Ten Simple (Empirical) Rules for Writing Science

Cody J. Weinberger, James A. Evans, Stefano Allesina

PLOS Computational Biology: published April 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004205

Ten Simple Rules for a Successful Cross-Disciplinary Collaboration

Bernhard Knapp, Rémi Bardenet, Miguel O. Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G. Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg McInerny, Timo Minssen, James Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A. Yates, David Gavaghan, Charlotte M. Deane

PLOS Computational Biology: published April 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004214

Ten Simple Rules for a Community Computational Challenge

Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac

PLOS Computational Biology: published April 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004150

Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research

Anne-Laure Boulesteix

PLOS Computational Biology: published April 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004191

Ten Simple Rules for Effective Online Outreach

Holly M. Bik, Alistair D. M. Dove, Miriam C. Goldstein, Rebecca R. Helm, Rick MacPherson, Kim Martini, Alexandria Warneke, Craig McClain

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1003906

Ten Simple Rules to Win a Nobel Prize

Richard J. Roberts

PLOS Computational Biology: published April 2, 2015 | https://doi.org/10.1371/journal.pcbi.1004084

The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences

Melanie I. Stefan, Johanna L. Gutlerner, Richard T. Born, Michael Springer

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004208

GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training

Teresa K. Atwood, Erik Bongcam-Rudloff, Michelle E. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder, GOBLET Consortium

PLOS Computational Biology: published April 9, 2015 | https://doi.org/10.1371/journal.pcbi.1004143

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What Is the Most Realistic Single-Compartment Model of Spike Initiation?

Romain Brette

PLOS Computational Biology: published April 9, 2015 | https://doi.org/10.1371/journal.pcbi.1004114

A Bayesian Ensemble Approach for Epidemiological Projections

Tom Lindström, Michael Tildesley, Colleen Webb

PLOS Computational Biology: published April 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004187

Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations

Albertas Janulevicius, Mark van Loosdrecht, Cristian Picioreanu

PLOS Computational Biology: published April 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004213

Cell-Specific Cardiac Electrophysiology Models

Willemijn Groenendaal, Francis A. Ortega, Armen R. Kherlopian, Andrew C. Zygmunt, Trine Krogh-Madsen, David J. Christini

PLOS Computational Biology: published April 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004242

Three-Dimensional Gradients of Cytokine Signaling between T Cells

Kevin Thurley, Daniel Gerecht, Elfriede Friedmann, Thomas Höfer

PLOS Computational Biology: published April 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004206

Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control

Simon Sponberg, Thomas L. Daniel, Adrienne L. Fairhall

PLOS Computational Biology: published April 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004168

Non-linear Membrane Properties in Entorhinal Cortical Stellate Cells Reduce Modulation of Input-Output Responses by Voltage Fluctuations

Fernando R. Fernandez, Paola Malerba, John A. White

PLOS Computational Biology: published April 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004188

Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans

Mei Zhan, Matthew M. Crane, Eugeni V. Entchev, Antonio Caballero, Diana Andrea Fernandes de Abreu, QueeLim Ch’ng, Hang Lu

PLOS Computational Biology: published April 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004194

Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer

Thomas W. Spiesser, Clemens Kühn, Marcus Krantz, Edda Klipp

PLOS Computational Biology: published April 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004223

Mixed Signal Learning by Spike Correlation Propagation in Feedback Inhibitory Circuits

Naoki Hiratani, Tomoki Fukai

PLOS Computational Biology: published April 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004227

Existence and Control of Go/No-Go Decision Transition Threshold in the Striatum

Jyotika Bahuguna, Ad Aertsen, Arvind Kumar

PLOS Computational Biology: published April 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004233

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism

Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff

PLOS Computational Biology: published April 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004236

Quantifying Spike Train Oscillations: Biases, Distortions and Solutions

Ayala Matzner, Izhar Bar-Gad

PLOS Computational Biology: published April 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004252

A Change in Vaccine Efficacy and Duration of Protection Explains Recent Rises in Pertussis Incidence in the United States

Manoj Gambhir, Thomas A. Clark, Simon Cauchemez, Sara Y. Tartof, David L. Swerdlow, Neil M. Ferguson

PLOS Computational Biology: published April 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004138

Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune Networks

Daniel K. Wells, Yishan Chuang, Louis M. Knapp, Dirk Brockmann, William L. Kath, Joshua N. Leonard

PLOS Computational Biology: published April 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004181

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling

Lorenza A. D’Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller

PLOS Computational Biology: published April 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004192

Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment

Hannah R. Meredith, Allison J. Lopatkin, Deverick J. Anderson, Lingchong You

PLOS Computational Biology: published April 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004201

Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences

Jian Tian, Jaie C. Woodard, Andrew Whitney, Eugene I. Shakhnovich

PLOS Computational Biology: published April 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004207

Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program

Noa Slater, Yoram Louzoun, Loren Gragert, Martin Maiers, Ansu Chatterjee, Mark Albrecht

PLOS Computational Biology: published April 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004204

Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations

Debabani Ganguly, Jianhan Chen

PLOS Computational Biology: published April 21, 2015 | https://doi.org/10.1371/journal.pcbi.1004247

Perturbation-Expression Analysis Identifies RUNX1 as a Regulator of Human Mammary Stem Cell Differentiation

Ethan S. Sokol, Sandhya Sanduja, Dexter X. Jin, Daniel H. Miller, Robert A. Mathis, Piyush B. Gupta

PLOS Computational Biology: published April 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004161

Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease

William F. Flynn, Max W. Chang, Zhiqiang Tan, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Bruce E. Torbett, Ronald M. Levy

PLOS Computational Biology: published April 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004249

Segmentation and Tracking of Adherens Junctions in 3D for the Analysis of Epithelial Tissue Morphogenesis

Rodrigo Cilla, Vinodh Mechery, Beatriz Hernandez de Madrid, Steven Del Signore, Ivan Dotu, Victor Hatini

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004124

Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts

Juan Palacios-Moreno, Lauren Foltz, Ailan Guo, Matthew P. Stokes, Emily D. Kuehn, Lynn George, Michael Comb, Mark L. Grimes

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004130

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel Rozowsky, William Meyerson, Mark B. Gerstein

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004132

Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth

Ka Wai Lin, Angela Liao, Amina A. Qutub

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004169

Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity

Paul Egan, Jeffrey Moore, Christian Schunn, Jonathan Cagan, Philip LeDuc

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004177

Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study

Nils A. Berglund, Thomas J. Piggot, Damien Jefferies, Richard B. Sessions, Peter J. Bond, Syma Khalid

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004180

The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition

Xiliang Zheng, Jin Wang

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004212

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response

Stuart Aitken, Shigeyuki Magi, Ahmad M. N. Alhendi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, the FANTOM Consortium, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. Semple

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004217

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MAGMA: Generalized Gene-Set Analysis of GWAS Data

Christiaan A. de Leeuw, Joris M. Mooij, Tom Heskes, Danielle Posthuma

PLOS Computational Biology: published April 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004219

NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation

Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs Greber, Holger Fröhlich, Niko Beerenwinkel

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004078

The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient

Michael D. O’Connell, Gregory T. Reeves

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004159

The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease

Stefan Flasche, Olivier Le Polain de Waroux, Katherine L. O’Brien, W. John Edmunds

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004173

The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information

Daniel Bendor

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004197

A Power-Law Dependence of Bacterial Invasion on Mammalian Host Receptors

Tae J. Lee, Jeffrey Wong, Sena Bae, Anna Jisu Lee, Allison Lopatkin, Fan Yuan, Lingchong You

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004203

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

Gabriel R. A. Margarido, David Heckerman

PLOS Computational Biology: published April 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004229

Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies

Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields

PLOS Computational Biology: published April 15, 2015 | https://doi.org/10.1371/journal.pcbi.1004119

A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions

Pedro Saa, Lars K. Nielsen

PLOS Computational Biology: published April 14, 2015 | https://doi.org/10.1371/journal.pcbi.1004195

General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks

Joon-Young Moon, UnCheol Lee, Stefanie Blain-Moraes, George A. Mashour

PLOS Computational Biology: published April 14, 2015 | https://doi.org/10.1371/journal.pcbi.1004225

Twisting Right to Left: A…A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation

Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan

PLOS Computational Biology: published April 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004162

Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees

Ickwon Choi, Amy W. Chung, Todd J. Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayaphan, Jaranit Kaewkungwal, Robert J. O'Connell, Donald Francis, Merlin L. Robb, Nelson L. Michael, Jerome H. Kim, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg

PLOS Computational Biology: published April 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004185

Optimising and Communicating Options for the Control of Invasive Plant Disease When There Is Epidemiological Uncertainty

Nik J. Cunniffe, Richard O. J. H. Stutt, R. Erik DeSimone, Tim R. Gottwald, Christopher A. Gilligan

PLOS Computational Biology: published April 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004211

Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae

Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana

PLOS Computational Biology: published April 10, 2015 | https://doi.org/10.1371/journal.pcbi.1004136

Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks

Adam J. Kucharski, W. John Edmunds

PLOS Computational Biology: published April 10, 2015 | https://doi.org/10.1371/journal.pcbi.1004154

Quantification of Diabetes Comorbidity Risks across Life Using Nation-Wide Big Claims Data

Peter Klimek, Alexandra Kautzky-Willer, Anna Chmiel, Irmgard Schiller-Frühwirth, Stefan Thurner

PLOS Computational Biology: published April 9, 2015 | https://doi.org/10.1371/journal.pcbi.1004125

A Bayesian Model of Category-Specific Emotional Brain Responses

Tor D. Wager, Jian Kang, Timothy D. Johnson, Thomas E. Nichols, Ajay B. Satpute, Lisa Feldman Barrett

PLOS Computational Biology: published April 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004066

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

Susan Dina Ghiassian, Jörg Menche, Albert-László Barabási

PLOS Computational Biology: published April 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004120

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

Tomáš Trnka, Stanislav Kozmon, Igor Tvaroška, Jaroslav Koča

PLOS Computational Biology: published April 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004061

Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery

Sébastien Giguère, François Laviolette, Mario Marchand, Denise Tremblay, Sylvain Moineau, Xinxia Liang, Éric Biron, Jacques Corbeil

PLOS Computational Biology: published April 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004074

Embodied Choice: How Action Influences Perceptual Decision Making

Nathan F. Lepora, Giovanni Pezzulo

PLOS Computational Biology: published April 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004110

Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable

Fabio Pardi, Celine Scornavacca

PLOS Computational Biology: published April 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004135

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Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models

Timo R. Maarleveld, Meike T. Wortel, Brett G. Olivier, Bas Teusink, Frank J. Bruggeman

PLOS Computational Biology: published April 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004166

Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency

Nancy K. Drew, Mackenzie A. Eagleson, Danny B. Baldo Jr., Kevin Kit Parker, Anna Grosberg

PLOS Computational Biology: published April 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004190

Cell Fate Reprogramming by Control of Intracellular Network Dynamics

Jorge G. T. Zañudo, Réka Albert

PLOS Computational Biology: published April 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004193

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Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills

Kai Olav Ellefsen, Jean-Baptiste Mouret, Jeff Clune

PLOS Computational Biology: published April 2, 2015 | https://doi.org/10.1371/journal.pcbi.1004128

Hybrid Spreading Mechanisms and T Cell Activation Shape the Dynamics of HIV-1 Infection

Changwang Zhang, Shi Zhou, Elisabetta Groppelli, Pierre Pellegrino, Ian Williams, Persephone Borrow, Benjamin M. Chain, Clare Jolly

PLOS Computational Biology: published April 2, 2015 | https://doi.org/10.1371/journal.pcbi.1004179

Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent

Andy Phaiboun, Yiming Zhang, Boryung Park, Minsu Kim

PLOS Computational Biology: published April 2, 2015 | https://doi.org/10.1371/journal.pcbi.1004198

The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction

Ross S. Williamson, Maneesh Sahani, Jonathan W. Pillow

PLOS Computational Biology: published April 1, 2015 | https://doi.org/10.1371/journal.pcbi.1004141

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