Table of Contents: November 2012

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.

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


The PLOS Computational Biology Software Section

Andreas Prlić, Hilmar Lapp

Ten Simple Rules to Protect Your Intellectual Property

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


Bioinformatics for the Human Microbiome Project

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

Research Articles

Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing

Luigi Acerbi, Daniel M. Wolpert, Sethu Vijayakumar

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

Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence

Jessica Nasica-Labouze, Normand Mousseau

Universal Pacemaker of Genome Evolution

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

How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population

Nicolas Perony, Claudio J. Tessone, Barbara König, Frank Schweitzer

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

Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories

Andreas Kubicek, Christopher Muhando, Hauke Reuter

Experimental Studies and Dynamics Modeling Analysis of the Swimming and Diving of Whirligig Beetles (Coleoptera: Gyrinidae)

Zhonghua Xu, Scott C. Lenaghan, Benjamin E. Reese, Xinghua Jia, Mingjun Zhang

Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e

Elisa Cilia, Geerten W. Vuister, Tom Lenaerts

Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles

Gergely Boza, Ádám Kun, István Scheuring, Ulf Dieckmann

This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes

Christian M. Zmasek, Adam Godzik

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

Elastic Energy Storage and Radial Forces in the Myofilament Lattice Depend on Sarcomere Length

C. David Williams, Michael Regnier, Thomas L. Daniel

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

The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors

Biman Jana, Changbong Hyeon, 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

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Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation

Anupam Saxena, Hod Lipson, Francisco J. Valero-Cuevas

Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies

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

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Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach

Yun Lee, Luis Escamilla-Treviño, Richard A. Dixon, Eberhard O. Voit

Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay

Filippo Cacace, Paola Paci, Valerio Cusimano, Alfredo Germani, Lorenzo Farina

Distinct Neurogenomic States in Basal Ganglia Subregions Relate Differently to Singing Behavior in Songbirds

Austin T. Hilliard, Julie E. Miller, Steve Horvath, Stephanie A. White

Evolution of Associative Learning in Chemical Networks

Simon McGregor, Vera Vasas, Phil Husbands, Chrisantha Fernando

Theory on the Coupled Stochastic Dynamics of Transcription and Splice-Site Recognition

Rajamanickam Murugan, Gabriel Kreiman

A Characterization of Scale Invariant Responses in Enzymatic Networks

Maja Skataric, Eduardo D. Sontag

The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains

Márton Münz, Jotun Hein, Philip C. Biggin

Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life

Marc P. Hoeppner, Paul P. Gardner, Anthony M. Poole

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

Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks

Ana Rita Brochado, Sergej Andrejev, Costas D. Maranas, Kiran R. Patil

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

Kailash Patil, Daniel Pressnitzer, Shihab Shamma, Mounya Elhilali

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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

Mesoscopic Model of Actin-Based Propulsion

Jie Zhu, Alex Mogilner

Structural Insights into the Inhibition of Actin-Capping Protein by Interactions with Phosphatidic Acid and Phosphatidylinositol (4,5)-Bisphosphate

Roman Pleskot, Přemysl Pejchar, Viktor Žárský, Christopher J. Staiger, Martin Potocký