Ten Simple Rules for Writing a PLOS Ten Simple Rules Article

Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003858

Establishing and Managing a Global Student Network

Avinash Shanmugam, Geoff Macintyre

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003920

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

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003849

Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle

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

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003857

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Synaptic Size Dynamics as an Effectively Stochastic Process

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

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003846

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Tanggis Bohnuud, Dima Kozakov, Sandor Vajda

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003872

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

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003843

Resolving Anatomical and Functional Structure in Human Brain Organization: Identifying Mesoscale Organization in Weighted Network Representations

Christian Lohse, Danielle S. Bassett, Kelvin O. Lim, Jean M. Carlson

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003712

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

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003835

Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity

David Higgins, Michael Graupner, Nicolas Brunel

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003834

Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups

Amos Korman, Efrat Greenwald, Ofer Feinerman

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003862

Expression Profile of the Schistosoma japonicum Degradome Reveals Differential Protease Expression Patterns and Potential Anti-schistosomal Intervention Targets

Shuai Liu, Pengfei Cai, Xianyu Piao, Nan Hou, Xiaosu Zhou, Chuang Wu, Heng Wang, Qijun Chen

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003856

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

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

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003865

Improving Contact Prediction along Three Dimensions

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

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003847

A Model for Sigma Factor Competition in Bacterial Cells

Marco Mauri, Stefan Klumpp

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003845

Hydrophobic Compounds Reshape Membrane Domains

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

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003873

Exploring the miRNA Regulatory Network Using Evolutionary Correlations

Benedikt Obermayer, Erel Levine

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003860

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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

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003874

In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells

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

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003839

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

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003863

Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks

Inhae Kim, Heetak Lee, Seong Kyu Han, Sanguk Kim

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003881

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

PLOS Computational Biology: published October 2, 2014 | https://doi.org/10.1371/journal.pcbi.1003866

Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle

Mary Hongying Cheng, Ivet Bahar

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003879

Reconstruction of the Gene Regulatory Network Involved in the Sonic Hedgehog Pathway with a Potential Role in Early Development of the Mouse Brain

Jinhua Liu, Xuelong Wang, Juan Li, Haifang Wang, Gang Wei, Jun Yan

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003884

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

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003877

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Reactive Searching and Infotaxis in Odor Source Localization

Nicole Voges, Antoine Chaffiol, Philippe Lucas, Dominique Martinez

PLOS Computational Biology: published October 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003861

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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

PLOS Computational Biology: published October 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003887

Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery

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

PLOS Computational Biology: published October 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003876

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

PLOS Computational Biology: published October 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003882

Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections

Frédéric Crevecoeur, Stephen H. Scott

PLOS Computational Biology: published October 9, 2014 | https://doi.org/10.1371/journal.pcbi.1003869

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Linking Myometrial Physiology to Intrauterine Pressure; How Tissue-Level Contractions Create Uterine Contractions of Labor

Roger C. Young, Peter Barendse

PLOS Computational Biology: published October 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003850

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

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

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003867

Predicting Chemical Environments of Bacteria from Receptor Signaling

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

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003870

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

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

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003871

Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia

Yue Li, Minggao Liang, Zhaolei Zhang

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003908

Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance

François Bertaux, Szymon Stoma, Dirk Drasdo, Gregory Batt

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003893

Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos

Bahman Nasseroleslami, Christopher J. Hasson, Dagmar Sternad

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003900

Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers

Heidi Koldsø, David Shorthouse, Jean Hélie, Mark S. P. Sansom

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003911

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

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003895

A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method

Seth D. Axen, Onur Erbilgin, Cheryl A. Kerfeld

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003898

Linking Macroscopic with Microscopic Neuroanatomy Using Synthetic Neuronal Populations

Calvin J. Schneider, Hermann Cuntz, Ivan Soltesz

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003921

Glycolysis Is Governed by Growth Regime and Simple Enzyme Regulation in Adherent MDCK Cells

Markus Rehberg, Joachim B. Ritter, Udo Reichl

PLOS Computational Biology: published October 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003885

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

Kei Moritsugu, Tohru Terada, Akinori Kidera

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003901

Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment

Robert Legenstein, Wolfgang Maass

PLOS Computational Biology: published October 23, 2014 | https://doi.org/10.1371/journal.pcbi.1003859

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

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003890

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

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

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003909

Estimating Location without External Cues

Allen Cheung

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003927

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations

Hai Fang

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003929

The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations

Rebecca Batorsky, Rinat A. Sergeev, Igor M. Rouzine

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003878

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

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003910

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

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003907

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

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003912

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

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

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003797

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FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units

Gang Peng, Yu Fan, Wenyi Wang

PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003880

Correction: Inferring on the Intentions of Others by Hierarchical Bayesian Learning

The PLOS Computational Biology Staff

PLOS Computational Biology: published October 16, 2014 | https://doi.org/10.1371/journal.pcbi.1003952

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Correction: Environmental Statistics and Optimal Regulation

The PLOS Computational Biology Staff

PLOS Computational Biology: published October 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003978

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Correction: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism

The PLOS Computational Biology Staff

PLOS Computational Biology: published October 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003989

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Correction: Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections

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PLOS Computational Biology: published October 30, 2014 | https://doi.org/10.1371/journal.pcbi.1003996

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