Ten simple rules to cultivate belonging in collaborative data science research teams

Kaitlyn M. Gaynor, Therese Azevedo, Clarissa Boyajian, Julien Brun, Amber E. Budden, Allie Cole, Samantha Csik, Joe DeCesaro, Halina Do-Linh, Joan Dudney, Carmen Galaz García, Scout Leonard, Nicholas J. Lyon, Althea Marks, Julia Parish, Alexandra A. Phillips, Courtney Scarborough, Joshua Smith, Marcus Thompson, Camila Vargas Poulsen, Caitlin R. Fong

PLOS Computational Biology: published November 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010567

Ten simple rules for running a summer research program

Joseph C. Ayoob, Juan S. Ramírez-Lugo

PLOS Computational Biology: published November 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010588

Ten simple rules for developing visualization tools in genomics

Eloi Durant, Mathieu Rouard, Eric W. Ganko, Cedric Muller, Alan M. Cleary, Andrew D. Farmer, Matthieu Conte, Francois Sabot

PLOS Computational Biology: published November 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010622

Reproducibility efforts as a teaching tool: A pilot study

Nestoras Karathanasis, Daniel Hwang, Vibol Heng, Rimal Abhimannyu, Phillip Slogoff-Sevilla, Gina Buchel, Victoria Frisbie, Peiyao Li, Dafni Kryoneriti, Isidore Rigoutsos

PLOS Computational Biology: published November 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010615

Ten simple rules for funding scientific open source software

Carly Strasser, Kate Hertweck, Josh Greenberg, Dario Taraborelli, Elizabeth Vu

PLOS Computational Biology: published November 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010627

Phylogenetic reconciliation

Hugo Menet, Vincent Daubin, Eric Tannier

PLOS Computational Biology: published November 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010621

Molecular source attribution

Elisa Chao, Connor Chato, Reid Vender, Abayomi S. Olabode, Roux-Cil Ferreira, Art F. Y. Poon

PLOS Computational Biology: published November 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010649

How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods

Brian A. Lerch, Derek A. Smith, Thomas Koffel, Sarah C. Bagby, Karen C. Abbott

PLOS Computational Biology: published November 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010666

Strength-dependent perturbation of whole-brain model working in different regimes reveals the role of fluctuations in brain dynamics

Yonatan Sanz Perl, Anira Escrichs, Enzo Tagliazucchi, Morten L. Kringelbach, Gustavo Deco

PLOS Computational Biology: published November 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010662

Training diversity promotes absolute-value-guided choice

Levi Solomyak, Paul B. Sharp, Eran Eldar

PLOS Computational Biology: published November 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010664

Synaptic reshaping of plastic neuronal networks by periodic multichannel stimulation with single-pulse and burst stimuli

Justus A. Kromer, Peter A. Tass

PLOS Computational Biology: published November 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010568

Inferring parameters of cancer evolution in chronic lymphocytic leukemia

Nathan D. Lee, Ivana Bozic

PLOS Computational Biology: published November 4, 2022 | https://doi.org/10.1371/journal.pcbi.1010677

Probabilistic program inference in network-based epidemiological simulations

Niklas Smedemark-Margulies, Robin Walters, Heiko Zimmermann, Lucas Laird, Christian van der Loo, Neela Kaushik, Rajmonda Caceres, Jan-Willem van de Meent

PLOS Computational Biology: published November 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010591

Network topology metrics explaining enrichment of hybrid epithelial/mesenchymal phenotypes in metastasis

Mubasher Rashid, Kishore Hari, John Thampi, Nived Krishnan Santhosh, Mohit Kumar Jolly

PLOS Computational Biology: published November 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010687

A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines

Xinyu Gu, Nicholas P. Schafer, Carlos Bueno, Wei Lu, Peter G. Wolynes

PLOS Computational Biology: published November 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010657

OrganoID: A versatile deep learning platform for tracking and analysis of single-organoid dynamics

Jonathan M. Matthews, Brooke Schuster, Sara Saheb Kashaf, Ping Liu, Rakefet Ben-Yishay, Dana Ishay-Ronen, Evgeny Izumchenko, Le Shen, Christopher R. Weber, Margaret Bielski, Sonia S. Kupfer, Mustafa Bilgic, Andrey Rzhetsky, Savaş Tay

PLOS Computational Biology: published November 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010584

AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers

Georgios D. Koutsovoulos, Solène Granjeon Noriot, Marc Bailly-Bechet, Etienne G. J. Danchin, Corinne Rancurel

PLOS Computational Biology: published November 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010686

Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners

Himangi Srivastava, Michael J. Lippincott, Jordan Currie, Robert Canfield, Maggie P. Y. Lam, Edward Lau

PLOS Computational Biology: published November 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010702

BIPS—A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library

Sigal Leviatan, Iris N. Kalka, Thomas Vogl, Shelley Klompas, Adina Weinberger, Eran Segal

PLOS Computational Biology: published November 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010663

Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm

Rahul Biswas, Eli Shlizerman

PLOS Computational Biology: published November 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010653

Adaptive multi-objective control explains how humans make lateral maneuvers while walking

David M. Desmet, Joseph P. Cusumano, Jonathan B. Dingwell

PLOS Computational Biology: published November 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010035

SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more

Hasan Balci, Ugur Dogrusoz, Yusuf Ziya Ozgul, Perman Atayev

PLOS Computational Biology: published November 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010635

Dosing time optimization of antihypertensive medications by including the circadian rhythm in pharmacokinetic-pharmacodynamic models

Javiera Cortés-Ríos, Ramón C. Hermida, Maria Rodriguez-Fernandez

PLOS Computational Biology: published November 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010711

Brain-wide connectome inferences using functional connectivity MultiVariate Pattern Analyses (fc-MVPA)

Alfonso Nieto-Castanon

PLOS Computational Biology: published November 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010634

Brain connectivity meets reservoir computing

Fabrizio Damicelli, Claus C. Hilgetag, Alexandros Goulas

PLOS Computational Biology: published November 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010639

Computationally efficient mechanism discovery for cell invasion with uncertainty quantification

Daniel J. VandenHeuvel, Christopher Drovandi, Matthew J. Simpson

PLOS Computational Biology: published November 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010599

Computational analysis of 5-fluorouracil anti-tumor activity in colon cancer using a mechanistic pharmacokinetic/pharmacodynamic model

Chenhui Ma, Alex Almasan, Evren Gurkan-Cavusoglu

PLOS Computational Biology: published November 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010685

A neurocomputational theory of action regulation predicts motor behavior in neurotypical individuals and patients with Parkinson’s disease

Shan Zhong, Jeong Woo Choi, Nadia G. Hashoush, Diana Babayan, Mahsa Malekmohammadi, Nader Pouratian, Vassilios Christopoulos

PLOS Computational Biology: published November 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010111

Soft disorder modulates the assembly path of protein complexes

Beatriz Seoane, Alessandra Carbone

PLOS Computational Biology: published November 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010713

Inferring a spatial code of cell-cell interactions across a whole animal body

Erick Armingol, Abbas Ghaddar, Chintan J. Joshi, Hratch Baghdassarian, Isaac Shamie, Jason Chan, Hsuan-Lin Her, Samuel Berhanu, Anushka Dar, Fabiola Rodriguez-Armstrong, Olivia Yang, Eyleen J. O’Rourke, Nathan E. Lewis

PLOS Computational Biology: published November 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010715

Sleep prevents catastrophic forgetting in spiking neural networks by forming a joint synaptic weight representation

Ryan Golden, Jean Erik Delanois, Pavel Sanda, Maxim Bazhenov

PLOS Computational Biology: published November 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010628

Operant conditioning of stochastic chemical reaction networks

David Arredondo, Matthew R. Lakin

PLOS Computational Biology: published November 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010676

HELIOS: High-speed sequence alignment in optics

Ehsan Maleki, Saeedeh Akbari Rokn Abadi, Somayyeh Koohi

PLOS Computational Biology: published November 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010665

Amino acid variants of SARS-CoV-2 papain-like protease have impact on drug binding

Agata P. Perlinska, Adam Stasiulewicz, Mai Lan Nguyen, Karolina Swiderska, Mikolaj Zmudzinski, Alicja W. Maksymiuk, Marcin Drag, Joanna I. Sulkowska

PLOS Computational Biology: published November 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010667

Coupling and heterogeneity modulate pacemaking capability in healthy and diseased two-dimensional sinoatrial node tissue models

Chiara Campana, Eugenio Ricci, Chiara Bartolucci, Stefano Severi, Eric A. Sobie

PLOS Computational Biology: published November 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010098

Deep reinforcement learning for optimal experimental design in biology

Neythen J. Treloar, Nathan Braniff, Brian Ingalls, Chris P. Barnes

PLOS Computational Biology: published November 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010695

Social dilemmas of sociality due to beneficial and costly contagion

Daniel B. Cooney, Dylan H. Morris, Simon A. Levin, Daniel I. Rubenstein, Pawel Romanczuk

PLOS Computational Biology: published November 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010670

Conflicting effects of recombination on the evolvability and robustness in neutrally evolving populations

Alexander Klug, Joachim Krug

PLOS Computational Biology: published November 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010710

Look twice: A generalist computational model predicts return fixations across tasks and species

Mengmi Zhang, Marcelo Armendariz, Will Xiao, Olivia Rose, Katarina Bendtz, Margaret Livingstone, Carlos Ponce, Gabriel Kreiman

PLOS Computational Biology: published November 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010654

Effective resistance against pandemics: Mobility network sparsification for high-fidelity epidemic simulations

Alexander Mercier, Samuel Scarpino, Cristopher Moore

PLOS Computational Biology: published November 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010650

Interpreting and de-noising genetically engineered barcodes in a DNA virus

Sylvain Blois, Benjamin M. Goetz, James J. Bull, Christopher S. Sullivan

PLOS Computational Biology: published November 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010131

Exploring the mono-/bistability range of positively autoregulated signaling systems in the presence of competing transcription factor binding sites

Rong Gao, Samantha E. Brokaw, Zeyue Li, Libby J. Helfant, Ti Wu, Muhammad Malik, Ann M. Stock

PLOS Computational Biology: published November 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010738

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

Mingyu Song, Persis A. Baah, Ming Bo Cai, Yael Niv

PLOS Computational Biology: published November 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010699

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Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021

Oliver Eales, Haowei Wang, David Haw, Kylie E. C. Ainslie, Caroline E. Walters, Christina Atchison, Graham Cooke, Wendy Barclay, Helen Ward, Ara Darzi, Deborah Ashby, Christl A. Donnelly, Paul Elliott, Steven Riley

PLOS Computational Biology: published November 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010724

Role of path information in visual perception of joint stiffness

A. Michael West Jr., Meghan E. Huber, Neville Hogan

PLOS Computational Biology: published November 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010729

The geometry of representational drift in natural and artificial neural networks

Kyle Aitken, Marina Garrett, Shawn Olsen, Stefan Mihalas

PLOS Computational Biology: published November 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010716

Experimental validation of computerised models of clustering of platelet glycoprotein receptors that signal via tandem SH2 domain proteins

Zahra Maqsood, Joanne C. Clark, Eleyna M. Martin, Yam Fung Hilaire Cheung, Luis A. Morán, Sean E. T. Watson, Jeremy A. Pike, Ying Di, Natalie S. Poulter, Alexandre Slater, Bodo M. H. Lange, Bernhard Nieswandt, Johannes A. Eble, Mike G. Tomlinson, Dylan M. Owen, David Stegner, Lloyd J. Bridge, Christoph Wierling, Steve P. Watson

PLOS Computational Biology: published November 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010708

Inference of B cell clonal families using heavy/light chain pairing information

Duncan K. Ralph, Frederick A. Matsen IV

PLOS Computational Biology: published November 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010723

A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion

Nikita Sivakumar, Helen V. Warner, Shayn M. Peirce, Matthew J. Lazzara

PLOS Computational Biology: published November 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010701

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Efficient inference and identifiability analysis for differential equation models with random parameters

Alexander P. Browning, Christopher Drovandi, Ian W. Turner, Adrianne L. Jenner, Matthew J. Simpson

PLOS Computational Biology: published November 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010734

Sampling effects and measurement overlap can bias the inference of neuronal avalanches

Joao Pinheiro Neto, F. Paul Spitzner, Viola Priesemann

PLOS Computational Biology: published November 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010678

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

Connor Chato, Yi Feng, Yuhua Ruan, Hui Xing, Joshua Herbeck, Marcia Kalish, Art F. Y. Poon

PLOS Computational Biology: published November 30, 2022 | https://doi.org/10.1371/journal.pcbi.1010745

Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: Killers and drivers of resistance evolution

Quentin J. Leclerc, Jodi A. Lindsay, Gwenan M. Knight

PLOS Computational Biology: published November 30, 2022 | https://doi.org/10.1371/journal.pcbi.1010746

Cluster detection with random neighbourhood covering: Application to invasive Group A Streptococcal disease

Massimo Cavallaro, Juliana Coelho, Derren Ready, Valerie Decraene, Theresa Lamagni, Noel D. McCarthy, Dan Todkill, Matt J. Keeling

PLOS Computational Biology: published November 30, 2022 | https://doi.org/10.1371/journal.pcbi.1010726

Tracking human skill learning with a hierarchical Bayesian sequence model

Noémi Éltető, Dezső Nemeth, Karolina Janacsek, Peter Dayan

PLOS Computational Biology: published November 30, 2022 | https://doi.org/10.1371/journal.pcbi.1009866

Correction: cytoNet: Spatiotemporal network analysis of cell communities

PLOS Computational Biology

PLOS Computational Biology: published November 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010644

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Correction: All²: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons

Vivekananda Sarangi, Yeongjun Jang, Milovan Suvakov, Taejeong Bae, Liana Fasching, Shobana Sekar, Livia Tomasini, Jessica Mariani, Flora M. Vaccarino, Alexej Abyzov

PLOS Computational Biology: published November 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010703

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Correction: A circuit model of auditory cortex

Youngmin Park, Maria N. Geffen

PLOS Computational Biology: published November 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010700

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