March 2020

Many diseases are known to impede the deformability of the red blood cell, which may adversely impact the transport of red blood cells (red) and platelets (yellow) in flow. Czaja et al. observes with increasing fractions of stiffened red blood cells (purple) in flow, a decrease of platelet margination to the vessel wall. Specifically, this is observed as a decrease of a fluorescent platelet signal at the wall of a glass channel with flowing human whole blood, and confirmed via cell resolved simulations.

Image Credit: Benjamin Czaja, The University of Amsterdam

Editorials

Ten Simple Rules for organizing a non–real-time web conference

Ana Arnal, Irene Epifanio, Pablo Gregori, Vicente Martínez

PLOS Computational Biology: published March 26, 2020 | https://doi.org/10.1371/journal.pcbi.1007667

Ten simple rules for providing effective bioinformatics research support

Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi, Lyndon Zass

PLOS Computational Biology: published March 26, 2020 | https://doi.org/10.1371/journal.pcbi.1007531

Education

Seven quick tips for analysis scripts in neuroimaging

Marijn van Vliet

PLOS Computational Biology: published March 26, 2020 | https://doi.org/10.1371/journal.pcbi.1007358

Research Articles

Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens

Jason C. Hyun, Erol S. Kavvas, Jonathan M. Monk, Bernhard O. Palsson

PLOS Computational Biology: published March 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007608

Direct coupling analysis of epistasis in allosteric materials

Barbara Bravi, Riccardo Ravasio, Carolina Brito, Matthieu Wyart

PLOS Computational Biology: published March 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007630

Modular analysis of the control of flagellar Ca²⁺-spike trains produced by CatSper and Ca_V channels in sea urchin sperm

Daniel A. Priego-Espinosa, Alberto Darszon, Adán Guerrero, Ana Laura González-Cota, Takuya Nishigaki, Gustavo Martínez-Mekler, Jorge Carneiro

PLOS Computational Biology: published March 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007605

Model-based analysis of response and resistance factors of cetuximab treatment in gastric cancer cell lines

Elba Raimúndez, Simone Keller, Gwen Zwingenberger, Karolin Ebert, Sabine Hug, Fabian J. Theis, Dieter Maier, Birgit Luber, Jan Hasenauer

PLOS Computational Biology: published March 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007147

Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila

Sebastian M. Bernasek, Nicolás Peláez, Richard W. Carthew, Neda Bagheri, Luís A. N. Amaral

PLOS Computational Biology: published March 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007406

Striated myocyte structural integrity: Automated analysis of sarcomeric z-discs

Tessa Altair Morris, Jasmine Naik, Kirby Sinclair Fibben, Xiangduo Kong, Tohru Kiyono, Kyoko Yokomori, Anna Grosberg

PLOS Computational Biology: published March 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007676

ASA³P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates

Oliver Schwengers, Andreas Hoek, Moritz Fritzenwanker, Linda Falgenhauer, Torsten Hain, Trinad Chakraborty, Alexander Goesmann

PLOS Computational Biology: published March 5, 2020 | https://doi.org/10.1371/journal.pcbi.1007134

Detecting critical slowing down in high-dimensional epidemiological systems

Tobias Brett, Marco Ajelli, Quan-Hui Liu, Mary G. Krauland, John J. Grefenstette, Willem G. van Panhuis, Alessandro Vespignani, John M. Drake, Pejman Rohani

PLOS Computational Biology: published March 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007679

Modeling binary and graded cone cell fate patterning in the mouse retina

Kiara C. Eldred, Cameron Avelis, Robert J. Johnston Jr, Elijah Roberts

PLOS Computational Biology: published March 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007691

ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

Arshag D. Mooradian, Sjoerd van der Post, Kristen M. Naegle, Jason M. Held

PLOS Computational Biology: published March 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007741

The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems

Michael A. Boemo, Luca Cardelli, Conrad A. Nieduszynski

PLOS Computational Biology: published March 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007651

Parallel Tempering with Lasso for model reduction in systems biology

Sanjana Gupta, Robin E. C. Lee, James R. Faeder

PLOS Computational Biology: published March 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007669

A plausible accelerating function of intermediate states in cancer metastasis

Hanah Goetz, Juan R. Melendez-Alvarez, Luonan Chen, Xiao-Jun Tian

PLOS Computational Biology: published March 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007682

Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization

Rafael R. Bravo, Etienne Baratchart, Jeffrey West, Ryan O. Schenck, Anna K. Miller, Jill Gallaher, Chandler D. Gatenbee, David Basanta, Mark Robertson-Tessi, Alexander R. A. Anderson

PLOS Computational Biology: published March 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007635

Estimation of neural network model parameters from local field potentials (LFPs)

Jan-Eirik W. Skaar, Alexander J. Stasik, Espen Hagen, Torbjørn V. Ness, Gaute T. Einevoll

PLOS Computational Biology: published March 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007725

The impact of news exposure on collective attention in the United States during the 2016 Zika epidemic

Michele Tizzoni, André Panisson, Daniela Paolotti, Ciro Cattuto

PLOS Computational Biology: published March 12, 2020 | https://doi.org/10.1371/journal.pcbi.1007633

Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex

Dmitrii S. Shcherbinin, Vlad A. Belousov, Mikhail Shugay

PLOS Computational Biology: published March 12, 2020 | https://doi.org/10.1371/journal.pcbi.1007714

The influence of red blood cell deformability on hematocrit profiles and platelet margination

Benjamin Czaja, Mario Gutierrez, Gábor Závodszky, David de Kanter, Alfons Hoekstra, Omolola Eniola-Adefeso

PLOS Computational Biology: published March 12, 2020 | https://doi.org/10.1371/journal.pcbi.1007716

Deconvolution of calcium imaging data using marked point processes

Ryohei Shibue, Fumiyasu Komaki

PLOS Computational Biology: published March 12, 2020 | https://doi.org/10.1371/journal.pcbi.1007650

Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

Mariama Jaiteh, Ismael Rodríguez-Espigares, Jana Selent, Jens Carlsson

PLOS Computational Biology: published March 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007680

Modelling the epidemiology of residual Plasmodium vivax malaria in a heterogeneous host population: A case study in the Amazon Basin

Rodrigo M. Corder, Marcelo U. Ferreira, M. Gabriela M. Gomes

PLOS Computational Biology: published March 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007377

Formation of phage lysis patterns and implications on co-propagation of phages and motile host bacteria

Xiaochu Li, Floricel Gonzalez, Nathaniel Esteves, Birgit E. Scharf, Jing Chen

PLOS Computational Biology: published March 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007236

Estimating epidemiological parameters from experiments in vector access to host plants, the method of matching gradients

Ruairí Donnelly, Geofrey W. Sikazwe, Christopher A. Gilligan

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007724

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

Lisa M. Bramer, Amanda M. White, Kelly G. Stratton, Allison M. Thompson, Daniel Claborne, Kirsten Hofmockel, Lee Ann McCue

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007654

Social behavioural adaptation in Autism

Baudouin Forgeot d'Arc, Marie Devaine, Jean Daunizeau

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007700

CAncer bioMarker Prediction Pipeline (CAMPP)—A standardized framework for the analysis of quantitative biological data

Thilde Terkelsen, Anders Krogh, Elena Papaleo

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007665

Learning to represent signals spike by spike

Wieland Brendel, Ralph Bourdoukan, Pietro Vertechi, Christian K. Machens, Sophie Denève

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007692

Computational and robotic modeling reveal parsimonious combinations of interactions between individuals in schooling fish

Liu Lei, Ramón Escobedo, Clément Sire, Guy Theraulaz

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007194

The use of mixture density networks in the emulation of complex epidemiological individual-based models

Christopher N. Davis, T. Deirdre Hollingsworth, Quentin Caudron, Michael A. Irvine

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1006869

A simplified modelling framework facilitates more complex representations of plant circadian clocks

Mathias Foo, Declan G. Bates, Ozgur E. Akman

PLOS Computational Biology: published March 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007671

SVXplorer: Three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures

Kunal Kathuria, Aakrosh Ratan

PLOS Computational Biology: published March 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007737

Methods detecting rhythmic gene expression are biologically relevant only for strong signal

David Laloum, Marc Robinson-Rechavi

PLOS Computational Biology: published March 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007666

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Guillaume Gautreau, Adelme Bazin, Mathieu Gachet, Rémi Planel, Laura Burlot, Mathieu Dubois, Amandine Perrin, Claudine Médigue, Alexandra Calteau, Stéphane Cruveiller, Catherine Matias, Christophe Ambroise, Eduardo P. C. Rocha, David Vallenet

PLOS Computational Biology: published March 19, 2020 | https://doi.org/10.1371/journal.pcbi.1007732

Computational design of substrate selective inhibition

Benny Da’adoosh, Kon Kaito, Keishi Miyashita, Minoru Sakaguchi, Amiram Goldblum

PLOS Computational Biology: published March 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007713

Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach

Isobel Routledge, Shengjie Lai, Katherine E. Battle, Azra C. Ghani, Manuel Gomez-Rodriguez, Kyle B. Gustafson, Swapnil Mishra, Juliette Unwin, Joshua L. Proctor, Andrew J. Tatem, Zhongjie Li, Samir Bhatt

PLOS Computational Biology: published March 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007707

Inference of coevolutionary dynamics and parameters from host and parasite polymorphism data of repeated experiments

Hanna Märkle, Aurélien Tellier

PLOS Computational Biology: published March 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007668

An Evolutionary Trace method defines functionally important bases and sites common to RNA families

Ilya B. Novikov, Angela D. Wilkins, Olivier Lichtarge

PLOS Computational Biology: published March 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007583

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Zhaleh Ghaemi, Joseph R. Peterson, Martin Gruebele, Zaida Luthey-Schulten

PLOS Computational Biology: published March 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007717

Quantifying the roles of vomiting, diarrhea, and residents vs. staff in norovirus transmission in U.S. nursing home outbreaks

Carly Adams, David Young, Paul A. Gastañaduy, Prabasaj Paul, Zach Marsh, Aron J. Hall, Benjamin A. Lopman

PLOS Computational Biology: published March 25, 2020 | https://doi.org/10.1371/journal.pcbi.1007271

A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015

Ellen Brooks-Pollock, Leon Danon, Hester Korthals Altes, Jennifer A. Davidson, Andrew M. T. Pollock, Dick van Soolingen, Colin Campbell, Maeve K. Lalor

PLOS Computational Biology: published March 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007687

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Increased fractions of stiffened red blood cells in flow decreases platelet margination

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