April 2020

Widefield calcium imaging provides a global view of neural activity in the mouse dorsal cortex. Saxena et al. developed LocaNMF (Localized semi-Nonnegative Matrix Factorization), allowing the decomposition of the recorded data into interpretable spatial and temporal components in a stable manner. This is done by mapping the inferred components onto well-defined brain regions using a widely-used brain atlas (here, the Allen Brain Atlas shown in black lines). Each color in this figure corresponds to a given region's spatial components in this mouse brain. Data collected by Simon Musall in the Churchland Laboratory at Cold Spring Harbor Laboratory.

Image Credit: Shreya Saxena, Columbia University

Editorials

Ten Simple Rules for landing on the right job after your PhD or postdoc

Kuan-lin Huang

PLOS Computational Biology: published April 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007723

Ten Simple Rules for writing algorithmic bioinformatics conference papers

Paul Medvedev

PLOS Computational Biology: published April 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007742

Ten simple rules for more objective decision-making

Anthony C. Fletcher, Georges A. Wagner, Philip E. Bourne

PLOS Computational Biology: published April 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007706

Ten simple rules for innovative dissemination of research

Tony Ross-Hellauer, Jonathan P. Tennant, Viltė Banelytė, Edit Gorogh, Daniela Luzi, Peter Kraker, Lucio Pisacane, Roberta Ruggieri, Electra Sifacaki, Michela Vignoli

PLOS Computational Biology: published April 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007704

Education Articles

Ten quick tips for homology modeling of high-resolution protein 3D structures

Yazan Haddad, Vojtech Adam, Zbynek Heger

PLOS Computational Biology: published April 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007449

On the choice of metric in gradient-based theories of brain function

Simone Carlo Surace, Jean-Pascal Pfister, Wulfram Gerstner, Johanni Brea

PLOS Computational Biology: published April 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007640

Reviews

Multiview learning for understanding functional multiomics

Nam D. Nguyen, Daifeng Wang

PLOS Computational Biology: published April 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007677

Multiple-target tracking in human and machine vision

Shiva Kamkar, Fatemeh Ghezloo, Hamid Abrishami Moghaddam, Ali Borji, Reza Lashgari

PLOS Computational Biology: published April 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007698

Research Articles

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

Cedoljub Bundalovic-Torma, Gregory B. Whitfield, Lindsey S. Marmont, P. Lynne Howell, John Parkinson

PLOS Computational Biology: published April 1, 2020 | https://doi.org/10.1371/journal.pcbi.1007721

The research and development process for multiscale models of infectious disease systems

Winston Garira

PLOS Computational Biology: published April 2, 2020 | https://doi.org/10.1371/journal.pcbi.1007734

PlasClass improves plasmid sequence classification

David Pellow, Itzik Mizrahi, Ron Shamir

PLOS Computational Biology: published April 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007781

Discovery of hierarchical representations for efficient planning

Momchil S. Tomov, Samyukta Yagati, Agni Kumar, Wanqian Yang, Samuel J. Gershman

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007594

Flocking in complex environments—Attention trade-offs in collective information processing

Parisa Rahmani, Fernando Peruani, Pawel Romanczuk

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007697

Ion channel noise shapes the electrical activity of endocrine cells

David M. Richards, Jamie J. Walker, Joel Tabak

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007769

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries

Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, J. Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007756

Network mechanisms and dysfunction within an integrated computational model of progression through mitosis in the human cell cycle

Scott S. Terhune, Yongwoon Jung, Katie M. Cataldo, Ranjan K. Dash

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007733

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data

Avtar Roopra

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007800

Complementary computational and experimental evaluation of missense variants in the ROMK potassium channel

Luca Ponzoni, Nga H. Nguyen, Ivet Bahar, Jeffrey L. Brodsky

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007749

Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic tracking

Sarah F. McGough, Michael A. Johansson, Marc Lipsitch, Nicolas A. Menzies

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007735

Robustness of the Dorsal morphogen gradient with respect to morphogen dosage

Hadel Al Asafen, Prasad U. Bandodkar, Sophia Carrell-Noel, Allison E. Schloop, Jeramey Friedman, Gregory T. Reeves

PLOS Computational Biology: published April 6, 2020 | https://doi.org/10.1371/journal.pcbi.1007750

Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks

Hans-Ulrich Klein, Martin Schäfer, David A. Bennett, Holger Schwender, Philip L. De Jager

PLOS Computational Biology: published April 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007771

Mechanistic models of PLC/PKC signaling implicate phosphatidic acid as a key amplifier of chemotactic gradient sensing

Jamie L. Nosbisch, Anisur Rahman, Krithika Mohan, Timothy C. Elston, James E. Bear, Jason M. Haugh

PLOS Computational Biology: published April 7, 2020 | https://doi.org/10.1371/journal.pcbi.1007708

Comparison of methods for rhythm analysis of complex animals’ acoustic signals

Lara S. Burchardt, Mirjam Knörnschild

PLOS Computational Biology: published April 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007755

Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2

Fude Sun, Carsten F. E. Schroer, Carlos R. Palacios, Lida Xu, Shi-Zhong Luo, Siewert J. Marrink

PLOS Computational Biology: published April 9, 2020 | https://doi.org/10.1371/journal.pcbi.1007777

Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa

Megan L. Matthews, Jack P. Wang, Ronald Sederoff, Vincent L. Chiang, Cranos M. Williams

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007197

Near-optimal combination of disparity across a log-polar scaled visual field

Guido Maiello, Manuela Chessa, Peter J. Bex, Fabio Solari

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007699

Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation

Luis Busto-Moner, Julien Morival, Honglei Ren, Arjang Fahim, Zachary Reitz, Timothy L. Downing, Elizabeth L. Read

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007195

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures

Jacob Pfeil, Lauren M. Sanders, Ioannis Anastopoulos, A. Geoffrey Lyle, Alana S. Weinstein, Yuanqing Xue, Andrew Blair, Holly C. Beale, Alex Lee, Stanley G. Leung, Phuong T. Dinh, Avanthi Tayi Shah, Marcus R. Breese, W. Patrick Devine, Isabel Bjork, Sofie R. Salama, E. Alejandro Sweet-Cordero, David Haussler, Olena Morozova Vaske

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007753

Deep reinforcement learning for the control of microbial co-cultures in bioreactors

Neythen J. Treloar, Alex J. H. Fedorec, Brian Ingalls, Chris P. Barnes

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007783

eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research

Augusto Anguita-Ruiz, Alberto Segura-Delgado, Rafael Alcalá, Concepción M. Aguilera, Jesús Alcalá-Fdez

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007792

Climbing Escher’s stairs: A way to approximate stability landscapes in multidimensional systems

Pablo Rodríguez-Sánchez, Egbert H. van Nes, Marten Scheffer

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007788

Resist or perish: Fate of a microbial population subjected to a periodic presence of antimicrobial

Loïc Marrec, Anne-Florence Bitbol

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007798

Ensemble modeling of auditory streaming reveals potential sources of bistability across the perceptual hierarchy

David F. Little, Joel S. Snyder, Mounya Elhilali

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007746

Molecular mechanisms of fentanyl mediated β-arrestin biased signaling

Parker W. de Waal, Jingjing Shi, Erli You, Xiaoxi Wang, Karsten Melcher, Yi Jiang, H. Eric Xu, Bradley M. Dickson

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007394

A powerful and versatile colocalization test

Yangqing Deng, Wei Pan

PLOS Computational Biology: published April 10, 2020 | https://doi.org/10.1371/journal.pcbi.1007778

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning

Jean-Baptiste Lugagne, Haonan Lin, Mary J. Dunlop

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007673

Generalizing to generalize: Humans flexibly switch between compositional and conjunctive structures during reinforcement learning

Nicholas T. Franklin, Michael J. Frank

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007720

Humans adapt their anticipatory eye movements to the volatility of visual motion properties

Chloé Pasturel, Anna Montagnini, Laurent Udo Perrinet

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007438

Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs

Marco Mauri, Jean-Luc Gouzé, Hidde de Jong, Eugenio Cinquemani

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007795

How to fit in: The learning principles of cell differentiation

Miguel Brun-Usan, Christoph Thies, Richard A. Watson

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1006811

DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data

Yi Jiang, Gina Giase, Kay Grennan, Annie W. Shieh, Yan Xia, Lide Han, Quan Wang, Qiang Wei, Rui Chen, Sihan Liu, Kevin P. White, Chao Chen, Bingshan Li, Chunyu Liu

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007522

A mathematical model describing the localization and spread of influenza A virus infection within the human respiratory tract

Christian Quirouette, Nada P. Younis, Micaela B. Reddy, Catherine A. A. Beauchemin

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007705

Improving the coverage of credible sets in Bayesian genetic fine-mapping

Anna Hutchinson, Hope Watson, Chris Wallace

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007829

Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data

Shreya Saxena, Ian Kinsella, Simon Musall, Sharon H. Kim, Jozsef Meszaros, David N. Thibodeaux, Carla Kim, John Cunningham, Elizabeth M. C. Hillman, Anne Churchland, Liam Paninski

PLOS Computational Biology: published April 13, 2020 | https://doi.org/10.1371/journal.pcbi.1007791

DOT: Gene-set analysis by combining decorrelated association statistics

Olga A. Vsevolozhskaya, Min Shi, Fengjiao Hu, Dmitri V. Zaykin

PLOS Computational Biology: published April 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007819

ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks

Pierre Millard, Uwe Schmitt, Patrick Kiefer, Julia A. Vorholt, Stéphanie Heux, Jean-Charles Portais

PLOS Computational Biology: published April 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007799

A molecular odorant transduction model and the complexity of spatio-temporal encoding in the Drosophila antenna

Aurel A. Lazar, Chung-Heng Yeh

PLOS Computational Biology: published April 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007751

Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis

Paul Curtin, Christine Austin, Austen Curtin, Chris Gennings, Claudia Figueroa-Romero, Kristen A. Mikhail, Tatiana M. Botero, Stephen A. Goutman, Eva L. Feldman, Manish Arora

PLOS Computational Biology: published April 15, 2020 | https://doi.org/10.1371/journal.pcbi.1007773

Unveiling dynamic metabolic signatures in human induced pluripotent and neural stem cells

João Vasconcelos e Sá, Daniel Simão, Ana P. Terrasso, Marta M. Silva, Catarina Brito, Inês A. Isidro, Paula M. Alves, Manuel J. T. Carrondo

PLOS Computational Biology: published April 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007780

Insights into adenosine A_2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions

Agustín Bruzzese, James A. R. Dalton, Jesús Giraldo

PLOS Computational Biology: published April 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007818

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments

Matthew L. Jenior, Thomas J. Moutinho Jr., Bonnie V. Dougherty, Jason A. Papin

PLOS Computational Biology: published April 16, 2020 | https://doi.org/10.1371/journal.pcbi.1007099

Striatal network modeling in Huntington’s Disease

Adam Ponzi, Scott J. Barton, Kendra D. Bunner, Claudia Rangel-Barajas, Emily S. Zhang, Benjamin R. Miller, George V. Rebec, James Kozloski

PLOS Computational Biology: published April 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007648

High-dimensional mediation analysis in survival models

Chengwen Luo, Botao Fa, Yuting Yan, Yang Wang, Yiwang Zhou, Yue Zhang, Zhangsheng Yu

PLOS Computational Biology: published April 17, 2020 | https://doi.org/10.1371/journal.pcbi.1007768

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE

Lisa-Katrin Schätzle, Ali Hadizadeh Esfahani, Andreas Schuppert

PLOS Computational Biology: published April 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007803

Flux-based hierarchical organization of Escherichia coli’s metabolic network

Semidán Robaina-Estévez, Zoran Nikoloski

PLOS Computational Biology: published April 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007832

Expression of quasi-equivalence and capsid dimorphism in the Hepadnaviridae

Weimin Wu, Norman R. Watts, Naiqian Cheng, Rick Huang, Alasdair C. Steven, Paul T. Wingfield

PLOS Computational Biology: published April 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007782

Low-rate firing limit for neurons with axon, soma and dendrites driven by spatially distributed stochastic synapses

Robert P. Gowers, Yulia Timofeeva, Magnus J. E. Richardson

PLOS Computational Biology: published April 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007175

Optimizing the deployment of ultra-low volume and targeted indoor residual spraying for dengue outbreak response

Sean M. Cavany, Guido España, Alun L. Lloyd, Lance A. Waller, Uriel Kitron, Helvio Astete, William H. Elson, Gonzalo M. Vazquez-Prokopec, Thomas W. Scott, Amy C. Morrison, Robert C. Reiner Jr., T. Alex Perkins

PLOS Computational Biology: published April 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007743

The drift diffusion model as the choice rule in inter-temporal and risky choice: A case study in medial orbitofrontal cortex lesion patients and controls

Jan Peters, Mark D’Esposito

PLOS Computational Biology: published April 20, 2020 | https://doi.org/10.1371/journal.pcbi.1007615

Structural and molecular insight into the pH-induced low-permeability of the voltage-gated potassium channel Kv1.2 through dewetting of the water cavity

Juhwan Lee, Mooseok Kang, Sangyeol Kim, Iksoo Chang

PLOS Computational Biology: published April 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007405

Accounting for red blood cell accessibility reveals distinct invasion strategies in Plasmodium falciparum strains

Francisco Y. Cai, Tiffany M. DeSimone, Elsa Hansen, Cameron V. Jennings, Amy K. Bei, Ambroise D. Ahouidi, Souleymane Mboup, Manoj T. Duraisingh, Caroline O. Buckee

PLOS Computational Biology: published April 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007702

Compounds without borders: A mechanism for quantifying complex odors and responses to scent-pollution in bumblebees

Jordanna D. H. Sprayberry

PLOS Computational Biology: published April 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007765

Vector bionomics and vectorial capacity as emergent properties of mosquito behaviors and ecology

Sean L. Wu, Héctor M. Sánchez C., John M. Henry, Daniel T. Citron, Qian Zhang, Kelly Compton, Biyonka Liang, Amit Verma, Derek A. T. Cummings, Arnaud Le Menach, Thomas W. Scott, Anne L. Wilson, Steven W. Lindsay, Catherine L. Moyes, Penny A. Hancock, Tanya L. Russell, Thomas R. Burkot, John M. Marshall, Samson Kiware, Robert C. Reiner Jr, David L. Smith

PLOS Computational Biology: published April 22, 2020 | https://doi.org/10.1371/journal.pcbi.1007446

Learning action-oriented models through active inference

Alexander Tschantz, Anil K. Seth, Christopher L. Buckley

PLOS Computational Biology: published April 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007805

Telling ecological networks apart by their structure: An environment-dependent approach

Chuliang Song, Serguei Saavedra

PLOS Computational Biology: published April 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007787

Biophysically grounded mean-field models of neural populations under electrical stimulation

Caglar Cakan, Klaus Obermayer

PLOS Computational Biology: published April 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007822

BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale

Qingyu Chen, Kyubum Lee, Shankai Yan, Sun Kim, Chih-Hsuan Wei, Zhiyong Lu

PLOS Computational Biology: published April 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007617

LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer

Junpeng Zhang, Taosheng Xu, Lin Liu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le

PLOS Computational Biology: published April 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007851

Dimensionality, information and learning in prefrontal cortex

Ramon Bartolo, Richard C. Saunders, Andrew R. Mitz, Bruno B. Averbeck

PLOS Computational Biology: published April 24, 2020 | https://doi.org/10.1371/journal.pcbi.1007514

Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression

Xiangyu Yao, Shihoko Kojima, Jing Chen

PLOS Computational Biology: published April 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007842

ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning

Xinmeng Li, James A. Van Deventer, Soha Hassoun

PLOS Computational Biology: published April 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007779

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

Andreas Haahr Larsen, Yong Wang, Sandro Bottaro, Sergei Grudinin, Lise Arleth, Kresten Lindorff-Larsen

PLOS Computational Biology: published April 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007870

Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species

Vinnu Bhardwaj, Massimo Franceschetti, Ramesh Rao, Pavel A. Pevzner, Yana Safonova

PLOS Computational Biology: published April 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007837

Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysis

Yuanchao Zhang, Man S. Kim, Erin R. Reichenberger, Ben Stear, Deanne M. Taylor

PLOS Computational Biology: published April 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007794

Decentralized control of insect walking: A simple neural network explains a wide range of behavioral and neurophysiological results

Malte Schilling, Holk Cruse

PLOS Computational Biology: published April 27, 2020 | https://doi.org/10.1371/journal.pcbi.1007804

Cover

LocaNMF for region-based decomposition of neural recordings from the mouse brain

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