December 2022

Schematic of the interacting active surface framework describing the dynamics of the tissue by the vertices of the triangular meshes representing each cell. This framework represents cortical flows, cortical tensions, intracellular pressures, bending moment, and forces arising from cell-cell interactions. Torres-Sánchez et al 2022

Image Credit: Alejandro Torres-Sánchez

Editorials

Ten simple rules for how you can help make your lab a better place as a graduate student or postdoc

Matthias C. Rillig

PLOS Computational Biology: published December 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010673

Ten simple rules for investigating (meta)genomic data from environmental ecosystems

Paton Vuong, Michael J. Wise, Andrew S. Whiteley, Parwinder Kaur

PLOS Computational Biology: published December 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010675

Ten simple rules for creating a sense of belonging in your research group

Nidia Ruedas-Gracia, Crystal M. Botham, Amber R. Moore, Courtney Peña

PLOS Computational Biology: published December 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010688

Ten simple rules for launching an academic research career

Jason A. Papin, Jessica Keim-Malpass, Sana Syed

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010689

Ten simple rules for failing successfully in academia

Stefan Gaillard, Tara van Viegen, Michele Veldsman, Melanie I. Stefan, Veronika Cheplygina

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010538

Education Articles

Ten quick tips for sequence-based prediction of protein properties using machine learning

Qingzhen Hou, Katharina Waury, Dea Gogishvili, K. Anton Feenstra

PLOS Computational Biology: published December 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010669

Ten simple rules and a template for creating workflows-as-applications

Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Papudeshi, Scott A. Handley, C. Titus Brown, Nathan S. Watson-Haigh, Robert A. Edwards

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010705

Eleven quick tips for data cleaning and feature engineering

Davide Chicco, Luca Oneto, Erica Tavazzi

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010718

Ten simple rules for empowering women in STEM

Patricia Guevara-Ramírez, Viviana A. Ruiz-Pozo, Santiago Cadena-Ullauri, Gabriela Salazar-Navas, Ana Acosta Bedón, J. Faustino V-Vázquez, Ana Karina Zambrano

PLOS Computational Biology: published December 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010731

Research Articles

Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution

Rikuto Kamiura, Ryo Mizuuchi, Norikazu Ichihashi

PLOS Computational Biology: published December 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010709

Interneuronal network model of theta-nested fast oscillations predicts differential effects of heterogeneity, gap junctions and short term depression for hyperpolarizing versus shunting inhibition

Guillem Via, Roman Baravalle, Fernando R. Fernandez, John A. White, Carmen C. Canavier

PLOS Computational Biology: published December 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010094

Monitoring real-time transmission heterogeneity from incidence data

Yunjun Zhang, Tom Britton, Xiaohua Zhou

PLOS Computational Biology: published December 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010078

Stability and learning in excitatory synapses by nonlinear inhibitory plasticity

Christoph Miehl, Julijana Gjorgjieva

PLOS Computational Biology: published December 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010682

Novel estimates reveal subnational heterogeneities in disease-relevant contact patterns in the United States

Casey F. Breen, Ayesha S. Mahmud, Dennis M. Feehan

PLOS Computational Biology: published December 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010742

A phylogenetic approach to inferring the order in which mutations arise during cancer progression

Yuan Gao, Jeff Gaither, Julia Chifman, Laura Kubatko

PLOS Computational Biology: published December 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010560

EEG-representational geometries and psychometric distortions in approximate numerical judgment

Stefan Appelhoff, Ralph Hertwig, Bernhard Spitzer

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010747

Input correlations impede suppression of chaos and learning in balanced firing-rate networks

Rainer Engelken, Alessandro Ingrosso, Ramin Khajeh, Sven Goedeke, L. F. Abbott

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010590

Leveraging infectious disease models to interpret randomized controlled trials: Controlling enteric pathogen transmission through water, sanitation, and hygiene interventions

Andrew F. Brouwer, Marisa C. Eisenberg, Kevin M. Bakker, Savannah N. Boerger, Mondal H. Zahid, Matthew C. Freeman, Joseph N. S. Eisenberg

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010748

Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission

Isaac H. Goldstein, Damon Bayer, Ivan Barilar, Balladiah Kizito, Ogopotse Matsiri, Chawangwa Modongo, Nicola M. Zetola, Stefan Niemann, Volodymyr M. Minin, Sanghyuk S. Shin

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010696

Regional mutational signature activities in cancer genomes

Caitlin Timmons, Quaid Morris, Caitlin F. Harrigan

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010733

Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data

Nana Wei, Yating Nie, Lin Liu, Xiaoqi Zheng, Hua-Jun Wu

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010753

ToMExO: A probabilistic tree-structured model for cancer progression

Mohammadreza Mohaghegh Neyshabouri, Jens Lagergren

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010732

Remeshing flexible membranes under the control of free energy

Xinxin Wang, Gaudenz Danuser

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010766

Orientation control strategies and adaptation to a visuomotor perturbation in rotational hand movements

Or Zruya, Ilana Nisky

PLOS Computational Biology: published December 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010248

Modelling the spatial dynamics of oncolytic virotherapy in the presence of virus-resistant tumour cells

Darshak Kartikey Bhatt, Thijs Janzen, Toos Daemen, Franz J. Weissing

PLOS Computational Biology: published December 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010076

Comparing T cell receptor repertoires using optimal transport

Branden J. Olson, Stefan A. Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen IV

PLOS Computational Biology: published December 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010681

Population coding strategies in human tactile afferents

Giulia Corniani, Miguel A. Casal, Stefano Panzeri, Hannes P. Saal

PLOS Computational Biology: published December 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010763

Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden

Fanny Bergström, Felix Günther, Michael Höhle, Tom Britton

PLOS Computational Biology: published December 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010767

Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods

Marion F. S. Fischer, James E. Crowe, Jens Meiler

PLOS Computational Biology: published December 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010230

Removal of reinforcement improves instrumental performance in humans by decreasing a general action bias rather than unmasking learnt associations

Hannah Kurtenbach, Eduard Ort, Monja Isabel Froböse, Gerhard Jocham

PLOS Computational Biology: published December 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010201

Metabolic reprogramming in Rheumatoid Arthritis Synovial Fibroblasts: A hybrid modeling approach

Sahar Aghakhani, Sylvain Soliman, Anna Niarakis

PLOS Computational Biology: published December 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010408

Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes

Yogita Sharma, Jared B. Bennett, Gordana Rašić, John M. Marshall

PLOS Computational Biology: published December 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010755

Mixed mechanism of conformational selection and induced fit as a molecular recognition process in the calreticulin family of proteins

Ashalatha Sreshty Mamidi, Avadhesha Surolia

PLOS Computational Biology: published December 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010661

Interpreting tree ensemble machine learning models with endoR

Albane Ruaud, Niklas Pfister, Ruth E. Ley, Nicholas D. Youngblut

PLOS Computational Biology: published December 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010714

Dissecting peripheral protein-membrane interfaces

Thibault Tubiana, Ian Sillitoe, Christine Orengo, Nathalie Reuter

PLOS Computational Biology: published December 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010346

Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation

Olivier Mailhot, Vincent Frappier, François Major, Rafael J. Najmanovich

PLOS Computational Biology: published December 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010777

CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data

Arda Söylev, Sevim Seda Çokoglu, Dilek Koptekin, Can Alkan, Mehmet Somel

PLOS Computational Biology: published December 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010788

Sparse RNNs can support high-capacity classification

Denis Turcu, L. F. Abbott

PLOS Computational Biology: published December 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010759

Using smartphone-GPS data to quantify human activity in green spaces

Alessandro Filazzola, Garland Xie, Kimberly Barrett, Andrea Dunn, Marc T. J. Johnson, James Scott MacIvor

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010725

Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation

Adrien Coulier, Prashant Singh, Marc Sturrock, Andreas Hellander

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010683

Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework

Yansong Wang, Zilong Hou, Yuning Yang, Ka-chun Wong, Xiangtao Li

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010779

Recalibrating probabilistic forecasts of epidemics

Aaron Rumack, Ryan J. Tibshirani, Roni Rosenfeld

PLOS Computational Biology: published December 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010771

Interacting active surfaces: A model for three-dimensional cell aggregates

Alejandro Torres-Sánchez, Max Kerr Winter, Guillaume Salbreux

PLOS Computational Biology: published December 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010762

Systematic comparison of differential expression networks in MTB mono-, HIV mono- and MTB/HIV co-infections for drug repurposing

Yao Jiang, Jia-Xuan Zhang, Rong Liu

PLOS Computational Biology: published December 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010744

Model-based prioritization for acquiring protection

Sarah M. Tashjian, Toby Wise, Dean Mobbs

PLOS Computational Biology: published December 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010805

scDSSC: Deep Sparse Subspace Clustering for scRNA-seq Data

HaiYun Wang, JianPing Zhao, ChunHou Zheng, YanSen Su

PLOS Computational Biology: published December 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010772

Environmental and ecological controls of the spatial distribution of microbial populations in aggregates

Eloi Martinez-Rabert, Chiel van Amstel, Cindy Smith, William T. Sloan, Rebeca Gonzalez-Cabaleiro

PLOS Computational Biology: published December 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010807

`tension`: A Python package for FORCE learning

Lu Bin Liu, Attila Losonczy, Zhenrui Liao

PLOS Computational Biology: published December 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010722

A mathematical model of potassium homeostasis: Effect of feedforward and feedback controls

Melissa M. Stadt, Jessica Leete, Sophia Devinyak, Anita T. Layton

PLOS Computational Biology: published December 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010607

Improved visualization of high-dimensional data using the distance-of-distance transformation

Jinke Liu, Martin Vinck

PLOS Computational Biology: published December 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010764

A method to estimate the cellular composition of the mouse brain from heterogeneous datasets

Dimitri Rodarie, Csaba Verasztó, Yann Roussel, Michael Reimann, Daniel Keller, Srikanth Ramaswamy, Henry Markram, Marc-Oliver Gewaltig

PLOS Computational Biology: published December 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010739

Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins

Jakub W. Wojciechowski, Emirhan Tekoglu, Marlena Gąsior-Głogowska, Virginie Coustou, Natalia Szulc, Monika Szefczyk, Marta Kopaczyńska, Sven J. Saupe, Witold Dyrka

PLOS Computational Biology: published December 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010787

Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant

Tingting Zhao, Nischal Karki, Brian D. Zoltowski, Devin A. Matthews

PLOS Computational Biology: published December 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010794

Mechanistic model for human brain metabolism and its connection to the neurovascular coupling

Nicolas Sundqvist, Sebastian Sten, Peter Thompson, Benjamin Jan Andersson, Maria Engström, Gunnar Cedersund

PLOS Computational Biology: published December 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010798

The effects of base rate neglect on sequential belief updating and real-world beliefs

Brandon K. Ashinoff, Justin Buck, Michael Woodford, Guillermo Horga

PLOS Computational Biology: published December 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010796

Mesoscopic description of hippocampal replay and metastability in spiking neural networks with short-term plasticity

Bastian Pietras, Valentin Schmutz, Tilo Schwalger

PLOS Computational Biology: published December 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010809

An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors

Xueer Chen, Lujia Chen, Cornelius H. L. Kürten, Fattaneh Jabbari, Lazar Vujanovic, Ying Ding, Binfeng Lu, Kevin Lu, Aditi Kulkarni, Tracy Tabib, Robert Lafyatis, Gregory F. Cooper, Robert Ferris, Xinghua Lu

PLOS Computational Biology: published December 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010761

The catecholamine precursor Tyrosine reduces autonomic arousal and decreases decision thresholds in reinforcement learning and temporal discounting

David Mathar, Mani Erfanian Abdoust, Tobias Marrenbach, Deniz Tuzsus, Jan Peters

PLOS Computational Biology: published December 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010785

Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images

Tomonori Ogane, Daisuke Noshiro, Toshio Ando, Atsuko Yamashita, Yuji Sugita, Yasuhiro Matsunaga

PLOS Computational Biology: published December 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010384

A fast lasso-based method for inferring higher-order interactions

Kieran Elmes, Astra Heywood, Zhiyi Huang, Alex Gavryushkin

PLOS Computational Biology: published December 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010730

Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes

Xuexia Jiang, Tadamoto Isogai, Joseph Chi, Gaudenz Danuser

PLOS Computational Biology: published December 30, 2022 | https://doi.org/10.1371/journal.pcbi.1009667

Correction

Correction: Humans combine value learning and hypothesis testing strategically in multi-dimensional probabilistic reward learning

The PLOS Computational Biology Staff

PLOS Computational Biology: published December 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010775