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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 2026-04-16T21:00:28-04:00.

Nguyen LTK, Tran DN, Nahar S, Kim TH, Jeong JW, Yoo JY. HDAC3 Regulates Transcriptional Networks Governing Decidualization. FASEB J, 40(8), pp. e71815. doi:10.1096/fj.202600629R (30 April 2026)

Horne J, Kaplan E, Jin B, Abbott K, Flores V, Petsolari E, Gradon J, Ntsogo Y, Harris A, Yu D, Zarkan A, Luisi BF. A lipoprotein partner for the Escherichia coli outer membrane protein TolC. Elife, 15. doi:10.7554/eLife.110666 (15 April 2026)

Ali A, Din TADAAT, Jalal MIA, Arifin WN, Abusalah MAHA, Abuarqoub AH, Ahmed N. Computational-based integrative methylome-transcriptome analysis reveals widespread enhancer hypomethylation in esophageal carcinoma. Epigenomics, pp. 1-14. doi:10.1080/17501911.2026.2654596 (14 April 2026)

Eyunni S, Chu SC, Guan ML, Louw M, Young E, Carson SE, Gong J, Cieslik M, Chinnaiyan AM, Parolia A. STAG2 loss amplifies EWS-FLI1-driven microsatellite enhancer activity promoting Ewing sarcoma aggressiveness. Proc Natl Acad Sci U S A, 123(15), pp. e2537425123. doi:10.1073/pnas.2537425123 (8 April 2026)

Maudet K, Samaniego J, Pradat Y, Bernard E. fRagmentomics: an R package for integrating cell-free DNA fragment features with mutational status to support liquid biopsy interpretation. Bioinformatics, 42(4). doi:10.1093/bioinformatics/btag152 (7 April 2026)

McClelland AJ, Hu B, Xu Y, Fang X, Wang C, Koch BL, Lovelace AH, Hawara E, Wang Y, Pang Z, De Francesco A, van Wier SP, Beekman AM, Levy A, Wang N, van der Hoorn RAL, Xu Q, Ma W. A secreted citrus protease cleaves an outer membrane protein of the Huanglongbing pathogen. Proc Natl Acad Sci U S A, 123(15), pp. e2528641123. doi:10.1073/pnas.2528641123 (7 April 2026)

Zhang C, Cao Z, Wei M, Zhu X, Yan Y, Wang Z, Zhang M. Combining bioinformatics prediction with experimental validation to explore the ameliorative effect of Psoralea corylifolia on vitiligo. Mol Med Rep, 33(6). doi:10.3892/mmr.2026.13868 (3 April 2026)

Zhang L, Cassol D, Gongol B, Girke T. systemPipeR: a multipurpose workflow management system for reproducible data analysis. NAR Genom Bioinform, 8(2), pp. lqag032. doi:10.1093/nargab/lqag032 (2 April 2026)

Easton CA, Wilmarth PA, Criss M, Kim K, Reddy AP, Tanne S, Boone JQ, Tran KD. Comparison of Transcript and Protein Abundance in Human Donor Retinas Support Extending Postmortem Interval From 12 to 18 Hours to Expand the Donor Pool for Biomedical Research. Invest Ophthalmol Vis Sci, 67(4), pp. 9. doi:10.1167/iovs.67.4.9 (1 April 2026)

Radulovich N, Pina PS, Udaskin ML, Li Q, Nixon KCJ, Xie IY, Nand A, Rosen JC, Li M, Hodgson A, Pham NA, Oza AM, Lupien M, Rottapel R, Tsao MS, Lheureux S. Preclinical Combination Targeting VEGF and PI3K in a Rare, Aggressive Mixed Endometrial Carcinoma: An Applied Case Report. Cancer Res Commun, 6(4), pp. 832-841. doi:10.1158/2767-9764.CRC-25-0634 (1 April 2026)