January 2022

Retinal microaneurysms (MAs) are one of the earliest clinically visible signs of diabetic retinopathy (DR). MA leakage or rupture may precipitate local pathology in the surrounding neural retina that impacts visual function. In this work, the authors perform computational modeling of blood cell transport in microvessels containing various MAs, a process that is very difficult to observe directly in vivo. The simulation results provide quantitative assessments of the impacts of MA morphology, microvascular hematocrit, hemodynamics and blood cell biomechanics on the perfusion status of MA lumen and unravel the mechanisms underlying the MA rupture and thrombosis in DR.

Image Credit: This image is created by Dr. Chensen Lin and Dr. He Li and they own the copyright.

Education Articles

Bringing bioinformatics to schools with the 4273pi project

Stevie A. Bain, Heleen Plaisier, Felicity Anderson, Nicola Cook, Kathryn Crouch, Thomas R. Meagher, Michael G. Ritchie, Edward W. J. Wallace, Daniel Barker

PLOS Computational Biology: published January 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009705

Project-based learning course on metabolic network modelling in computational systems biology

Thomas Sauter, Tamara Bintener, Ali Kishk, Luana Presta, Tessy Prohaska, Daniel Guignard, Ni Zeng, Claudia Cipriani, Sundas Arshad, Thomas Pfau, Patricia Martins Conde, Maria Pires Pacheco

PLOS Computational Biology: published January 27, 2022 | https://doi.org/10.1371/journal.pcbi.1009711

Perspectives

Beyond advertising: New infrastructures for publishing integrated research objects

Elizabeth DuPre, Chris Holdgraf, Agah Karakuzu, Loïc Tetrel, Pierre Bellec, Nikola Stikov, Jean-Baptiste Poline

PLOS Computational Biology: published January 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009651

Ten simple rules for researchers who want to develop web apps

Sheila M. Saia, Natalie G. Nelson, Sierra N. Young, Stanton Parham, Micah Vandegrift

PLOS Computational Biology: published January 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009663

Research Articles

Formation, collective motion, and merging of macroscopic bacterial aggregates

George Courcoubetis, Manasi S. Gangan, Sean Lim, Xiaokan Guo, Stephan Haas, James Q. Boedicker

PLOS Computational Biology: published January 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009153

Microsimulation based quantitative analysis of COVID-19 management strategies

István Z. Reguly, Dávid Csercsik, János Juhász, Kálmán Tornai, Zsófia Bujtár, Gergely Horváth, Bence Keömley-Horváth, Tamás Kós, György Cserey, Kristóf Iván, Sándor Pongor, Gábor Szederkényi, Gergely Röst, Attila Csikász-Nagy

PLOS Computational Biology: published January 4, 2022 | https://doi.org/10.1371/journal.pcbi.1009693

Computational investigation of blood cell transport in retinal microaneurysms

He Li, Yixiang Deng, Konstantina Sampani, Shengze Cai, Zhen Li, Jennifer K. Sun, George E. Karniadakis

PLOS Computational Biology: published January 5, 2022 | https://doi.org/10.1371/journal.pcbi.1009728

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

Raga Krishnakumar, Anne M. Ruffing

PLOS Computational Biology: published January 5, 2022 | https://doi.org/10.1371/journal.pcbi.1009731

Increasing neural network robustness improves match to macaque V1 eigenspectrum, spatial frequency preference and predictivity

Nathan C. L. Kong, Eshed Margalit, Justin L. Gardner, Anthony M. Norcia

PLOS Computational Biology: published January 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009739

A lexical approach for identifying behavioural action sequences

Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat, Claire Wyart

PLOS Computational Biology: published January 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009672

Interpretable machine learning for high-dimensional trajectories of aging health

Spencer Farrell, Arnold Mitnitski, Kenneth Rockwood, Andrew D. Rutenberg

PLOS Computational Biology: published January 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009746

Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation

Benjamin Martin, Pablo D. Dans, Milosz Wieczór, Nuria Villegas, Isabelle Brun-Heath, Federica Battistini, Montserrat Terrazas, Modesto Orozco

PLOS Computational Biology: published January 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009749

Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data

Yan Wu, Lingfeng Xue, Wen Huang, Minghua Deng, Yihan Lin

PLOS Computational Biology: published January 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009762

Asymmetries around the visual field: From retina to cortex to behavior

Eline R. Kupers, Noah C. Benson, Marisa Carrasco, Jonathan Winawer

PLOS Computational Biology: published January 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009771

Self-organization of collective escape in pigeon flocks

Marina Papadopoulou, Hanno Hildenbrandt, Daniel W. E. Sankey, Steven J. Portugal, Charlotte K. Hemelrijk

PLOS Computational Biology: published January 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009772

The activity of human enhancers is modulated by the splicing of their associated lncRNAs

Jennifer Yihong Tan, Ana Claudia Marques

PLOS Computational Biology: published January 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009722

Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables

Arno Strouwen, Bart M. Nicolaï, Peter Goos

PLOS Computational Biology: published January 12, 2022 | https://doi.org/10.1371/journal.pcbi.1009610

Optimism and pessimism in optimised replay

Georgy Antonov, Christopher Gagne, Eran Eldar, Peter Dayan

PLOS Computational Biology: published January 12, 2022 | https://doi.org/10.1371/journal.pcbi.1009634

Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff

Le Khanh Ngan Nguyen, Itamar Megiddo, Susan Howick

PLOS Computational Biology: published January 12, 2022 | https://doi.org/10.1371/journal.pcbi.1009780

Dominating lengthscales of zebrafish collective behaviour

Yushi Yang, Francesco Turci, Erika Kague, Chrissy L. Hammond, John Russo, C. Patrick Royall

PLOS Computational Biology: published January 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009394

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

Zhi Ming Xu, Sina Rüeger, Michaela Zwyer, Daniela Brites, Hellen Hiza, Miriam Reinhard, Liliana Rutaihwa, Sonia Borrell, Faima Isihaka, Hosiana Temba, Thomas Maroa, Rastard Naftari, Jerry Hella, Mohamed Sasamalo, Klaus Reither, Damien Portevin, Sebastien Gagneux, Jacques Fellay

PLOS Computational Biology: published January 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009628

An initial ‘snapshot’ of sensory information biases the likelihood and speed of subsequent changes of mind

William Turner, Daniel Feuerriegel, Robert Hester, Stefan Bode

PLOS Computational Biology: published January 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009738

Identification of periodic attractors in Boolean networks using a priori information

Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp, Tatsuya Akutsu

PLOS Computational Biology: published January 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009702

A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series

Jann Paul Mattern, Kristof Glauninger, Gregory L. Britten, John R. Casey, Sangwon Hyun, Zhen Wu, E. Virginia Armbrust, Zaid Harchaoui, François Ribalet

PLOS Computational Biology: published January 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009733

Computable early Caenorhabditis elegans embryo with a phase field model

Xiangyu Kuang, Guoye Guan, Ming-Kin Wong, Lu-Yan Chan, Zhongying Zhao, Chao Tang, Lei Zhang

PLOS Computational Biology: published January 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009755

Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors

Joanna E. Handzlik, Manu

PLOS Computational Biology: published January 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009779

A deep generative model of 3D single-cell organization

Rory M. Donovan-Maiye, Jackson M. Brown, Caleb K. Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg, Gregory R. Johnson

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009155

The evolutionary maintenance of Lévy flight foraging

Winston Campeau, Andrew M. Simons, Brett Stevens

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009490

Controlling gene expression timing through gene regulatory architecture

Md Zulfikar Ali, Robert C. Brewster

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009745

Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach

Marcell Miski, Bence Márk Keömley-Horváth, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy, Zoltán Gáspári

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009758

Ultrafast population coding and axo-somatic compartmentalization

Chenfei Zhang, David Hofmann, Andreas Neef, Fred Wolf

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009775

Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes

Gorka Lasso, Saad Khan, Stephanie A. Allen, Margarette Mariano, Catalina Florez, Erika P. Orner, Jose A. Quiroz, Gregory Quevedo, Aldo Massimi, Aditi Hegde, Ariel S. Wirchnianski, Robert H. Bortz III, Ryan J. Malonis, George I. Georgiev, Karen Tong, Natalia G. Herrera, Nicholas C. Morano, Scott J. Garforth, Avinash Malaviya, Ahmed Khokhar, Ethan Laudermilch, M. Eugenia Dieterle, J. Maximilian Fels, Denise Haslwanter, Rohit K. Jangra, Jason Barnhill, Steven C. Almo, Kartik Chandran, Jonathan R. Lai, Libusha Kelly, Johanna P. Daily, Olivia Vergnolle

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009778

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes

Alexander J. Bryer, Tyler Reddy, Edward Lyman, Juan R. Perilla

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009781

Ictal wavefront propagation in slices and simulations with conductance-based refractory density model

Anton V. Chizhov, Dmitry V. Amakhin, Elena Yu. Smirnova, Aleksey V. Zaitsev

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009782

Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants—An exemplar of how human disturbance impacts group-living species

Maggie Wiśniewska, Ivan Puga-Gonzalez, Phyllis Lee, Cynthia Moss, Gareth Russell, Simon Garnier, Cédric Sueur

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009792

Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach

Chen Jia, Abhyudai Singh, Ramon Grima

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009793

DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics

Owen M. O’Connor, Razan N. Alnahhas, Jean-Baptiste Lugagne, Mary J. Dunlop

PLOS Computational Biology: published January 18, 2022 | https://doi.org/10.1371/journal.pcbi.1009797

Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution

Tadamune Kaneko, Macoto Kikuchi

PLOS Computational Biology: published January 19, 2022 | https://doi.org/10.1371/journal.pcbi.1009796

Extended ensemble simulations of a SARS-CoV-2 nsp1–5’-UTR complex

Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono

PLOS Computational Biology: published January 19, 2022 | https://doi.org/10.1371/journal.pcbi.1009804

Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution

Vladimír Palivec, Christian Johannessen, Jakub Kaminský, Hector Martinez-Seara

PLOS Computational Biology: published January 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009678

Fine-scale estimation of effective reproduction numbers for dengue surveillance

Janet Ong, Stacy Soh, Soon Hoe Ho, Annabel Seah, Borame Sue Dickens, Ken Wei Tan, Joel Ruihan Koo, Alex R. Cook, Daniel R. Richards, Leon Yan-Feng Gaw, Lee Ching Ng, Jue Tao Lim

PLOS Computational Biology: published January 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009791

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach

Mengting Niu, Quan Zou, Chen Lin

PLOS Computational Biology: published January 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009798

Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices

Arish Alreja, Ilya Nemenman, Christopher J. Rozell

PLOS Computational Biology: published January 21, 2022 | https://doi.org/10.1371/journal.pcbi.1009642

Discovering adaptation-capable biological network structures using control-theoretic approaches

Priyan Bhattacharya, Karthik Raman, Arun K. Tangirala

PLOS Computational Biology: published January 21, 2022 | https://doi.org/10.1371/journal.pcbi.1009769

Efficient ReML inference in variance component mixed models using a Min-Max algorithm

Fabien Laporte, Alain Charcosset, Tristan Mary-Huard

PLOS Computational Biology: published January 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009659

McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems

André Bogdanowski, Thomas Banitz, Linea Katharina Muhsal, Christian Kost, Karin Frank

PLOS Computational Biology: published January 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009777

Polypolish: Short-read polishing of long-read bacterial genome assemblies

Ryan R. Wick, Kathryn E. Holt

PLOS Computational Biology: published January 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009802

Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection

Alasdair D. F. Clarke, Amelia R. Hunt, Anna E. Hughes

PLOS Computational Biology: published January 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009813

The structural coverage of the human proteome before and after AlphaFold

Eduard Porta-Pardo, Victoria Ruiz-Serra, Samuel Valentini, Alfonso Valencia

PLOS Computational Biology: published January 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009818

Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data

Qi Jiang, Shuo Zhang, Lin Wan

PLOS Computational Biology: published January 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009821

Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy

Alexander B. Brummer, Xin Yang, Eric Ma, Margarita Gutova, Christine E. Brown, Russell C. Rockne

PLOS Computational Biology: published January 26, 2022 | https://doi.org/10.1371/journal.pcbi.1009504

Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9

Elodie Goldwaser, Catherine Laurent, Nathalie Lagarde, Sylvie Fabrega, Laure Nay, Bruno O. Villoutreix, Christian Jelsch, Arnaud B. Nicot, Marie-Anne Loriot, Maria A. Miteva

PLOS Computational Biology: published January 26, 2022 | https://doi.org/10.1371/journal.pcbi.1009820

AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments

Tianwei Yu

PLOS Computational Biology: published January 26, 2022 | https://doi.org/10.1371/journal.pcbi.1009826

Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences

Quinn Dickinson, Jesse G. Meyer

PLOS Computational Biology: published January 28, 2022 | https://doi.org/10.1371/journal.pcbi.1009736

Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships

Nina Kudryashova, Theoklitos Amvrosiadis, Nathalie Dupuy, Nathalie Rochefort, Arno Onken

PLOS Computational Biology: published January 28, 2022 | https://doi.org/10.1371/journal.pcbi.1009799

Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model

Alexander Nestor-Bergmann, Guy B. Blanchard, Nathan Hervieux, Alexander G. Fletcher, Jocelyn Étienne, Bénédicte Sanson

PLOS Computational Biology: published January 28, 2022 | https://doi.org/10.1371/journal.pcbi.1009812

From complete cross-docking to partners identification and binding sites predictions

Chloé Dequeker, Yasser Mohseni Behbahani, Laurent David, Elodie Laine, Alessandra Carbone

PLOS Computational Biology: published January 28, 2022 | https://doi.org/10.1371/journal.pcbi.1009825

Traveling waves in the prefrontal cortex during working memory

Sayak Bhattacharya, Scott L. Brincat, Mikael Lundqvist, Earl K. Miller

PLOS Computational Biology: published January 28, 2022 | https://doi.org/10.1371/journal.pcbi.1009827

Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle

Chunrui Xu, Henry Hollis, Michelle Dai, Xiangyu Yao, Layne T. Watson, Yang Cao, Minghan Chen

PLOS Computational Biology: published January 28, 2022 | https://doi.org/10.1371/journal.pcbi.1009847

A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution

Kaushik N. Shankar, Yiyuan Zhang, Talid Sinno, Scott L. Diamond

PLOS Computational Biology: published January 28, 2022 | https://doi.org/10.1371/journal.pcbi.1009850

Fast and accurate influenza forecasting in the United States with Inferno

Dave Osthus

PLOS Computational Biology: published January 31, 2022 | https://doi.org/10.1371/journal.pcbi.1008651

Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students

Tomiko Oskotsky, Ruchika Bajaj, Jillian Burchard, Taylor Cavazos, Ina Chen, William T. Connell, Stephanie Eaneff, Tianna Grant, Ishan Kanungo, Karla Lindquist, Douglas Myers-Turnbull, Zun Zar Chi Naing, Alice Tang, Bianca Vora, Jon Wang, Isha Karim, Claire Swadling, Janice Yang, AI4ALL Student Cohort 2020, Bill Lindstaedt, Marina Sirota

PLOS Computational Biology: published January 31, 2022 | https://doi.org/10.1371/journal.pcbi.1009719

Corrections

Correction: SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data

Jing Qi, Yang Zhou, Zicen Zhao, Shuilin Jin

PLOS Computational Biology: published January 5, 2022 | https://doi.org/10.1371/journal.pcbi.1009770

Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models

Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O’Rourke, Nathan E. Lewis

PLOS Computational Biology: published January 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009776

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Computational modeling of blood cell transport in retinal microaneurysms

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