February 2022

DHFR exploits this alternate anomeric configuration of NADPH to evade inhibition by certain inhibitors.

Image Credit: Graham Holt, Donald Laboratory, Duke University.

Editorials

Ten simple rules for large-scale data processing

Arkarachai Fungtammasan, Alexandra Lee, Jaclyn Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey Greene

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009757

Ten simple rules for improving research data discovery

Nicole Contaxis, Jason Clark, Anthony Dellureficio, Sara Gonzales, Sara Mannheimer, Peter R. Oxley, Melissa A. Ratajeski, Alisa Surkis, Amy M. Yarnell, Michelle Yee, Kristi Holmes

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009768

Ten simple rules for initial data analysis

Mark Baillie, Saskia le Cessie, Carsten Oliver Schmidt, Lara Lusa, Marianne Huebner, for the Topic Group “Initial Data Analysis” of the STRATOS Initiative

PLOS Computational Biology: published February 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009819

Education Articles

Hidden Markov Modeling with HMMTeacher

Camilo Fuentes-Beals, Alejandro Valdés-Jiménez, Gonzalo Riadi

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009703

Twelve quick tips for software design

Greg Wilson

PLOS Computational Biology: published February 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009809

Perspective

There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk

Jon Zelner, Nina B. Masters, Ramya Naraharisetti, Sanyu A. Mojola, Merlin Chowkwanyun, Ryan Malosh

PLOS Computational Biology: published February 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009795

Review

Classification of bursting patterns: A tale of two ducks

Mathieu Desroches, John Rinzel, Serafim Rodrigues

PLOS Computational Biology: published February 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009752

Research Articles

Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth

Stefan Müller, Diana Széliová, Jürgen Zanghellini

PLOS Computational Biology: published February 1, 2022 | https://doi.org/10.1371/journal.pcbi.1009843

Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens

Myo T. Naung, Elijah Martin, Jacob Munro, Somya Mehra, Andrew J. Guy, Moses Laman, G. L. Abby Harrison, Livingstone Tavul, Manuel Hetzel, Dominic Kwiatkowski, Ivo Mueller, Melanie Bahlo, Alyssa E. Barry

PLOS Computational Biology: published February 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009801

RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins

Ignacio Sanchez-Burgos, Jorge R. Espinosa, Jerelle A. Joseph, Rosana Collepardo-Guevara

PLOS Computational Biology: published February 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009810

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

Gabriela Canto-Encalada, Diego Tec-Campos, Juan D. Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, Cristal Zuñiga

PLOS Computational Biology: published February 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009828

Thunderstruck: The ACDC model of flexible sequences and rhythms in recurrent neural circuits

Cristian Buc Calderon, Tom Verguts, Michael J. Frank

PLOS Computational Biology: published February 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009854

Classical mathematical models for prediction of response to chemotherapy and immunotherapy

Narmin Ghaffari Laleh, Chiara Maria Lavinia Loeffler, Julia Grajek, Kateřina Staňková, Alexander T. Pearson, Hannah Sophie Muti, Christian Trautwein, Heiko Enderling, Jan Poleszczuk, Jakob Nikolas Kather

PLOS Computational Biology: published February 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009822

Modelling brain representations of abstract concepts

Daniel Kaiser, Arthur M. Jacobs, Radoslaw M. Cichy

PLOS Computational Biology: published February 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009837

Estimating the glutamate transporter surface density in distinct sub-cellular compartments of mouse hippocampal astrocytes

Anca R. Rǎdulescu, Gabrielle C. Todd, Cassandra L. Williams, Benjamin A. Bennink, Alex A. Lemus, Haley E. Chesbro, Justin R. Bourgeois, Ashley M. Kopec, Damian G. Zuloaga, Annalisa Scimemi

PLOS Computational Biology: published February 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009845

The properties of human disease mutations at protein interfaces

Benjamin J. Livesey, Joseph A. Marsh

PLOS Computational Biology: published February 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009858

The SAMBA tool uses long reads to improve the contiguity of genome assemblies

Aleksey V. Zimin, Steven L. Salzberg

PLOS Computational Biology: published February 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009860

INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation

Marzia Di Filippo, Dario Pescini, Bruno Giovanni Galuzzi, Marcella Bonanomi, Daniela Gaglio, Eleonora Mangano, Clarissa Consolandi, Lilia Alberghina, Marco Vanoni, Chiara Damiani

PLOS Computational Biology: published February 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009337

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions

Thomas J. Moutinho Jr., Benjamin C. Neubert, Matthew L. Jenior, Jason A. Papin

PLOS Computational Biology: published February 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009341

Evaluating supervised and unsupervised background noise correction in human gut microbiome data

Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin, Nandita R. Garud

PLOS Computational Biology: published February 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009838

Connectivity and dynamics in the olfactory bulb

David E. Chen Kersen, Gaia Tavoni, Vijay Balasubramanian

PLOS Computational Biology: published February 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009856

In silico prediction of HIV-1-host molecular interactions and their directionality

Haiting Chai, Quan Gu, Joseph Hughes, David L. Robertson

PLOS Computational Biology: published February 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009720

Inference of trajectory presence by tree dimension and subset specificity by subtree cover

Lovemore Tenha, Mingzhou Song

PLOS Computational Biology: published February 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009829

Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights

Ramin Khajeh, Francesco Fumarola, LF Abbott

PLOS Computational Biology: published February 9, 2022 | https://doi.org/10.1371/journal.pcbi.1008836

Known allosteric proteins have central roles in genetic disease

György Abrusán, David B. Ascher, Michael Inouye

PLOS Computational Biology: published February 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009806

Evaluating spatially adaptive guidelines for the treatment of gonorrhea to reduce the incidence of gonococcal infection and increase the effective lifespan of antibiotics

Reza Yaesoubi, Ted Cohen, Katherine Hsu, Thomas L. Gift, Sancta B. St. Cyr, Joshua A. Salomon, Yonatan H. Grad

PLOS Computational Biology: published February 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009842

STENCIL: A web templating engine for visualizing and sharing life science datasets

Qi Sun, Ali Nematbakhsh, Prashant K. Kuntala, Gretta Kellogg, B. Franklin Pugh, William K. M. Lai

PLOS Computational Biology: published February 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009859

Combination and competition between path integration and landmark navigation in the estimation of heading direction

Sevan K. Harootonian, Arne D. Ekstrom, Robert C. Wilson

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009222

Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2

Anna Foix, Daniel López, Francisco Díez-Fuertes, Michael J. McConnell, Antonio J. Martín-Galiano

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009726

Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts

Robert C. Mines, Tomasz Lipniacki, Xiling Shen

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009811

Homeostatic control of synaptic rewiring in recurrent networks induces the formation of stable memory engrams

Júlia V. Gallinaro, Nebojša Gašparović, Stefan Rotter

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009836

Machine learning modeling of family wide enzyme-substrate specificity screens

Samuel Goldman, Ria Das, Kevin K. Yang, Connor W. Coley

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009853

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus

Siyu Wang, Stephanie M. Reeve, Graham T. Holt, Adegoke A. Ojewole, Marcel S. Frenkel, Pablo Gainza, Santosh Keshipeddy, Vance G. Fowler, Dennis L. Wright, Bruce R. Donald

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009855

A computationally tractable birth-death model that combines phylogenetic and epidemiological data

Alexander Eugene Zarebski, Louis du Plessis, Kris Varun Parag, Oliver George Pybus

PLOS Computational Biology: published February 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009805

Bias-free estimation of information content in temporally sparse neuronal activity

Liron Sheintuch, Alon Rubin, Yaniv Ziv

PLOS Computational Biology: published February 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009832

A mechanistic modeling framework reveals the key principles underlying tumor metabolism

Shubham Tripathi, Jun Hyoung Park, Shivanand Pudakalakatti, Pratip K. Bhattacharya, Benny Abraham Kaipparettu, Herbert Levine

PLOS Computational Biology: published February 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009841

Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics

Leonie van Steijn, Inge M. N. Wortel, Clément Sire, Loïc Dupré, Guy Theraulaz, Roeland M. H. Merks

PLOS Computational Biology: published February 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009156

Elucidating multi-input processing 3-node gene regulatory network topologies capable of generating striped gene expression patterns

Juan Camilo Arboleda-Rivera, Gloria Machado-Rodríguez, Boris A. Rodríguez, Jayson Gutiérrez

PLOS Computational Biology: published February 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009704

Evidence for the emergence of β-trefoils by ‘Peptide Budding’ from an IgG-like β-sandwich

Liam M. Longo, Rachel Kolodny, Shawn E. McGlynn

PLOS Computational Biology: published February 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009833

gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support

M. Eric Irrgang, Caroline Davis, Peter M. Kasson

PLOS Computational Biology: published February 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009835

Patient contrastive learning: A performant, expressive, and practical approach to electrocardiogram modeling

Nathaniel Diamant, Erik Reinertsen, Steven Song, Aaron D. Aguirre, Collin M. Stultz, Puneet Batra

PLOS Computational Biology: published February 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009862

Shape analysis of gamma rhythm supports a superlinear inhibitory regime in an inhibition-stabilized network

R Krishnakumaran, Mohammed Raees, Supratim Ray

PLOS Computational Biology: published February 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009886

Individual risk perception and empirical social structures shape the dynamics of infectious disease outbreaks

Valeria d’Andrea, Riccardo Gallotti, Nicola Castaldo, Manlio De Domenico

PLOS Computational Biology: published February 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009760

Near-term forecasting of companion animal tick paralysis incidence: An iterative ensemble model

Nicholas J. Clark, Tatiana Proboste, Guyan Weerasinghe, Ricardo J. Soares Magalhães

PLOS Computational Biology: published February 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009874

Tool evaluation for the detection of variably sized indels from next generation whole genome and targeted sequencing data

Ning Wang, Vladislav Lysenkov, Katri Orte, Veli Kairisto, Juhani Aakko, Sofia Khan, Laura L. Elo

PLOS Computational Biology: published February 17, 2022 | https://doi.org/10.1371/journal.pcbi.1009269

Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates

Alessandra Løchen, James E. Truscott, Nicholas J. Croucher

PLOS Computational Biology: published February 17, 2022 | https://doi.org/10.1371/journal.pcbi.1009389

Blood and brain gene expression signatures of chronic intermittent ethanol consumption in mice

Laura B. Ferguson, Amanda J. Roberts, R. Dayne Mayfield, Robert O. Messing

PLOS Computational Biology: published February 17, 2022 | https://doi.org/10.1371/journal.pcbi.1009800

Regulatory network-based imputation of dropouts in single-cell RNA sequencing data

Ana Carolina Leote, Xiaohui Wu, Andreas Beyer

PLOS Computational Biology: published February 17, 2022 | https://doi.org/10.1371/journal.pcbi.1009849

High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication

Nithya Ramakrishnan, Sibi Raj B. Pillai, Ranjith Padinhateeri

PLOS Computational Biology: published February 17, 2022 | https://doi.org/10.1371/journal.pcbi.1009861

Computational exploration of treadmilling and protrusion growth observed in fire ant rafts

Robert J. Wagner, Franck J. Vernerey

PLOS Computational Biology: published February 17, 2022 | https://doi.org/10.1371/journal.pcbi.1009869

High-frequency oscillations and sequence generation in two-population models of hippocampal region CA1

Wilhelm Braun, Raoul-Martin Memmesheimer

PLOS Computational Biology: published February 17, 2022 | https://doi.org/10.1371/journal.pcbi.1009891

Towards the prediction of non-peptidic epitopes

Paul F. Zierep, Randi Vita, Nina Blazeska, Aurélien F. A. Moumbock, Jason A. Greenbaum, Bjoern Peters, Stefan Günther

PLOS Computational Biology: published February 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009151

The correlation between cell and nucleus size is explained by an eukaryotic cell growth model

Yufei Wu, Adrian F. Pegoraro, David A. Weitz, Paul Janmey, Sean X. Sun

PLOS Computational Biology: published February 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009400

Quantitative modeling identifies critical cell mechanics driving bile duct lumen formation

Paul Van Liedekerke, Lila Gannoun, Axelle Loriot, Tim Johann, Frédéric P. Lemaigre, Dirk Drasdo

PLOS Computational Biology: published February 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009653

Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage

Emmanuel E. Moutoussamy, Qaiser Waheed, Greta J. Binford, Hanif M. Khan, Shane M. Moran, Anna R. Eitel, Matthew H. J. Cordes, Nathalie Reuter

PLOS Computational Biology: published February 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009871

Phylogenetic inference of changes in amino acid propensities with single-position resolution

Galya V. Klink, Olga V. Kalinina, Georgii A. Bazykin

PLOS Computational Biology: published February 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009878

Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1

Genelle F. Harrison, Laura Ann Leaton, Erica A. Harrison, Katherine M. Kichula, Marte K. Viken, Jonathan Shortt, Christopher R. Gignoux, Benedicte A. Lie, Damjan Vukcevic, Stephen Leslie, Paul J. Norman

PLOS Computational Biology: published February 22, 2022 | https://doi.org/10.1371/journal.pcbi.1009059

Retinal optic flow during natural locomotion

Jonathan Samir Matthis, Karl S. Muller, Kathryn L. Bonnen, Mary M. Hayhoe

PLOS Computational Biology: published February 22, 2022 | https://doi.org/10.1371/journal.pcbi.1009575

RecPD: A Recombination-aware measure of phylogenetic diversity

Cedoljub Bundalovic-Torma, Darrell Desveaux, David S. Guttman

PLOS Computational Biology: published February 22, 2022 | https://doi.org/10.1371/journal.pcbi.1009899

Learning as filtering: Implications for spike-based plasticity

Jannes Jegminat, Simone Carlo Surace, Jean-Pascal Pfister

PLOS Computational Biology: published February 23, 2022 | https://doi.org/10.1371/journal.pcbi.1009721

Bayesian data assimilation for estimating instantaneous reproduction numbers during epidemics: Applications to COVID-19

Xian Yang, Shuo Wang, Yuting Xing, Ling Li, Richard Yi Da Xu, Karl J. Friston, Yike Guo

PLOS Computational Biology: published February 23, 2022 | https://doi.org/10.1371/journal.pcbi.1009807

Comparative analyses of parasites with a comprehensive database of genome-scale metabolic models

Maureen A. Carey, Gregory L. Medlock, Michał Stolarczyk, William A. Petri Jr., Jennifer L. Guler, Jason A. Papin

PLOS Computational Biology: published February 23, 2022 | https://doi.org/10.1371/journal.pcbi.1009870

Multi-omics data integration reveals metabolome as the top predictor of the cervicovaginal microenvironment

Nicholas A. Bokulich, Paweł Łaniewski, Anja Adamov, Dana M. Chase, J. Gregory Caporaso, Melissa M. Herbst-Kralovetz

PLOS Computational Biology: published February 23, 2022 | https://doi.org/10.1371/journal.pcbi.1009876

Evolutionary information helps understand distinctive features of the angiotensin II receptors AT1 and AT2 in amniota

Rym Ben Boubaker, Asma Tiss, Daniel Henrion, Hajer Guissouma, Marie Chabbert

PLOS Computational Biology: published February 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009732

Inferring RNA-binding protein target preferences using adversarial domain adaptation

Ying Liu, Ruihui Li, Jiawei Luo, Zhaolei Zhang

PLOS Computational Biology: published February 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009863

Measuring the repertoire of age-related behavioral changes in Drosophila melanogaster

Katherine E. Overman, Daniel M. Choi, Kawai Leung, Joshua W. Shaevitz, Gordon J. Berman

PLOS Computational Biology: published February 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009867

SiteMotif: A graph-based algorithm for deriving structural motifs in Protein Ligand binding sites

Santhosh Sankar, Nagasuma Chandra

PLOS Computational Biology: published February 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009901

Bacterial age distribution in soil – Generational gaps in adjacent hot and cold spots

Benedict Borer, Dani Or

PLOS Computational Biology: published February 25, 2022 | https://doi.org/10.1371/journal.pcbi.1009857

The role of childrens’ vaccination for COVID-19—Pareto-optimal allocations of vaccines

Nir Gavish, Guy Katriel

PLOS Computational Biology: published February 25, 2022 | https://doi.org/10.1371/journal.pcbi.1009872

Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic

Yuen Ler Chow, Shantanu Singh, Anne E. Carpenter, Gregory P. Way

PLOS Computational Biology: published February 25, 2022 | https://doi.org/10.1371/journal.pcbi.1009888

Mapping the gene network landscape of Alzheimer’s disease through integrating genomics and transcriptomics

Sara Brin Rosenthal, Hao Wang, Da Shi, Cin Liu, Ruben Abagyan, Linda K. McEvoy, Chi-Hua Chen

PLOS Computational Biology: published February 25, 2022 | https://doi.org/10.1371/journal.pcbi.1009903

IQCELL: A platform for predicting the effect of gene perturbations on developmental trajectories using single-cell RNA-seq data

Tiam Heydari, Matthew A. Langley, Cynthia L. Fisher, Daniel Aguilar-Hidalgo, Shreya Shukla, Ayako Yachie-Kinoshita, Michael Hughes, Kelly M. McNagny, Peter W. Zandstra

PLOS Computational Biology: published February 25, 2022 | https://doi.org/10.1371/journal.pcbi.1009907

Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery

Daniel Domingo-Fernández, Yojana Gadiya, Abhishek Patel, Sarah Mubeen, Daniel Rivas-Barragan, Chris W. Diana, Biswapriya B. Misra, David Healey, Joe Rokicki, Viswa Colluru

PLOS Computational Biology: published February 25, 2022 | https://doi.org/10.1371/journal.pcbi.1009909

Corrections

Correction: 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 February 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009851

Correction: Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans

Yashika Arora, Pushpinder Walia, Mitsuhiro Hayashibe, Makii Muthalib, Shubhajit Roy Chowdhury, Stephane Perrey, Anirban Dutta

PLOS Computational Biology: published February 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009734

Cover

High resolution structure of Staphyloccus aureus dihydrofolate reductase (DHFR) with inhibitor R-27 (top, white) and t-NADPH (bottom, black)