September 2020

The novel coronavirus responsible for COVID-19, SARS-CoV-2, has resulted in over 32 million confirmed infections worldwide (as of September 25, 2020). Zhao et al have proposed an efficient methodology for genetically subtyping the SARS-CoV-2 virus. DNA sequence entropy identifies variable nucleotide sites, which are used to generate genetic signatures called informative subtype markers (ISMs). This image shows the resulting global distribution of predominant genetic subtypes of the virus. Spatiotemporal mapping of the distribution of ISM subtypes can track the progress of the pandemic. ISM patterns can also be analyzed to identify emerging sets of covarying mutations.

Image Credit: Zhao et al

Editorials

Ten simple rules for an inclusive summer coding program for non-computer-science undergraduates

Pleuni Pennings, Mayra M. Banuelos, Francisca L. Catalan, Victoria R. Caudill, Bozhidar Chakalov, Selena Hernandez, Jeanice Jones, Chinomnso Okorie, Sepideh Modrek, Rori Rohlfs, Nicole Adelstein

PLOS Computational Biology: published September 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007833

Ten simple rules for open human health research

Aïda Bafeta, Jason Bobe, Jon Clucas, Pattie Pramila Gonsalves, Célya Gruson-Daniel, Kathy L. Hudson, Arno Klein, Anirudh Krishnakumar, Anna McCollister-Slipp, Ariel B. Lindner, Dusan Misevic, John A. Naslund, Camille Nebeker, Aki Nikolaidis, Irene Pasquetto, Gabriela Sanchez, Matthieu Schapira, Tohar Scheininger, Félix Schoeller, Anibal Sólon Heinsfeld, François Taddei

PLOS Computational Biology: published September 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007846

Ten simple rules on how to write a standard operating procedure

Susanne Hollmann, Marcus Frohme, Christoph Endrullat, Andreas Kremer, Domenica D’Elia, Babette Regierer, Alina Nechyporenko, on behalf of Cost Action CA15110

PLOS Computational Biology: published September 3, 2020 | https://doi.org/10.1371/journal.pcbi.1008095

Education Articles

Ten quick tips for teaching with participatory live coding

Alexander Nederbragt, Rayna Michelle Harris, Alison Presmanes Hill, Greg Wilson

PLOS Computational Biology: published September 10, 2020 | https://doi.org/10.1371/journal.pcbi.1008090

Ten simple rules to make your research more sustainable

Anne-Laure Ligozat, Aurélie Névéol, Bénédicte Daly, Emmanuelle Frenoux

PLOS Computational Biology: published September 24, 2020 | https://doi.org/10.1371/journal.pcbi.1008148

Perspective

Ten simple rules for writing scientific op-ed articles

Hoe-Han Goh, Philip Bourne

PLOS Computational Biology: published September 17, 2020 | https://doi.org/10.1371/journal.pcbi.1008187

Research Articles

Microtubule instability driven by longitudinal and lateral strain propagation

Maxim Igaev, Helmut Grubmüller

PLOS Computational Biology: published September 2, 2020 | https://doi.org/10.1371/journal.pcbi.1008132

Direction-selective motion discrimination by traveling waves in visual cortex

Stewart Heitmann, G. Bard Ermentrout

PLOS Computational Biology: published September 2, 2020 | https://doi.org/10.1371/journal.pcbi.1008164

Basal leakage in oscillation: Coupled transcriptional and translational control using feed-forward loops

Ignasius Joanito, Ching-Cher Sanders Yan, Jhih-Wei Chu, Shu-Hsing Wu, Chao-Ping Hsu

PLOS Computational Biology: published September 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007740

Shape-to-graph mapping method for efficient characterization and classification of complex geometries in biological images

William Pilcher, Xingyu Yang, Anastasia Zhurikhina, Olga Chernaya, Yinghan Xu, Peng Qiu, Denis Tsygankov

PLOS Computational Biology: published September 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007758

Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention

Yunjun Zhang, Thomas Leitner, Jan Albert, Tom Britton

PLOS Computational Biology: published September 3, 2020 | https://doi.org/10.1371/journal.pcbi.1008122

Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state

Lia Papadopoulos, Christopher W. Lynn, Demian Battaglia, Danielle S. Bassett

PLOS Computational Biology: published September 4, 2020 | https://doi.org/10.1371/journal.pcbi.1008144

VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution

Wei Xiong Wen, Adam J. Mead, Supat Thongjuea

PLOS Computational Biology: published September 8, 2020 | https://doi.org/10.1371/journal.pcbi.1008195

Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures

Bo Chen, Wei Xu

PLOS Computational Biology: published September 8, 2020 | https://doi.org/10.1371/journal.pcbi.1008108

Integration of social cues and individual experiences during instrumental avoidance learning

Philip Pärnamets, Andreas Olsson

PLOS Computational Biology: published September 8, 2020 | https://doi.org/10.1371/journal.pcbi.1008163

Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion

Nikolaus Korfhage, Markus Mühling, Stephan Ringshandl, Anke Becker, Bernd Schmeck, Bernd Freisleben

PLOS Computational Biology: published September 8, 2020 | https://doi.org/10.1371/journal.pcbi.1008179

Similarities and differences in spatial and non-spatial cognitive maps

Charley M. Wu, Eric Schulz, Mona M. Garvert, Björn Meder, Nicolas W. Schuck

PLOS Computational Biology: published September 9, 2020 | https://doi.org/10.1371/journal.pcbi.1008149

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data

Thinh N. Tran, Gary D. Bader

PLOS Computational Biology: published September 9, 2020 | https://doi.org/10.1371/journal.pcbi.1008205

A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway

Gabriella J. Gerlach, Rachel Carrock, Robyn Stix, Elliott J. Stollar, K. Aurelia Ball

PLOS Computational Biology: published September 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007815

Genetic buffering and potentiation in metabolism

Juan F. Poyatos

PLOS Computational Biology: published September 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008185

Kinetic modeling of H₂O₂ dynamics in the mitochondria of HeLa cells

Kassi T. Stein, Sun Jin Moon, Athena N. Nguyen, Hadley D. Sikes

PLOS Computational Biology: published September 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008202

NuSeT: A deep learning tool for reliably separating and analyzing crowded cells

Linfeng Yang, Rajarshi P. Ghosh, J. Matthew Franklin, Simon Chen, Chenyu You, Raja R. Narayan, Marc L. Melcher, Jan T. Liphardt

PLOS Computational Biology: published September 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008193

Effects of spatial heterogeneity on bacterial genetic circuits

Carlos Barajas, Domitilla Del Vecchio

PLOS Computational Biology: published September 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008159

Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

Cristina Herencias, Sergio Salgado-Briegas, M. Auxiliadora Prieto, Juan Nogales

PLOS Computational Biology: published September 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007646

MONET: Multi-omic module discovery by omic selection

Nimrod Rappoport, Roy Safra, Ron Shamir

PLOS Computational Biology: published September 15, 2020 | https://doi.org/10.1371/journal.pcbi.1008182

A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology

Ziqiang Wei, Bei-Jung Lin, Tsai-Wen Chen, Kayvon Daie, Karel Svoboda, Shaul Druckmann

PLOS Computational Biology: published September 15, 2020 | https://doi.org/10.1371/journal.pcbi.1008198

DeepHE: Accurately predicting human essential genes based on deep learning

Xue Zhang, Wangxin Xiao, Weijia Xiao

PLOS Computational Biology: published September 16, 2020 | https://doi.org/10.1371/journal.pcbi.1008229

Discovering functional sequences with RELICS, an analysis method for CRISPR screens

Patrick C. Fiaux, Hsiuyi V. Chen, Poshen B. Chen, Aaron R. Chen, Graham McVicker

PLOS Computational Biology: published September 16, 2020 | https://doi.org/10.1371/journal.pcbi.1008194

Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization

Zhengqiao Zhao, Bahrad A. Sokhansanj, Charvi Malhotra, Kitty Zheng, Gail L. Rosen

PLOS Computational Biology: published September 17, 2020 | https://doi.org/10.1371/journal.pcbi.1008269

Response nonlinearities in networks of spiking neurons

Alessandro Sanzeni, Mark H. Histed, Nicolas Brunel

PLOS Computational Biology: published September 17, 2020 | https://doi.org/10.1371/journal.pcbi.1008165

A new Graph Gaussian embedding method for analyzing the effects of cognitive training

Mengjia Xu, Zhijiang Wang, Haifeng Zhang, Dimitrios Pantazis, Huali Wang, Quanzheng Li

PLOS Computational Biology: published September 17, 2020 | https://doi.org/10.1371/journal.pcbi.1008186

The relative contributions of infectious and mitotic spread to HTLV-1 persistence

Daniel J. Laydon, Vikram Sunkara, Lies Boelen, Charles R. M. Bangham, Becca Asquith

PLOS Computational Biology: published September 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007470

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

Hyeon-Jin Kim, Galip Gürkan Yardımcı, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B. Ware, Jay Shendure, Zhijun Duan, William Stafford Noble

PLOS Computational Biology: published September 18, 2020 | https://doi.org/10.1371/journal.pcbi.1008173

All-atom simulation of the HET-s prion replication

Luca Terruzzi, Giovanni Spagnolli, Alberto Boldrini, Jesús R. Requena, Emiliano Biasini, Pietro Faccioli

PLOS Computational Biology: published September 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007922

Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance

Cody Baker, Vicky Zhu, Robert Rosenbaum

PLOS Computational Biology: published September 18, 2020 | https://doi.org/10.1371/journal.pcbi.1008192

Fast estimation of time-varying infectious disease transmission rates

Mikael Jagan, Michelle S. deJonge, Olga Krylova, David J. D. Earn

PLOS Computational Biology: published September 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008124

Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination

Ryan E. Pavlovicz, Hahnbeom Park, Frank DiMaio

PLOS Computational Biology: published September 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008103

Prospects for detecting early warning signals in discrete event sequence data: Application to epidemiological incidence data

Emma Southall, Michael J. Tildesley, Louise Dyson

PLOS Computational Biology: published September 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007836

Alcoholic liver disease: A registry view on comorbidities and disease prediction

Dhouha Grissa, Ditlev Nytoft Rasmussen, Aleksander Krag, Søren Brunak, Lars Juhl Jensen

PLOS Computational Biology: published September 22, 2020 | https://doi.org/10.1371/journal.pcbi.1008244

A compiler for biological networks on silicon chips

J. Kyle Medley, Jonathan Teo, Sung Sik Woo, Joseph Hellerstein, Rahul Sarpeshkar, Herbert M. Sauro

PLOS Computational Biology: published September 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008063

Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data

Camila P. E. de Souza, Mirela Andronescu, Tehmina Masud, Farhia Kabeer, Justina Biele, Emma Laks, Daniel Lai, Patricia Ye, Jazmine Brimhall, Beixi Wang, Edmund Su, Tony Hui, Qi Cao, Marcus Wong, Michelle Moksa, Richard A. Moore, Martin Hirst, Samuel Aparicio, Sohrab P. Shah

PLOS Computational Biology: published September 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008270

Identifying locations of re-entrant drivers from patient-specific distribution of fibrosis in the left atrium

Aditi Roy, Marta Varela, Henry Chubb, Robert MacLeod, Jules C. Hancox, Tobias Schaeffter, Oleg Aslanidi

PLOS Computational Biology: published September 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008086

Efficient sensory coding of multidimensional stimuli

Thomas E. Yerxa, Eric Kee, Michael R. DeWeese, Emily A. Cooper

PLOS Computational Biology: published September 24, 2020 | https://doi.org/10.1371/journal.pcbi.1008146

Buffering and total calcium levels determine the presence of oscillatory regimes in cardiac cells

Miquel Marchena, Blas Echebarria, Yohannes Shiferaw, Enrique Alvarez-Lacalle

PLOS Computational Biology: published September 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007728

Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms

Rajib Mukherjee, Burcu Beykal, Adam T. Szafran, Melis Onel, Fabio Stossi, Maureen G. Mancini, Dillon Lloyd, Fred A. Wright, Lan Zhou, Michael A. Mancini, Efstratios N. Pistikopoulos

PLOS Computational Biology: published September 24, 2020 | https://doi.org/10.1371/journal.pcbi.1008191

A greedy classifier optimization strategy to assess ion channel blocking activity and pro-arrhythmia in hiPSC-cardiomyocytes

Fabien Raphel, Tessa De Korte, Damiano Lombardi, Stefan Braam, Jean-Frederic Gerbeau

PLOS Computational Biology: published September 25, 2020 | https://doi.org/10.1371/journal.pcbi.1008203

Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes

Quirine A. ten Bosch, Joseph M. Wagman, Fanny Castro-Llanos, Nicole L. Achee, John P. Grieco, T. Alex Perkins

PLOS Computational Biology: published September 25, 2020 | https://doi.org/10.1371/journal.pcbi.1008190

Short-term depression and long-term plasticity together tune sensitive range of synaptic plasticity

Nicolas Deperrois, Michael Graupner

PLOS Computational Biology: published September 25, 2020 | https://doi.org/10.1371/journal.pcbi.1008265

A simple, scalable approach to building a cross-platform transcriptome atlas

Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim-Anh Lê Cao, Jarny Choi, Christine A. Wells

PLOS Computational Biology: published September 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008219

Modeling the efficiency of filovirus entry into cells in vitro: Effects of SNP mutations in the receptor molecule

Kwang Su Kim, Tatsunari Kondoh, Yusuke Asai, Ayato Takada, Shingo Iwami

PLOS Computational Biology: published September 28, 2020 | https://doi.org/10.1371/journal.pcbi.1007612

Mutation bias interacts with composition bias to influence adaptive evolution

Alejandro V. Cano, Joshua L. Payne

PLOS Computational Biology: published September 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008296

Characterizing chromatin folding coordinate and landscape with deep learning

Wen Jun Xie, Yifeng Qi, Bin Zhang

PLOS Computational Biology: published September 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008262

A bacterial size law revealed by a coarse-grained model of cell physiology

François Bertaux, Julius von Kügelgen, Samuel Marguerat, Vahid Shahrezaei

PLOS Computational Biology: published September 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008245

Tuning network dynamics from criticality to an asynchronous state

Jingwen Li, Woodrow L. Shew

PLOS Computational Biology: published September 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008268

Domino-like transient dynamics at seizure onset in epilepsy

Jennifer Creaser, Congping Lin, Thomas Ridler, Jonathan T. Brown, Wendyl D’Souza, Udaya Seneviratne, Mark Cook, John R. Terry, Krasimira Tsaneva-Atanasova

PLOS Computational Biology: published September 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008206

Minimizing the number of optimizations for efficient community dynamic flux balance analysis

James D. Brunner, Nicholas Chia

PLOS Computational Biology: published September 29, 2020 | https://doi.org/10.1371/journal.pcbi.1007786

Inferring a complete genotype-phenotype map from a small number of measured phenotypes

Zachary R. Sailer, Sarah H. Shafik, Robert L. Summers, Alex Joule, Alice Patterson-Robert, Rowena E. Martin, Michael J. Harms

PLOS Computational Biology: published September 29, 2020 | https://doi.org/10.1371/journal.pcbi.1008243

Cyclic transitions between higher order motifs underlie sustained asynchronous spiking in sparse recurrent networks

Kyle Bojanek, Yuqing Zhu, Jason MacLean

PLOS Computational Biology: published September 30, 2020 | https://doi.org/10.1371/journal.pcbi.1007409

Increased comparability between RNA-Seq and microarray data by utilization of gene sets

Frans M. van der Kloet, Jeroen Buurmans, Martijs J. Jonker, Age K. Smilde, Johan A. Westerhuis

PLOS Computational Biology: published September 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008295

Aberrant computational mechanisms of social learning and decision-making in schizophrenia and borderline personality disorder

Lara Henco, Andreea O. Diaconescu, Juha M. Lahnakoski, Marie-Luise Brandi, Sophia Hörmann, Johannes Hennings, Alkomiet Hasan, Irina Papazova, Wolfgang Strube, Dimitris Bolis, Leonhard Schilbach, Christoph Mathys

PLOS Computational Biology: published September 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008162

IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis

Gianfranco Politano, Alfredo Benso

PLOS Computational Biology: published September 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008238

Uncertainty-driven regulation of learning and exploration in adolescents: A computational account

Marieke Jepma, Jessica V. Schaaf, Ingmar Visser, Hilde M. Huizenga

PLOS Computational Biology: published September 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008276

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Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization

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