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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 2026-01-09T06:00:06-05:00.

Singh A, Herman A, Dey D, Menge S, Singh S, Tran A, Matson A, Mourad A, Rangarajan P, Masuria R, Sato N, Vadnais S, Rao JS, Singh G, Graham ML, Ramachandran S, Hering BJ. Allospecific splenic Tr1 cells drive effector T cell exhaustion through up-regulated Areg-EGFR signaling to promote transplant tolerance Sci Adv, 12(2), pp. eaea0567. doi:10.1126/sciadv.aea0567 (7 January 2026)

Kar R, Sinha S, Khatun Z, Sharma A, Patil VS. A distinct subset of stem-cell memory is poised for the cytotoxicity program in CD4+ T cells in humans Sci Adv, 12(2), pp. eady6423. doi:10.1126/sciadv.ady6423 (7 January 2026)

Chen R, Chen J, Shi L, He J. iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm Brief Bioinform, 27(1), pp. bbaf704. doi:10.1093/bib/bbaf704 (7 January 2026)

Suffiotti M, Tanner L, Kozera L, Sebastian A, van Maurik A, Strasser D. Sjögren’s disease metabolome reveals biomarker signatures to characterise patients and assess disease activity RMD Open, 12(1), pp. e006312. doi:10.1136/rmdopen-2025-006312 (5 January 2026)

Chen C, Han C, Xue L, Wu W, Zhang L, Lu X. PERP suppresses breast cancer metastasis via the ATF3–HSPA6 signaling pathway J Int Med Res, 53(12), pp. 03000605251406800. doi:10.1177/03000605251406800 (28 December 2025)

Xiao W, Fang X, Luo S, Song J, Sun J, Chen J, Chen Z. Prognostic implications of a programmed cell death-related long non-coding RNA signature and its relevance to immune features in esophageal carcinoma Transl Cancer Res, 14(12), pp. 8705-8724. doi:10.21037/tcr-2025-1598 (11 December 2025)

Langon X, Mosca M, Milhau N, Legain M, Idée A, Pin D. Assessing D-Squame as a Minimally Invasive Technique to Evaluate the Cutaneous Immune Response mRNA in a Dog Model of Canine Atopic Dermatitis. Vet Dermatol. doi:10.1111/vde.70042 (10 December 2025)

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, 97(50), pp. 27639-27645. doi:10.1021/acs.analchem.5c04338 (8 December 2025)

Joy P, Datta S, Sahoo S, Som TK, Tripathy PR, Gaikwad MR, Ayyanar P, Raghav SK. Congenital Anomalies in a Neonate With Partial Monosomy of Chromosome 21 q Arm: A Case Report Cureus, 17(12), pp. e98751. doi:10.7759/cureus.98751 (8 December 2025)