Ten Simple Rules for Effective Computational Research

James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David J. Gavaghan, Stephen Emmott, Charlotte Deane

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003506

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies

Lonnie Welch, Fran Lewitter, Russell Schwartz, Cath Brooksbank, Predrag Radivojac, Bruno Gaeta, Maria Victoria Schneider

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003496

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Crossing Borders for Science

Sebastian J. Schultheiss, Joshua SungWoo Yang, Wataru Iwasaki, Shu-Hsi Lin, Angela Jean, Magali Michaut

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003519

If You Can't Measure It, You Can't Manage It

Jean Peccoud

PLOS Computational Biology: published March 20, 2014 | https://doi.org/10.1371/journal.pcbi.1003462

The Rise and Fall of HIV in High-Prevalence Countries: A Challenge for Mathematical Modeling

Nico J. D. Nagelkerke, Paul Arora, Prabhat Jha, Brian Williams, Lyle McKinnon, Sake J. de Vlas

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003459

Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane

Navneet Bung, Meenakshi Pradhan, Harini Srinivasan, Gopalakrishnan Bulusu

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003484

Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell-Driven Cancers

Alexandra Jilkine, Ryan N. Gutenkunst

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003481

Epigenetics Decouples Mutational from Environmental Robustness. Did It Also Facilitate Multicellularity?

Saurabh Gombar, Thomas MacCarthy, Aviv Bergman

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003450

Slowness and Sparseness Have Diverging Effects on Complex Cell Learning

Jörn-Philipp Lies, Ralf M. Häfner, Matthias Bethge

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003468

Universal Count Correction for High-Throughput Sequencing

Tatsunori B. Hashimoto, Matthew D. Edwards, David K. Gifford

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003494

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Bidirectional Control of Absence Seizures by the Basal Ganglia: A Computational Evidence

Mingming Chen, Daqing Guo, Tiebin Wang, Wei Jing, Yang Xia, Peng Xu, Cheng Luo, Pedro A. Valdes-Sosa, Dezhong Yao

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003495

Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars

Partha S. Bhagavatula, Charles Claudianos, Michael R. Ibbotson, Mandyam V. Srinivasan

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003473

Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating

Ramya Gamini, Wei Han, John E. Stone, Klaus Schulten

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003488

Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation

Michael Pargett, Ann E. Rundell, Gregery T. Buzzard, David M. Umulis

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003498

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

Lit-Hsin Loo, Danai Laksameethanasan, Yi-Ling Tung

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003504

Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

Md. Abul Hassan Samee, Saurabh Sinha

PLOS Computational Biology: published March 6, 2014 | https://doi.org/10.1371/journal.pcbi.1003467

Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains

Vladimir Kazeev, Mustafa Khammash, Michael Nip, Christoph Schwab

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003359

Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver

Lars Ole Schwen, Markus Krauss, Christoph Niederalt, Felix Gremse, Fabian Kiessling, Andrea Schenk, Tobias Preusser, Lars Kuepfer

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003499

Modular Composition of Gene Transcription Networks

Andras Gyorgy, Domitilla Del Vecchio

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003486

Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases

Teresa Szczepińska, Jan Kutner, Michał Kopczyński, Krzysztof Pawłowski, Andrzej Dziembowski, Andrzej Kudlicki, Krzysztof Ginalski, Maga Rowicka

PLOS Computational Biology: published March 20, 2014 | https://doi.org/10.1371/journal.pcbi.1003514

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Computational Analyses of Synergism in Small Molecular Network Motifs

Yili Zhang, Paul Smolen, Douglas A. Baxter, John H. Byrne

PLOS Computational Biology: published March 20, 2014 | https://doi.org/10.1371/journal.pcbi.1003524

Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations

Hazem Toutounji, Gordon Pipa

PLOS Computational Biology: published March 20, 2014 | https://doi.org/10.1371/journal.pcbi.1003512

Dynamic Alignment Models for Neural Coding

Sepp Kollmorgen, Richard H. R. Hahnloser

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003508

Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map

Nguyen T. Nguyen, Xiaolin Zhang, Cathy Wu, Richard A. Lange, Robert J. Chilton, Merry L. Lindsey, Yu-Fang Jin

PLOS Computational Biology: published March 20, 2014 | https://doi.org/10.1371/journal.pcbi.1003472

An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway

James Lu, Katrin Hübner, M. Nazeem Nanjee, Eliot A. Brinton, Norman A. Mazer

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003509

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Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability

Andrey Rzhetsky, Steven C. Bagley, Kanix Wang, Christopher S. Lyttle, Edwin H. Cook Jr, Russ B. Altman, Robert D. Gibbons

PLOS Computational Biology: published March 13, 2014 | https://doi.org/10.1371/journal.pcbi.1003518

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003500

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Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing

Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq

PLOS Computational Biology: published March 20, 2014 | https://doi.org/10.1371/journal.pcbi.1003517

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Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities

Arnaud Messé, David Rudrauf, Habib Benali, Guillaume Marrelec

PLOS Computational Biology: published March 20, 2014 | https://doi.org/10.1371/journal.pcbi.1003530

Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain

Alexandros Goulas, Matteo Bastiani, Gleb Bezgin, Harry B. M. Uylings, Alard Roebroeck, Peter Stiers

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003529

Modeling Mutual Exclusivity of Cancer Mutations

Ewa Szczurek, Niko Beerenwinkel

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003503

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A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects

Adrien Fauré, Barbara M. I. Vreede, Élio Sucena, Claudine Chaouiya

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003527

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003501

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Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT)

Chase Cockrell, Scott Christley, Gary An

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003507

STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning

David Kappel, Bernhard Nessler, Wolfgang Maass

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003511

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Global Quantitative Modeling of Chromatin Factor Interactions

Jian Zhou, Olga G. Troyanskaya

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003525

Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems

Samanthe M. Lyons, Wenlong Xu, June Medford, Ashok Prasad

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003533

Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence

Megan A. Cummins, Pavan J. Dalal, Marco Bugana, Stefano Severi, Eric A. Sobie

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003543

Resolving Structural Variability in Network Models and the Brain

Florian Klimm, Danielle S. Bassett, Jean M. Carlson, Peter J. Mucha

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003491

Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model

Wondimu Teka, Toma M. Marinov, Fidel Santamaria

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003526

Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy

Noah C. Benson, Omar H. Butt, David H. Brainard, Geoffrey K. Aguirre

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003538

Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data

Colin J. Worby, Marc Lipsitch, William P. Hanage

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003549

Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach

Fabian Konrath, Johannes Witt, Thomas Sauter, Dagmar Kulms

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003528

Viral Quasispecies Assembly via Maximal Clique Enumeration

Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003515

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HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

Emily Berger, Deniz Yorukoglu, Jian Peng, Bonnie Berger

PLOS Computational Biology: published March 27, 2014 | https://doi.org/10.1371/journal.pcbi.1003502

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Correction: A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes

The PLOS Computational Biology Staff

PLOS Computational Biology: published March 26, 2014 | https://doi.org/10.1371/journal.pcbi.1003582