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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 2026-05-26T00:00:20-04:00.

Radke MH, Badillo Lisakowski V, Meinke S, Britto-Borges T, Schneider-Lunitz V, Hummel O, van Heesch S, Ruiz Orera J, Hubner N, Granzier H, Dieterich C, Gotthardt M. RBM20 isoform regulation by independent transcription start sites adapts alternative splicing in development and disease. Nat Commun, 17(1). doi:10.1038/s41467-026-73230-w (23 May 2026)

Pashapu AR, Dalmannsdottir S, Jørgensen M, Kovi MR, Rognli OA. Allele frequency and gene expression differences under key winter stresses in temporal populations of two timothy cultivars. Theor Appl Genet, 139(6). doi:10.1007/s00122-026-05270-1 (23 May 2026)

Zhang Z, Zhou L, Yao L, Ma T, Xu Y. Mendelian Randomization Revealed Potential of mTOR Inhibitors for Treatment of Osteoporosis: Evidence From GWAS and Transcriptome Data. Int J Endocrinol, 2026, pp. 5562148. doi:10.1155/ije/5562148 (23 May 2026)

Suomi T, Kettunen J, Pusa T, Elo LL. Clarifying the scope and capabilities of ROTS in differential expression analysis. Bioinformatics. doi:10.1093/bioinformatics/btag335 (22 May 2026)

Galfrè SG, Fantozzi M, Sîrbu A, Testa I, Tolloso M, Alberti A, Priami C, Morandin F. From gene correlations to cell clusters: COTAN improved scRNA-seq analysis. NAR Genom Bioinform, 8(2), pp. lqag048. doi:10.1093/nargab/lqag048 (21 May 2026)

Brown EM, Druskat S, Hébert-Dufresne L, Howison J, Mietchen D, Nesbitt A, Pimentel JF, Veytsman B. Biomedical open source software: Crucial packages and hidden heroes. PLoS Comput Biol, 22(5), pp. e1014260. doi:10.1371/journal.pcbi.1014260 (13 May 2026)

Si CD, Peek CT, Fatah SR, Beaudoin AJ, Zhelonkin AR, Eichelberger KR, Hahn SL, Watson RO, Mogilenko DA, Cassat JE. RANKL inhibits macrophage proinflammatory Toll-like receptor 2 and 4 signaling and impairs killing of intracellular bacteria. Immunohorizons, 10(5). doi:10.1093/immhor/vlag023 (13 May 2026)

Landis JT, Love MI. Efficient and Tidy Manipulation of Annotated Matrix Data with plyxp. bioRxiv. doi:10.64898/2026.05.06.721669 (11 May 2026)

Deconinck L, Zappia L, Cannoodt R, Morgan M, Core S, Virshup I, Sang-Aram C, Bredikhin D, Schilder B, Seurinck R, Saeys Y. anndataR improves interoperability between R and Python in single-cell transcriptomics. Bioinformatics. doi:10.1093/bioinformatics/btag288 (9 May 2026)

Zhu Z, Hu J, Li L. Exploring the mechanism of saffron in treating viral myocarditis using network pharmacology and molecular docking. Medicine (Baltimore), 105(19), pp. e48736. doi:10.1097/MD.0000000000048736 (8 May 2026)