Table of Contents

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


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

Ana Arnal, Irene Epifanio, Pablo Gregori, Vicente Martínez

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


Seven quick tips for analysis scripts in neuroimaging

Marijn van Vliet

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

Direct coupling analysis of epistasis in allosteric materials

Barbara Bravi, Riccardo Ravasio, Carolina Brito, Matthieu Wyart

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Parallel Tempering with Lasso for model reduction in systems biology

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

A plausible accelerating function of intermediate states in cancer metastasis

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

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

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

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

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

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

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

Deconvolution of calcium imaging data using marked point processes

Ryohei Shibue, Fumiyasu Komaki

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

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

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

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

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

Social behavioural adaptation in Autism

Baudouin Forgeot d'Arc, Marie Devaine, Jean Daunizeau

Learning to represent signals spike by spike

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

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

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

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

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

David Laloum, Marc Robinson-Rechavi

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

Computational design of substrate selective inhibition

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

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

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

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

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

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

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

Comparative study of population genomic approaches for mapping colony-level traits

Shani Inbar, Pnina Cohen, Tal Yahav, Eyal Privman

Mechanisms underlying attraction to odors in walking Drosophila

Liangyu Tao, Siddhi Ozarkar, Vikas Bhandawat

Uncoupling the roles of firing rates and spike bursts in shaping the STN-GPe beta band oscillations

Jyotika Bahuguna, Ajith Sahasranamam, Arvind Kumar

Dynamical model of the CLC-2 ion channel reveals conformational changes associated with selectivity-filter gating

Keri A. McKiernan, Anna K. Koster, Merritt Maduke, Vijay S. Pande

The spread of a wild plant pathogen is driven by the road network

Elina Numminen, Anna-Liisa Laine

ProteinVR: Web-based molecular visualization in virtual reality

Kevin C. Cassidy, Jan Šefčík, Yogindra Raghav, Alexander Chang, Jacob D. Durrant