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Table of Contents: March 2012

COVER

Nerve cell on worn paper.

Image Credit: Dimitrios V. Vavoulis and Volko A. Straub, the Universities of Warwick and Leicester, United Kingdom, 2012.
Issue Image

This image illustrates a B4 neuron from the mollusk Lymnaea stagnalis on a background of mathematical expressions, simulation data, and binary digits, which represent the implicit assumption that nervous systems can be modeled and simulated in a digital computer. In this issue, Vavoulis et al. (10.1371/journal.pcbi.1002401) present a method for estimating dynamic states and parameters in data-driven models of neurons and neural networks based on principles of Bayesian statistics and Sequential Monte Carlo simulation.

Editorials

Ten Simple Rules for Starting a Company

Anthony C. Fletcher, Philip E. Bourne

Topic Pages: PLoS Computational Biology Meets Wikipedia

Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne

Education

Topic Page

Circular Permutation in Proteins

Spencer Bliven, Andreas Prlić

Research Articles

Collective Dynamics Differentiates Functional Divergence in Protein Evolution

Tyler J. Glembo, Daniel W. Farrell, Z. Nevin Gerek, M. F. Thorpe, S. Banu Ozkan

Comprehensive Modelling of the Neurospora Circadian Clock and Its Temperature Compensation

Yu-Yao Tseng, Suzanne M. Hunt, Christian Heintzen, Susan K. Crosthwaite, Jean-Marc Schwartz

Impact of Network Structure and Cellular Response on Spike Time Correlations

James Trousdale, Yu Hu, Eric Shea-Brown, Krešimir Josić

Hemodynamic Traveling Waves in Human Visual Cortex

Kevin M. Aquino, Mark M. Schira, P. A. Robinson, Peter M. Drysdale, Michael Breakspear

Dynamic Effective Connectivity of Inter-Areal Brain Circuits

Demian Battaglia, Annette Witt, Fred Wolf, Theo Geisel

Traffic Instabilities in Self-Organized Pedestrian Crowds

Mehdi Moussaïd, Elsa G. Guillot, Mathieu Moreau, Jérôme Fehrenbach, Olivier Chabiron, Samuel Lemercier, Julien Pettré, Cécile Appert-Rolland, Pierre Degond, Guy Theraulaz

Cell Shape Dynamics: From Waves to Migration

Meghan K. Driscoll, Colin McCann, Rael Kopace, Tess Homan, John T. Fourkas, Carole Parent, Wolfgang Losert

AutoClickChem: Click Chemistry in Silico

Jacob D. Durrant, J. Andrew McCammon

Network Evolution: Rewiring and Signatures of Conservation in Signaling

Mark G. F. Sun, Martin Sikora, Michael Costanzo, Charles Boone, Philip M. Kim

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

Alexander R. Macalalad, Michael C. Zody, Patrick Charlebois, Niall J. Lennon, Ruchi M. Newman, Christine M. Malboeuf, Elizabeth M. Ryan, Christian L. Boutwell, Karen A. Power, Doug E. Brackney, Kendra N. Pesko, Joshua Z. Levin, Gregory D. Ebel, Todd M. Allen, Bruce W. Birren, Matthew R. Henn

The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation

Ying-Ying Jiang, De-Xin Kong, Tao Qin, Xiao Li, Gustavo Caetano-Anollés, Hong-Yu Zhang

Entropic Tension in Crowded Membranes

Martin Lindén, Pierre Sens, Rob Phillips

Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex

Cyril F. Reboul, Grischa R. Meyer, Benjamin T. Porebski, Natalie A. Borg, Ashley M. Buckle

Bonsai Trees in Your Head: How the Pavlovian System Sculpts Goal-Directed Choices by Pruning Decision Trees

Quentin J. M. Huys, Neir Eshel, Elizabeth O'Nions, Luke Sheridan, Peter Dayan, Jonathan P. Roiser

Inferring Epidemic Contact Structure from Phylogenetic Trees

Gabriel E. Leventhal, Roger Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer

Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?

Carlos J. Melián, David Alonso, Stefano Allesina, Richard S. Condit, Rampal S. Etienne

Mitochondrial Variability as a Source of Extrinsic Cellular Noise

Iain G. Johnston, Bernadett Gaal, Ricardo Pires das Neves, Tariq Enver, Francisco J. Iborra, Nick S. Jones

Ensemble Models of Neutrophil Trafficking in Severe Sepsis

Sang O. K. Song, Justin Hogg, Zhi-Yong Peng, Robert Parker, John A. Kellum, Gilles Clermont

Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria

David M. Richards, Antje M. Hempel, Klas Flärdh, Mark J. Buttner, Martin Howard

Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza

Ken T. D. Eames, Natasha L. Tilston, Ellen Brooks-Pollock, W. John Edmunds

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

Stefan J. Jol, Anne Kümmel, Marco Terzer, Jörg Stelling, Matthias Heinemann

Living on Three Time Scales: The Dynamics of Plasma Cell and Antibody Populations Illustrated for Hepatitis A Virus

Mathieu Andraud, Olivier Lejeune, Jammbe Z. Musoro, Benson Ogunjimi, Philippe Beutels, Niel Hens