August 2021

A mosaic image of an anopheles mosquito was created by representing each pixel of the template with a deep ultraviolet microscopy image of an individual red blood cell. The red blood cell images were drawn from a pool containing healthy cells and P.falciparum-infected cells. Red blood cell images were adjusted in their mean intensity values to reflect template pixel intensities. Lebel et al 2021

Image Credit: The template anopheles mosquito image was modified from a BioRender.com icon (Anopheles mosquito, 2020). The mosaic was created using custom software written by Paul Lebel and is being shared under the creative commons license (CC BY 4.0).

Editorials

Ten simple rules for teaching applied programming in an authentic and immersive online environment

Frances Hooley, Peter J. Freeman, Angela C. Davies

PLOS Computational Biology: published August 5, 2021 | https://doi.org/10.1371/journal.pcbi.1009184

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries

Benjamin Moore, Patricia Carvajal-López, Paballo Abel Chauke, Marco Cristancho, Victoria Dominguez Del Angel, Selene L. Fernandez-Valverde, Amel Ghouila, Piraveen Gopalasingam, Fatma Zahra Guerfali, Alice Matimba, Sarah L. Morgan, Guilherme Oliveira, Verena Ras, Alejandro Reyes, Javier De Las Rivas, Nicola Mulder

PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009218

Ten simple rules for creating reusable pathway models for computational analysis and visualization

Kristina Hanspers, Martina Kutmon, Susan L. Coort, Daniela Digles, Lauren J. Dupuis, Friederike Ehrhart, Finterly Hu, Elisson N. Lopes, Marvin Martens, Nhung Pham, Woosub Shin, Denise N. Slenter, Andra Waagmeester, Egon L. Willighagen, Laurent A. Winckers, Chris T. Evelo, Alexander R. Pico

PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009226

Ten simple rules for conducting a mendelian randomization study

Sarah A. Gagliano Taliun, David M. Evans

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009238

Ten simple rules for aspiring graduate students

Andrea I. Luppi, Charlotte Coco Newton, Lynde Folsom, Elisa Galliano, Rafael Romero-Garcia

PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009276

Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South

Danny Haelewaters, Tina A. Hofmann, Adriana L. Romero-Olivares

PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009277

Education

Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster

Jamie J. Alnasir

PLOS Computational Biology: published August 5, 2021 | https://doi.org/10.1371/journal.pcbi.1009207

Review

Review of machine learning methods for RNA secondary structure prediction

Qi Zhao, Zheng Zhao, Xiaoya Fan, Zhengwei Yuan, Qian Mao, Yudong Yao

PLOS Computational Biology: published August 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009291

Research Articles

Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime

Marc Durand

PLOS Computational Biology: published August 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008576

Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells

Leif Zinn-Brooks, Marcus L. Roper

PLOS Computational Biology: published August 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008828

PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions

Seyed Ziaeddin Alborzi, Amina Ahmed Nacer, Hiba Najjar, David W. Ritchie, Marie-Dominique Devignes

PLOS Computational Biology: published August 9, 2021 | https://doi.org/10.1371/journal.pcbi.1008844

Using machine learning and big data to explore the drug resistance landscape in HIV

Luc Blassel, Anna Tostevin, Christian Julian Villabona-Arenas, Martine Peeters, Stéphane Hué, Olivier Gascuel, On behalf of the UK HIV Drug Resistance Database

PLOS Computational Biology: published August 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008873

Critical behaviour of the stochastic Wilson-Cowan model

Antonio de Candia, Alessandro Sarracino, Ilenia Apicella, Lucilla de Arcangelis

PLOS Computational Biology: published August 30, 2021 | https://doi.org/10.1371/journal.pcbi.1008884

High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING

Wesley M. Marin, Ravi Dandekar, Danillo G. Augusto, Tasneem Yusufali, Bianca Heyn, Jan Hofmann, Vinzenz Lange, Jürgen Sauter, Paul J. Norman, Jill A. Hollenbach

PLOS Computational Biology: published August 2, 2021 | https://doi.org/10.1371/journal.pcbi.1008904

Identification of structures for ion channel kinetic models

Kathryn E. Mangold, Wei Wang, Eric K. Johnson, Druv Bhagavan, Jonathan D. Moreno, Jeanne M. Nerbonne, Jonathan R. Silva

PLOS Computational Biology: published August 16, 2021 | https://doi.org/10.1371/journal.pcbi.1008932

A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex

Anton V. Chizhov, Lyle J. Graham

PLOS Computational Biology: published August 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009007

A modular approach for modeling the cell cycle based on functional response curves

Jolan De Boeck, Jan Rombouts, Lendert Gelens

PLOS Computational Biology: published August 11, 2021 | https://doi.org/10.1371/journal.pcbi.1009008

Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism

Leo Zhu, William Pei, Ines Thiele, Radhakrishnan Mahadevan

PLOS Computational Biology: published August 5, 2021 | https://doi.org/10.1371/journal.pcbi.1009110

Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread

John R. Giles, Derek A. T. Cummings, Bryan T. Grenfell, Andrew J. Tatem, Elisabeth zu Erbach-Schoenberg, CJE Metcalf, Amy Wesolowski

PLOS Computational Biology: published August 10, 2021 | https://doi.org/10.1371/journal.pcbi.1009127

An uncertainty-based model of the effects of fixation on choice

Zhi-Wei Li, Wei Ji Ma

PLOS Computational Biology: published August 16, 2021 | https://doi.org/10.1371/journal.pcbi.1009190

Wing structure and neural encoding jointly determine sensing strategies in insect flight

Alison I. Weber, Thomas L. Daniel, Bingni W. Brunton

PLOS Computational Biology: published August 11, 2021 | https://doi.org/10.1371/journal.pcbi.1009195

Dendritic normalisation improves learning in sparsely connected artificial neural networks

Alex D. Bird, Peter Jedlicka, Hermann Cuntz

PLOS Computational Biology: published August 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009202

Models of heterogeneous dopamine signaling in an insect learning and memory center

Linnie Jiang, Ashok Litwin-Kumar

PLOS Computational Biology: published August 10, 2021 | https://doi.org/10.1371/journal.pcbi.1009205

A multi-approach and multi-scale platform to model CD4+ T cells responding to infections

Kenneth Y. Wertheim, Bhanwar Lal Puniya, Alyssa La Fleur, Ab Rauf Shah, Matteo Barberis, Tomáš Helikar

PLOS Computational Biology: published August 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009209

The unbiased estimation of the fraction of variance explained by a model

Dean A. Pospisil, Wyeth Bair

PLOS Computational Biology: published August 4, 2021 | https://doi.org/10.1371/journal.pcbi.1009212

Topology-preserving smoothing of retinotopic maps

Yanshuai Tu, Duyan Ta, Zhong-Lin Lu, Yalin Wang

PLOS Computational Biology: published August 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009216

Evaluation and comparison of multi-omics data integration methods for cancer subtyping

Ran Duan, Lin Gao, Yong Gao, Yuxuan Hu, Han Xu, Mingfeng Huang, Kuo Song, Hongda Wang, Yongqiang Dong, Chaoqun Jiang, Chenxing Zhang, Songwei Jia

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009224

Relating simulation studies by provenance—Developing a family of Wnt signaling models

Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M. Uhrmacher

PLOS Computational Biology: published August 5, 2021 | https://doi.org/10.1371/journal.pcbi.1009227

A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes

Karoline Horgmo Jæger, Andrew G. Edwards, Wayne R. Giles, Aslak Tveito

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009233

Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic

Ritabrata Dutta, Susana N. Gomes, Dante Kalise, Lorenzo Pacchiardi

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009236

Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space

Daisuke Imoto, Nen Saito, Akihiko Nakajima, Gen Honda, Motohiko Ishida, Toyoko Sugita, Sayaka Ishihara, Koko Katagiri, Chika Okimura, Yoshiaki Iwadate, Satoshi Sawai

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009237

Improving the understanding of cytoneme-mediated morphogen gradients by in silico modeling

Adrián Aguirre-Tamaral, Isabel Guerrero

PLOS Computational Biology: published August 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009245

A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers

Frances L. Heredia, Abiel Roche-Lima, Elsie I. Parés-Matos

PLOS Computational Biology: published August 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009247

IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA

Zhonghe Shao, Ting Wang, Meng Zhang, Zhou Jiang, Shuiping Huang, Ping Zeng

PLOS Computational Biology: published August 31, 2021 | https://doi.org/10.1371/journal.pcbi.1009250

Mathematical framework for place coding in the auditory system

Alex D. Reyes

PLOS Computational Biology: published August 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009251

A large-scale brain network mechanism for increased seizure propensity in Alzheimer’s disease

Luke Tait, Marinho A. Lopes, George Stothart, John Baker, Nina Kazanina, Jiaxiang Zhang, Marc Goodfellow

PLOS Computational Biology: published August 11, 2021 | https://doi.org/10.1371/journal.pcbi.1009252

Using de novo assembly to identify structural variation of eight complex immune system gene regions

Jia-Yuan Zhang, Hannah Roberts, David S. C. Flores, Antony J. Cutler, Andrew C. Brown, Justin P. Whalley, Olga Mielczarek, David Buck, Helen Lockstone, Barbara Xella, Karen Oliver, Craig Corton, Emma Betteridge, Rachael Bashford-Rogers, Julian C. Knight, John A. Todd, Gavin Band

PLOS Computational Biology: published August 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009254

Computational identification and experimental characterization of preferred downstream positions in human core promoters

René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009256

Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining

Paul Lebel, Rebekah Dial, Venkata N. P. Vemuri, Valentina Garcia, Joseph DeRisi, Rafael Gómez-Sjöberg

PLOS Computational Biology: published August 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009257

Bistability in fatty-acid oxidation resulting from substrate inhibition

Fentaw Abegaz, Anne-Claire M. F. Martines, Marcel A. Vieira-Lara, Melany Rios-Morales, Dirk-Jan Reijngoud, Ernst C. Wit, Barbara M. Bakker

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009259

Interspike interval correlations in neuron models with adaptation and correlated noise

Lukas Ramlow, Benjamin Lindner

PLOS Computational Biology: published August 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009261

A multi-objective genetic algorithm to find active modules in multiplex biological networks

Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaïs Baudot

PLOS Computational Biology: published August 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009263

Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting

Simon Mauras, Vincent Cohen-Addad, Guillaume Duboc, Max Dupré la Tour, Paolo Frasca, Claire Mathieu, Lulla Opatowski, Laurent Viennot

PLOS Computational Biology: published August 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009264

Model checking via testing for direct effects in Mendelian Randomization and transcriptome-wide association studies

Yangqing Deng, Wei Pan

PLOS Computational Biology: published August 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009266

Unveiling functions of the visual cortex using task-specific deep neural networks

Kshitij Dwivedi, Michael F. Bonner, Radoslaw Martin Cichy, Gemma Roig

PLOS Computational Biology: published August 13, 2021 | https://doi.org/10.1371/journal.pcbi.1009267

Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows

Daniel Schindler, Ted Moldenhawer, Maike Stange, Valentino Lepro, Carsten Beta, Matthias Holschneider, Wilhelm Huisinga

PLOS Computational Biology: published August 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009268

Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations

Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gómez-Sjöberg

PLOS Computational Biology: published August 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009274

SiGMoiD: A super-statistical generative model for binary data

Xiaochuan Zhao, Germán Plata, Purushottam D. Dixit

PLOS Computational Biology: published August 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009275

The evolutionary history of topological variations in the CPA/AT transporters

Govindarajan Sudha, Claudio Bassot, John Lamb, Nanjiang Shu, Yan Huang, Arne Elofsson

PLOS Computational Biology: published August 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009278

A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms

Indie C. Garwood, Sourish Chakravarty, Jacob Donoghue, Meredith Mahnke, Pegah Kahali, Shubham Chamadia, Oluwaseun Akeju, Earl K. Miller, Emery N. Brown

PLOS Computational Biology: published August 18, 2021 | https://doi.org/10.1371/journal.pcbi.1009280

Optimal closed-loop deep brain stimulation using multiple independently controlled contacts

Gihan Weerasinghe, Benoit Duchet, Christian Bick, Rafal Bogacz

PLOS Computational Biology: published August 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009281

Discovering differential genome sequence activity with interpretable and efficient deep learning

Jennifer Hammelman, David K. Gifford

PLOS Computational Biology: published August 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009282

Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base

Tomasz Konopka, Sandra Ng, Damian Smedley

PLOS Computational Biology: published August 11, 2021 | https://doi.org/10.1371/journal.pcbi.1009283

Deep geometric representations for modeling effects of mutations on protein-protein binding affinity

Xianggen Liu, Yunan Luo, Pengyong Li, Sen Song, Jian Peng

PLOS Computational Biology: published August 4, 2021 | https://doi.org/10.1371/journal.pcbi.1009284

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants

Natália Teruel, Olivier Mailhot, Rafael J. Najmanovich

PLOS Computational Biology: published August 5, 2021 | https://doi.org/10.1371/journal.pcbi.1009286

Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria

Jason A. Hendry, Dominic Kwiatkowski, Gil McVean

PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009287

Estimating the conditional probability of developing human papilloma virus related oropharyngeal cancer by combining machine learning and inverse Bayesian modelling

Prerna Tewari, Eugene Kashdan, Cathal Walsh, Cara M. Martin, Andrew C. Parnell, John J. O’Leary

PLOS Computational Biology: published August 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009289

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

Ariel A. Hippen, Matias M. Falco, Lukas M. Weber, Erdogan Pekcan Erkan, Kaiyang Zhang, Jennifer Anne Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks

PLOS Computational Biology: published August 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009290

Multiscale representations of community structures in attractor neural networks

Tatsuya Haga, Tomoki Fukai

PLOS Computational Biology: published August 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009296

Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters

Natalie Schaworonkow, Bradley Voytek

PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009298

Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection

Lubna Pinky, Crystal W. Burke, Charles J. Russell, Amber M. Smith

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009299

Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions

Jason Liu, Daniel J. Spakowicz, Garrett I. Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang, Shaoke Lou, Donghoon Lee, Jing Zhang, Carolyn Presley, Ann Greene, Matthew Stults-Kolehmainen, Laura M. Nally, Julien S. Baker, Lisa M. Fucito, Stuart A. Weinzimer, Andrew V. Papachristos, Mark Gerstein

PLOS Computational Biology: published August 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009303

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach

Nikolas Dovrolis, Katerina Kassela, Konstantinos Konstantinidis, Adamantia Kouvela, Stavroula Veletza, Ioannis Karakasiliotis

PLOS Computational Biology: published August 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009304

The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus

Sam R. Hill, Reidun Twarock, Eric C. Dykeman

PLOS Computational Biology: published August 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009306

Epigenetic instability may alter cell state transitions and anticancer drug resistance

Anshul Saini, James M. Gallo

PLOS Computational Biology: published August 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009307

DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions

Vincent Rocher, Matthieu Genais, Elissar Nassereddine, Raphael Mourad

PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009308

A probabilistic model for the ultradian timing of REM sleep in mice

Sung-Ho Park, Justin Baik, Jiso Hong, Hanna Antila, Benjamin Kurland, Shinjae Chung, Franz Weber

PLOS Computational Biology: published August 25, 2021 | https://doi.org/10.1371/journal.pcbi.1009316

The interplay between vaccination and social distancing strategies affects COVID19 population-level outcomes

Sharon Guerstein, Victoria Romeo-Aznar, Ma’ayan Dekel, Oren Miron, Nadav Davidovitch, Rami Puzis, Shai Pilosof

PLOS Computational Biology: published August 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009319

Neurally-constrained modeling of human gaze strategies in a change blindness task

Akshay Jagatap, Simran Purokayastha, Hritik Jain, Devarajan Sridharan

PLOS Computational Biology: published August 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009322

Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence

Simon M. Lichtinger, Adiran Garaizar, Rosana Collepardo-Guevara, Aleks Reinhardt

PLOS Computational Biology: published August 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009328

Ankyrin repeats in context with human population variation

Javier S. Utgés, Maxim I. Tsenkov, Noah J. M. Dietrich, Stuart A. MacGowan, Geoffrey J. Barton

PLOS Computational Biology: published August 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009335

The role of memory in non-genetic inheritance and its impact on cancer treatment resistance

Tyler Cassidy, Daniel Nichol, Mark Robertson-Tessi, Morgan Craig, Alexander R. A. Anderson

PLOS Computational Biology: published August 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009348

Targeted pandemic containment through identifying local contact network bottlenecks

Shenghao Yang, Priyabrata Senapati, Di Wang, Chris T. Bauch, Kimon Fountoulakis

PLOS Computational Biology: published August 30, 2021 | https://doi.org/10.1371/journal.pcbi.1009351

AIM: A network model of attention in auditory cortex

Kenny F. Chou, Kamal Sen

PLOS Computational Biology: published August 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009356

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