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Eleven quick tips for writing a Bioconductor package

Charlotte Soneson, Lori Shepherd, Marcel Ramos, Kevin Rue-Albrecht, Johannes Rainer, Hervé Pagès, Vincent J. Carey

PLoS Comput Biol. 2025 Mar; 21(3): e1012856. Published online 2025 Mar 19. doi: 10.1371/journal.pcbi.1012856

PMCID:: PMC11922196

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Select item 119184032.

Modeling decision-making under uncertainty with qualitative outcomes

Nachshon Korem, Or Duek, Ruonan Jia, Emily Wertheimer, Sierra Metviner, Michael Grubb, Ifat Levy

PLoS Comput Biol. 2025 Mar; 21(3): e1012440. Published online 2025 Mar 3. doi: 10.1371/journal.pcbi.1012440

PMCID:: PMC11918403

Article PDF–901K

Select item 119021993.

DySCo: A general framework for dynamic functional connectivity

Giuseppe de Alteriis, Oliver Sherwood, Alessandro Ciaramella, Robert Leech, Joana Cabral, Federico E Turkheimer, Paul Expert

PLoS Comput Biol. 2025 Mar; 21(3): e1012795. Published online 2025 Mar 7. doi: 10.1371/journal.pcbi.1012795

PMCID:: PMC11902199

Article PDF–11M

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Post-processing and weighted combination of infectious disease nowcasts

André Victor Ribeiro Amaral, Daniel Wolffram, Paula Moraga, Johannes Bracher

PLoS Comput Biol. 2025 Mar; 21(3): e1012836. Published online 2025 Mar 3. doi: 10.1371/journal.pcbi.1012836

PMCID:: PMC11902281

Article PDF–9.9M

Select item 118820505.

Impact of increased diagnosis of early HIV infection and immediate antiretroviral treatment initiation on HIV transmission among men who have sex with men in the Netherlands

Alexandra Teslya, Janneke Cornelia Maria Heijne, Maarten Franciscus Schim van der Loeff, Ard van Sighem, Jacob Aiden Roberts, Maartje Dijkstra, Godelieve J de Bree, Axel Jeremias Schmidt, Kai J Jonas, Mirjam E Kretzschmar, Ganna Rozhnova

PLoS Comput Biol. 2025 Feb; 21(2): e1012055. Published online 2025 Feb 27. doi: 10.1371/journal.pcbi.1012055

PMCID:: PMC11882050

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Select item 119030426.

Noradrenergic and Dopaminergic modulation of meta-cognition and meta-control

Sara Ershadmanesh, Sahar Rajabi, Reza Rostami, Rani Moran, Peter Dayan

PLoS Comput Biol. 2025 Feb; 21(2): e1012675. Published online 2025 Feb 26. doi: 10.1371/journal.pcbi.1012675

PMCID:: PMC11903042

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An agent-based model to simulate the transmission dynamics of bloodborne pathogens within hospitals

Paul Henriot, Mohamed El-Kassas, Wagida Anwar, Samia A. Girgis, Maha El Gaafary, Kévin Jean, Laura Temime

PLoS Comput Biol. 2025 Feb; 21(2): e1012850. Published online 2025 Feb 24. doi: 10.1371/journal.pcbi.1012850

PMCID:: PMC11882061

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Information transmission in a cell monolayer: A numerical study

Paweł Nałęcz-Jawecki, Przemysław Szyc, Frederic Grabowski, Marek Kochańczyk, Tomasz Lipniacki

PLoS Comput Biol. 2025 Feb; 21(2): e1012846. Published online 2025 Feb 21. doi: 10.1371/journal.pcbi.1012846

PMCID:: PMC11902151

Article PDF–3.0M

Select item 118673999.

Quantifying infectious disease epidemic risks: A practical approach for seasonal pathogens

Alexander R Kaye, Giorgio Guzzetta, Michael J Tildesley, Robin N Thompson

PLoS Comput Biol. 2025 Feb; 21(2): e1012364. Published online 2025 Feb 19. doi: 10.1371/journal.pcbi.1012364

PMCID:: PMC11867399

Article PDF–1.9M

Select item 1184998310.

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment

Mai Chan Lau, Jennifer Borowsky, Juha P. Väyrynen, Koichiro Haruki, Melissa Zhao, Andressa Dias Costa, Simeng Gu, Annacarolina da Silva, Tomotaka Ugai, Kota Arima, Minh N. Nguyen, Yasutoshi Takashima, Joe Yeong, David Tai, Tsuyoshi Hamada, Jochen K. Lennerz, Charles S. Fuchs, Catherine J. Wu, Jeffrey A. Meyerhardt, Shuji Ogino, Jonathan A. Nowak

PLoS Comput Biol. 2025 Feb; 21(2): e1012707. Published online 2025 Feb 18. doi: 10.1371/journal.pcbi.1012707

PMCID:: PMC11849983

Article PDF–2.9M

Select item 1184998111.

ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization

Laura M. Gunsalus, Michael J. Keiser, Katherine S. Pollard

PLoS Comput Biol. 2025 Feb; 21(2): e1012841. Published online 2025 Feb 18. doi: 10.1371/journal.pcbi.1012841

PMCID:: PMC11849981

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Select item 1184191712.

Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data

Xueda Shen, Aaron Rumack, Bryan Wilder, Ryan J Tibshirani

PLoS Comput Biol. 2025 Feb; 21(2): e1012717. Published online 2025 Feb 18. doi: 10.1371/journal.pcbi.1012717

PMCID:: PMC11841917

Article PDF–6.7M

Select item 1182840813.

Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern

Wenxuan Li, Xu Chen, Suli Liu, Chiyu Zhang, Guyue Liu

PLoS Comput Biol. 2025 Feb; 21(2): e1012778. Published online 2025 Feb 14. doi: 10.1371/journal.pcbi.1012778

PMCID:: PMC11828408

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Select item 1187035414.

Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction

Xianghao Zhan, Qinmei Xu, Yuanning Zheng, Guangming Lu, Olivier Gevaert

PLoS Comput Biol. 2025 Feb; 21(2): e1012803. Published online 2025 Feb 13. doi: 10.1371/journal.pcbi.1012803

PMCID:: PMC11870354

Article PDF–40M

Select item 1184191515.

Hexagons all the way down: grid cells as a conformal isometric map of space

Vemund Sigmundson Schøyen, Kosio Beshkov, Markus Borud Pettersen, Erik Hermansen, Konstantin Holzhausen, Anders Malthe-Sørenssen, Marianne Fyhn, Mikkel Elle Lepperød

PLoS Comput Biol. 2025 Feb; 21(2): e1012804. Published online 2025 Feb 13. doi: 10.1371/journal.pcbi.1012804

PMCID:: PMC11841915

Article PDF–6.2M

Select item 1183537816.

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities

Lars Berling, Jonathan Klawitter, Remco Bouckaert, Dong Xie, Alex Gavryushkin, Alexei J Drummond

PLoS Comput Biol. 2025 Feb; 21(2): e1012789. Published online 2025 Feb 13. doi: 10.1371/journal.pcbi.1012789

PMCID:: PMC11835378

Article PDF–3.5M

Select item 1182500517.

AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis

Rui Miao, Hao-Yang Yu, Bing-Jie Zhong, Hong-Xia Sun, Qiang Xia

PLoS Comput Biol. 2025 Feb; 21(2): e1012773. Published online 2025 Feb 13. doi: 10.1371/journal.pcbi.1012773

PMCID:: PMC11825005

Article PDF–2.1M

Select item 1184490118.

ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature

Luca Musella, Alejandro Afonso Castro, Xin Lai, Max Widmann, Julio Vera

PLoS Comput Biol. 2025 Feb; 21(2): e1012745. Published online 2025 Feb 11. doi: 10.1371/journal.pcbi.1012745

PMCID:: PMC11844901

Article PDF–3.1M

Select item 1184189319.

Decoding biomolecular condensate dynamics: an energy landscape approach

Subhadip Biswas, Davit A Potoyan

PLoS Comput Biol. 2025 Feb; 21(2): e1012826. Published online 2025 Feb 10. doi: 10.1371/journal.pcbi.1012826

PMCID:: PMC11841893

Article PDF–30M

Select item 1180542620.

Challenging a paradigm: Staggered versus single-pulse mass dog vaccination strategy for rabies elimination

Brinkley Raynor Bellotti, Elvis W. Díaz, Micaela De la Puente-León, Maria T. Rieders, Sergio E. Recuenco, Michael Z. Levy, Ricardo Castillo-Neyra

PLoS Comput Biol. 2025 Feb; 21(2): e1012780. Published online 2025 Feb 7. doi: 10.1371/journal.pcbi.1012780

PMCID:: PMC11805426

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"PLoS Comput Biol"[jour] (11191)
PMC
Homo sapiens vacuolar protein sorting 13 homolog D (VPS13D), transcript variant ...
Homo sapiens vacuolar protein sorting 13 homolog D (VPS13D), transcript variant 1, mRNA
gi|1388704174|ref|NM_015378.4|

Nucleotide
intermembrane lipid transfer protein VPS13D isoform 1 [Homo sapiens]
intermembrane lipid transfer protein VPS13D isoform 1 [Homo sapiens]
gi|54607139|ref|NP_056193.2|

Protein
Mus musculus vacuolar protein sorting 13A (Vps13a), mRNA
Mus musculus vacuolar protein sorting 13A (Vps13a), mRNA
gi|355390275|ref|NM_173028.4|

Nucleotide
Mus musculus X-linked Kx blood group (Xk), mRNA
Mus musculus X-linked Kx blood group (Xk), mRNA
gi|134053936|ref|NM_023500.2|

Nucleotide

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