December 2020

The in silico proton irradiation of 3D genome structure derived from Hi-C geometry. The track-structure of the primary protons (red) traversing through the IMR90 cell nucleus, producing secondary electrons (green) as they travel, the energy depositions of these particles damage the DNA. This damage to the DNA is then scored as single- or double-stranded breaks and the distribution of these are analysed. Ingram et al.

Image Credit: Samuel P Ingram Nicholas T Henthorn

Editorial

Ten simple rules for creating a brand-new virtual academic meeting (even amid a pandemic)

Scott Rich, Andreea O. Diaconescu, John D. Griffiths, Milad Lankarany

PLOS Computational Biology: published December 18, 2020 | https://doi.org/10.1371/journal.pcbi.1008485

Education Articles

Ten simple rules for typographically appealing scientific texts

Lars Ole Schwen

PLOS Computational Biology: published December 31, 2020 | https://doi.org/10.1371/journal.pcbi.1008458

Ten quick tips for making things findable

Sarah Lin, Ibraheem Ali, Greg Wilson

PLOS Computational Biology: published December 31, 2020 | https://doi.org/10.1371/journal.pcbi.1008469

Perspective

Practical considerations for measuring the effective reproductive number, R_t

Katelyn M. Gostic, Lauren McGough, Edward B. Baskerville, Sam Abbott, Keya Joshi, Christine Tedijanto, Rebecca Kahn, Rene Niehus, James A. Hay, Pablo M. De Salazar, Joel Hellewell, Sophie Meakin, James D. Munday, Nikos I. Bosse, Katharine Sherrat, Robin N. Thompson, Laura F. White, Jana S. Huisman, Jérémie Scire, Sebastian Bonhoeffer, Tanja Stadler, Jacco Wallinga, Sebastian Funk, Marc Lipsitch, Sarah Cobey

PLOS Computational Biology: published December 10, 2020 | https://doi.org/10.1371/journal.pcbi.1008409

Reviews

Bridging from single to collective cell migration: A review of models and links to experiments

Andreas Buttenschön, Leah Edelstein-Keshet

PLOS Computational Biology: published December 10, 2020 | https://doi.org/10.1371/journal.pcbi.1008411

The two kinds of free energy and the Bayesian revolution

Sebastian Gottwald, Daniel A. Braun

PLOS Computational Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pcbi.1008420

Research Articles

Accurate prediction of kinase-substrate networks using knowledge graphs

Vít Nováček, Gavin McGauran, David Matallanas, Adrián Vallejo Blanco, Piero Conca, Emir Muñoz, Luca Costabello, Kamalesh Kanakaraj, Zeeshan Nawaz, Brian Walsh, Sameh K. Mohamed, Pierre-Yves Vandenbussche, Colm J. Ryan, Walter Kolch, Dirk Fey

PLOS Computational Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pcbi.1007578

A generative spiking neural-network model of goal-directed behaviour and one-step planning

Ruggero Basanisi, Andrea Brovelli, Emilio Cartoni, Gianluca Baldassarre

PLOS Computational Biology: published December 8, 2020 | https://doi.org/10.1371/journal.pcbi.1007579

A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits

Jack E. Bowyer, Chloe Ding, Benjamin H. Weinberg, Wilson W. Wong, Declan G. Bates

PLOS Computational Biology: published December 18, 2020 | https://doi.org/10.1371/journal.pcbi.1007849

A mathematical model of local and global attention in natural scene viewing

Noa Malem-Shinitski, Manfred Opper, Sebastian Reich, Lisa Schwetlick, Stefan A. Seelig, Ralf Engbert

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1007880

Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity

Stefano Masoli, Alessandra Ottaviani, Stefano Casali, Egidio D’Angelo

PLOS Computational Biology: published December 30, 2020 | https://doi.org/10.1371/journal.pcbi.1007937

Computational study on ratio-sensing in yeast galactose utilization pathway

Jiayin Hong, Bo Hua, Michael Springer, Chao Tang

PLOS Computational Biology: published December 4, 2020 | https://doi.org/10.1371/journal.pcbi.1007960

Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network

Bánk G. Fenyves, Gábor S. Szilágyi, Zsolt Vassy, Csaba Sőti, Peter Csermely

PLOS Computational Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pcbi.1007974

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases

Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter

PLOS Computational Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pcbi.1007988

Quantifying the impact of COVID-19 control measures using a Bayesian model of physical distancing

Sean C. Anderson, Andrew M. Edwards, Madi Yerlanov, Nicola Mulberry, Jessica E. Stockdale, Sarafa A. Iyaniwura, Rebeca C. Falcao, Michael C. Otterstatter, Michael A. Irvine, Naveed Z. Janjua, Daniel Coombs, Caroline Colijn

PLOS Computational Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pcbi.1008274

Reconciling emergences: An information-theoretic approach to identify causal emergence in multivariate data

Fernando E. Rosas, Pedro A. M. Mediano, Henrik J. Jensen, Anil K. Seth, Adam B. Barrett, Robin L. Carhart-Harris, Daniel Bor

PLOS Computational Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008289

Orientation processing by synaptic integration across first-order tactile neurons

Etay Hay, J. Andrew Pruszynski

PLOS Computational Biology: published December 2, 2020 | https://doi.org/10.1371/journal.pcbi.1008303

Approximating complex musculoskeletal biomechanics using multidimensional autogenerating polynomials

Anton Sobinov, Matthew T. Boots, Valeriya Gritsenko, Lee E. Fisher, Robert A. Gaunt, Sergiy Yakovenko

PLOS Computational Biology: published December 16, 2020 | https://doi.org/10.1371/journal.pcbi.1008350

Population variability in the generation and selection of T-cell repertoires

Zachary Sethna, Giulio Isacchini, Thomas Dupic, Thierry Mora, Aleksandra M. Walczak, Yuval Elhanati

PLOS Computational Biology: published December 9, 2020 | https://doi.org/10.1371/journal.pcbi.1008394

Bacteria use structural imperfect mimicry to hijack the host interactome

Natalia Sanchez de Groot, Marc Torrent Burgas

PLOS Computational Biology: published December 4, 2020 | https://doi.org/10.1371/journal.pcbi.1008395

Tracking collective cell motion by topological data analysis

Luis L. Bonilla, Ana Carpio, Carolina Trenado

PLOS Computational Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008407

Quantification of nematic cell polarity in three-dimensional tissues

André Scholich, Simon Syga, Hernán Morales-Navarrete, Fabián Segovia-Miranda, Hidenori Nonaka, Kirstin Meyer, Walter de Back, Lutz Brusch, Yannis Kalaidzidis, Marino Zerial, Frank Jülicher, Benjamin M. Friedrich

PLOS Computational Biology: published December 10, 2020 | https://doi.org/10.1371/journal.pcbi.1008412

Differential effects of propofol and ketamine on critical brain dynamics

Thomas F. Varley, Olaf Sporns, Aina Puce, John Beggs

PLOS Computational Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008418

Evaluation of CD8 T cell killing models with computer simulations of 2-photon imaging experiments

Ananya Rastogi, Philippe A. Robert, Stephan Halle, Michael Meyer-Hermann

PLOS Computational Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008428

Empirical model for short-time prediction of COVID-19 spreading

Martí Català, Sergio Alonso, Enrique Alvarez-Lacalle, Daniel López, Pere-Joan Cardona, Clara Prats

PLOS Computational Biology: published December 9, 2020 | https://doi.org/10.1371/journal.pcbi.1008431

Mapping molar shapes on signaling pathways

Wataru Morita, Naoki Morimoto, Jukka Jernvall

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008436

Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation

Hayden Nunley, Mikiko Nagashima, Kamirah Martin, Alcides Lorenzo Gonzalez, Sachihiro C. Suzuki, Declan A. Norton, Rachel O. L. Wong, Pamela A. Raymond, David K. Lubensky

PLOS Computational Biology: published December 15, 2020 | https://doi.org/10.1371/journal.pcbi.1008437

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

Jennifer Lu, Steven L. Salzberg

PLOS Computational Biology: published December 4, 2020 | https://doi.org/10.1371/journal.pcbi.1008439

Control of filament length by a depolymerizing gradient

Arnab Datta, David Harbage, Jane Kondev

PLOS Computational Biology: published December 4, 2020 | https://doi.org/10.1371/journal.pcbi.1008440

Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging

Julienne LaChance, Daniel J. Cohen

PLOS Computational Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008443

Optimal adjustment of the human circadian clock in the real world

Samuel Christensen, Yitong Huang, Olivia J. Walch, Daniel B. Forger

PLOS Computational Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008445

Estimating individuals’ genetic and non-genetic effects underlying infectious disease transmission from temporal epidemic data

Christopher M. Pooley, Glenn Marion, Stephen C. Bishop, Richard I. Bailey, Andrea B. Doeschl-Wilson

PLOS Computational Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008447

Neural diffusivity and pre-emptive epileptic seizure intervention

Erik D. Fagerholm, Chayanin Tangwiriyasakul, Karl J. Friston, Inês R. Violante, Steven Williams, David W. Carmichael, Suejen Perani, Federico E. Turkheimer, Rosalyn J. Moran, Robert Leech, Mark P. Richardson

PLOS Computational Biology: published December 1, 2020 | https://doi.org/10.1371/journal.pcbi.1008448

Insights on cross-species transmission of SARS-CoV-2 from structural modeling

João P. G. L. M. Rodrigues, Susana Barrera-Vilarmau, João M. C. Teixeira, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt

PLOS Computational Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pcbi.1008449

In silico mutagenesis of human ACE2 with S protein and translational efficiency explain SARS-CoV-2 infectivity in different species

Javier Delgado Blanco, Xavier Hernandez-Alias, Damiano Cianferoni, Luis Serrano

PLOS Computational Biology: published December 7, 2020 | https://doi.org/10.1371/journal.pcbi.1008450

A modular framework for multiscale, multicellular, spatiotemporal modeling of acute primary viral infection and immune response in epithelial tissues and its application to drug therapy timing and effectiveness

T. J. Sego, Josua O. Aponte-Serrano, Juliano Ferrari Gianlupi, Samuel R. Heaps, Kira Breithaupt, Lutz Brusch, Jessica Crawshaw, James M. Osborne, Ellen M. Quardokus, Richard K. Plemper, James A. Glazier

PLOS Computational Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008451

Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain

Sreejan Kumar, Cameron T. Ellis, Thomas P. O’Connell, Marvin M. Chun, Nicholas B. Turk-Browne

PLOS Computational Biology: published December 3, 2020 | https://doi.org/10.1371/journal.pcbi.1008457

Proteostasis is adaptive: Balancing chaperone holdases against foldases

Adam MR de Graff, David E. Mosedale, Tilly Sharp, Ken A. Dill, David J. Grainger

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008460

Targeting TMPRSS2 and Cathepsin B/L together may be synergistic against SARS-CoV-2 infection

Pranesh Padmanabhan, Rajat Desikan, Narendra M. Dixit

PLOS Computational Biology: published December 8, 2020 | https://doi.org/10.1371/journal.pcbi.1008461

Biologically-informed neural networks guide mechanistic modeling from sparse experimental data

John H. Lagergren, John T. Nardini, Ruth E. Baker, Matthew J. Simpson, Kevin B. Flores

PLOS Computational Biology: published December 1, 2020 | https://doi.org/10.1371/journal.pcbi.1008462

Bursting in cerebellar stellate cells induced by pharmacological agents: Non-sequential spike adding

Saeed Farjami, Ryan P. D. Alexander, Derek Bowie, Anmar Khadra

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008463

Drug2ways: Reasoning over causal paths in biological networks for drug discovery

Daniel Rivas-Barragan, Sarah Mubeen, Francesc Guim Bernat, Martin Hofmann-Apitius, Daniel Domingo-Fernández

PLOS Computational Biology: published December 2, 2020 | https://doi.org/10.1371/journal.pcbi.1008464

A mechanistic framework for a priori pharmacokinetic predictions of orally inhaled drugs

Niklas Hartung, Jens Markus Borghardt

PLOS Computational Biology: published December 15, 2020 | https://doi.org/10.1371/journal.pcbi.1008466

The COVID-19 outbreak in Sichuan, China: Epidemiology and impact of interventions

Quan-Hui Liu, Ana I. Bento, Kexin Yang, Hang Zhang, Xiaohan Yang, Stefano Merler, Alessandro Vespignani, Jiancheng Lv, Hongjie Yu, Wei Zhang, Tao Zhou, Marco Ajelli

PLOS Computational Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008467

NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions

Andrey Kechin, Viktoria Borobova, Ulyana Boyarskikh, Evgeniy Khrapov, Sergey Subbotin, Maxim Filipenko

PLOS Computational Biology: published December 30, 2020 | https://doi.org/10.1371/journal.pcbi.1008468

Development of a hybrid model for a partially known intracellular signaling pathway through correction term estimation and neural network modeling

Dongheon Lee, Arul Jayaraman, Joseph S. Kwon

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008472

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease

Pamela N. Luna, Jonathan M. Mansbach, Chad A. Shaw

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008473

IOCBIO Kinetics: An open-source software solution for analysis of data traces

Marko Vendelin, Martin Laasmaa, Mari Kalda, Jelena Branovets, Niina Karro, Karina Barsunova, Rikke Birkedal

PLOS Computational Biology: published December 22, 2020 | https://doi.org/10.1371/journal.pcbi.1008475

Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage

Samuel P. Ingram, Nicholas T. Henthorn, John W. Warmenhoven, Norman F. Kirkby, Ranald I. Mackay, Karen J. Kirkby, Michael J. Merchant

PLOS Computational Biology: published December 16, 2020 | https://doi.org/10.1371/journal.pcbi.1008476

The DIOS framework for optimizing infectious disease surveillance: Numerical methods for simulation and multi-objective optimization of surveillance network architectures

Qu Cheng, Philip A. Collender, Alexandra K. Heaney, Xintong Li, Rohini Dasan, Charles Li, Joseph A. Lewnard, Jonathan L. Zelner, Song Liang, Howard H. Chang, Lance A. Waller, Benjamin A. Lopman, Changhong Yang, Justin V. Remais

PLOS Computational Biology: published December 4, 2020 | https://doi.org/10.1371/journal.pcbi.1008477

FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy

Daniel F. Nino, Daniel Djayakarsana, Joshua N. Milstein

PLOS Computational Biology: published December 8, 2020 | https://doi.org/10.1371/journal.pcbi.1008479

A functional theory of bistable perception based on dynamical circular inference

Pantelis Leptourgos, Vincent Bouttier, Renaud Jardri, Sophie Denève

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008480

Evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages

Amjad Khan, Alita R. Burmeister, Lindi M. Wahl

PLOS Computational Biology: published December 4, 2020 | https://doi.org/10.1371/journal.pcbi.1008482

Unbiased and efficient log-likelihood estimation with inverse binomial sampling

Bas van Opheusden, Luigi Acerbi, Wei Ji Ma

PLOS Computational Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008483

A Bayesian computational model reveals a failure to adapt interoceptive precision estimates across depression, anxiety, eating, and substance use disorders

Ryan Smith, Rayus Kuplicki, Justin Feinstein, Katherine L. Forthman, Jennifer L. Stewart, Martin P. Paulus, Tulsa 1000 investigators, Sahib S. Khalsa

PLOS Computational Biology: published December 14, 2020 | https://doi.org/10.1371/journal.pcbi.1008484

On the NF-Y regulome as in ENCODE (2019)

Mirko Ronzio, Andrea Bernardini, Giulio Pavesi, Roberto Mantovani, Diletta Dolfini

PLOS Computational Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008488

A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro

Haiping Zhang, Yang Yang, Junxin Li, Min Wang, Konda Mani Saravanan, Jinli Wei, Justin Tze-Yang Ng, Md. Tofazzal Hossain, Maoxuan Liu, Huiling Zhang, Xiaohu Ren, Yi Pan, Yin Peng, Yi Shi, Xiaochun Wan, Yingxia Liu, Yanjie Wei

PLOS Computational Biology: published December 31, 2020 | https://doi.org/10.1371/journal.pcbi.1008489

Context-specific network modeling identifies new crosstalk in β-adrenergic cardiac hypertrophy

Ali Khalilimeybodi, Alexander M. Paap, Steven L. M. Christiansen, Jeffrey J. Saucerman

PLOS Computational Biology: published December 18, 2020 | https://doi.org/10.1371/journal.pcbi.1008490

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness

Ivan Carcamo-Orive, Marc Y. R. Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang

PLOS Computational Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008491

Crosstalk and ultrasensitivity in protein degradation pathways

Abhishek Mallela, Maulik K. Nariya, Eric J. Deeds

PLOS Computational Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008492

OpenSim Moco: Musculoskeletal optimal control

Christopher L. Dembia, Nicholas A. Bianco, Antoine Falisse, Jennifer L. Hicks, Scott L. Delp

PLOS Computational Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008493

Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology

Ivan Borisov, Evgeny Metelkin

PLOS Computational Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008495

Robust detection of point mutations involved in multidrug-resistant Mycobacterium tuberculosis in the presence of co-occurrent resistance markers

Julian Libiseller-Egger, Jody Phelan, Susana Campino, Fady Mohareb, Taane G. Clark

PLOS Computational Biology: published December 21, 2020 | https://doi.org/10.1371/journal.pcbi.1008518

Multi-scale modeling of macrophage—T cell interactions within the tumor microenvironment

Colin G. Cess, Stacey D. Finley

PLOS Computational Biology: published December 23, 2020 | https://doi.org/10.1371/journal.pcbi.1008519

Systems biology predicts that fibrosis in tuberculous granulomas may arise through macrophage-to-myofibroblast transformation

Stephanie Evans, J. Russell Butler, Joshua T. Mattila, Denise E. Kirschner

PLOS Computational Biology: published December 28, 2020 | https://doi.org/10.1371/journal.pcbi.1008520

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