April 2014

The image depicts the HoneyComb experimental paradigm: on a virtual playfield, each player controls their avatar-dot with the mouse, navigating by clicking into adjacent fields. The key idea of the HoneyComb paradigm is indicated by laying the local perspective of the red-dot player over the global perspective of the experimenter. In this experiment, six goal fields rendering monetary payoffs (€ for a majority and €€ for a minority) and an incentive for group cohesion were implemented. The red and the yellow circles indicate varying dispersion rates of the players. See Boos et al.

Image Credit: Johannes Pritz, Courant Research Centre Evolution of Social Behavior, University of Gõttingen, Germany.

Editorial

Ten Simple Rules for the Care and Feeding of Scientific Data

Alyssa Goodman, Alberto Pepe, Alexander W. Blocker, Christine L. Borgman, Kyle Cranmer, Merce Crosas, Rosanne Di Stefano, Yolanda Gil, Paul Groth, Margaret Hedstrom, David W. Hogg, Vinay Kashyap, Ashish Mahabal, Aneta Siemiginowska, Aleksandra Slavkovic

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003542

Message from ISCB

ISMB 2014—The Premier Conference for the World's Computational Biologists

Christiana N. Fogg, Diane E. Kovats

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003566

Education

A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences

Michelle D. Brazas, Fran Lewitter, Maria Victoria Schneider, Celia W. G. van Gelder, Patricia M. Palagi

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003510

Perspective

Computational Biology and Bioinformatics in Nigeria

Segun A. Fatumo, Moses P. Adoga, Opeolu O. Ojo, Olugbenga Oluwagbemi, Tolulope Adeoye, Itunuoluwa Ewejobi, Marion Adebiyi, Ezekiel Adebiyi, Clement Bewaji, Oyekanmi Nashiru

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003516

Review

The Influence of Spatiotemporal Structure of Noisy Stimuli in Decision Making

Andrea Insabato, Laura Dempere-Marco, Mario Pannunzi, Gustavo Deco, Ranulfo Romo

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003492

Research Articles

Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs

Ambuj Kumar, Rituraj Purohit

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003318

Rates of CTL Killing in Persistent Viral Infection In Vivo

Marjet Elemans, Arnaud Florins, Luc Willems, Becca Asquith

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003534

Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems

Justin S. Hogg, Leonard A. Harris, Lori J. Stover, Niketh S. Nair, James R. Faeder

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003544

Leadership in Moving Human Groups

Margarete Boos, Johannes Pritz, Simon Lange, Michael Belz

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003541

Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity

David Samu, Anil K. Seth, Thomas Nowotny

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003557

Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics

Jeffrey P. Perley, Judith Mikolajczak, Marietta L. Harrison, Gregery T. Buzzard, Ann E. Rundell

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003546

Dynamics of Cellular Responses to Radiation

Dominik Wodarz, Ron Sorace, Natalia L. Komarova

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003513

The Evolution of Multivariate Maternal Effects

Bram Kuijper, Rufus A. Johnstone, Stuart Townley

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003550

Spike-Threshold Adaptation Predicted by Membrane Potential Dynamics In Vivo

Bertrand Fontaine, José Luis Peña, Romain Brette

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003560

Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment

Kirill Serkh, Daniel B. Forger

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003523

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoît Roux

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003521

The Spatial Resolution of Epidemic Peaks

Harriet L. Mills, Steven Riley

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003561

Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex

Yunqiang Bian, Cheng Tan, Jun Wang, Yuebiao Sheng, Jian Zhang, Wei Wang

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003562

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Paul J. McMurdie, Susan Holmes

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003531

Chemical, Target, and Bioactive Properties of Allosteric Modulation

Gerard J. P. van Westen, Anna Gaulton, John P. Overington

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003559

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

Bram Vrancken, Andrew Rambaut, Marc A. Suchard, Alexei Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, Philippe Lemey

PLOS Computational Biology: published April 3, 2014 | https://doi.org/10.1371/journal.pcbi.1003505

Sensing Membrane Stresses by Protein Insertions

Felix Campelo, Michael M. Kozlov

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003556

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003537

Biophysical Properties of Intrinsically Disordered p130Cas Substrate Domain — Implication in Mechanosensing

Kinya Hotta, Soumya Ranganathan, Ruchuan Liu, Fei Wu, Hiroaki Machiyama, Rong Gao, Hiroaki Hirata, Neelesh Soni, Takashi Ohe, Christopher W. V. Hogue, M. S. Madhusudhan, Yasuhiro Sawada

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003532

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, Nicolas Foloppe, A. Beatriz Garmendia-Doval, Szilveszter Juhos, Peter Schmidtke, Xavier Barril, Roderick E. Hubbard, S. David Morley

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003571

A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation

Thomas D. Cuypers, Paulien Hogeweg

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003547

Active Learning to Understand Infectious Disease Models and Improve Policy Making

Lander Willem, Sean Stijven, Ekaterina Vladislavleva, Jan Broeckhove, Philippe Beutels, Niel Hens

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003563

Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers

ManChon U, Eric Talevich, Samiksha Katiyar, Khaled Rasheed, Natarajan Kannan

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003545

Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells

Bailu Si, Sandro Romani, Misha Tsodyks

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003558

Phylogenetic Quantification of Intra-tumour Heterogeneity

Roland F. Schwarz, Anne Trinh, Botond Sipos, James D. Brenton, Nick Goldman, Florian Markowetz

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003535

Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study

Laetitia Canini, Jessica M. Conway, Alan S. Perelson, Fabrice Carrat

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003568

Timing of Neuropeptide Coupling Determines Synchrony and Entrainment in the Mammalian Circadian Clock

Bharath Ananthasubramaniam, Erik D. Herzog, Hanspeter Herzel

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003565

Phylodynamic Inference for Structured Epidemiological Models

David A. Rasmussen, Erik M. Volz, Katia Koelle

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003570

Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time

David J. McIver, John S. Brownstein

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003581

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors

Lars Boukharta, Hugo Gutiérrez-de-Terán, Johan Åqvist

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003585

Evolutionary Game Dynamics in Populations with Heterogenous Structures

Wes Maciejewski, Feng Fu, Christoph Hauert

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003567

A Toolbox for Representational Similarity Analysis

Hamed Nili, Cai Wingfield, Alexander Walther, Li Su, William Marslen-Wilson, Nikolaus Kriegeskorte

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003553

Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals

Robert Brown, Bogdan Pasaniuc

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003555

Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin

Qing-Miao Nie, Akio Togashi, Takeshi N. Sasaki, Mitsunori Takano, Masaki Sasai, Tomoki P. Terada

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003552

How the Brain Decides When to Work and When to Rest: Dissociation of Implicit-Reactive from Explicit-Predictive Computational Processes

Florent Meyniel, Lou Safra, Mathias Pessiglione

PLOS Computational Biology: published April 17, 2014 | https://doi.org/10.1371/journal.pcbi.1003584

Mechanisms of Zero-Lag Synchronization in Cortical Motifs

Leonardo L. Gollo, Claudio Mirasso, Olaf Sporns, Michael Breakspear

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003548

A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations

Vincent Frappier, Rafael J. Najmanovich

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003569

Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method

Ke Tang, Jinfeng Zhang, Jie Liang

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003539

Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes

Aleksej Zelezniak, Steven Sheridan, Kiran Raosaheb Patil

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003572

Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

Daniel Machado, Markus Herrgård

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003580

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens

Adam M. Feist, Harish Nagarajan, Amelia-Elena Rotaru, Pier-Luc Tremblay, Tian Zhang, Kelly P. Nevin, Derek R. Lovley, Karsten Zengler

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003575

Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model

Matteo Farinella, Daniel T. Ruedt, Padraig Gleeson, Frederic Lanore, R. Angus Silver

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003590

Knowledge-based Fragment Binding Prediction

Grace W. Tang, Russ B. Altman

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003589

Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis

Thomas Walenda, Thomas Stiehl, Hanna Braun, Julia Fröbel, Anthony D. Ho, Thomas Schroeder, Tamme W. Goecke, Björn Rath, Ulrich Germing, Anna Marciniak-Czochra, Wolfgang Wagner

PLOS Computational Biology: published April 24, 2014 | https://doi.org/10.1371/journal.pcbi.1003599

Correction: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson’s Leukocytes Identified by RNA Sequencing

The PLOS Computational Biology Staff

PLOS Computational Biology: published May 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003647

Cover

Computer-based multi-client game for investigating human group movement.

Editorial

Message from ISCB

Education

Perspective

Review

Research Articles

Related Articles

Related Articles

Related Articles

Related Articles

Related Articles

Related Articles

Related Articles

Related Articles

Corrections

Related Articles

Related Articles

Related Articles

Related Articles