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Table of Contents: April 2015

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Using single-unit recordings from awake marmosets (Callithrix jacchus), we validate several model predictions, including differences in the temporal fidelity, discharge rates and temporal dynamics of stimulus-evoked responses between neurons with rate and temporal representations. Together these data suggest that feedforward inhibition provides a parsimonious explanation of the neural coding dichotomy observed in auditory cortex. Bendor.

Editorials

Ten Simple (Empirical) Rules for Writing Science

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

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

Ten Simple Rules for a Community Computational Challenge

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

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

Education

Perspective

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

Review

Research Articles

A Bayesian Ensemble Approach for Epidemiological Projections

Tom Lindström, Michael Tildesley, Colleen Webb

Cell-Specific Cardiac Electrophysiology Models

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

Three-Dimensional Gradients of Cytokine Signaling between T Cells

Kevin Thurley, Daniel Gerecht, Elfriede Friedmann, Thomas Höfer

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

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

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

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

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

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

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

Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment

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

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

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

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

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

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

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

Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity

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

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

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, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. Semple , the FANTOM Consortium

MAGMA: Generalized Gene-Set Analysis of GWAS Data

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

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

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

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

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

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

Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae

Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana

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

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

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

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

Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency

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

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

Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent

Andy Phaiboun, Yiming Zhang, Boryung Park, Minsu Kim