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Table of Contents: November 2012

COVER

Snapshot of the virtual coral reef patch (top view).

Image Credit: Andreas Kubicek, Leibniz Center for Tropical Marine Ecology.
Issue Image

The simulation of small-scale processes allows the analysis of ecosystem responses to environmental change. Colonies of two massive (polygons) and two branching (stars) coral species compete for space with each other and algae (macroalgae as green spots; turf algae as grid). Higher level properties, such as population dynamics and community composition, emerge from local interactions of neighboring organisms, which are additionally influenced by environmental conditions. See Kubicek et al.

Editorials

Ten Simple Rules to Protect Your Intellectual Property

Mark Jolly, Anthony C. Fletcher, Philip E. Bourne

Perspective

Bioinformatics for the Human Microbiome Project

Dirk Gevers, Mihai Pop, Patrick D. Schloss, Curtis Huttenhower

Research Articles

Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle

Yihan Lin, Ying Li, Sean Crosson, Aaron R. Dinner, Norbert F. Scherer

Temporal Expression-based Analysis of Metabolism

Sara B. Collins, Ed Reznik, Daniel Segrè

Universal Pacemaker of Genome Evolution

Sagi Snir, Yuri I. Wolf, Eugene V. Koonin

Weakly Circadian Cells Improve Resynchrony

Alexis B. Webb, Stephanie R. Taylor, Kurt A. Thoroughman, Francis J. Doyle III, Erik D. Herzog

Reconstructing Mammalian Sleep Dynamics with Data Assimilation

Madineh Sedigh-Sarvestani, Steven J. Schiff, Bruce J. Gluckman

Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens

Renske M. A. Vroomans, Athanasius F. M. Marée, Rob J. de Boer, Joost B. Beltman

A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data

Marco J. Morelli, Gaël Thébaud, Joël Chadœuf, Donald P. King, Daniel T. Haydon, Samuel Soubeyrand

Sensorimotor Learning Biases Choice Behavior: A Learning Neural Field Model for Decision Making

Christian Klaes, Sebastian Schneegans, Gregor Schöner, Alexander Gail

Functional Connectivity and Tuning Curves in Populations of Simultaneously Recorded Neurons

Ian H. Stevenson, Brian M. London, Emily R. Oby, Nicholas A. Sachs, Jacob Reimer, Bernhard Englitz, Stephen V. David, Shihab A. Shamma, Timothy J. Blanche, Kenji Mizuseki, Amin Zandvakili, Nicholas G. Hatsopoulos, Lee E. Miller, Konrad P. Kording

The Dominant Folding Route Minimizes Backbone Distortion in SH3

Heiko Lammert, Jeffrey K. Noel, José N. Onuchic

Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis

Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C. Crowley, Matthias Kaschube, Fred Wolf

Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies

Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C. Crowley, Matthias Kaschube, Fred Wolf

Evolution of Associative Learning in Chemical Networks

Simon McGregor, Vera Vasas, Phil Husbands, Chrisantha Fernando

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

Art F. Y. Poon, Luke C. Swenson, Evelien M. Bunnik, Diana Edo-Matas, Hanneke Schuitemaker, Angélique B. van 't Wout, P. Richard Harrigan

Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network

Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd J. de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin

A Mathematical Model of CR3/TLR2 Crosstalk in the Context of Francisella tularensis Infection

Rachel Leander, Shipan Dai, Larry S. Schlesinger, Avner Friedman

Music in Our Ears: The Biological Bases of Musical Timbre Perception

Kailash Patil, Daniel Pressnitzer, Shihab Shamma, Mounya Elhilali

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

Natali V. Di Russo, Dario A. Estrin, Marcelo A. Martí, Adrian E. Roitberg

Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient

Samuel M. D. Seaver, Marta Sales-Pardo, Roger Guimerà, Luís A. Nunes Amaral