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Table of Contents: October 2014

Editorial

Ten Simple Rules for Writing a PLOS Ten Simple Rules Article

Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne

Message from ISCB

Establishing and Managing a Global Student Network

Avinash Shanmugam, Geoff Macintyre

Perspective

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems

Maxwell L. Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari

Research Articles

Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble

Mary A. Rohrdanz, Wenwei Zheng, Bradley Lambeth, Jocelyne Vreede, Cecilia Clementi

Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices

Munia Amin, Varun B. Kothamachu, Elisenda Feliu, Birgit E. Scharf, Steven L. Porter, Orkun S. Soyer

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling

Stinus Lindgreen, Sinan Uğur Umu, Alicia Sook-Wei Lai, Hisham Eldai, Wenting Liu, Stephanie McGimpsey, Nicole E. Wheeler, Patrick J. Biggs, Nick R. Thomson, Lars Barquist, Anthony M. Poole, Paul P. Gardner

Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro

Sophia Rudorf, Michael Thommen, Marina V. Rodnina, Reinhard Lipowsky

Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root?

Dirk De Vos, Kris Vissenberg, Jan Broeckhove, Gerrit T. S. Beemster

Bistable Forespore Engulfment in Bacillus subtilis by a Zipper Mechanism in Absence of the Cell Wall

Nikola Ojkic, Javier López-Garrido, Kit Pogliano, Robert G. Endres

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, Leonid A. Mirny

Predicting Chemical Environments of Bacteria from Receptor Signaling

Diana Clausznitzer, Gabriele Micali, Silke Neumann, Victor Sourjik, Robert G. Endres

Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells

Christian L. Althaus, Beda Joos, Alan S. Perelson, Huldrych F. Günthard

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant

Paraskevi Gkeka, Thomas Evangelidis, Maria Pavlaki, Vasiliki Lazani, Savvas Christoforidis, Bogos Agianian, Zoe Cournia

Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos

Bahman Nasseroleslami, Christopher J. Hasson, Dagmar Sternad

Reactive Searching and Infotaxis in Odor Source Localization

Nicole Voges, Antoine Chaffiol, Philippe Lucas, Dominique Martinez

Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery

Jose A. Seoane, Colin Campbell, Ian N. M. Day, Juan P. Casas, Tom R. Gaunt

Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

Matthew N. Benedict, Michael B. Mundy, Christopher S. Henry, Nicholas Chia, Nathan D. Price

Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness

Srivas Chennu, Paola Finoia, Evelyn Kamau, Judith Allanson, Guy B. Williams, Martin M. Monti, Valdas Noreika, Aurina Arnatkeviciute, Andrés Canales-Johnson, Francisco Olivares, Daniela Cabezas-Soto, David K. Menon, John D. Pickard, Adrian M. Owen, Tristan A. Bekinschtein

In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells

Roy Malka, Francisco Feijó Delgado, Scott R. Manalis, John M. Higgins

Improving Contact Prediction along Three Dimensions

Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell

The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion

Nicole Dölker, Maria W. Górna, Ludovico Sutto, Antonio S. Torralba, Giulio Superti-Furga, Francesco L. Gervasio

Hydrophobic Compounds Reshape Membrane Domains

Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, Luca Monticelli

Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach

Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holiday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson

Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling

Mariliis Tark-Dame, Hansjoerg Jerabek, Erik M. M. Manders, Dieter W. Heermann, Roel van Driel

Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters

Rafael Tapia-Rojo, Juan José Mazo, José Ángel Hernández, María Luisa Peleato, María F. Fillat, Fernando Falo

Fast Synchronization of Ultradian Oscillators Controlled by Delta-Notch Signaling with Cis-Inhibition

Hendrik B. Tiedemann, Elida Schneltzer, Stefan Zeiser, Wolfgang Wurst, Johannes Beckers, Gerhard K. H. Przemeck, Martin Hrabě de Angelis

Synaptic Size Dynamics as an Effectively Stochastic Process

Adiel Statman, Maya Kaufman, Amir Minerbi, Noam E. Ziv, Naama Brenner

Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle

Andrew J. Fritz, Branislav Stojkovic, Hu Ding, Jinhui Xu, Sambit Bhattacharya, Ronald Berezney

Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis

Nathalie Poupin, François Mariotti, Jean-François Huneau, Dominique Hermier, Hélène Fouillet

Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics

Michael J. Prerau, Katie E. Hartnack, Gabriel Obregon-Henao, Aaron Sampson, Margaret Merlino, Karen Gannon, Matt T. Bianchi, Jeffrey M. Ellenbogen, Patrick L. Purdon

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