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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 2026-09-26T23:00:07-04:00.

Chang W, Yuan J, Zhang H, Yu Y, Ma Y, Li M, Li W, Yan H, Sun C, Zhang P, Tian Y, Guo F, Li P, Sun Y. A four‑gene signature identifies TKI‑induced persister cells and uncovers a ZLN005‑induced pyroptotic vulnerability via the GSDME pathway in EGFR‑mutant lung cancer. Mol Med Rep, 34(5). doi:10.3892/mmr.2026.14017 (18 September 2026)

Song X, Pan C, Li Z, Zhou X, Xiong A, Zhao Z, Luo H, Zhou C. Longitudinal spatial multi-omics delineates tumor microenvironment remodeling across sequential EGFR-TKIs in EGFR-mutant NSCLC. J Transl Med, 24(1). doi:10.1186/s12967-026-08897-2 (2 September 2026)

Osuntoki IG, Harrison A, Dai H, Bao Y, Zabet NR. HiCPotts: an R/bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of bias. Bioinformatics, 42(9). doi:10.1093/bioinformatics/btag673 (31 August 2026)

Zhang M, Fields S, Zhang Q, Ouyang Y, Xin Y, Zhang J, Liu H, Shen J, Xu B, Chen J, Wu D, Li C, Xu P. Rbm5 sustains leukemia stem cells through a Myc-driven transcriptional circuitry. Leukemia, 40(10), pp. 2167-2180. doi:10.1038/s41375-026-03064-4 (16 July 2026)

Baumgartl C, Becker J, Naber L, Xu M, Gerstmann E, Gonzalez-Calero JG, Suppacher J, Heß S, Bubeck F, Grimm D. Distinct YY dinucleotide periodicity in adeno-associated virus DNA. Mol Ther, 34(9), pp. 5527-5541. doi:10.1016/j.ymthe.2026.07.003 (8 July 2026)

Patchen BK, Saw WY, Phillips EK, Levy BD, Rosario A, Cho MH, Silverman EK, Hancock DB, Cassano PA, DeMeo DL. Polyunsaturated fatty acids modulation of smoking-related epigenetics and pulmonary outcomes. Genes Nutr, 21(1). doi:10.1186/s12263-026-00812-0 (7 July 2026)

Susaimanickam PJ, Capowski E, Xiong MN, Edwards KL, Phanse Y, Welch MJ, Pier A, Mayerl SJ, Zepeda MAF, Peterson KD, Phillips MJ, Sinha D, Gomez TM, Gamm DM. Identification and enrichment of human retinal organoid-derived red/green cone-competent precursors with enhanced axon dynamics. Stem Cell Res Ther, 17(1). doi:10.1186/s13287-026-05128-9 (4 July 2026)

Becquard T, Benatar C, Bretot C, Eluard B, Bordereaux D, Thirouard L, Hammoutene A, Montagne A, Dingli F, Loew D, Ransy C, Alves-Guerra MC, Caradeuc C, Cagnard N, Boissan M, Giraud N, Bouillaud F, Bertho G, Paradis V, Chiron D, Dentin R, Prip-Buus C, Baud V. The alternative NF-κB RelB subunit is a novel critical sensor of lipid metabolism to promote tumor development. Cell Death Dis, 17(1). doi:10.1038/s41419-026-09064-7 (4 July 2026)

Zheng Z, Xu T, Pathak JL, Xu S, Lu J, Yu S, Fu Z, Xie W, Zhu H, Jaspers RT, Zheng H, Wu L, Li J. SERINC3 promotes osteogenic differentiation of BMSCs via IL-32/AMPK-mediated autophagy and mitochondrial energy metabolism. Stem Cell Res Ther, 17(1). doi:10.1186/s13287-026-05135-w (3 July 2026)

Cornell CR, Olatinwo RO, Kozhar O, Wharton K, Stewart JE. Emerging Threats in Southern U.S. Pine Plantations: Temporal Dynamics of Fungal Communities and the Impact of Lecanosticta acicola. Microb Ecol, 89(1). doi:10.1007/s00248-026-02825-z (3 July 2026)