March 2013

The yellow bundle in the foreground represents a coarse-grained, computer-generated conformation of human Chromosome 19. The structure was obtained by using steered molecular dynamics simulations to enforce a comprehensive set of knowledge-based constraints. Specifically, the simulations were used to promote the spatial proximity of hundreds of gene pairs that are known to be significantly co-regulated. Conformations were obtained with LAMMPS and visualized by VMD. See Di Stefano, et al.

Image Credit: Marco Di Stefano, Angelo Rosa, Cristian Micheletti

Editorial

New Methods Section in PLOS Computational Biology

Thomas Lengauer, Ruth Nussinov

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002972

Topic Pages

Viral Phylodynamics

Erik M. Volz, Katia Koelle, Trevor Bedford

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002947

Evolving Digital Ecological Networks

Miguel A. Fortuna, Luis Zaman, Aaron P. Wagner, Charles Ofria

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002928

Research Articles

Do Ants Need to Estimate the Geometrical Properties of Trail Bifurcations to Find an Efficient Route? A Swarm Robotics Test Bed

Simon Garnier, Maud Combe, Christian Jost, Guy Theraulaz

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002903

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

Tina Toni, Bruce Tidor

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002960

The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks

Clive G. Bowsher, Margaritis Voliotis, Peter S. Swain

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002965

Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action

James B. Gilmore, Anthony D. Kelleher, David A. Cooper, John M. Murray

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002971

Automated Analysis of a Diverse Synapse Population

Brad Busse, Stephen Smith

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002976

Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds

Michael A. Carlin, Mounya Elhilali

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002982

Stability and Responsiveness in a Self-Organized Living Architecture

Simon Garnier, Tucker Murphy, Matthew Lutz, Edward Hurme, Simon Leblanc, Iain D. Couzin

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002984

A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana

Christoph Schmal, Peter Reimann, Dorothee Staiger

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002986

A Model of Binocular Rivalry and Cross-orientation Suppression

Christopher P. Said, David J. Heeger

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002991

The Fate of Cooperation during Range Expansions

Kirill S. Korolev

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002994

Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain

Marta I. Garrido, Maneesh Sahani, Raymond J. Dolan

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1002999

Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq

Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1003000

Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity

Himadri Mukhopadhyay, Shaun-Paul Cordoba, Philip K. Maini, P. Anton van der Merwe, Omer Dushek

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1003004

An Integrated Computational/Experimental Model of Lymphoma Growth

Hermann B. Frieboes, Bryan R. Smith, Yao-Li Chuang, Ken Ito, Allison M. Roettgers, Sanjiv S. Gambhir, Vittorio Cristini

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1003008

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes

Syed Abbas Bukhari, Gustavo Caetano-Anollés

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1003009

Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit

Yuguo Yu, Thomas S. McTavish, Michael L. Hines, Gordon M. Shepherd, Cesare Valenti, Michele Migliore

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1003014

Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19

Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti

PLOS Computational Biology: published March 28, 2013 | https://doi.org/10.1371/journal.pcbi.1003019

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

Philip Stegmaier, Alexander Kel, Edgar Wingender, Jürgen Borlak

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002958

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection

Richard P. Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E. Herbert-Read, David J. T. Sumpter, Ashley J. W. Ward

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002961

Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza

Laura Matrajt, M. Elizabeth Halloran, Ira M. Longini Jr

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002964

Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases

Alane Izu, Ted Cohen, Victor DeGruttola

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002973

Bursts of Vertex Activation and Epidemics in Evolving Networks

Luis E. C. Rocha, Vincent D. Blondel

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002974

Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment

Wei Zhang, Takayo Ota, Viji Shridhar, Jeremy Chien, Baolin Wu, Rui Kuang

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002975

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

Katarzyna Bozek, Thomas Lengauer, Saleta Sierra, Rolf Kaiser, Francisco S. Domingues

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002977

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002980

Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences

Dazhi Jiao, Yuzhen Ye, Haixu Tang

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002981

Angiogenesis: An Adaptive Dynamic Biological Patterning Problem

Timothy W. Secomb, Jonathan P. Alberding, Richard Hsu, Mark W. Dewhirst, Axel R. Pries

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002983

Neuronal Avalanches Differ from Wakefulness to Deep Sleep – Evidence from Intracranial Depth Recordings in Humans

Viola Priesemann, Mario Valderrama, Michael Wibral, Michel Le Van Quyen

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002985

Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements

Sergio Rossell, Martijn A. Huynen, Richard A. Notebaart

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002988

A Multi-scale Analysis of Influenza A Virus Fitness Trade-offs due to Temperature-dependent Virus Persistence

Andreas Handel, Justin Brown, David Stallknecht, Pejman Rohani

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002989

In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase – Cytochrome c

Frank H. Wallrapp, Alexander A. Voityuk, Victor Guallar

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002990

Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids

Alexander J. Stewart, Robert M. Seymour, Andrew Pomiankowski, Max Reuter

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002992

Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins

Hyun-Jun Nam, Seong Kyu Han, James U. Bowie, Sanguk Kim

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002997

Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network

Jialiang Huang, Chaoqun Niu, Christopher D. Green, Lun Yang, Hongkang Mei, Jing-Dong J. Han

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1002998

Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field

Silvio a Beccara, Tatjana Škrbić, Roberto Covino, Cristian Micheletti, Pietro Faccioli

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003002

Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

Paul C. Whitford, Scott C. Blanchard, Jamie H. D. Cate, Karissa Y. Sanbonmatsu

PLOS Computational Biology: published March 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003003

Stimulus-dependent Maximum Entropy Models of Neural Population Codes

Einat Granot-Atedgi, Gašper Tkačik, Ronen Segev, Elad Schneidman

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002922

Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming

Robert W. Mill, Tamás M. Bőhm, Alexandra Bendixen, István Winkler, Susan L. Denham

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002925

Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic

Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric Schadt

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002935

A Dynamical Role for Acetylcholine in Synaptic Renormalization

Christian G. Fink, Geoffrey G. Murphy, Michal Zochowski, Victoria Booth

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002939

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002946

Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering

Mehrdad Mehrbod, Mohammad R. K. Mofrad

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002948

Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling

Douglas E. White, Melissa A. Kinney, Todd C. McDevitt, Melissa L. Kemp

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002952

Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity

BoHung Kim, Sarah L. Hawes, Fawad Gillani, Lane J. Wallace, Kim T. Blackwell

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002953

Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes

Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars A. Bongo, Rebecca D. Burdine, Olga G. Troyanskaya

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002957

Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model

Libin Rong, Jeremie Guedj, Harel Dahari, Daniel J. Coffield Jr, Micha Levi, Patrick Smith, Alan S. Perelson

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002959

Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch, Jens Boch

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002962

Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock

Stefanie Hertel, Christian Brettschneider, Ilka M. Axmann

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002966

Differential Expression Analysis for Pathways

Winston A. Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins, Eugene Kolker

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002967

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002968

Directional Summation in Non-direction Selective Retinal Ganglion Cells

Syed Y. Abbas, Khaldoun C. Hamade, Ellen J. Yang, Scott Nawy, Robert G. Smith, Diana L. Pettit

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002969

Chaste: An Open Source C++ Library for Computational Physiology and Biology

Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David J. Gavaghan

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002970

Processing of Multi-dimensional Sensorimotor Information in the Spinal and Cerebellar Neuronal Circuitry: A New Hypothesis

Anton Spanne, Henrik Jörntell

PLOS Computational Biology: published March 14, 2013 | https://doi.org/10.1371/journal.pcbi.1002979

Interpretation of Genomic Variants Using a Unified Biological Network Approach

Ekta Khurana, Yao Fu, Jieming Chen, Mark Gerstein

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002886

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability

Pouria Dasmeh, Adrian W. R. Serohijos, Kasper P. Kepp, Eugene I. Shakhnovich

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002929

High Prevalence of Multistability of Rest States and Bursting in a Database of a Model Neuron

Bóris Marin, William H. Barnett, Anca Doloc-Mihu, Ronald L. Calabrese, Gennady S. Cymbalyuk

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002930

Dual Coordination of Post Translational Modifications in Human Protein Networks

Jonathan Woodsmith, Atanas Kamburov, Ulrich Stelzl

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002933

Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects

Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel, Eran Segal

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002934

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema

Ron Stewart, Cynthia Alexander Rascón, Shulan Tian, Jeff Nie, Chris Barry, Li-Fang Chu, Hamisha Ardalani, Ryan J. Wagner, Mitchell D. Probasco, Jennifer M. Bolin, Ning Leng, Srikumar Sengupta, Michael Volkmer, Bianca Habermann, Elly M. Tanaka, James A. Thomson, Colin N. Dewey

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002936

Trade-off between Multiple Constraints Enables Simultaneous Formation of Modules and Hubs in Neural Systems

Yuhan Chen, Shengjun Wang, Claus C. Hilgetag, Changsong Zhou

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002937

A Simple Iterative Model Accurately Captures Complex Trapline Formation by Bumblebees Across Spatial Scales and Flower Arrangements

Andrew M. Reynolds, Mathieu Lihoreau, Lars Chittka

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002938

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

Per Larsson, Peter M. Kasson

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002950

Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface

David K. Johnson, John Karanicolas

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002951

Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression

David Amar, Hershel Safer, Ron Shamir

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002955

Integrative Analysis Using Module-Guided Random Forests Reveals Correlated Genetic Factors Related to Mouse Weight

Zheng Chen, Weixiong Zhang

PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002956

Cover

Ensemble conformations of human Chromosome 19 generated by computer simulations

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