Table of Contents: 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.


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

Messages from ISCB

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

Christiana N. Fogg, Diane E. Kovats

Education Articles

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


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


The Influence of Spatiotemporal Structure of Noisy Stimuli in Decision Making

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

Research Articles

Rates of CTL Killing in Persistent Viral Infection In Vivo

Marjet Elemans, Arnaud Florins, Luc Willems, Becca Asquith

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

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Leadership in Moving Human Groups

Margarete Boos, Johannes Pritz, Simon Lange, Michael Belz

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

David Samu, Anil K. Seth, Thomas Nowotny

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

Dynamics of Cellular Responses to Radiation

Dominik Wodarz, Ron Sorace, Natalia L. Komarova

The Evolution of Multivariate Maternal Effects

Bram Kuijper, Rufus A. Johnstone, Stuart Townley

Spike-Threshold Adaptation Predicted by Membrane Potential Dynamics In Vivo

Bertrand Fontaine, José Luis Peña, Romain Brette

Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment

Kirill Serkh, Daniel B. Forger

The Spatial Resolution of Epidemic Peaks

Harriet L. Mills, Steven Riley

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

Chemical, Target, and Bioactive Properties of Allosteric Modulation

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

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

Sensing Membrane Stresses by Protein Insertions

Felix Campelo, Michael M. Kozlov

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

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

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

Active Learning to Understand Infectious Disease Models and Improve Policy Making

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

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

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

Bailu Si, Sandro Romani, Misha Tsodyks

Phylogenetic Quantification of Intra-tumour Heterogeneity

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

Related Articles

  1. New Methods Section in PLOS Computational Biology

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

Bharath Ananthasubramaniam, Erik D. Herzog, Hanspeter Herzel

Phylodynamic Inference for Structured Epidemiological Models

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

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

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

Evolutionary Game Dynamics in Populations with Heterogenous Structures

Wes Maciejewski, Feng Fu, Christoph Hauert

A Toolbox for Representational Similarity Analysis

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

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

Mechanisms of Zero-Lag Synchronization in Cortical Motifs

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

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

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

Knowledge-based Fragment Binding Prediction

Grace W. Tang, Russ B. Altman

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

Bayesian Analysis for Inference of an Emerging Epidemic: Citrus Canker in Urban Landscapes

Franco M. Neri, Alex R. Cook, Gavin J. Gibson, Tim R. Gottwald, Christopher A. Gilligan

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

Thomas S. B. Schmidt, João F. Matias Rodrigues, Christian von Mering

Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli

Hao Bai, Matthew D. Rolfe, Wenjing Jia, Simon Coakley, Robert K. Poole, Jeffrey Green, Mike Holcombe