Table of Contents: April 2014


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

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

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.


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

Message from ISCB


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

Mechanisms of Zero-Lag Synchronization in Cortical Motifs

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

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

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

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

Knowledge-based Fragment Binding Prediction

Grace W. Tang, Russ B. Altman

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

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

Phylogenetic Quantification of Intra-tumour Heterogeneity

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

A Toolbox for Representational Similarity Analysis

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

Active Learning to Understand Infectious Disease Models and Improve Policy Making

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

Phylodynamic Inference for Structured Epidemiological Models

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

Dynamics of Cellular Responses to Radiation

Dominik Wodarz, Ron Sorace, Natalia L. Komarova

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

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

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

The Evolution of Multivariate Maternal Effects

Bram Kuijper, Rufus A. Johnstone, Stuart Townley

Sensing Membrane Stresses by Protein Insertions

Felix Campelo, Michael M. Kozlov

Spike-Threshold Adaptation Predicted by Membrane Potential Dynamics In Vivo

Bertrand Fontaine, José Luis Peña, Romain Brette

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

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

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

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

Rates of CTL Killing in Persistent Viral Infection In Vivo

Marjet Elemans, Arnaud Florins, Luc Willems, Becca Asquith

Leadership in Moving Human Groups

Margarete Boos, Johannes Pritz, Simon Lange, Michael Belz

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

Chemical, Target, and Bioactive Properties of Allosteric Modulation

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