Ten Simple Rules for Starting a Regional Student Group

Avinash Kumar Shanmugam, Geoff Macintyre, Magali Michaut, Thomas Abeel

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003340

Learning How to Run a Lab: Interviews with Principal Investigators

Theodore Alexandrov, Philip E. Bourne

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003349

Breaking the Ice and Forging Links: The Importance of Socializing in Research

Miranda Stobbe, Tarun Mishra, Geoff Macintyre

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003355

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003326

Ten Quick Tips for Using the Gene Ontology

Judith A. Blake

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003343

About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium

Lennart Martens

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003332

Leading a Statistical Bioinformatics Lab: It's All About Finding Balance

Olga Vitek

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003333

The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013

Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P. Satagopam, Manuel Corpas, Geoff Macintyre, Theodore Alexandrov

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003350

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK

Peter Man-Un Ung, Andrea D. Thompson, Lyra Chang, Jason E. Gestwicki, Heather A. Carlson

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003279

Cell-Based Multi-Parametric Model of Cleft Progression during Submandibular Salivary Gland Branching Morphogenesis

Shayoni Ray, Daniel Yuan, Nimit Dhulekar, Basak Oztan, Bülent Yener, Melinda Larsen

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003319

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale

Nickolay A. Khazanov, Heather A. Carlson

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003321

A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions

Xiaoxia Wang, Sarada Panchanathan, Gerardo Chowell

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003328

A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection

Luca Albergante, Jon Timmis, Lynette Beattie, Paul M. Kaye

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003334

Dread and the Disvalue of Future Pain

Giles W. Story, Ivaylo Vlaev, Ben Seymour, Joel S. Winston, Ara Darzi, Raymond J. Dolan

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003335

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Genetic Architecture Promotes the Evolution and Maintenance of Cooperation

Antoine Frénoy, François Taddei, Dusan Misevic

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003339

Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data

Weronika Sikora-Wohlfeld, Marit Ackermann, Eleni G. Christodoulou, Kalaimathy Singaravelu, Andreas Beyer

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003342

Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of Macroevolution

Erez Persi, David Horn

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003346

MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms

Rotem Ben-Hamo, Sol Efroni

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003351

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

Guillem Portella, Federica Battistini, Modesto Orozco

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003354

Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification

Lucas Theis, Andrè Maia Chagas, Daniel Arnstein, Cornelius Schwarz, Matthias Bethge

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003356

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks

Takeshi Hase, Samik Ghosh, Ryota Yamanaka, Hiroaki Kitano

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003361

Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins

Debabani Ganguly, Weihong Zhang, Jianhan Chen

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003363

Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals

Frank S. Heldt, Timo Frensing, Antje Pflugmacher, Robin Gröpler, Britta Peschel, Udo Reichl

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003372

Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution

Tobias Warnecke, Erin A. Becker, Marc T. Facciotti, Corey Nislow, Ben Lehner

PLOS Computational Biology: published November 21, 2013 | https://doi.org/10.1371/journal.pcbi.1003373

Predictive Coding of Dynamical Variables in Balanced Spiking Networks

Martin Boerlin, Christian K. Machens, Sophie Denève

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003258

A Tunable Coarse-Grained Model for Ligand-Receptor Interaction

Teresa Ruiz-Herrero, Javier Estrada, Raúl Guantes, David G. Miguez

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003274

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Evidence for Finely-Regulated Asynchronous Growth of Toxoplasma gondii Cysts Based on Data-Driven Model Selection

Adam M. Sullivan, Xiaopeng Zhao, Yasuhiro Suzuki, Eri Ochiai, Stephen Crutcher, Michael A. Gilchrist

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003283

Dynamical Adaptation in Photoreceptors

Damon A. Clark, Raphael Benichou, Markus Meister, Rava Azeredo da Silveira

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003289

In Silico Analysis of Cell Cycle Synchronisation Effects in Radiotherapy of Tumour Spheroids

Harald Kempf, Haralampos Hatzikirou, Marcus Bleicher, Michael Meyer-Hermann

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003295

Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations

Noa Chapal-Ilani, Yosef E. Maruvka, Adam Spiro, Yitzhak Reizel, Rivka Adar, Liran I. Shlush, Ehud Shapiro

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003297

Receptor Concentration and Diffusivity Control Multivalent Binding of Sv40 to Membrane Bilayers

Oliwia M. Szklarczyk, Nélido González-Segredo, Philipp Kukura, Ariella Oppenheim, Daniel Choquet, Vahid Sandoghdar, Ari Helenius, Ivo F. Sbalzarini, Helge Ewers

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003310

Stochastic Computations in Cortical Microcircuit Models

Stefan Habenschuss, Zeno Jonke, Wolfgang Maass

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003311

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Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

Noah Ollikainen, Tanja Kortemme

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003313

Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells

Kazunari Mouri, Yasushi Sako

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003320

Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli

Alex Dickson, Charles L. Brooks III

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003324

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

Hannah Edwards, Sanne Abeln, Charlotte M. Deane

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003325

Synaptic Plasticity in Neural Networks Needs Homeostasis with a Fast Rate Detector

Friedemann Zenke, Guillaume Hennequin, Wulfram Gerstner

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003330

Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

Guido Polles, Giuliana Indelicato, Raffaello Potestio, Paolo Cermelli, Reidun Twarock, Cristian Micheletti

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003331

Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code

Christophe Micheyl, Paul R. Schrater, Andrew J. Oxenham

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003336

Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein

Davi R. Ortega, Guoya Mo, Kwangwoon Lee, Hongjun Zhou, Jerome Baudry, Frederick W. Dahlquist, Igor B. Zhulin

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003337

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

Janez Konc, Milan Hodošček, Mitja Ogrizek, Joanna Trykowska Konc, Dušanka Janežič

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003341

Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos

Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Christian Kramer, Klaus R. Liedl

PLOS Computational Biology: published November 14, 2013 | https://doi.org/10.1371/journal.pcbi.1003353

Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations

Murat Çetinbaş, Eugene I. Shakhnovich

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003269

Communication and Common Interest

Peter Godfrey-Smith, Manolo Martínez

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003282

A Neurocomputational Model of the Mismatch Negativity

Falk Lieder, Klaas E. Stephan, Jean Daunizeau, Marta I. Garrido, Karl J. Friston

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003288

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A Computational Model of Liver Iron Metabolism

Simon Mitchell, Pedro Mendes

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003299

Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations

Jakob J. Metzger, Stephan Eule

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003303

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay Nakhleh

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003306

Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon

Denis Valle, James Clark

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003312

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data

Ridvan Eksi, Hong-Dong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003314

Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity

Kejian Wang, Jiazhi Sun, Shufeng Zhou, Chunling Wan, Shengying Qin, Can Li, Lin He, Lun Yang

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003315

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Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell

Varun B. Kothamachu, Elisenda Feliu, Carsten Wiuf, Luca Cardelli, Orkun S. Soyer

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003322

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response

Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003323

Mapping the Structural and Dynamical Features of Kinesin Motor Domains

Guido Scarabelli, Barry J. Grant

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003329

Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance

Biyu J. He, John M. Zempel

PLOS Computational Biology: published November 7, 2013 | https://doi.org/10.1371/journal.pcbi.1003348