Ten simple rules for using public biological data for your research

Vishal H. Oza, Jordan H. Whitlock, Elizabeth J. Wilk, Angelina Uno-Antonison, Brandon Wilk, Manavalan Gajapathy, Timothy C. Howton, Austyn Trull, Lara Ianov, Elizabeth A. Worthey, Brittany N. Lasseigne

PLOS Computational Biology: published January 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010749

Ten quick tips for computational analysis of medical images

Davide Chicco, Rakesh Shiradkar

PLOS Computational Biology: published January 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010778

Galaxy Training: A powerful framework for teaching!

Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D. Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A. Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, Galaxy Training Network, Björn Grüning, Bérénice Batut

PLOS Computational Biology: published January 9, 2023 | https://doi.org/10.1371/journal.pcbi.1010752

Ten simple rules for defining a computational biology project

William Stafford Noble

PLOS Computational Biology: published January 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010786

Ten simple rules for implementing open and reproducible research practices after attending a training course

Verena Heise, Constance Holman, Hung Lo, Ekaterini Maria Lyras, Mark Christopher Adkins, Maria Raisa Jessica Aquino, Konstantinos I. Bougioukas, Katherine O. Bray, Martyna Gajos, Xuanzong Guo, Corinna Hartling, Rodrigo Huerta-Gutierrez, Miroslava Jindrová, Joanne P. M. Kenney, Adrianna P. Kępińska, Laura Kneller, Elena Lopez-Rodriguez, Felix Mühlensiepen, Angela Richards, Gareth Richards, Maximilian Siebert, James A. Smith, Natalie Smith, Nicolai Stransky, Sirpa Tarvainen, Daniela Sofia Valdes, Kayleigh L. Warrington, Nina-Maria Wilpert, Disa Witkowska, Mirela Zaneva, Jeanette Zanker, Tracey L. Weissgerber

PLOS Computational Biology: published January 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010750

Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load

Migle Gabrielaite, Marc Bennedbæk, Malthe Sebro Rasmussen, Virginia Kan, Hansjakob Furrer, Robert Flisiak, Marcelo Losso, Jens D. Lundgren, INSIGHT START Study Group, Rasmus L. Marvig

PLOS Computational Biology: published January 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010756

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks

Polina Lakrisenko, Paul Stapor, Stephan Grein, Łukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl, Jan Hasenauer

PLOS Computational Biology: published January 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010783

Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections

Frédéric Labbé, Qixin He, Qi Zhan, Kathryn E. Tiedje, Dionne C. Argyropoulos, Mun Hua Tan, Anita Ghansah, Karen P. Day, Mercedes Pascual

PLOS Computational Biology: published January 3, 2023 | https://doi.org/10.1371/journal.pcbi.1010816

Mapping of morpho-electric features to molecular identity of cortical inhibitory neurons

Yann Roussel, Csaba Verasztó, Dimitri Rodarie, Tanguy Damart, Michael Reimann, Srikanth Ramaswamy, Henry Markram, Daniel Keller

PLOS Computational Biology: published January 5, 2023 | https://doi.org/10.1371/journal.pcbi.1010058

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One dimensional approximations of neuronal dynamics reveal computational strategy

Connor Brennan, Adeeti Aggarwal, Rui Pei, David Sussillo, Alex Proekt

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010784

A quantitative model for human neurovascular coupling with translated mechanisms from animals

Sebastian Sten, Henrik Podéus, Nicolas Sundqvist, Fredrik Elinder, Maria Engström, Gunnar Cedersund

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010818

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks

Souvik Seal, Qunhua Li, Elle Butler Basner, Laura M. Saba, Katerina Kechris

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010758

A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures

Hongxuan Zhai, Julia Fukuyama

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010821

Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions

Nicola Catenacci Volpi, Martin Greaves, Dari Trendafilov, Christoph Salge, Giovanni Pezzulo, Daniel Polani

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010810

Novel modelling approaches to predict the role of antivirals in reducing influenza transmission

Jason Asher, Annabelle Lemenuel-Diot, Matthew Clay, David P. Durham, Luis Mier-y-Teran-Romero, Carlos J. Arguello, Sebastien Jolivet, Diana Y. Wong, Klaus Kuhlbusch, Barry Clinch, Jean-Eric Charoin

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010797

SurvivalPath:A R package for conducting personalized survival path mapping based on time-series survival data

Lujun Shen, Jinqing Mo, Changsheng Yang, Yiquan Jiang, Liangru Ke, Dan Hou, Jingdong Yan, Tao Zhang, Weijun Fan

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010830

HiSV: A control-free method for structural variation detection from Hi-C data

Junping Li, Lin Gao, Yusen Ye

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010760

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Humans account for cognitive costs when finding shortcuts: An information-theoretic analysis of navigation

Gian Luca Lancia, Mattia Eluchans, Marco D’Alessandro, Hugo J. Spiers, Giovanni Pezzulo

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010829

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering

Theresa Ullmann, Stefanie Peschel, Philipp Finger, Christian L. Müller, Anne-Laure Boulesteix

PLOS Computational Biology: published January 6, 2023 | https://doi.org/10.1371/journal.pcbi.1010820

Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus

Jiani Chen, Swan Tan, Vasanthi Avadhanula, Leonard Moise, Pedro A. Piedra, Anne S. De Groot, Justin Bahl

PLOS Computational Biology: published January 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010360

Interspecific comparison of gene expression profiles using machine learning

Artem S. Kasianov, Anna V. Klepikova, Alexey V. Mayorov, Gleb S. Buzanov, Maria D. Logacheva, Aleksey A. Penin

PLOS Computational Biology: published January 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010743

Ecological landscapes guide the assembly of optimal microbial communities

Ashish B. George, Kirill S. Korolev

PLOS Computational Biology: published January 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010570

Chaotic dynamics in spatially distributed neuronal networks generate population-wide shared variability

Noga Mosheiff, Bard Ermentrout, Chengcheng Huang

PLOS Computational Biology: published January 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010843

Spikebench: An open benchmark for spike train time-series classification

Ivan Lazarevich, Ilya Prokin, Boris Gutkin, Victor Kazantsev

PLOS Computational Biology: published January 10, 2023 | https://doi.org/10.1371/journal.pcbi.1010792

Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability

Ryan J. Murphy, Gency Gunasingh, Nikolas K. Haass, Matthew J. Simpson

PLOS Computational Biology: published January 12, 2023 | https://doi.org/10.1371/journal.pcbi.1010833

A unitary model of auditory frequency change perception

Kai Siedenburg, Jackson Graves, Daniel Pressnitzer

PLOS Computational Biology: published January 12, 2023 | https://doi.org/10.1371/journal.pcbi.1010307

Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni

Kahlan E. Newman, Syma Khalid

PLOS Computational Biology: published January 13, 2023 | https://doi.org/10.1371/journal.pcbi.1010841

Systematic design of pulse dosing to eradicate persister bacteria

Garima Singh, Mehmet A. Orman, Jacinta C. Conrad, Michael Nikolaou

PLOS Computational Biology: published January 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010243

Examining the efficacy of localised gemcitabine therapy for the treatment of pancreatic cancer using a hybrid agent-based model

Adrianne L. Jenner, Wayne Kelly, Michael Dallaston, Robyn Araujo, Isobelle Parfitt, Dominic Steinitz, Pantea Pooladvand, Peter S. Kim, Samantha J. Wade, Kara L. Vine

PLOS Computational Biology: published January 17, 2023 | https://doi.org/10.1371/journal.pcbi.1010104

End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins

Tian Cai, Li Xie, Shuo Zhang, Muge Chen, Di He, Amitesh Badkul, Yang Liu, Hari Krishna Namballa, Michael Dorogan, Wayne W. Harding, Cameron Mura, Philip E. Bourne, Lei Xie

PLOS Computational Biology: published January 18, 2023 | https://doi.org/10.1371/journal.pcbi.1010851

Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis

Caleb M. Phillips, Ernesto A. B. F. Lima, Manasa Gadde, Angela M. Jarrett, Marissa Nichole Rylander, Thomas E. Yankeelov

PLOS Computational Biology: published January 18, 2023 | https://doi.org/10.1371/journal.pcbi.1009499

Modelling continual learning in humans with Hebbian context gating and exponentially decaying task signals

Timo Flesch, David G. Nagy, Andrew Saxe, Christopher Summerfield

PLOS Computational Biology: published January 19, 2023 | https://doi.org/10.1371/journal.pcbi.1010808

Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments

Yuki Sugiyama, Kohei Uno, Yusuke Matsui

PLOS Computational Biology: published January 19, 2023 | https://doi.org/10.1371/journal.pcbi.1009989

Surround suppression in mouse auditory cortex underlies auditory edge detection

Omri David Gilday, Benedikt Praegel, Ido Maor, Tav Cohen, Israel Nelken, Adi Mizrahi

PLOS Computational Biology: published January 19, 2023 | https://doi.org/10.1371/journal.pcbi.1010861

Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics

Oshane O. Thomas, Hongyu Shen, Ryan L. Raaum, William E. H. Harcourt-Smith, John D. Polk, Mark Hasegawa-Johnson

PLOS Computational Biology: published January 19, 2023 | https://doi.org/10.1371/journal.pcbi.1009061

Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates

Alexander P. Browning, Matthew J. Simpson

PLOS Computational Biology: published January 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010844

A new model of Notch signalling: Control of Notch receptor cis-inhibition via Notch ligand dimers

Daipeng Chen, Zary Forghany, Xinxin Liu, Haijiang Wang, Roeland M. H. Merks, David A. Baker

PLOS Computational Biology: published January 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010169

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Carlos Gueto-Tettay, Di Tang, Lotta Happonen, Moritz Heusel, Hamed Khakzad, Johan Malmström, Lars Malmström

PLOS Computational Biology: published January 20, 2023 | https://doi.org/10.1371/journal.pcbi.1010457

A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting

Solveig Engebretsen, Alfonso Diz-Lois Palomares, Gunnar Rø, Anja Bråthen Kristoffersen, Jonas Christoffer Lindstrøm, Kenth Engø-Monsen, Meghana Kamineni, Louis Yat Hin Chan, Ørjan Dale, Jørgen Eriksson Midtbø, Kristian Lindalen Stenerud, Francesco Di Ruscio, Richard White, Arnoldo Frigessi, Birgitte Freiesleben de Blasio

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Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction

Gregory J. Kimmel, Richard J. Beck, Xiaoqing Yu, Thomas Veith, Samuel Bakhoum, Philipp M. Altrock, Noemi Andor

PLOS Computational Biology: published January 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010815

Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases

Arash Mehrjou, Ashkan Soleymani, Amin Abyaneh, Samir Bhatt, Bernhard Schölkopf, Stefan Bauer

PLOS Computational Biology: published January 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010799

Relating local connectivity and global dynamics in recurrent excitatory-inhibitory networks

Yuxiu Shao, Srdjan Ostojic

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Deciphering the RRM-RNA recognition code: A computational analysis

Joel Roca-Martínez, Hrishikesh Dhondge, Michael Sattler, Wim F. Vranken

PLOS Computational Biology: published January 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010859

Modelling ribosome kinetics and translational control on dynamic mRNA

Eric C. Dykeman

PLOS Computational Biology: published January 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010870

Improving the validity of neuroimaging decoding tests of invariant and configural neural representation

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PLOS Computational Biology: published January 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010819

Shape-specific characterization of colorectal adenoma growth and transition to cancer with stochastic cell-based models

Cristoforo Simonetto, Ulrich Mansmann, Jan Christian Kaiser

PLOS Computational Biology: published January 23, 2023 | https://doi.org/10.1371/journal.pcbi.1010831

Mechanisms of hemoglobin cycling in anemia patients treated with erythropoiesis-stimulating agents

David J. Jörg, Doris H. Fuertinger, Peter Kotanko

PLOS Computational Biology: published January 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010850

neuroWalknet, a controller for hexapod walking allowing for context dependent behavior

Malte Schilling, Holk Cruse

PLOS Computational Biology: published January 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010136

Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants

Sören von Bülow, Mateusz Sikora, Florian E. C. Blanc, Roberto Covino, Gerhard Hummer

PLOS Computational Biology: published January 24, 2023 | https://doi.org/10.1371/journal.pcbi.1010822

Injury-related cell death and proteoglycan loss in articular cartilage: Numerical model combining necrosis, reactive oxygen species, and inflammatory cytokines

Joonas P. Kosonen, Atte S. A. Eskelinen, Gustavo A. Orozco, Petteri Nieminen, Donald D. Anderson, Alan J. Grodzinsky, Rami K. Korhonen, Petri Tanska

PLOS Computational Biology: published January 26, 2023 | https://doi.org/10.1371/journal.pcbi.1010337

A dual graph neural network for drug–drug interactions prediction based on molecular structure and interactions

Mei Ma, Xiujuan Lei

PLOS Computational Biology: published January 26, 2023 | https://doi.org/10.1371/journal.pcbi.1010812

Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia

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PLOS Computational Biology: published January 26, 2023 | https://doi.org/10.1371/journal.pcbi.1010380

Bayesian reconstruction of memories stored in neural networks from their connectivity

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PLOS Computational Biology: published January 30, 2023 | https://doi.org/10.1371/journal.pcbi.1010813

Community composition exceeds area as a predictor of long-term conservation value

Jacob D. O’Sullivan, J. Christopher D. Terry, Ramesh Wilson, Axel G. Rossberg

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Environmental uncertainty and the advantage of impulsive choice strategies

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Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit

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maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

Tareian A. Cazares, Faiz W. Rizvi, Balaji Iyer, Xiaoting Chen, Michael Kotliar, Anthony T. Bejjani, Joseph A. Wayman, Omer Donmez, Benjamin Wronowski, Sreeja Parameswaran, Leah C. Kottyan, Artem Barski, Matthew T. Weirauch, V. B. Surya Prasath, Emily R. Miraldi

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Correction: Time to revisit the endpoint dilution assay and to replace the TCID₅₀ as a measure of a virus sample’s infection concentration

Daniel Cresta, Donald C. Warren, Christian Quirouette, Amanda P. Smith, Lindey C. Lane, Amber M. Smith, Catherine A. A. Beauchemin

PLOS Computational Biology: published January 31, 2023 | https://doi.org/10.1371/journal.pcbi.1010877

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