakibara

A Probabilistic Model of RNA Conformational Space pp. 1-11

Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V Mardia, Jesper Ferkinghoff-Borg and Thomas Hamelryck

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

Exploring the Free Energy Landscape: From Dynamics to Networks and Back pp. 1-9

Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique and Fernando Falo

Ten Simple Rules for Choosing between Industry and Academia pp. 1-4

David B Searls

Volume 5, issue 5, 2009

Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings pp. 1-16

Quentin J M Huys and Liam Paninski

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

How to Get the Most out of Your Curation Effort pp. 1-13

Andrey Rzhetsky, Hagit Shatkay and W John Wilbur

Fast Statistical Alignment pp. 1-15

Robert K Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes and Lior Pachter

SHRiMP: Accurate Mapping of Short Color-space Reads pp. 1-11

Stephen M Rumble, Phil Lacroute, Adrian V Dalca, Marc Fiume, Arend Sidow and Michael Brudno

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

Prediction of Protein Binding Regions in Disordered Proteins pp. 1-18

Bálint Mészáros, István Simon and Zsuzsanna Dosztányi

Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't pp. 1-18

Yasser Roudi, Sheila Nirenberg and Peter E Latham

Volume 5, issue 4, 2009

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

Cheng Ly and Brent Doiron

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples pp. 1-11

James Robert White, Niranjan Nagarajan and Mihai Pop

Ten Simple Rules To Combine Teaching and Research pp. 1-2

Quentin Vicens and Philip E Bourne

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

Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL pp. 1-21

Zheng Yang, Peter Májek and Ivet Bahar

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

Yosef E Maruvka and Nadav M Shnerb

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

Gitanjali Yadav, Rajesh S Gokhale and Debasisa Mohanty

Volume 5, issue 3, 2009

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures pp. 1-20

Alberto Pascual-García, David Abia, Ángel R Ortiz and Ugo Bastolla

BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis pp. 1-11

Allen W Bryan, Matthew Menke, Lenore J Cowen, Susan L Lindquist and Bonnie Berger

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

Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter pp. 1-10

Boian S Alexandrov, Vladimir Gelev, Sang Wook Yoo, Alan R Bishop, Kim Ø Rasmussen and Anny Usheva

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

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

Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior pp. 1-9

Jeremy E Purvis, Ravi Radhakrishnan and Scott L Diamond

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

Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System pp. 1-24

Patrick Blomquist, Anna Devor, Ulf G Indahl, Istvan Ulbert, Gaute T Einevoll and Anders M Dale

T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules pp. 1-7

Aidan MacNamara, Ulrich Kadolsky, Charles R M Bangham and Becca Asquith

Volume 5, issue 2, 2009

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

Maoz Shamir

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

Michael D Daily and Jeffrey J Gray

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

Volume 5, issue 1, 2009

Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches pp. 1-20

Sinisa Pajevic and Dietmar Plenz

Estimating the Location and Spatial Extent of a Covert Anthrax Release pp. 1-9

Judith Legrand, Joseph R Egan, Ian M Hall, Simon Cauchemez, Steve Leach and Neil M Ferguson

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

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

Lucy J Colwell and Michael P Brenner

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