PLOS Computational Biology 2017 Reviewer and Editorial Board Thank You

PLOS Computational Biology: published March 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006066

Ten simple rules to create a serious game, illustrated with examples from structural biology

Marc Baaden, Olivier Delalande, Nicolas Ferey, Samuela Pasquali, Jérôme Waldispühl, Antoine Taly

PLOS Computational Biology: published March 8, 2018 | https://doi.org/10.1371/journal.pcbi.1005955

Ten simple rules for collaborative lesson development

Gabriel A. Devenyi, Rémi Emonet, Rayna M. Harris, Kate L. Hertweck, Damien Irving, Ian Milligan, Greg Wilson

PLOS Computational Biology: published March 1, 2018 | https://doi.org/10.1371/journal.pcbi.1005963

Eleven quick tips for running an interdisciplinary short course for new graduate students

Timothy E. Saunders, Cynthia Y. He, Patrice Koehl, L. L. Sharon Ong, Peter T. C. So

PLOS Computational Biology: published March 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006039

Eleven quick tips for architecting biomedical informatics workflows with cloud computing

Brian S. Cole, Jason H. Moore

PLOS Computational Biology: published March 29, 2018 | https://doi.org/10.1371/journal.pcbi.1005994

Meet-U: Educating through research immersion

Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphael Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes

PLOS Computational Biology: published March 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005992

A FAIR guide for data providers to maximise sharing of human genomic data

Manuel Corpas, Nadezda V. Kovalevskaya, Amanda McMurray, Fiona G. G. Nielsen

PLOS Computational Biology: published March 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005873

An open source tool for automatic spatiotemporal assessment of calcium transients and local ‘signal-close-to-noise’ activity in calcium imaging data

Juan Prada, Manju Sasi, Corinna Martin, Sibylle Jablonka, Thomas Dandekar, Robert Blum

PLOS Computational Biology: published March 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006054

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data

Ivan Dotu, Scott I. Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras, Jeffrey H. Chuang

PLOS Computational Biology: published March 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006078

Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets

Soroush Samadian, Jeff P. Bruce, Trevor J. Pugh

PLOS Computational Biology: published March 28, 2018 | https://doi.org/10.1371/journal.pcbi.1006080

Modeling the dynamics of oligodendrocyte precursor cells and the genesis of gliomas

Aloys Dufour, Emilie Gontran, Christophe Deroulers, Pascale Varlet, Johan Pallud, Basile Grammaticos, Mathilde Badoual

PLOS Computational Biology: published March 28, 2018 | https://doi.org/10.1371/journal.pcbi.1005977

Astrocytic Kir4.1 channels and gap junctions account for spontaneous epileptic seizure

Mengmeng Du, Jiajia Li, Liang Chen, Yuguo Yu, Ying Wu

PLOS Computational Biology: published March 28, 2018 | https://doi.org/10.1371/journal.pcbi.1005877

Dynamic combination of sensory and reward information under time pressure

Shiva Farashahi, Chih-Chung Ting, Chang-Hao Kao, Shih-Wei Wu, Alireza Soltani

PLOS Computational Biology: published March 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006070

Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch

Roman Vaxenburg, Isis Wyche, Karel Svoboda, Alexander L. Efros, Samuel Andrew Hires

PLOS Computational Biology: published March 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006032

From correlation to causation: Estimating effective connectivity from zero-lag covariances of brain signals

Jonathan Schiefer, Alexander Niederbühl, Volker Pernice, Carolin Lennartz, Jürgen Hennig, Pierre LeVan, Stefan Rotter

PLOS Computational Biology: published March 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006056

Scabies in residential care homes: Modelling, inference and interventions for well-connected population sub-units

Timothy Kinyanjui, Jo Middleton, Stefan Güttel, Jackie Cassell, Joshua Ross, Thomas House

PLOS Computational Biology: published March 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006046

A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens

Mehdi Bouhaddou, Anne Marie Barrette, Alan D. Stern, Rick J. Koch, Matthew S. DiStefano, Eric A. Riesel, Luis C. Santos, Annie L. Tan, Alex E. Mertz, Marc R. Birtwistle

PLOS Computational Biology: published March 26, 2018 | https://doi.org/10.1371/journal.pcbi.1005985

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1. Correction: A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens

Population dynamics of engineered underdominance and killer-rescue gene drives in the control of disease vectors

Matthew P. Edgington, Luke S. Alphey

PLOS Computational Biology: published March 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006059

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules

Albert Solernou, Benjamin S. Hanson, Robin A. Richardson, Robert Welch, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris

PLOS Computational Biology: published March 23, 2018 | https://doi.org/10.1371/journal.pcbi.1005897

Model-based analysis of competing-endogenous pathways (MACPath) in human cancers

Hyun Jung Park, Soyeon Kim, Wei Li

PLOS Computational Biology: published March 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006074

Activation gating in HCN2 channels

Sabine Hummert, Susanne Thon, Thomas Eick, Ralf Schmauder, Eckhard Schulz, Klaus Benndorf

PLOS Computational Biology: published March 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006045

Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders

Guillaume Viejo, Thomas Cortier, Adrien Peyrache

PLOS Computational Biology: published March 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006041

Haptic communication between humans is tuned by the hard or soft mechanics of interaction

Atsushi Takagi, Francesco Usai, Gowrishankar Ganesh, Vittorio Sanguineti, Etienne Burdet

PLOS Computational Biology: published March 22, 2018 | https://doi.org/10.1371/journal.pcbi.1005971

Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza

Narmada Sambaturu, Sumanta Mukherjee, Martín López-García, Carmen Molina-París, Gautam I. Menon, Nagasuma Chandra

PLOS Computational Biology: published March 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006069

Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells

Yanting Luo, Jianlin He, Xiguang Xu, Ming-an Sun, Xiaowei Wu, Xuemei Lu, Hehuang Xie

PLOS Computational Biology: published March 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006034

The Pathway Coexpression Network: Revealing pathway relationships

Yered Pita-Juárez, Gabriel Altschuler, Sokratis Kariotis, Wenbin Wei, Katjuša Koler, Claire Green, Rudolph E. Tanzi, Winston Hide

PLOS Computational Biology: published March 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006042

The exclusive effects of chaperonin on the behavior of proteins with 5₂ knot

Yani Zhao, Pawel Dabrowski-Tumanski, Szymon Niewieczerzal, Joanna I. Sulkowska

PLOS Computational Biology: published March 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005970

Epigenetic regulation of cell fate reprogramming in aging and disease: A predictive computational model

Núria Folguera-Blasco, Elisabet Cuyàs, Javier A. Menéndez, Tomás Alarcón

PLOS Computational Biology: published March 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006052

Imbalanced amplification: A mechanism of amplification and suppression from local imbalance of excitation and inhibition in cortical circuits

Christopher Ebsch, Robert Rosenbaum

PLOS Computational Biology: published March 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006048

iDREM: Interactive visualization of dynamic regulatory networks

Jun Ding, James S. Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph

PLOS Computational Biology: published March 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006019

Closely related, yet unique: Distinct homo- and heterodimerization patterns of G protein coupled chemokine receptors and their fine-tuning by cholesterol

Stefan Gahbauer, Kristyna Pluhackova, Rainer A. Böckmann

PLOS Computational Biology: published March 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006062

LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions

Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange

PLOS Computational Biology: published March 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006058

Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state

Hao Ge, Pingping Wu, Hong Qian, Xiaoliang Sunney Xie

PLOS Computational Biology: published March 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006051

Gap junction plasticity as a mechanism to regulate network-wide oscillations

Guillaume Pernelle, Wilten Nicola, Claudia Clopath

PLOS Computational Biology: published March 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006025

Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation

Michael Pablo, Samuel A. Ramirez, Timothy C. Elston

PLOS Computational Biology: published March 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006016

In silico study of multicellular automaticity of heterogeneous cardiac cell monolayers: Effects of automaticity strength and structural linear anisotropy

James Elber Duverger, Vincent Jacquemet, Alain Vinet, Philippe Comtois

PLOS Computational Biology: published March 12, 2018 | https://doi.org/10.1371/journal.pcbi.1005978

Across-subjects classification of stimulus modality from human MEG high frequency activity

Britta U. Westner, Sarang S. Dalal, Simon Hanslmayr, Tobias Staudigl

PLOS Computational Biology: published March 12, 2018 | https://doi.org/10.1371/journal.pcbi.1005938

The importance of geometry in the corneal micropocket angiogenesis assay

James A. Grogan, Anthony J. Connor, Joe M. Pitt-Francis, Philip K. Maini, Helen M. Byrne

PLOS Computational Biology: published March 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006049

Use of temperature to improve West Nile virus forecasts

Nicholas B. DeFelice, Zachary D. Schneider, Eliza Little, Christopher Barker, Kevin A. Caillouet, Scott R. Campbell, Dan Damian, Patrick Irwin, Herff M. P. Jones, John Townsend, Jeffrey Shaman

PLOS Computational Biology: published March 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006047

4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data

Ibai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, Ignacio Maeso, José Luis Gómez-Skarmeta, Damien P. Devos

PLOS Computational Biology: published March 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006030

Neuronal gain modulability is determined by dendritic morphology: A computational optogenetic study

Sarah Jarvis, Konstantin Nikolic, Simon R. Schultz

PLOS Computational Biology: published March 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006027

ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy

Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney

PLOS Computational Biology: published March 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006002

Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis

David O. Holland, Margaret E. Johnson

PLOS Computational Biology: published March 8, 2018 | https://doi.org/10.1371/journal.pcbi.1006022

Bat detective—Deep learning tools for bat acoustic signal detection

Oisin Mac Aodha, Rory Gibb, Kate E. Barlow, Ella Browning, Michael Firman, Robin Freeman, Briana Harder, Libby Kinsey, Gary R. Mead, Stuart E. Newson, Ivan Pandourski, Stuart Parsons, Jon Russ, Abigel Szodoray-Paradi, Farkas Szodoray-Paradi, Elena Tilova, Mark Girolami, Gabriel Brostow, Kate E. Jones

PLOS Computational Biology: published March 8, 2018 | https://doi.org/10.1371/journal.pcbi.1005995

Method for the simulation of blood platelet shape and its evolution during activation

Alexander E. Moskalensky, Maxim A. Yurkin, Artem R. Muliukov, Alena L. Litvinenko, Vyacheslav M. Nekrasov, Andrei V. Chernyshev, Valeri P. Maltsev

PLOS Computational Biology: published March 8, 2018 | https://doi.org/10.1371/journal.pcbi.1005899

Deploying digital health data to optimize influenza surveillance at national and local scales

Elizabeth C. Lee, Ali Arab, Sandra M. Goldlust, Cécile Viboud, Bryan T. Grenfell, Shweta Bansal

PLOS Computational Biology: published March 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006020

Cytosolic proteins can exploit membrane localization to trigger functional assembly

Osman N. Yogurtcu, Margaret E. Johnson

PLOS Computational Biology: published March 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006031

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA

Hidetoshi Kono, Shun Sakuraba, Hisashi Ishida

PLOS Computational Biology: published March 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006024

Related Articles

1. Correction: Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA

Factors affecting basket catheter detection of real and phantom rotors in the atria: A computational study

Laura Martinez-Mateu, Lucia Romero, Ana Ferrer-Albero, Rafael Sebastian, José F. Rodríguez Matas, José Jalife, Omer Berenfeld, Javier Saiz

PLOS Computational Biology: published March 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006017

A computational model for how cells choose temporal or spatial sensing during chemotaxis

Rui Zhen Tan, Keng-Hwee Chiam

PLOS Computational Biology: published March 5, 2018 | https://doi.org/10.1371/journal.pcbi.1005966

Increased T cell trafficking as adjunct therapy for HIV-1

Helen R. Fryer, Steven M. Wolinsky, Angela R. McLean

PLOS Computational Biology: published March 2, 2018 | https://doi.org/10.1371/journal.pcbi.1006028

Classifying dynamic transitions in high dimensional neural mass models: A random forest approach

Lauric A. Ferrat, Marc Goodfellow, John R. Terry

PLOS Computational Biology: published March 2, 2018 | https://doi.org/10.1371/journal.pcbi.1006009

Population-specific design of de-immunized protein biotherapeutics

Benjamin Schubert, Charlotta Schärfe, Pierre Dönnes, Thomas Hopf, Debora Marks, Oliver Kohlbacher

PLOS Computational Biology: published March 2, 2018 | https://doi.org/10.1371/journal.pcbi.1005983

An entropic barriers diffusion theory of decision-making in multiple alternative tasks

Diego Fernandez Slezak, Mariano Sigman, Guillermo A. Cecchi

PLOS Computational Biology: published March 2, 2018 | https://doi.org/10.1371/journal.pcbi.1005961

Inverse tissue mechanics of cell monolayer expansion

Yohei Kondo, Kazuhiro Aoki, Shin Ishii

PLOS Computational Biology: published March 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006029

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

Charlie Beirnaert, Pieter Meysman, Trung Nghia Vu, Nina Hermans, Sandra Apers, Luc Pieters, Adrian Covaci, Kris Laukens

PLOS Computational Biology: published March 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006018

Receptor recharge time drastically reduces the number of captured particles

Gregory Handy, Sean D. Lawley, Alla Borisyuk

PLOS Computational Biology: published March 1, 2018 | https://doi.org/10.1371/journal.pcbi.1006015

An evolutionary learning and network approach to identifying key metabolites for osteoarthritis

Ting Hu, Karoliina Oksanen, Weidong Zhang, Ed Randell, Andrew Furey, Guang Sun, Guangju Zhai

PLOS Computational Biology: published March 1, 2018 | https://doi.org/10.1371/journal.pcbi.1005986

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

J. Kenneth Baillie, Andrew Bretherick, Christopher S. Haley, Sara Clohisey, Alan Gray, Lucile P. A. Neyton, Jeffrey Barrett, Eli A. Stahl, Albert Tenesa, Robin Andersson, J. Ben Brown, Geoffrey J. Faulkner, Marina Lizio, Ulf Schaefer, Carsten Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, IIBDGC Consortium, Damian Mole, Vladimir B. Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A. Wells, Nir Hacohen, Thomas C. Freeman, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, David A. Hume

PLOS Computational Biology: published March 1, 2018 | https://doi.org/10.1371/journal.pcbi.1005934