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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 2026-06-21T18:00:28-04:00.

Song Y, Huang B, Wu J, Lin J, Xin K, Gao B, Kemp GJ, Guo B, Gong Q. Variations of structural-functional coupling in post-traumatic stress disorder are associated with underlying molecular and transcriptional features. Psychol Med, 56, pp. e196. doi:10.1017/S0033291726104838 (18 June 2026)

Müller FE, Bahr FS, Erschow S, Kasten M, Heimerl M, Benen N, Jung M, Schmidt A, Scherr M, Falk CS, Bustamante C, Ponomarev I, Bauersachs J, Hilfiker-Kleiner D, Thum T, Ponimaskin EG, Ricke-Hoch M. Serotonin 5-HT7 receptor signaling modulates inflammatory responses and survival after myocardial infarction. J Transl Med, 24(1). doi:10.1186/s12967-026-08423-4 (17 June 2026)

Fei L, Maksimovic J, Oshlack A. barbieQ: an R software package for analysing barcode count data from clonal tracking experiments. Bioinformatics. doi:10.1093/bioinformatics/btag397 (16 June 2026)

Hao X, Zhao B, Yan Q, Yano M, Matsuoka A, Qi Y, Liao L, Zielinski RJ, Tang HY, Kossenkov AV, Zal MA, Sarma K, Zhang R. Nuclear export of R-loop by the DDX1 and XPO1 complex promotes senescence-associated secretory phenotype and inflammaging. Nat Aging, 6(6), pp. 1208-1226. doi:10.1038/s43587-026-01147-6 (16 June 2026)

Kenney GE, Sherpa RN, Burgess JD, Boyle AP, Phanstiel DH. SEMPLR: an R package for transcription factor binding prediction. Bioinformatics. doi:10.1093/bioinformatics/btag383 (12 June 2026)

Wright ES. Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria. Mol Ecol Resour, 26(5), pp. e70163. doi:10.1111/1755-0998.70163 (10 June 2026)

Chen Y, Yoo S, Ahn S, Imran HZB, Reyes YA, Nguyen DV, Soltani T, Wu D. Mesospace-domain biochar regulates electron transfer to enhance elemental sulfur-driven autotrophic denitrification for low-carbon mariculture wastewater treatment. Water Res, 303, pp. 126268. doi:10.1016/j.watres.2026.126268 (8 June 2026)

Lu A, Chen WT, Dalby M, Sainz Garcia D, Vanheusden M, de Vries LE, van Lieshout V, Martirosyan A, Craessaerts K, Moonen S, Zielonka M, Chrysidou I, Misbaer A, Wolfs L, Pavie B, Swaab D, Thal DR, Huitinga I, Rozemuller A, Rohde SK, Hulsman M, Holstege H, Balice-Gordon R, Plath N, Fiers M, De Strooper B. Human microglial transitions at the Aβ-tau inflection point associate with divergent pathways to dementia and resilience. Nat Med, 32(6), pp. 2047-2059. doi:10.1038/s41591-026-04393-8 (4 June 2026)

Del Azodi CB, Dunstone AM, McCarthy DJ. Orchestrating multi-state QTL analysis with bioconductor. BMC Bioinformatics. doi:10.1186/s12859-026-06472-6 (3 June 2026)

Kaur H, Das P, Camphausen K, Shankavaram U. CPSM: An R Package for Cancer Patient Survival Risk Model Using Transcriptomics and Clinical Data. Gigascience. doi:10.1093/gigascience/giag067 (2 June 2026)