August 2014

Animal groups, such as the starling murmuration (Sturnus vulgaris) shown here, must frequently make consensus decisions. These collective decisions may be based on various environmental cues that individuals in the group observe, and these individual opinions must be integrated into a collective decision through movement dynamics. Associative learning, which is ubiquitous across animal taxa, can alter the degree to which group members rely on particular cues. The learned behavior can differ dramatically when learning within a group context compared to learning in isolation, which can lead to substantially enhanced collective wisdom. See Kao et al.

Image Credit: Albert Kao

Editorials

Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era

Qiang Cui, Ruth Nussinov

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003786

Ten Simple Rules of Live Tweeting at Scientific Conferences

Sean Ekins, Ethan O. Perlstein

PLOS Computational Biology: published August 21, 2014 | https://doi.org/10.1371/journal.pcbi.1003789

Message from ISCB

The Upside of Failure: How Regional Student Groups Learn from Their Mistakes

Tarun Mishra, R. Gonzalo Parra, Thomas Abeel

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003768

Research Articles

Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study

Bernhard Knapp, James Dunbar, Charlotte M. Deane

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003748

Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes

Alex H. Lang, Hu Li, James J. Collins, Pankaj Mehta

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003734

Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images

Umut Güçlü, Marcel A. J. van Gerven

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003724

Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus

Nik J. Cunniffe, Francisco F. Laranjeira, Franco M. Neri, R. Erik DeSimone, Christopher A. Gilligan

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003753

Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment

Johannes Textor, Sarah E. Henrickson, Judith N. Mandl, Ulrich H. von Andrian, Jürgen Westermann, Rob J. de Boer, Joost B. Beltman

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003752

A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis

Jessica M. Conway, Alan S. Perelson

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003769

A Micellar On-Pathway Intermediate Step Explains the Kinetics of Prion Amyloid Formation

Erwan Hingant, Pascaline Fontes, Maria Teresa Alvarez-Martinez, Jacques-Damien Arnaud, Jean-Pierre Liautard, Laurent Pujo-Menjouet

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003735

Phenotypic Signatures Arising from Unbalanced Bacterial Growth

Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003751

Collective Learning and Optimal Consensus Decisions in Social Animal Groups

Albert B. Kao, Noam Miller, Colin Torney, Andrew Hartnett, Iain D. Couzin

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003762

Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque

Fang-Chieh Chou, Jan Lipfert, Rhiju Das

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003756

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

Jaclyn K. Mann, John P. Barton, Andrew L. Ferguson, Saleha Omarjee, Bruce D. Walker, Arup Chakraborty, Thumbi Ndung'u

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003776

SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

Christopher A. Miller, Brian S. White, Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, Matthew J. Ellis, William Schierding, John F. DiPersio, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003665

Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis

Shuo Gu, Daniel-Adriano Silva, Luming Meng, Alexander Yue, Xuhui Huang

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003767

Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment

Eric L. Haseltine, Sandra De Meyer, Inge Dierynck, Doug J. Bartels, Anne Ghys, Andrew Davis, Eileen Z. Zhang, Ann M. Tigges, Joan Spanks, Gaston Picchio, Tara L. Kieffer, James C. Sullivan

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003772

Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions

Kanghoon Jung, Hyeran Jang, Jerald D. Kralik, Jaeseung Jeong

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003759

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

Yuan Zhang, Yanni Sun, James R. Cole

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003737

Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells

Huilei Xu, Yen-Sin Ang, Ana Sevilla, Ihor R. Lemischka, Avi Ma'ayan

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003777

A Simple Model of Optimal Population Coding for Sensory Systems

Eizaburo Doi, Michael S. Lewicki

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003761

Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro

René F. M. van Oers, Elisabeth G. Rens, Danielle J. LaValley, Cynthia A. Reinhart-King, Roeland M. H. Merks

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003774

A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells

Pengxing Cao, Xiahui Tan, Graham Donovan, Michael J. Sanderson, James Sneyd

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003783

Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes

Anne-Florence Bitbol, David J. Schwab

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003778

Memory Capacity of Networks with Stochastic Binary Synapses

Alexis M. Dubreuil, Yali Amit, Nicolas Brunel

PLOS Computational Biology: published August 7, 2014 | https://doi.org/10.1371/journal.pcbi.1003727

Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks

Dov A. Pechenick, Joshua L. Payne, Jason H. Moore

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003780

Top-Down Inputs Enhance Orientation Selectivity in Neurons of the Primary Visual Cortex during Perceptual Learning

Samat Moldakarimov, Maxim Bazhenov, Terrence J. Sejnowski

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003770

Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens

Delphine Pessoa, Caetano Souto-Maior, Erida Gjini, Joao S. Lopes, Bruno Ceña, Cláudia T. Codeço, M. Gabriela M. Gomes

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003773

Optimal Behavioral Hierarchy

Alec Solway, Carlos Diuk, Natalia Córdova, Debbie Yee, Andrew G. Barto, Yael Niv, Matthew M. Botvinick

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003779

Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection

Miri Adler, Avi Mayo, Uri Alon

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003781

Kinetic Memory Based on the Enzyme-Limited Competition

Tetsuhiro S. Hatakeyama, Kunihiko Kaneko

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003784

MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis

Seungyeul Yoo, Tao Huang, Joshua D. Campbell, Eunjee Lee, Zhidong Tu, Mark W. Geraci, Charles A. Powell, Eric E. Schadt, Avrum Spira, Jun Zhu

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003790

The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage

Peter T. McHale, Arthur D. Lander

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003802

Dynamic Mechanisms of Neocortical Focal Seizure Onset

Yujiang Wang, Marc Goodfellow, Peter Neal Taylor, Gerold Baier

PLOS Computational Biology: published August 14, 2014 | https://doi.org/10.1371/journal.pcbi.1003787

Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework

Ken Daigoro Yokoyama, Yang Zhang, Jian Ma

PLOS Computational Biology: published August 21, 2014 | https://doi.org/10.1371/journal.pcbi.1003771

Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions

Piero Dalle Pezze, Glyn Nelson, Elsje G. Otten, Viktor I. Korolchuk, Thomas B. L. Kirkwood, Thomas von Zglinicki, Daryl P. Shanley

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003728

A New Model for Pore Formation by Cholesterol-Dependent Cytolysins

Cyril F. Reboul, James C. Whisstock, Michelle A. Dunstone

PLOS Computational Biology: published August 21, 2014 | https://doi.org/10.1371/journal.pcbi.1003791

Sparsity and Compressed Coding in Sensory Systems

Victor J. Barranca, Gregor Kovačič, Douglas Zhou, David Cai

PLOS Computational Biology: published August 21, 2014 | https://doi.org/10.1371/journal.pcbi.1003793

Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography

Xiakun Chu, Jin Wang

PLOS Computational Biology: published August 21, 2014 | https://doi.org/10.1371/journal.pcbi.1003782

VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials

Brian Y. Chen

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003792

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model

Andries J. van Tonder, Shilan Mistry, James E. Bray, Dorothea M. C. Hill, Alison J. Cody, Chris L. Farmer, Keith P. Klugman, Anne von Gottberg, Stephen D. Bentley, Julian Parkhill, Keith A. Jolley, Martin C. J. Maiden, Angela B. Brueggemann

PLOS Computational Biology: published August 21, 2014 | https://doi.org/10.1371/journal.pcbi.1003788

Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism

Rui Xia, Selina Vattathil, Paul Scheet

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003765

Spatially Distributed Dendritic Resonance Selectively Filters Synaptic Input

Jonathan Laudanski, Benjamin Torben-Nielsen, Idan Segev, Shihab Shamma

PLOS Computational Biology: published August 21, 2014 | https://doi.org/10.1371/journal.pcbi.1003775

Possible Role of Interleukin-1β in Type 2 Diabetes Onset and Implications for Anti-inflammatory Therapy Strategies

Gang Zhao, Gitanjali Dharmadhikari, Kathrin Maedler, Michael Meyer-Hermann

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003798

Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth

Sébastien Benzekry, Clare Lamont, Afshin Beheshti, Amanda Tracz, John M. L. Ebos, Lynn Hlatky, Philip Hahnfeldt

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003800

Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network

Frantisek Honti, Stephen Meader, Caleb Webber

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003815

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003806

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

Geir Villy Isaksen, Johan Åqvist, Bjørn Olav Brandsdal

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003813

Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution

Priscilla Ambrosi, Juan Sebastian Chahda, Hannah R. Koslen, Hillel J. Chiel, Claudia Mieko Mizutani

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003807

Communication through Resonance in Spiking Neuronal Networks

Gerald Hahn, Alejandro F. Bujan, Yves Frégnac, Ad Aertsen, Arvind Kumar

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003811

Corrections

Correction: Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks

The PLOS Computational Biology Staff

PLOS Computational Biology: published August 11, 2014 | https://doi.org/10.1371/journal.pcbi.1003816

Correction: The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation

The PLOS Computational Biology Staff

PLOS Computational Biology: published August 8, 2014 | https://doi.org/10.1371/journal.pcbi.1003832

Correction: A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction

The PLOS Computational Biology Staff

PLOS Computational Biology: published August 28, 2014 | https://doi.org/10.1371/journal.pcbi.1003864

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

The PLOS Computational Biology Staff

PLOS Computational Biology: published August 29, 2014 | https://doi.org/10.1371/journal.pcbi.1003868

Cover

Using a model of collective learning to understand how individual learning affects consensus group decisions.

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