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📖 Bioconductor Publications

Publications

This is a select list of featured and recent publications that cite Bioconductor, along with select books, book chapters, and original Bioconductor technical reports.

Featured

Alexander TA, Irizarry RA, Bravo HC. Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 1:kxab030. doi: 10.1093/biostatistics/kxab030. Epub ahead of print. PMID: 34467372.

Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nat Commun. 2022 Jun 27;13(1):3695. doi: 10.1038/s41467-022-31411-3. PMID: 35760813; PMCID: PMC9237024

Schatz MC, Philippakis AA, Afgan E, Banks E, Carey VJ, Carroll RJ, Culotti A, Ellrott K, Goecks J, Grossman RL, Hall IM, Hansen KD, Lawson J, Leek JT, Luria AO, Mosher S, Morgan M, Nekrutenko A, O'Connor BD, Osborn K, Paten B, Patterson C, Tan FJ, Taylor CO, Vessio J, Waldron L, Wang T, Wuichet K. Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space. Cell Genom. 2022 Jan 12;2(1):100085. doi: 10.1016/j.xgen.2021.100085. Epub 2022 Jan 13. PMID: 35199087; PMCID: PMC8863334

He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R. Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods. 2022 Mar;19(3):316-322. doi: 10.1038/s41592-022-01408-3. Epub 2022 Mar 11. PMID: 35277707; PMCID: PMC8933848

Recent

10 most recent PubMed and PubMed Central citations mentioning "*Bioconductor*". For a complete list, go to PubMed and PubMed Central. Last updated 2025-12-09T09:00:06-05:00.

Lu Z, Lu Y, Zhou J, Zhu Y. [Construction of a prognostic model for breast cancer based on lipid metabolism-related genes and functional verification of ALDH2]. Zhejiang Da Xue Xue Bao Yi Xue Ban, pp. 1-10. doi:10.3724/zdxbyxb-2025-0567 (8 December 2025)

Louail P, Brunius C, Garcia-Aloy M, Kumler W, Storz N, Stanstrup J, Treutler H, Vangeenderhuysen P, Witting M, Neumann S, Rainer J. xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem. Anal Chem. doi:10.1021/acs.analchem.5c04338 (8 December 2025)

Nedwed AS, Ustjanzew A, Abassi N, Dammer L, Schulze A, Helbich SS, Delacher M, Strauch K, Marini F. GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor. BMC Bioinformatics. doi:10.1186/s12859-025-06335-6 (7 December 2025)

Baldoni PL, Chen L, Li M, Chen Y, Smyth GK. Dividing out quantification uncertainty enables assessment of differential transcript usage with limma and edgeR. Nucleic Acids Res, 53(22). doi:10.1093/nar/gkaf1305 (26 November 2025)

Wheeler W, Wang D, Zhao I, Vale FF, Jin Y, Rabkin CS. GrafGen: distance-based inference of population ancestry for Helicobacter pylori genomes. BMC Bioinformatics. doi:10.1186/s12859-025-06294-y (26 November 2025)

Xu Y, Sargeant CJ, You Y, You Y, Su S, Wang C, Tian L, Chen Y, Ritchie ME. stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data. NAR Genom Bioinform, 7(4), pp. lqaf167. doi:10.1093/nargab/lqaf167 (22 November 2025)

Crowell HL, Dong Y, Billato I, Cai P, Emons M, Gunz S, Guo B, Li M, Mahmoud A, Manukyan A, Pagès H, Panwar P, Rao S, Sargeant CJ, Shepherd Kern L, Ramos M, Sun J, Totty M, Carey VJ, Chen Y, Collado-Torres L, Ghazanfar S, Hansen KD, Martinowich K, Maynard KR, Patrick E, Righelli D, Risso D, Tiberi S, Waldron L, Gottardo R, Robinson MD, Hicks SC, Weber LM. Orchestrating Spatial Transcriptomics Analysis with Bioconductor. bioRxiv. doi:10.1101/2025.11.20.688607 (21 November 2025)

Türei D, Schaul J, Palacio-Escat N, Bohár B, Bai Y, Ceccarelli F, Çevrim E, Daley M, Darcan M, Dimitrov D, Doğan T, Domingo-Fernández D, Dugourd A, Gábor A, Gul L, Hall BA, Hoyt CT, Ivanova O, Klein M, Lawrence T, Mañanes D, Módos D, Müller-Dott S, Ölbei M, Schmidt C, Şen B, Theis FJ, Ünlü A, Ulusoy E, Valdeolivas A, Korcsmáros T, Saez-Rodriguez J. OmniPath: integrated knowledgebase for multi-omics analysis. Nucleic Acids Res. doi:10.1093/nar/gkaf1126 (18 November 2025)

Al Ajami A, Schuck J, Marini F, Imkeller K. Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data. NAR Genom Bioinform, 7(4), pp. lqaf149. doi:10.1093/nargab/lqaf149 (11 November 2025)

Billato I, Pages H, Carey V, Waldron L, Sales G, Romualdi C, Risso D. Benchmarking large-scale single-cell RNA-seq analysis. bioRxiv. doi:10.1101/2025.10.28.681564 (29 October 2025)