Ten simple rules for reading a scientific paper

Maureen A. Carey, Kevin L. Steiner, William A. Petri Jr

PLOS Computational Biology: published July 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008032

A framework to assess the quality and impact of bioinformatics training across ELIXIR

Kim T. Gurwitz, Prakash Singh Gaur, Louisa J. Bellis, Lee Larcombe, Eva Alloza, Balint Laszlo Balint, Alexander Botzki, Jure Dimec, Victoria Dominguez del Angel, Pedro L. Fernandes, Eija Korpelainen, Roland Krause, Mateusz Kuzak, Loredana Le Pera, Brane Leskošek, Jessica M. Lindvall, Diana Marek, Paula A. Martinez, Tuur Muyldermans, Ståle Nygård, Patricia M. Palagi, Hedi Peterson, Fotis Psomopoulos, Vojtech Spiwok, Celia W. G. van Gelder, Allegra Via, Marko Vidak, Daniel Wibberg, Sarah L. Morgan, Gabriella Rustici

PLOS Computational Biology: published July 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007976

Nine quick tips for efficient bioinformatics curriculum development and training

Susan McClatchy, Kristin M. Bass, Daniel M. Gatti, Adam Moylan, Gary Churchill

PLOS Computational Biology: published July 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008007

A simple model for learning in volatile environments

Payam Piray, Nathaniel D. Daw

PLOS Computational Biology: published July 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007963

Extracellular loops of BtuB facilitate transport of vitamin B₁₂ through the outer membrane of E. coli

Tomasz Pieńko, Joanna Trylska

PLOS Computational Biology: published July 1, 2020 | https://doi.org/10.1371/journal.pcbi.1008024

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1. Correction: Extracellular loops of BtuB facilitate transport of vitamin B₁₂ through the outer membrane of E. coli

Using information theory to optimise epidemic models for real-time prediction and estimation

Kris V. Parag, Christl A. Donnelly

PLOS Computational Biology: published July 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007990

A systems-biology approach to molecular machines: Exploration of alternative transporter mechanisms

August George, Paola Bisignano, John M. Rosenberg, Michael Grabe, Daniel M. Zuckerman

PLOS Computational Biology: published July 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007884

A kinetic mechanism for enhanced selectivity of membrane transport

Paola Bisignano, Michael A. Lee, August George, Daniel M. Zuckerman, Michael Grabe, John M. Rosenberg

PLOS Computational Biology: published July 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007789

Computational models to improve surveillance for cassava brown streak disease and minimize yield loss

Alex C. Ferris, Richard O. J. H. Stutt, David Godding, Christopher A. Gilligan

PLOS Computational Biology: published July 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007823

Brain-optimized extraction of complex sound features that drive continuous auditory perception

Julia Berezutskaya, Zachary V. Freudenburg, Umut Güçlü, Marcel A. J. van Gerven, Nick F. Ramsey

PLOS Computational Biology: published July 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007992

Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices

Joe Hilton, Matt J. Keeling

PLOS Computational Biology: published July 2, 2020 | https://doi.org/10.1371/journal.pcbi.1008031

Trade-off between local transmission and long-range dispersal drives infectious disease outbreak size in spatially structured populations

Elisa Benincà, Thomas Hagenaars, Gert Jan Boender, Jan van de Kassteele, Michiel van Boven

PLOS Computational Biology: published July 6, 2020 | https://doi.org/10.1371/journal.pcbi.1008009

Electrostatic and bending energies predict staggering and splaying in nonmuscle myosin II minifilaments

Tom L. Kaufmann, Ulrich S. Schwarz

PLOS Computational Biology: published July 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007801

Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections

Madison S. Krieger, Carson E. Denison, Thayer L. Anderson, Martin A. Nowak, Alison L. Hill

PLOS Computational Biology: published July 6, 2020 | https://doi.org/10.1371/journal.pcbi.1008010

Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality

Thuy T. T. Le, Frederick R. Adler

PLOS Computational Biology: published July 6, 2020 | https://doi.org/10.1371/journal.pcbi.1008036

OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling

Konstantin Butenko, Christian Bahls, Max Schröder, Rüdiger Köhling, Ursula van Rienen

PLOS Computational Biology: published July 6, 2020 | https://doi.org/10.1371/journal.pcbi.1008023

Winter is coming: Pathogen emergence in seasonal environments

Philippe Carmona, Sylvain Gandon

PLOS Computational Biology: published July 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007954

Real time structural search of the Protein Data Bank

Dmytro Guzenko, Stephen K. Burley, Jose M. Duarte

PLOS Computational Biology: published July 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007970

Socioeconomic bias in influenza surveillance

Samuel V. Scarpino, James G. Scott, Rosalind M. Eggo, Bruce Clements, Nedialko B. Dimitrov, Lauren Ancel Meyers

PLOS Computational Biology: published July 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007941

Immunization strategies in networks with missing data

Samuel F. Rosenblatt, Jeffrey A. Smith, G. Robin Gauthier, Laurent Hébert-Dufresne

PLOS Computational Biology: published July 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007897

AncesTree: An interactive immunoglobulin lineage tree visualizer

Mathilde Foglierini, Leontios Pappas, Antonio Lanzavecchia, Davide Corti, Laurent Perez

PLOS Computational Biology: published July 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007731

Whole cell biophysical modeling of codon-tRNA competition reveals novel insights related to translation dynamics

Doron Levin, Tamir Tuller

PLOS Computational Biology: published July 10, 2020 | https://doi.org/10.1371/journal.pcbi.1008038

Unravelling the γ-butyrolactone network in Streptomyces coelicolor by computational ensemble modelling

Areti Tsigkinopoulou, Eriko Takano, Rainer Breitling

PLOS Computational Biology: published July 10, 2020 | https://doi.org/10.1371/journal.pcbi.1008039

The interplay between somatic and dendritic inhibition promotes the emergence and stabilization of place fields

Victor Pedrosa, Claudia Clopath

PLOS Computational Biology: published July 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007955

Heterogeneous, delayed-onset killing by multiple-hitting T cells: Stochastic simulations to assess methods for analysis of imaging data

Richard J. Beck, Dario I. Bijker, Joost B. Beltman

PLOS Computational Biology: published July 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007972

Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data

Xian F. Mallory, Mohammadamin Edrisi, Nicholas Navin, Luay Nakhleh

PLOS Computational Biology: published July 13, 2020 | https://doi.org/10.1371/journal.pcbi.1008012

Heart failure-induced atrial remodelling promotes electrical and conduction alternans

Na Zhao, Qince Li, Kevin Zhang, Kuanquan Wang, Runnan He, Yongfeng Yuan, Henggui Zhang

PLOS Computational Biology: published July 13, 2020 | https://doi.org/10.1371/journal.pcbi.1008048

Towards optogenetic vision restoration with high resolution

Ulisse Ferrari, Stéphane Deny, Abhishek Sengupta, Romain Caplette, Francesco Trapani, José-Alain Sahel, Deniz Dalkara, Serge Picaud, Jens Duebel, Olivier Marre

PLOS Computational Biology: published July 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007857

iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding

Huiyuan Chen, Feixiong Cheng, Jing Li

PLOS Computational Biology: published July 15, 2020 | https://doi.org/10.1371/journal.pcbi.1008040

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line

Elin Nyman, Richard R. Stein, Xiaohong Jing, Weiqing Wang, Benjamin Marks, Ioannis K. Zervantonakis, Anil Korkut, Nicholas P. Gauthier, Chris Sander

PLOS Computational Biology: published July 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007909

A mathematical model for persistent post-CSD vasoconstriction

Shixin Xu, Joshua C. Chang, Carson C. Chow, KC Brennan, Huaxiong Huang

PLOS Computational Biology: published July 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007996

Data-driven contact structures: From homogeneous mixing to multilayer networks

Alberto Aleta, Guilherme Ferraz de Arruda, Yamir Moreno

PLOS Computational Biology: published July 16, 2020 | https://doi.org/10.1371/journal.pcbi.1008035

Estimation of neuron parameters from imperfect observations

Joseph D. Taylor, Samuel Winnall, Alain Nogaret

PLOS Computational Biology: published July 16, 2020 | https://doi.org/10.1371/journal.pcbi.1008053

Interactions between calmodulin and neurogranin govern the dynamics of CaMKII as a leaky integrator

Mariam Ordyan, Tom Bartol, Mary Kennedy, Padmini Rangamani, Terrence Sejnowski

PLOS Computational Biology: published July 17, 2020 | https://doi.org/10.1371/journal.pcbi.1008015

AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

Andrew J. Page, Sarah Bastkowski, Muhammad Yasir, A. Keith Turner, Thanh Le Viet, George M. Savva, Mark A. Webber, Ian G. Charles

PLOS Computational Biology: published July 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007980

Computational principles of neural adaptation for binaural signal integration

Timo Oess, Marc O. Ernst, Heiko Neumann

PLOS Computational Biology: published July 17, 2020 | https://doi.org/10.1371/journal.pcbi.1008020

Cross-species regulatory sequence activity prediction

David R. Kelley

PLOS Computational Biology: published July 20, 2020 | https://doi.org/10.1371/journal.pcbi.1008050

Mathematical modeling of plant cell fate transitions controlled by hormonal signals

Filip Z. Klawe, Thomas Stiehl, Peter Bastian, Christophe Gaillochet, Jan U. Lohmann, Anna Marciniak-Czochra

PLOS Computational Biology: published July 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007523

A novel riboswitch classification based on imbalanced sequences achieved by machine learning

Solomon Shiferaw Beyene, Tianyi Ling, Blagoj Ristevski, Ming Chen

PLOS Computational Biology: published July 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007760

Multidimensional phenotyping predicts lifespan and quantifies health in Caenorhabditis elegans

Céline N. Martineau, André E. X. Brown, Patrick Laurent

PLOS Computational Biology: published July 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008002

Capsule networks as recurrent models of grouping and segmentation

Adrien Doerig, Lynn Schmittwilken, Bilge Sayim, Mauro Manassi, Michael H. Herzog

PLOS Computational Biology: published July 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008017

Bayesian modelling of high-throughput sequencing assays with malacoda

Andrew R. Ghazi, Xianguo Kong, Ed S. Chen, Leonard C. Edelstein, Chad A. Shaw

PLOS Computational Biology: published July 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007504

Predicting lymphatic filariasis elimination in data-limited settings: A reconstructive computational framework for combining data generation and model discovery

Morgan E. Smith, Emily Griswold, Brajendra K. Singh, Emmanuel Miri, Abel Eigege, Solomon Adelamo, John Umaru, Kenrick Nwodu, Yohanna Sambo, Jonathan Kadimbo, Jacob Danyobi, Frank O. Richards, Edwin Michael

PLOS Computational Biology: published July 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007506

Beyond ranking nodes: Predicting epidemic outbreak sizes by network centralities

Doina Bucur, Petter Holme

PLOS Computational Biology: published July 22, 2020 | https://doi.org/10.1371/journal.pcbi.1008052

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes

David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz

PLOS Computational Biology: published July 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007553

The location of the axon initial segment affects the bandwidth of spike initiation dynamics

Christophe Verbist, Michael G. Müller, Huibert D. Mansvelder, Robert Legenstein, Michele Giugliano

PLOS Computational Biology: published July 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008087

An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias

Jennifer L. Wilson, Dan Lu, Nick Corr, Aaron Fullerton, James Lu

PLOS Computational Biology: published July 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007620

Signaling models for dopamine-dependent temporal contiguity in striatal synaptic plasticity

Hidetoshi Urakubo, Sho Yagishita, Haruo Kasai, Shin Ishii

PLOS Computational Biology: published July 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008078

Depth in convolutional neural networks solves scene segmentation

Noor Seijdel, Nikos Tsakmakidis, Edward H. F. de Haan, Sander M. Bohte, H. Steven Scholte

PLOS Computational Biology: published July 24, 2020 | https://doi.org/10.1371/journal.pcbi.1008022

A practical application of generative adversarial networks for RNA-seq analysis to predict the molecular progress of Alzheimer's disease

Jinhee Park, Hyerin Kim, Jaekwang Kim, Mookyung Cheon

PLOS Computational Biology: published July 24, 2020 | https://doi.org/10.1371/journal.pcbi.1008099

scPADGRN: A preconditioned ADMM approach for reconstructing dynamic gene regulatory network using single-cell RNA sequencing data

Xiao Zheng, Yuan Huang, Xiufen Zou

PLOS Computational Biology: published July 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007471

Temperature-robust activity patterns arise from coordinated axonal Sodium channel properties

Margaret L. DeMaegd, Wolfgang Stein

PLOS Computational Biology: published July 27, 2020 | https://doi.org/10.1371/journal.pcbi.1008057

An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets

Philipp Schneider, Axel von Kamp, Steffen Klamt

PLOS Computational Biology: published July 27, 2020 | https://doi.org/10.1371/journal.pcbi.1008110

Spatial and temporal patterns of nitric oxide diffusion and degradation drive emergent cerebrovascular dynamics

William Davis Haselden, Ravi Teja Kedarasetti, Patrick J. Drew

PLOS Computational Biology: published July 27, 2020 | https://doi.org/10.1371/journal.pcbi.1008069

A circuit model of auditory cortex

Youngmin Park, Maria N. Geffen

PLOS Computational Biology: published July 27, 2020 | https://doi.org/10.1371/journal.pcbi.1008016

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Quorum sensing via dynamic cytokine signaling comprehensively explains divergent patterns of effector choice among helper T cells

Edward C. Schrom II, Simon A. Levin, Andrea L. Graham

PLOS Computational Biology: published July 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008051

ADP is the dominant controller of AMP-activated protein kinase activity dynamics in skeletal muscle during exercise

Ian F. Coccimiglio, David C. Clarke

PLOS Computational Biology: published July 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008079

Electrical coupling controls dimensionality and chaotic firing of inferior olive neurons

Huu Hoang, Eric J. Lang, Yoshito Hirata, Isao T. Tokuda, Kazuyuki Aihara, Keisuke Toyama, Mitsuo Kawato, Nicolas Schweighofer

PLOS Computational Biology: published July 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008075

Emergent neutrality in consumer-resource dynamics

Rafael D’Andrea, Theo Gibbs, James P. O’Dwyer

PLOS Computational Biology: published July 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008102

Regional sequence expansion or collapse in heterozygous genome assemblies

Kathryn C. Asalone, Kara M. Ryan, Maryam Yamadi, Annastelle L. Cohen, William G. Farmer, Deborah J. George, Claudia Joppert, Kaitlyn Kim, Madeeha Froze Mughal, Rana Said, Metin Toksoz-Exley, Evgeny Bisk, John R. Bracht

PLOS Computational Biology: published July 31, 2020 | https://doi.org/10.1371/journal.pcbi.1008104

Cortical ignition dynamics is tightly linked to the core organisation of the human connectome

Samy Castro, Wael El-Deredy, Demian Battaglia, Patricio Orio

PLOS Computational Biology: published July 31, 2020 | https://doi.org/10.1371/journal.pcbi.1007686