Ten Simple Rules for Developing Public Biological Databases

Mohamed Helmy, Alexander Crits-Christoph, Gary D. Bader

PLOS Computational Biology: published November 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005128

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

Hulda S. Haraldsdóttir, Ronan M. T. Fleming

PLOS Computational Biology: published November 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004999

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine

Ayush Singhal, Michael Simmons, Zhiyong Lu

PLOS Computational Biology: published November 30, 2016 | https://doi.org/10.1371/journal.pcbi.1005017

Network Receptive Field Modeling Reveals Extensive Integration and Multi-feature Selectivity in Auditory Cortical Neurons

Nicol S. Harper, Oliver Schoppe, Ben D. B. Willmore, Zhanfeng Cui, Jan W. H. Schnupp, Andrew J. King

PLOS Computational Biology: published November 11, 2016 | https://doi.org/10.1371/journal.pcbi.1005113

Real-Time Control of an Articulatory-Based Speech Synthesizer for Brain Computer Interfaces

Florent Bocquelet, Thomas Hueber, Laurent Girin, Christophe Savariaux, Blaise Yvert

PLOS Computational Biology: published November 23, 2016 | https://doi.org/10.1371/journal.pcbi.1005119

Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion

Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R. Petzold

PLOS Computational Biology: published November 28, 2016 | https://doi.org/10.1371/journal.pcbi.1005122

Improved Measures of Integrated Information

Max Tegmark

PLOS Computational Biology: published November 21, 2016 | https://doi.org/10.1371/journal.pcbi.1005123

Error-Robust Modes of the Retinal Population Code

Jason S. Prentice, Olivier Marre, Mark L. Ioffe, Adrianna R. Loback, Gašper Tkačik, Michael J. Berry II

PLOS Computational Biology: published November 17, 2016 | https://doi.org/10.1371/journal.pcbi.1005148

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Interrogating Emergent Transport Properties for Molecular Motor Ensembles: A Semi-analytical Approach

Shreyas Bhaban, Donatello Materassi, Mingang Li, Thomas Hays, Murti Salapaka

PLOS Computational Biology: published November 3, 2016 | https://doi.org/10.1371/journal.pcbi.1005152

Machine Learning for Characterization of Insect Vector Feeding

Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe

PLOS Computational Biology: published November 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005158

Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012

William J. Love, Kelson A. Zawack, James G. Booth, Yrjo T. Grӧhn, Cristina Lanzas

PLOS Computational Biology: published November 16, 2016 | https://doi.org/10.1371/journal.pcbi.1005160

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World

Ye Eun Kim, Paul G. Higgs

PLOS Computational Biology: published November 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005161

Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1

Jeffrey S. Seely, Matthew T. Kaufman, Stephen I. Ryu, Krishna V. Shenoy, John P. Cunningham, Mark M. Churchland

PLOS Computational Biology: published November 4, 2016 | https://doi.org/10.1371/journal.pcbi.1005164

High-Frequency Resonance in the Gerbil Medial Superior Olive

Jason Mikiel-Hunter, Vibhakar Kotak, John Rinzel

PLOS Computational Biology: published November 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005166

The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization

Elad Noor, Avi Flamholz, Arren Bar-Even, Dan Davidi, Ron Milo, Wolfram Liebermeister

PLOS Computational Biology: published November 3, 2016 | https://doi.org/10.1371/journal.pcbi.1005167

Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4

Kristyna Pluhackova, Stefan Gahbauer, Franziska Kranz, Tsjerk A. Wassenaar, Rainer A. Böckmann

PLOS Computational Biology: published November 3, 2016 | https://doi.org/10.1371/journal.pcbi.1005169

Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning

Jonathan A. Michaels, Benjamin Dann, Hansjörg Scherberger

PLOS Computational Biology: published November 4, 2016 | https://doi.org/10.1371/journal.pcbi.1005175

Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments

David A. Van Valen, Takamasa Kudo, Keara M. Lane, Derek N. Macklin, Nicolas T. Quach, Mialy M. DeFelice, Inbal Maayan, Yu Tanouchi, Euan A. Ashley, Markus W. Covert

PLOS Computational Biology: published November 4, 2016 | https://doi.org/10.1371/journal.pcbi.1005177

Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan

Elizabeth N. Davison, Benjamin O. Turner, Kimberly J. Schlesinger, Michael B. Miller, Scott T. Grafton, Danielle S. Bassett, Jean M. Carlson

PLOS Computational Biology: published November 23, 2016 | https://doi.org/10.1371/journal.pcbi.1005178

Topology, Cross-Frequency, and Same-Frequency Band Interactions Shape the Generation of Phase-Amplitude Coupling in a Neural Mass Model of a Cortical Column

Roberto C. Sotero

PLOS Computational Biology: published November 1, 2016 | https://doi.org/10.1371/journal.pcbi.1005180

WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning

George L. Sutphin, J. Matthew Mahoney, Keith Sheppard, David O. Walton, Ron Korstanje

PLOS Computational Biology: published November 3, 2016 | https://doi.org/10.1371/journal.pcbi.1005182

A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging

Sagi Snir, Bridgett M. vonHoldt, Matteo Pellegrini

PLOS Computational Biology: published November 11, 2016 | https://doi.org/10.1371/journal.pcbi.1005183

NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents

Sophia S. Liu, Adam J. Hockenberry, Andrea Lancichinetti, Michael C. Jewett, Luís A. N. Amaral

PLOS Computational Biology: published November 11, 2016 | https://doi.org/10.1371/journal.pcbi.1005184

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways

Lefteris Koumakis, Alexandros Kanterakis, Evgenia Kartsaki, Maria Chatzimina, Michalis Zervakis, Manolis Tsiknakis, Despoina Vassou, Dimitris Kafetzopoulos, Kostas Marias, Vassilis Moustakis, George Potamias

PLOS Computational Biology: published November 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005187

Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay

Adam F. Prasanphanich, Douglas E. White, Margaret A. Gran, Melissa L. Kemp

PLOS Computational Biology: published November 16, 2016 | https://doi.org/10.1371/journal.pcbi.1005188

Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains

Arno Onken, Jian K. Liu, P. P. Chamanthi R. Karunasekara, Ioannis Delis, Tim Gollisch, Stefano Panzeri

PLOS Computational Biology: published November 4, 2016 | https://doi.org/10.1371/journal.pcbi.1005189

Malaria Elimination Campaigns in the Lake Kariba Region of Zambia: A Spatial Dynamical Model

Milen Nikolov, Caitlin A. Bever, Alexander Upfill-Brown, Busiku Hamainza, John M. Miller, Philip A. Eckhoff, Edward A. Wenger, Jaline Gerardin

PLOS Computational Biology: published November 23, 2016 | https://doi.org/10.1371/journal.pcbi.1005192

Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue

Geir Halnes, Tuomo Mäki-Marttunen, Daniel Keller, Klas H. Pettersen, Ole A. Andreassen, Gaute T. Einevoll

PLOS Computational Biology: published November 7, 2016 | https://doi.org/10.1371/journal.pcbi.1005193

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Drivers of Inter-individual Variation in Dengue Viral Load Dynamics

Rotem Ben-Shachar, Scott Schmidler, Katia Koelle

PLOS Computational Biology: published November 17, 2016 | https://doi.org/10.1371/journal.pcbi.1005194

PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases

Marzieh Ayati, Mehmet Koyutürk

PLOS Computational Biology: published November 11, 2016 | https://doi.org/10.1371/journal.pcbi.1005195

The Environment Shapes the Inner Vestibule of LeuT

Azmat Sohail, Kumaresan Jayaraman, Santhoshkannan Venkatesan, Kamil Gotfryd, Markus Daerr, Ulrik Gether, Claus J. Loland, Klaus T. Wanner, Michael Freissmuth, Harald H. Sitte, Walter Sandtner, Thomas Stockner

PLOS Computational Biology: published November 11, 2016 | https://doi.org/10.1371/journal.pcbi.1005197

Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City

Wan Yang, Donald R. Olson, Jeffrey Shaman

PLOS Computational Biology: published November 17, 2016 | https://doi.org/10.1371/journal.pcbi.1005201

Induced Fit in Protein Multimerization: The HFBI Case

Laura Riccardi, Paolo Mereghetti

PLOS Computational Biology: published November 10, 2016 | https://doi.org/10.1371/journal.pcbi.1005202

Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints

Fang-Cheng Yeh, Jean M. Vettel, Aarti Singh, Barnabas Poczos, Scott T. Grafton, Kirk I. Erickson, Wen-Yih I. Tseng, Timothy D. Verstynen

PLOS Computational Biology: published November 15, 2016 | https://doi.org/10.1371/journal.pcbi.1005203

An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production

Adaoha E. C. Ihekwaba, Ivan Mura, John Walshaw, Michael W. Peck, Gary C. Barker

PLOS Computational Biology: published November 17, 2016 | https://doi.org/10.1371/journal.pcbi.1005205

Extending Integrate-and-Fire Model Neurons to Account for the Effects of Weak Electric Fields and Input Filtering Mediated by the Dendrite

Florian Aspart, Josef Ladenbauer, Klaus Obermayer

PLOS Computational Biology: published November 28, 2016 | https://doi.org/10.1371/journal.pcbi.1005206

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

Mona Habibi, Jörg Rottler, Steven S. Plotkin

PLOS Computational Biology: published November 29, 2016 | https://doi.org/10.1371/journal.pcbi.1005211

Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference

Kieran R. Campbell, Christopher Yau

PLOS Computational Biology: published November 21, 2016 | https://doi.org/10.1371/journal.pcbi.1005212

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Antioxidant Properties of Kynurenines: Density Functional Theory Calculations

Aleksandr V. Zhuravlev, Gennady A. Zakharov, Boris F. Shchegolev, Elena V. Savvateeva-Popova

PLOS Computational Biology: published November 18, 2016 | https://doi.org/10.1371/journal.pcbi.1005213

A Biophysical Systems Approach to Identifying the Pathways of Acute and Chronic Doxorubicin Mitochondrial Cardiotoxicity

Bernardo L. de Oliveira, Steven Niederer

PLOS Computational Biology: published November 21, 2016 | https://doi.org/10.1371/journal.pcbi.1005214

Combined Changes in Chloride Regulation and Neuronal Excitability Enable Primary Afferent Depolarization to Elicit Spiking without Compromising its Inhibitory Effects

Petri Takkala, Yi Zhu, Steven A. Prescott

PLOS Computational Biology: published November 11, 2016 | https://doi.org/10.1371/journal.pcbi.1005215

Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle

Peter Rashkov, Ian P. Barrett, Robert E. Beardmore, Claus Bendtsen, Ivana Gudelj

PLOS Computational Biology: published November 29, 2016 | https://doi.org/10.1371/journal.pcbi.1005216

Creating High-Resolution Multiscale Maps of Human Tissue Using Multi-beam SEM

André F. Pereira, Daniel J. Hageman, Tomasz Garbowski, Christof Riedesel, Ulf Knothe, Dirk Zeidler, Melissa L. Knothe Tate

PLOS Computational Biology: published November 21, 2016 | https://doi.org/10.1371/journal.pcbi.1005217

Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction

Edgar D. Coelho, Joel P. Arrais, José Luís Oliveira

PLOS Computational Biology: published November 28, 2016 | https://doi.org/10.1371/journal.pcbi.1005219

Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway

Kazunari Iwamoto, Yuki Shindo, Koichi Takahashi

PLOS Computational Biology: published November 30, 2016 | https://doi.org/10.1371/journal.pcbi.1005222

Do Vascular Networks Branch Optimally or Randomly across Spatial Scales?

Elif Tekin, David Hunt, Mitchell G. Newberry, Van M. Savage

PLOS Computational Biology: published November 30, 2016 | https://doi.org/10.1371/journal.pcbi.1005223