PLOS Computational Biology

2005 - 2022

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Volume 5, issue 12, 2009

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

Distributed Dynamical Computation in Neural Circuits with Propagating Coherent Activity Patterns pp. 1-11

Pulin Gong and Cees van Leeuwen

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

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

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

Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus pp. 1-19

Julijana Gjorgjieva, Taro Toyoizumi and Stephen J Eglen

A Quick Guide for Developing Effective Bioinformatics Programming Skills pp. 1-7

Joel T Dudley and Atul J Butte

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

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

Yue Zhao, David Granas and Gary D Stormo

Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR pp. 1-12

Sean Ekins, Sandhya Kortagere, Manisha Iyer, Erica J Reschly, Markus A Lill, Matthew R Redinbo and Matthew D Krasowski

Defining an Essence of Structure Determining Residue Contacts in Proteins pp. 1-10

R Sathyapriya, Jose M Duarte, Henning Stehr, Ioannis Filippis and Michael Lappe

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

Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening pp. 1-10

Vebjorn Ljosa and Anne E Carpenter

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

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 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

Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle pp. 1-11

Kenneth S Campbell

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

Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary pp. 1-16

Dominik M Wittmann, Florian Blöchl, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash and Fabian J Theis

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

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

Quantification of Circadian Rhythms in Single Cells pp. 1-10

Pål O Westermark, David K Welsh, Hitoshi Okamura and Hanspeter Herzel

Volume 5, issue 10, 2009

Specific Entrainment of Mitral Cells during Gamma Oscillation in the Rat Olfactory Bulb pp. 1-19

François O David, Etienne Hugues, Tristan Cenier, Nicolas Fourcaud-Trocmé and Nathalie Buonviso

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

Vassilios N Christopoulos and Paul R Schrater

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

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

High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations pp. 1-13

Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi and Makoto Taiji

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

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

Volume 5, issue 9, 2009

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

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

Species Tree Inference by Minimizing Deep Coalescences pp. 1-12

Cuong Than and Luay Nakhleh

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

Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models pp. 1-10

Timothy R Lezon, Andrej Sali and Ivet Bahar

Noise Management by Molecular Networks pp. 1-11

Frank J Bruggeman, Nils Blüthgen and Hans V Westerhoff

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 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

The Role of Ongoing Dendritic Oscillations in Single-Neuron Dynamics pp. 1-15

Michiel W H Remme, Máté Lengyel and Boris S Gutkin

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

Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine pp. 1-17

Jiyong Park, Byungnam Kahng and Wonmuk Hwang

Volume 5, issue 8, 2009

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

Strong Inference for Systems Biology pp. 1-10

Daniel A Beard and Martin J Kushmerick

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

Brian A Kidd, David Baker and Wendy E Thomas

A Quick Guide to Teaching R Programming to Computational Biology Students pp. 1-4

Stephen J Eglen

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations pp. 1-18

Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio and Stefano Piana

Towards Reproducible Descriptions of Neuronal Network Models pp. 1-18

Eilen Nordlie, Marc-Oliver Gewaltig and Hans Ekkehard Plesser

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

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

Daniel A Braun, Pedro A Ortega and Daniel M Wolpert

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

Evolutionary Triplet Models of Structured RNA pp. 1-20

Robert K Bradley and Ian Holmes

Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo pp. 1-20

Yurie Okabe-Oho, Hiroki Murakami, Suguru Oho and Masaki Sasai

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

Recognizing Sequences of Sequences pp. 1-13

Stefan J Kiebel, Katharina von Kriegstein, Jean Daunizeau and Karl J Friston

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

Jochen S Hub and Bert L de Groot

The Origins of Lactase Persistence in Europe pp. 1-13

Yuval Itan, Adam Powell, Mark A Beaumont, Joachim Burger and Mark G Thomas

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

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

A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation pp. 1-7

Stefan Auer, Antonio Trovato and Michele Vendruscolo

Can Molecular Motors Drive Distance Measurements in Injured Neurons? pp. 1-14

Naaman Kam, Yitzhak Pilpel and Mike Fainzilber

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

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations pp. 1-10

Lucy R Allen, Sergei V Krivov and Emanuele Paci

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation pp. 1-10

Olgun Guvench and Alexander D MacKerell

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

A Quick Guide to Organizing Computational Biology Projects pp. 1-5

William Stafford Noble

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

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants pp. 1-15

Jiang Du, Robert D Bjornson, Zhengdong D Zhang, Yong Kong, Michael Snyder and Mark B Gerstein

Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View pp. 1-11

Yongping Pan and Ruth Nussinov

An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility pp. 1-14

Susanne M Rafelski, Jonathan B Alberts and Garrett M Odell

Volume 5, issue 6, 2009

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

Modeling and Inferring Cleavage Patterns in Proliferating Epithelia pp. 1-8

Ankit B Patel, William T Gibson, Matthew C Gibson and Radhika Nagpal

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

Active Dendrites Enhance Neuronal Dynamic Range pp. 1-12

Leonardo L Gollo, Osame Kinouchi and Mauro Copelli

Establishing a Successful Bioinformatics Core Facility Team pp. 1-3

Fran Lewitter and Michael Rebhan

Optimal Control Predicts Human Performance on Objects with Internal Degrees of Freedom pp. 1-15

Arne Nagengast, Daniel A Braun and Daniel M Wolpert

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

David B Searls

The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls pp. 1-10

Yossi Yovel, Mariana Laura Melcon, Matthias O Franz, Annette Denzinger and Hans-Ulrich Schnitzler

The Need for Centralization of Computational Biology Resources pp. 1-2

Fran Lewitter, Michael Rebhan, Brent Richter and David Sexton

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

Volume 5, issue 5, 2009

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

Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling pp. 1-14

Smita Agrawal, Colin Archer and David V Schaffer

A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation pp. 1-15

Nicholas J Hudson, Antonio Reverter and Brian P Dalrymple

Fast Statistical Alignment pp. 1-15

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

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

Andrey Rzhetsky, Hagit Shatkay and W John Wilbur

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

Hypergraphs and Cellular Networks pp. 1-6

Steffen Klamt, Utz-Uwe Haus and Fabian Theis

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

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

BioLINK Special Interest Group Session on the Future of Scientific Publishing pp. 1-2

Scott Markel

Getting Started in Computational Mass Spectrometry–Based Proteomics pp. 1-4

Olga Vitek

Volume 5, issue 4, 2009

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

Cheng Ly and Brent Doiron

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling pp. 1-13

Bree B Aldridge, Julio Saez-Rodriguez, Jeremy L Muhlich, Peter K Sorger and Douglas A Lauffenburger

Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article pp. 1-17

David Shotton, Katie Portwin, Graham Klyne and Alistair Miles

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

James Robert White, Niranjan Nagarajan and Mihai Pop

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

Jan Eichhorn, Fabian Sinz and Matthias Bethge

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

Gitanjali Yadav, Rajesh S Gokhale and Debasisa Mohanty

An Analytically Solvable Model for Rapid Evolution of Modular Structure pp. 1-14

Nadav Kashtan, Avi E Mayo, Tomer Kalisky and Uri Alon

A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1) pp. 1-10

Srinivas Ramachandran, Adrian W R Serohijos, Le Xu, Gerhard Meissner and Nikolay V Dokholyan

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

The Role of the Frank–Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis pp. 1-18

Steven A Niederer and Nicolas P Smith

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

Quentin Vicens and Philip E Bourne

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

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

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors pp. 1-15

Manu, Svetlana Surkova, Alexander V Spirov, Vitaly V Gursky, Hilde Janssens, Ah-Ram Kim, Ovidiu Radulescu, Carlos E Vanario-Alonso, David H Sharp, Maria Samsonova and John Reinitz

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

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

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

Jeremy E Purvis, Ravi Radhakrishnan and Scott L Diamond

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

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

Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution pp. 1-14

Xin He, Xu Ling and Saurabh Sinha

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

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

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

Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer pp. 1-16

Giulia Morra, Gennady Verkhivker and Giorgio Colombo

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

Volume 5, issue 2, 2009

Stochastically Gating Ion Channels Enable Patterned Spike Firing through Activity-Dependent Modulation of Spike Probability pp. 1-20

Joshua T Dudman and Matthew F Nolan

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

Maoz Shamir

Rapid Sampling of Molecular Motions with Prior Information Constraints pp. 1-17

Barak Raveh, Angela Enosh, Ora Schueler-Furman and Dan Halperin

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

Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments pp. 1-12

Vincent A Voelz, M Scott Shell and Ken A Dill

Volume 5, issue 1, 2009

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

Lucy J Colwell and Michael P Brenner

A Review of 2008 for PLoS Computational Biology pp. 1-1

Evie Browne, Rosemary Dickin and Philip E Bourne

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

Sinisa Pajevic and Dietmar Plenz

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

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

State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture pp. 1-12

Adam B Barrett, Guy O Billings, Richard G M Morris and Mark C W van Rossum

Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures pp. 1-12

Dirk Müller and Jörg Stelling

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

Microblogging the ISMB: A New Approach to Conference Reporting pp. 1-5

Neil Saunders, Pedro Beltrão, Lars Jensen, Daniel Jurczak, Roland Krause, Michael Kuhn and Shirley Wu