Ten simple rules for responsible referencing

Bart Penders

PLOS Computational Biology: published April 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006036

New computational approaches to understanding molecular protein function

Jacquelyn S. Fetrow, Patricia C. Babbitt

PLOS Computational Biology: published April 5, 2018 | https://doi.org/10.1371/journal.pcbi.1005756

Eleven quick tips for finding research data

Kathleen Gregory, Siri Jodha Khalsa, William K. Michener, Fotis E. Psomopoulos, Anita de Waard, Mingfang Wu

PLOS Computational Biology: published April 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006038

Ten quick tips for teaching programming

Neil C. C. Brown, Greg Wilson

PLOS Computational Biology: published April 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006023

Automated plant species identification—Trends and future directions

Jana Wäldchen, Michael Rzanny, Marco Seeland, Patrick Mäder

PLOS Computational Biology: published April 5, 2018 | https://doi.org/10.1371/journal.pcbi.1005993

Quantitative analysis reveals crosstalk mechanisms of heat shock-induced attenuation of NF-κB signaling at the single cell level

Małgorzata Kardyńska, Anna Paszek, Jarosław Śmieja, David Spiller, Wiesława Widłak, Michael R. H. White, Pawel Paszek, Marek Kimmel

PLOS Computational Biology: published April 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006130

Automated evaluation of quaternary structures from protein crystals

Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte

PLOS Computational Biology: published April 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006104

Topological and statistical analyses of gene regulatory networks reveal unifying yet quantitatively different emergent properties

Wilberforce Zachary Ouma, Katja Pogacar, Erich Grotewold

PLOS Computational Biology: published April 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006098

Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape

David R. J. Pleydell, Samuel Soubeyrand, Sylvie Dallot, Gérard Labonne, Joël Chadœuf, Emmanuel Jacquot, Gaël Thébaud

PLOS Computational Biology: published April 30, 2018 | https://doi.org/10.1371/journal.pcbi.1006085

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Effects of growth rate, cell size, motion, and elemental stoichiometry on nutrient transport kinetics

Kevin J. Flynn, David O. F. Skibinski, Christian Lindemann

PLOS Computational Biology: published April 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006118

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design

Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D. Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack Jr.

PLOS Computational Biology: published April 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006112

Material and shape perception based on two types of intensity gradient information

Masataka Sawayama, Shin'ya Nishida

PLOS Computational Biology: published April 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006061

Organization of the core respiratory network: Insights from optogenetic and modeling studies

Jessica Ausborn, Hidehiko Koizumi, William H. Barnett, Tibin T. John, Ruli Zhang, Yaroslav I. Molkov, Jeffrey C. Smith, Ilya A. Rybak

PLOS Computational Biology: published April 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006148

Effects of spatiotemporal HSV-2 lesion dynamics and antiviral treatment on the risk of HIV-1 acquisition

Catherine M. Byrne, Soren Gantt, Daniel Coombs

PLOS Computational Biology: published April 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006129

Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin

Vasyl V. Mykuliak, Alexander William M. Haining, Magdaléna von Essen, Armando del Río Hernández, Vesa P. Hytönen

PLOS Computational Biology: published April 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006126

RIDDLE: Race and ethnicity Imputation from Disease history with Deep LEarning

Ji-Sung Kim, Xin Gao, Andrey Rzhetsky

PLOS Computational Biology: published April 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006106

Personalizing physical exercise in a computational model of fuel homeostasis

Maria Concetta Palumbo, Micaela Morettini, Paolo Tieri, Fasma Diele, Massimo Sacchetti, Filippo Castiglione

PLOS Computational Biology: published April 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006073

Rational metareasoning and the plasticity of cognitive control

Falk Lieder, Amitai Shenhav, Sebastian Musslick, Thomas L. Griffiths

PLOS Computational Biology: published April 25, 2018 | https://doi.org/10.1371/journal.pcbi.1006043

Switchable slow cellular conductances determine robustness and tunability of network states

Guillaume Drion, Julie Dethier, Alessio Franci, Rodolphe Sepulchre

PLOS Computational Biology: published April 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006125

Identifying robust hysteresis in networks

Tomáš Gedeon, Bree Cummins, Shaun Harker, Konstantin Mischaikow

PLOS Computational Biology: published April 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006121

Black-boxing and cause-effect power

William Marshall, Larissa Albantakis, Giulio Tononi

PLOS Computational Biology: published April 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006114

Computational mechanisms underlying cortical responses to the affordance properties of visual scenes

Michael F. Bonner, Russell A. Epstein

PLOS Computational Biology: published April 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006111

Correcting for batch effects in case-control microbiome studies

Sean M. Gibbons, Claire Duvallet, Eric J. Alm

PLOS Computational Biology: published April 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006102

A machine learning based framework to identify and classify long terminal repeat retrotransposons

Leander Schietgat, Celine Vens, Ricardo Cerri, Carlos N. Fischer, Eduardo Costa, Jan Ramon, Claudia M. A. Carareto, Hendrik Blockeel

PLOS Computational Biology: published April 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006097

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

Sneha Mitra, Anushua Biswas, Leelavati Narlikar

PLOS Computational Biology: published April 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006090

Exploiting glycan topography for computational design of Env glycoprotein antigenicity

Wen-Han Yu, Peng Zhao, Monia Draghi, Claudia Arevalo, Christina B. Karsten, Todd J. Suscovich, Bronwyn Gunn, Hendrik Streeck, Abraham L. Brass, Michael Tiemeyer, Michael Seaman, John R. Mascola, Lance Wells, Douglas A. Lauffenburger, Galit Alter

PLOS Computational Biology: published April 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006093

Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse

Reuben M. Buckley, R. Daniel Kortschak, David L. Adelson

PLOS Computational Biology: published April 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006091

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

Benjamin Schott, Manuel Traub, Cornelia Schlagenhauf, Masanari Takamiya, Thomas Antritter, Andreas Bartschat, Katharina Löffler, Denis Blessing, Jens C. Otte, Andrei Y. Kobitski, G. Ulrich Nienhaus, Uwe Strähle, Ralf Mikut, Johannes Stegmaier

PLOS Computational Biology: published April 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006128

Compositional clustering in task structure learning

Nicholas T. Franklin, Michael J. Frank

PLOS Computational Biology: published April 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006116

Decision making improves sperm chemotaxis in the presence of noise

Justus A. Kromer, Steffen Märcker, Steffen Lange, Christel Baier, Benjamin M. Friedrich

PLOS Computational Biology: published April 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006109

Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer

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PLOS Computational Biology: published April 19, 2018 | https://doi.org/10.1371/journal.pcbi.1006087

Bayesian reconstruction of transmission within outbreaks using genomic variants

Nicola De Maio, Colin J. Worby, Daniel J. Wilson, Nicole Stoesser

PLOS Computational Biology: published April 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006117

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Geoffrey D. Hannigan, Melissa B. Duhaime, Danai Koutra, Patrick D. Schloss

PLOS Computational Biology: published April 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006099

Propagating annotations of molecular networks using in silico fragmentation

Ricardo R. da Silva, Mingxun Wang, Louis-Félix Nothias, Justin J. J. van der Hooft, Andrés Mauricio Caraballo-Rodríguez, Evan Fox, Marcy J. Balunas, Jonathan L. Klassen, Norberto Peporine Lopes, Pieter C. Dorrestein

PLOS Computational Biology: published April 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006089

A computational model of shared fine-scale structure in the human connectome

J. Swaroop Guntupalli, Ma Feilong, James V. Haxby

PLOS Computational Biology: published April 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006120

On the role of extrinsic noise in microRNA-mediated bimodal gene expression

Marco Del Giudice, Stefano Bo, Silvia Grigolon, Carla Bosia

PLOS Computational Biology: published April 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006063

A modelling approach for exploring muscle dynamics during cyclic contractions

Stephanie A. Ross, Nilima Nigam, James M. Wakeling

PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006123

Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations

Russell B. Davidson, Josie Hendrix, Brian J. Geiss, Martin McCullagh

PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006103

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

Florian Kaiser, Sebastian Bittrich, Sebastian Salentin, Christoph Leberecht, V. Joachim Haupt, Sarah Krautwurst, Michael Schroeder, Dirk Labudde

PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006101

Using pseudoalignment and base quality to accurately quantify microbial community composition

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PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006096

Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilms

Ricardo Martínez-García, Carey D. Nadell, Raimo Hartmann, Knut Drescher, Juan A. Bonachela

PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006094

Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly

Juan Francisco Viso, Patricia Belelli, Matías Machado, Humberto González, Sergio Pantano, María Julia Amundarain, Fernando Zamarreño, Maria Marta Branda, Diego M. A. Guérin, Marcelo D. Costabel

PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006082

Whole-body iron transport and metabolism: Mechanistic, multi-scale model to improve treatment of anemia in chronic kidney disease

Joydeep Sarkar, Alka A. Potdar, Gerald M. Saidel

PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006060

A computational study of astrocytic glutamate influence on post-synaptic neuronal excitability

Bronac Flanagan, Liam McDaid, John Wade, KongFatt Wong-Lin, Jim Harkin

PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006040

Origins of scale invariance in vocalization sequences and speech

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PLOS Computational Biology: published April 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005996

Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy

Martin Weigert, Kaushikaram Subramanian, Sebastian T. Bundschuh, Eugene W. Myers, Moritz Kreysing

PLOS Computational Biology: published April 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006079

Principles that govern competition or co-existence in Rho-GTPase driven polarization

Jian-Geng Chiou, Samuel A. Ramirez, Timothy C. Elston, Thomas P. Witelski, David G. Schaeffer, Daniel J. Lew

PLOS Computational Biology: published April 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006095

Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens

Loup Rimbaud, Julien Papaïx, Jean-François Rey, Luke G. Barrett, Peter H. Thrall

PLOS Computational Biology: published April 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006067

Physics-based simulations of aerial attacks by peregrine falcons reveal that stooping at high speed maximizes catch success against agile prey

Robin Mills, Hanno Hildenbrandt, Graham K. Taylor, Charlotte K. Hemelrijk

PLOS Computational Biology: published April 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006044

Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data

Travers Ching, Xun Zhu, Lana X. Garmire

PLOS Computational Biology: published April 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006076

Interactions of spatial strategies producing generalization gradient and blocking: A computational approach

Laurent Dollé, Ricardo Chavarriaga, Agnès Guillot, Mehdi Khamassi

PLOS Computational Biology: published April 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006092

Toward a theory of coactivation patterns in excitable neural networks

Arnaud Messé, Marc-Thorsten Hütt, Claus C. Hilgetag

PLOS Computational Biology: published April 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006084

Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction

Wolfgang Giese, Gregor Milicic, Andreas Schröder, Edda Klipp

PLOS Computational Biology: published April 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006075

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa

Huanan Zhang, Catherine A. A. Lee, Zhuliu Li, John R. Garbe, Cindy R. Eide, Raphael Petegrosso, Rui Kuang, Jakub Tolar

PLOS Computational Biology: published April 9, 2018 | https://doi.org/10.1371/journal.pcbi.1006053

Need for speed: An optimized gridding approach for spatially explicit disease simulations

Stefan Sellman, Kimberly Tsao, Michael J. Tildesley, Peter Brommesson, Colleen T. Webb, Uno Wennergren, Matt J. Keeling, Tom Lindström

PLOS Computational Biology: published April 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006086

Effect of Ca²⁺ on the promiscuous target-protein binding of calmodulin

Annie M. Westerlund, Lucie Delemotte

PLOS Computational Biology: published April 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006072

Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1

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PLOS Computational Biology: published April 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006065

Computational analysis of the oscillatory behavior at the translation level induced by mRNA levels oscillations due to finite intracellular resources

Yoram Zarai, Tamir Tuller

PLOS Computational Biology: published April 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006055

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PLOS Computational Biology: published April 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006033