October 2022

Bats perceive the three-dimensional environment by emitting ultrasound pulses from their nose or mouth and receiving echoes through both ears. To determine the position of a target object, it is necessary to know the distance and direction of the target. Certain bat species that use a combined signal of long constant frequency and short frequency modulated ultrasounds synchronize their pinnae movement with pulse emission, and this behavior has been regarded as helpful for localizing the elevation angle of a reflective sound source. This paper describes a simple mathematical model for investigating the active listening strategy employed by bats. Hiraga et al 2022

Image Credit: Yasufumi Yamada, Hiroshima University, Japan.

Editorials

Ten simple rules for successfully supporting first-generation/low-income (FLI) students in STEM

Courtney Peña, Nidia Ruedas-Gracia, Jennifer R. Cohen, Ngoc Tran, Miranda B. Stratton

PLOS Computational Biology: published October 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010499

Ten simple rules for reporting a bug

Benjamin C. Haller

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010540

Ten simple rules on how to develop a stakeholder engagement plan

Susanne Hollmann, Babette Regierer, Jaele Bechis, Lesley Tobin, Domenica D’Elia

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010520

Ten simple rules for a successful international consortium in big data omics

Miranda D. Stobbe, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Ivo Glynne Gut

PLOS Computational Biology: published October 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010546

Ten simple rules for writing a Registered Report

Emma L. Henderson, Christopher D. Chambers

PLOS Computational Biology: published October 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010571

Ten simple rules for creating a global network in computational biology

Jenea Imani Adams, Taylor Ferebee, Melyssa Minto, Kayla K. Pennerman, Nyasha Chambwe

PLOS Computational Biology: published October 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010528

Education

Ten simple rules for creating and sustaining antiracist graduate programs

Edgar Perez-Lopez, Larisa Gavrilova, Janice Disla, Melissa Goodlad, Dalena Ngo, Arabi Seshappan, Farhana Sharmin, Jesus Cisneros, Christopher T. Kello, Asmeret Asefaw Berhe

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010516

Perspectives

Ten simple rules for unbiased teaching

Dean Mobbs, Sarah M. Tashjian

PLOS Computational Biology: published October 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010344

Ten simple rules in biomedical engineering to improve healthcare equity

Olivia L. Lanier, Mykel D. Green, Gilda A. Barabino, Elizabeth Cosgriff-Hernandez

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010525

Review

Calibrating spatiotemporal models of microbial communities to microscopy data: A review

Aaron Yip, Julien Smith-Roberge, Sara Haghayegh Khorasani, Marc G. Aucoin, Brian P. Ingalls

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010533

Research Articles

Spatial models of pattern formation during phagocytosis

John Cody Herron, Shiqiong Hu, Bei Liu, Takashi Watanabe, Klaus M. Hahn, Timothy C. Elston

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010092

HAL-X: Scalable hierarchical clustering for rapid and tunable single-cell analysis

James Anibal, Alexandre G. Day, Erol Bahadiroglu, Liam O’Neil, Long Phan, Alec Peltekian, Amir Erez, Mariana Kaplan, Grégoire Altan-Bonnet, Pankaj Mehta

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010349

A fibrin enhanced thrombosis model for medical devices operating at low shear regimes or large surface areas

Rodrigo Méndez Rojano, Angela Lai, Mansur Zhussupbekov, Greg W. Burgreen, Keith Cook, James F. Antaki

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010277

Cross-scale excitability in networks of quadratic integrate-and-fire neurons

Daniele Avitabile, Mathieu Desroches, G. Bard Ermentrout

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010569

Variant calling enhances the identification of cancer cells in single-cell RNA sequencing data

William Gasper, Francesca Rossi, Matteo Ligorio, Dario Ghersi

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010576

Modulation of working memory duration by synaptic and astrocytic mechanisms

Sophia Becker, Andreas Nold, Tatjana Tchumatchenko

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010543

Magnitude-sensitive reaction times reveal non-linear time costs in multi-alternative decision-making

James A. R. Marshall, Andreagiovanni Reina, Célia Hay, Audrey Dussutour, Angelo Pirrone

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010523

mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations

Alexandra O. M. Holmes, Adrian Goldman, Antreas C. Kalli

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010578

Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains

Sabrin Hilau, Sophia Katz, Tanya Wasserman, Ruth Hershberg, Yonatan Savir

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010565

The value of confidence: Confidence prediction errors drive value-based learning in the absence of external feedback

Lena Esther Ptasczynski, Isa Steinecker, Philipp Sterzer, Matthias Guggenmos

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010580

Fast and interpretable consensus clustering via minipatch learning

Luqin Gan, Genevera I. Allen

PLOS Computational Biology: published October 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010577

Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis

Chen Jia, Abhyudai Singh, Ramon Grima

PLOS Computational Biology: published October 4, 2022 | https://doi.org/10.1371/journal.pcbi.1010574

Dual STDP processes at Purkinje cells contribute to distinct improvements in accuracy and speed of saccadic eye movements

Lorenzo Fruzzetti, Hari Teja Kalidindi, Alberto Antonietti, Cristiano Alessandro, Alice Geminiani, Claudia Casellato, Egidio Falotico, Egidio D’Angelo

PLOS Computational Biology: published October 4, 2022 | https://doi.org/10.1371/journal.pcbi.1010564

Scalable workflow for characterization of cell-cell communication in COVID-19 patients

Yingxin Lin, Lipin Loo, Andy Tran, David M. Lin, Cesar Moreno, Daniel Hesselson, G. Gregory Neely, Jean Y. H. Yang

PLOS Computational Biology: published October 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010495

Random-effects meta-analysis of effect sizes as a unified framework for gene set analysis

Mohammad A. Makrooni, Dónal O’Shea, Paul Geeleher, Cathal Seoighe

PLOS Computational Biology: published October 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010278

Efficient Bayesian inference for stochastic agent-based models

Andreas Christ Sølvsten Jørgensen, Atiyo Ghosh, Marc Sturrock, Vahid Shahrezaei

PLOS Computational Biology: published October 5, 2022 | https://doi.org/10.1371/journal.pcbi.1009508

Measuring impact of vaccination among wildlife: The case of bait vaccine campaigns for classical swine fever epidemic among wild boar in Japan

Ryota Matsuyama, Takehisa Yamamoto, Yoko Hayama, Ryosuke Omori

PLOS Computational Biology: published October 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010510

Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies

Marie Locard-Paulet, Oana Palasca, Lars Juhl Jensen

PLOS Computational Biology: published October 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010604

An ensemble n-sub-epidemic modeling framework for short-term forecasting epidemic trajectories: Application to the COVID-19 pandemic in the USA

Gerardo Chowell, Sushma Dahal, Amna Tariq, Kimberlyn Roosa, James M. Hyman, Ruiyan Luo

PLOS Computational Biology: published October 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010602

Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins

Javier A. Romero, Paulina Putko, Mateusz Urbańczyk, Krzysztof Kazimierczuk, Anna Zawadzka-Kazimierczuk

PLOS Computational Biology: published October 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010258

Disentangling choice value and choice conflict in sequential decisions under risk

Laura Fontanesi, Amitai Shenhav, Sebastian Gluth

PLOS Computational Biology: published October 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010478

Understanding molecular mechanisms and predicting phenotypic effects of pathogenic tubulin mutations

Thomas J. Attard, Julie P. I. Welburn, Joseph A. Marsh

PLOS Computational Biology: published October 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010611

Prioritizing interventions for preventing COVID-19 outbreaks in military basic training

Guido España, T. Alex Perkins, Simon D. Pollett, Morgan E. Smith, Sean M. Moore, Paul O. Kwon, Tara L. Hall, Milford H. Beagle Jr., Clinton K. Murray, Shilpa Hakre, Sheila A. Peel, Kayvon Modjarrad, Paul T. Scott

PLOS Computational Biology: published October 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010489

Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin

Annie M. Westerlund, Akshay Sridhar, Leo Dahl, Alma Andersson, Anna-Yaroslava Bodnar, Lucie Delemotte

PLOS Computational Biology: published October 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010583

DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes

Siguo Wang, Qinhu Zhang, Ying He, Zhen Cui, Zhenghao Guo, Kyungsook Han, De-Shuang Huang

PLOS Computational Biology: published October 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010572

Rule-based and stimulus-based cues bias auditory decisions via different computational and physiological mechanisms

Nathan Tardiff, Lalitta Suriya-Arunroj, Yale E. Cohen, Joshua I. Gold

PLOS Computational Biology: published October 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010601

Theoretical investigation of active listening behavior based on the echolocation of CF-FM bats

Takahiro Hiraga, Yasufumi Yamada, Ryo Kobayashi

PLOS Computational Biology: published October 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009784

Credibility assessment of patient-specific computational modeling using patient-specific cardiac modeling as an exemplar

Suran Galappaththige, Richard A. Gray, Caroline Mendonca Costa, Steven Niederer, Pras Pathmanathan

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010541

Structured random receptive fields enable informative sensory encodings

Biraj Pandey, Marius Pachitariu, Bingni W. Brunton, Kameron Decker Harris

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010484

EpiLPS: A fast and flexible Bayesian tool for estimation of the time-varying reproduction number

Oswaldo Gressani, Jacco Wallinga, Christian L. Althaus, Niel Hens, Christel Faes

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010618

Multiple bumps can enhance robustness to noise in continuous attractor networks

Raymond Wang, Louis Kang

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010547

Probabilistic edge weights fine-tune Boolean network dynamics

Dávid Deritei, Nina Kunšič, Péter Csermely

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010536

Chaos in synthetic microbial communities

Behzad D. Karkaria, Angelika Manhart, Alex J. H. Fedorec, Chris P. Barnes

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010548

Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans

Yuxiang Wu, Shang Wu, Xin Wang, Chengtian Lang, Quanshi Zhang, Quan Wen, Tianqi Xu

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010594

Obsessive-compulsive disorder is characterized by decreased Pavlovian influence on instrumental behavior

Ziwen Peng, Luning He, Rongzhen Wen, Tom Verguts, Carol A. Seger, Qi Chen

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1009945

Experimental guidance for discovering genetic networks through hypothesis reduction on time series

Breschine Cummins, Francis C. Motta, Robert C. Moseley, Anastasia Deckard, Sophia Campione, Marcio Gameiro, Tomáš Gedeon, Konstantin Mischaikow, Steven B. Haase

PLOS Computational Biology: published October 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010145

Correcting the hebbian mistake: Toward a fully error-driven hippocampus

Yicong Zheng, Xiaonan L. Liu, Satoru Nishiyama, Charan Ranganath, Randall C. O’Reilly

PLOS Computational Biology: published October 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010589

Spatial clustering in vaccination hesitancy: The role of social influence and social selection

Lucila G. Alvarez-Zuzek, Casey M. Zipfel, Shweta Bansal

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010437

Bounded rational decision-making models suggest capacity-limited concurrent motor planning in human posterior parietal and frontal cortex

Sonja Schach, Axel Lindner, Daniel Alexander Braun

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010585

CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data

Zubair Lalani, Gillian Chu, Silas Hsu, Shaw Kagawa, Michael Xiang, Simone Zaccaria, Mohammed El-Kebir

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010614

A machine learning model trained on a high-throughput antibacterial screen increases the hit rate of drug discovery

A. S. M. Zisanur Rahman, Chengyou Liu, Hunter Sturm, Andrew M. Hogan, Rebecca Davis, Pingzhao Hu, Silvia T. Cardona

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010613

How do (perceptual) distracters distract?

Tsvetomira Dumbalska, Katarzyna Rudzka, Hannah E. Smithson, Christopher Summerfield

PLOS Computational Biology: published October 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010609

A deep learning approach to real-time HIV outbreak detection using genetic data

Michael D. Kupperman, Thomas Leitner, Ruian Ke

PLOS Computational Biology: published October 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010598

Modulation of signaling cross-talk between pJNK and pAKT generates optimal apoptotic response

Sharmila Biswas, Baishakhi Tikader, Sandip Kar, Ganesh A. Viswanathan

PLOS Computational Biology: published October 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010626

Optimal noise level for coding with tightly balanced networks of spiking neurons in the presence of transmission delays

Jonathan Timcheck, Jonathan Kadmon, Kwabena Boahen, Surya Ganguli

PLOS Computational Biology: published October 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010593

A new computational model illuminates the extraordinary eyes of Phronima

Zahra M. Bagheri, Anna-Lee Jessop, Julian C. Partridge, Karen J. Osborn, Jan M. Hemmi

PLOS Computational Biology: published October 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010545

Kinetic and data-driven modeling of pancreatic β-cell central carbon metabolism and insulin secretion

Patrick E. Gelbach, Dongqing Zheng, Scott E. Fraser, Kate L. White, Nicholas A. Graham, Stacey D. Finley

PLOS Computational Biology: published October 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010555

Modelling membrane reshaping by staged polymerization of ESCRT-III filaments

Xiuyun Jiang, Lena Harker-Kirschneck, Christian Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, Anđela Šarić

PLOS Computational Biology: published October 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010586

A new machine learning method for cancer mutation analysis

Mahnaz Habibi, Golnaz Taheri

PLOS Computational Biology: published October 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010332

Hippocampal and medial prefrontal cortices encode structural task representations following progressive and interleaved training schedules

Sam C. Berens, Chris M. Bird

PLOS Computational Biology: published October 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010566

Altered expression response upon repeated gene repression in single yeast cells

Lea Schuh, Igor Kukhtevich, Poonam Bheda, Melanie Schulz, Maria Bordukova, Robert Schneider, Carsten Marr

PLOS Computational Biology: published October 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010640

Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

Zi-Chun Mu, Ya-Lan Tan, Ben-Gong Zhang, Jie Liu, Ya-Zhou Shi

PLOS Computational Biology: published October 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010501

Integrated experimental-computational analysis of a HepaRG liver-islet microphysiological system for human-centric diabetes research

Belén Casas, Liisa Vilén, Sophie Bauer, Kajsa P. Kanebratt, Charlotte Wennberg Huldt, Lisa Magnusson, Uwe Marx, Tommy B. Andersson, Peter Gennemark, Gunnar Cedersund

PLOS Computational Biology: published October 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010587

DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets

Elena Tea Russo, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio

PLOS Computational Biology: published October 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010610

Global and gene-specific translational regulation in Escherichia coli across different conditions

Di Zhang, Sophia Hsin-Jung Li, Christopher G. King, Ned S. Wingreen, Zemer Gitai, Zhiyuan Li

PLOS Computational Biology: published October 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010641

Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models

Stephen Malina, Daniel Cizin, David A. Knowles

PLOS Computational Biology: published October 20, 2022 | https://doi.org/10.1371/journal.pcbi.1009880

MetaLP: An integrative linear programming method for protein inference in metaproteomics

Shichao Feng, Hong-Long Ji, Huan Wang, Bailu Zhang, Ryan Sterzenbach, Chongle Pan, Xuan Guo

PLOS Computational Biology: published October 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010603

Bayesian parameter estimation for dynamical models in systems biology

Nathaniel J. Linden, Boris Kramer, Padmini Rangamani

PLOS Computational Biology: published October 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010651

Stochastic dynamics of Type-I interferon responses

Benjamin D. Maier, Luis U. Aguilera, Sven Sahle, Pascal Mutz, Priyata Kalra, Christopher Dächert, Ralf Bartenschlager, Marco Binder, Ursula Kummer

PLOS Computational Biology: published October 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010623

Novel methods for estimating the instantaneous and overall COVID-19 case fatality risk among care home residents in England

Christopher E. Overton, Luke Webb, Uma Datta, Mike Fursman, Jo Hardstaff, Iina Hiironen, Karthik Paranthaman, Heather Riley, James Sedgwick, Julia Verne, Steve Willner, Lorenzo Pellis, Ian Hall

PLOS Computational Biology: published October 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010554

Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond

Kody A. Waldstein, Jirong Yi, Myung Cho, Raghu Mudumbai, Xiaodong Wu, Steven M. Varga, Weiyu Xu

PLOS Computational Biology: published October 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010629

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

Gabriel Foley, Ariane Mora, Connie M. Ross, Scott Bottoms, Leander Sützl, Marnie L. Lamprecht, Julian Zaugg, Alexandra Essebier, Brad Balderson, Rhys Newell, Raine E. S. Thomson, Bostjan Kobe, Ross T. Barnard, Luke Guddat, Gerhard Schenk, Jörg Carsten, Yosephine Gumulya, Burkhard Rost, Dietmar Haltrich, Volker Sieber, Elizabeth M. J. Gillam, Mikael Bodén

PLOS Computational Biology: published October 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010633

Modelling the first wave of COVID-19 in India

Dhiraj Kumar Hazra, Bhalchandra S. Pujari, Snehal M. Shekatkar, Farhina Mozaffer, Sitabhra Sinha, Vishwesha Guttal, Pinaki Chaudhuri, Gautam I. Menon

PLOS Computational Biology: published October 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010632

Understanding the impact of third-party species on pairwise coexistence

Jie Deng, Washington Taylor, Serguei Saavedra

PLOS Computational Biology: published October 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010630

Mechanics of lung cancer: A finite element model shows strain amplification during early tumorigenesis

Rebecca G. Zitnay, Michael R. Herron, Keith R. Carney, Scott Potter, Lyska L. Emerson, Jeffrey A. Weiss, Michelle C. Mendoza

PLOS Computational Biology: published October 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010153

Structural spine plasticity: Learning and forgetting of odor-specific subnetworks in the olfactory bulb

John Hongyu Meng, Hermann Riecke

PLOS Computational Biology: published October 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010338

Emergent multilevel selection in a simple spatial model of the evolution of altruism

Rutger Hermsen

PLOS Computational Biology: published October 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010612

CHOIRBM: An R package for exploratory data analysis and interactive visualization of pain patient body map data

Eric Cramer, Maisa Ziadni, Kristen Hymel Scherrer, Sean Mackey, Ming-Chih Kao

PLOS Computational Biology: published October 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010496

Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data

Che Yu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu, Mark Gerstein, Jing Zhang

PLOS Computational Biology: published October 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010636

Unsupervised machine learning predicts future sexual behaviour and sexually transmitted infections among HIV-positive men who have sex with men

Sara Andresen, Suraj Balakrishna, Catrina Mugglin, Axel J. Schmidt, Dominique L. Braun, Alex Marzel, Thanh Doco Lecompte, Katharine EA Darling, Jan A. Roth, Patrick Schmid, Enos Bernasconi, Huldrych F. Günthard, Andri Rauch, Roger D. Kouyos, Luisa Salazar-Vizcaya, the Swiss HIV Cohort Study

PLOS Computational Biology: published October 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010559

Controlling microbial co-culture based on substrate pulsing can lead to stability through differential fitness advantages

J. Andres Martinez, Matheo Delvenne, Lucas Henrion, Fabian Moreno, Samuel Telek, Christian Dusny, Frank Delvigne

PLOS Computational Biology: published October 31, 2022 | https://doi.org/10.1371/journal.pcbi.1010674

Correction

Correction: Evaluating epidemic forecasts in an interval format

Johannes Bracher, Evan L. Ray, Tilmann Gneiting, Nicholas G. Reich

PLOS Computational Biology: published October 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010592

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