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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 2026-09-28T00:00:15-04:00.

Koike TE, Fuziwara CS, Santos AR, Delpupo FVB, Nascimento TL, Rozanski A, Pereira MG, Brum PC, Kimura ET, Rando TA, Miyabara EH. β2 Adrenoceptor Signaling Modulates Myoblast Differentiation via miR‐374b‐5p/GSK3β and miR‐326‐3p/Tnfrsf11a Axes. Cell Biol Int, 50(10). doi:10.1002/cbin.70214 (26 September 2026)

Nguyen H, Nguyen K, Bya P, Alafif T, Quan TT, Nguyen T. DeOPUS: cellular deconvolution via optimized power-transformed unmixing with shrinkage. Brief Bioinform, 27(5). doi:10.1093/bib/bbag524 (26 September 2026)

Yang L, Mo W, Wang G, Wu X. Integrative Transcriptomic and Genetic Analyses Identify CDC20 as a Potential Biomarker Associated with Cell Cycle and Immune-Inflammatory Processes in Psoriasis. Clin Cosmet Investig Dermatol, 19, pp. 636697. doi:10.2147/CCID.S636697 (21 September 2026)

Khumpan T, Chewe K, Vijayvergia N, Eleam E, Quiñones-Romero JN, Peri S, Yulan G, Engstrom PF, Cai KQ, Pei J, Alekbaeva GD, Campbell KS, Whetstine JR, Astsaturov I, Lee H. AI-powered histopathology classifiers identify transcriptomic biomarkers associated with cell cycle regulation and increased mitotic activity in poorly differentiated neuroendocrine carcinoma. Hum Genomics, 20. doi:10.1186/s40246-026-01032-8 (15 September 2026)

Shaikh N, Teasdale M, Walker LJ, Wilson L, Howarth R, Saleem S, Logsdon J, Hepburn AC, Nelson R, Lian Q, Elizondo AC, Hussain R, Coxhead J, Gaughan L, Lako M, Scott E, Robson CN, Simons B, Hayward SW, Strand DW, Heer R, Buskin A. A xeno-free human iPSC-derived prostate organoid platform for multilineage differentiation and genetic manipulation. Cell Rep Methods, 6(9). doi:10.1016/j.crmeth.2026.101538 (29 July 2026)

Liu M, Li H, Jin H, Xiao Y, He P, Tan C, Wang HL, Lassance JM, Löfstedt C, Ding BJ. Paving the Way for Plant-Based Bioproduction of (Z)-13-Octadecenoic Moth Pheromone Compounds. Plant Biotechnol J, 24(10), pp. 5554-5569. doi:10.1111/pbi.70733 (28 July 2026)

Wang Y, Lei X, de Wit T, Schrama E, Welters MJP, van Leeuwen K, de Kivit S, de Boer M, van den Bulk J, de Miranda NFCC, Schumacher TN, Sun C, Borst J, Xiao Y. Efficient generation of human cDC1-like cells to detect and enhance tumor-reactive T cells via CD4(+) T cell help. Cell Rep Methods, 6(9). doi:10.1016/j.crmeth.2026.101533 (22 July 2026)

Qian G, Kim J, Tiwari R, Polacco BJ, Forget A, Schaffer LV, Kim HK, Gao J, Zhou Y, Jang GM, Kelly MR, Zhao X, Foussard H, Zhang L, Krogan N, Ideker T, Chavez A. HIT-MAP: A scalable approach to multimodal mapping of subcellular organization. Cell Rep Methods, 6(9). doi:10.1016/j.crmeth.2026.101534 (22 July 2026)

Esteban-Serna S, Widén T, Seliner S, Grosemans H, Farquhar I, Swaffer MP, Granneman S. ABA-AA: A simple, reversible, and non-toxic anchor-away system for effective nuclear protein depletion. Cell Rep Methods, 6(9). doi:10.1016/j.crmeth.2026.101517 (8 July 2026)

Zhang T, Li J, Tang C, Wu Y, Wu H, Zhu XT, Luo Z, Qin H, Ding L, Zeng Y, Lee SY, Shen X, Gao S, Tian Z, Tang Q, Li M, Qamar MTU, Dong Y, Dossa K, Zhang Y, Chen H, An S, Yu X, Chen L, Wang D, Li S, Chen LL, Li Y. Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes. Imeta, 5(3), pp. e70136. doi:10.1002/imt2.70136 (1 July 2026)