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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 2025-12-07T08:00:07-05:00.

Shen W, Rajrani R, Reyes MI, Wheeler E, Deppong D, Mickelson‐Young L, Ndunguru J, Hanley‐Bowdoin L, Ascencio‐Ibáñez JT. A TIR‐NLR gene from Arabidopsis Pla‐1 confers resistance to geminivirus infection Plant J, 124(5), pp. e70628. doi:10.1111/tpj.70628 (6 December 2025)

Duran-Ortiz S, Young JA, List EO, Basu R, Walsh C, Gotte EA, Berryman DE, Kopchick JJ. Sex-Specific transcriptomic changes in adipose tissue following adult-onset disruption of growth hormone receptor Pituitary, 29(1), pp. 5. doi:10.1007/s11102-025-01603-3 (5 December 2025)

Zheng S, Yu X, Wang X, Ma Y, Han Y, Zhang J, Wu W, Sun C, He L. DNA methylation-driven gene-based drug response prediction model for liver cancer: The critical role of GLS PLoS One, 20(12), pp. e0338091. doi:10.1371/journal.pone.0338091 (5 December 2025)

Paredes-Vázquez A, Balsa-Canto E, Banga JR. Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls PLoS Comput Biol, 21(12), pp. e1013204. doi:10.1371/journal.pcbi.1013204 (1 December 2025)

Song MA, Gupta A, Park SY, Kim J, Archer KJ, Tiirikainen M, Franke A, Wilkens LR, Le Marchand L, Chung D, Lim U. Differential blood DNA methylation loci between Native Hawaiian and White women are associated with dietary patterns and metabolic biomarkers Sci Rep, 15, pp. 43191. doi:10.1038/s41598-025-25253-4 (28 November 2025)

Taskiran I, Orenay-Boyacioglu S, Boyacioglu O, Erdogdu IH, Culhaci N, Meteoglu I. DNA polymerase epsilon-mutant colorectal cancers: Insights into non-exonuclease domain mutation variants, microsatellite instability status, and co-mutation profiles World J Gastroenterol, 31(44), pp. 112524. doi:10.3748/wjg.v31.i44.112524 (28 November 2025)

Choi WY, Zhao X, Holt J, Jain R, Jo H, Hoadley KA, Hayes DN, Choi HY. The offonome reveals on and off states of gene expression near the detection limit of RNA-seq Sci Rep, 15, pp. 43141. doi:10.1038/s41598-025-27185-5 (28 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)