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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 2026-03-14T22:00:28-04:00.

Lin J, Wen Y, Tang J, Zhang X, Zhang H, Zhu H. Human-specific lncRNAs contributed critically to human evolution by distinctly regulating gene expression. Elife, 12. doi:10.7554/eLife.89001 (13 March 2026)

Duan D, Ma W, Tang W, Wu H, Zhang L, Feng H. mist: a hierarchical Bayesian framework for detecting differential DNA methylation dynamics in single-cell data. Nat Commun. doi:10.1038/s41467-026-70523-y (12 March 2026)

Pacwa-Płociniczak M, Daszkowska-Golec A, Gobetti S, Sinkkonen A, Płociniczak T. Plant and soil transcriptomics reveal the consequences of bioaugmentation of co-contaminated soil with Pseudomonas qingdaonensis ZCR6 during bacteria-assisted phytoremediation. Appl Microbiol Biotechnol, 110(1). doi:10.1007/s00253-026-13763-8 (11 March 2026)

Brown JR, Pedersen B, Long GV, Maher NG, Lim SY, Rizos H, Shklovskaya E. Prednisolone modulates CD8⁺ and regulatory T-cell activity to dampen response to immune checkpoint inhibitor therapy in melanoma. Oncoimmunology, 15(1), pp. 2643494. doi:10.1080/2162402X.2026.2643494 (10 March 2026)

Bergstrom K, Smith H, Johnson RK, Vanderlinden LA, Seifert J, Hohsfield KR, Yang IV, Slack SD, Dong F, Kechris K, Rewers M, Norris JM, Carry PM. Longitudinal changes in epigenetic age acceleration prior to type 1 diabetes onset in the Diabetes Autoimmunity Study in the Young (DAISY). BMJ Open Diabetes Res Care, 14(2). doi:10.1136/bmjdrc-2025-005725 (10 March 2026)

Langleib M, Fontenla S, Domínguez F, Sankaranarayanan G, Wlodek S, Berriman M, Rinaldi G, Iriarte A, Tort JF. Transcriptome profiling of intra-snail stages of the liver fluke Fasciola hepatica reveals key mediators underlying parasite development and interaction with the host. BMC Genomics, 27(1). doi:10.1186/s12864-026-12670-6 (9 March 2026)

Ruf WP, Kühlwein JK, Meier L, Brockmann SJ, LeeBae J, Sadri-Vakili G, Yilmazer-Hanke D, Petri S, Thal DR, Grozdanov V, Danzer KM. Multi-modal dissection of cell-type specific TDP-43 pathology in the motor cortex. Nat Commun, 17(1). doi:10.1038/s41467-026-69944-6 (9 March 2026)

Peng S, Chen Y, Wu J, Huang X, Hong L, Xie Y, Lei Y, Wei X, Yang P, Zhang J, Yang Q, Liu G, Li A, Liu S, Li J, Dai W, Hu Y, Wang J, Xiong J, Wang J. RNA‑binding protein DAZAP1 promotes gastric cancer metastasis by enhancing NOTCH1 and JAG1 mRNA stability. Int J Oncol, 68(5). doi:10.3892/ijo.2026.5863 (6 March 2026)

Boukas L, Délot EC, Pitsava G, Lambert C, Fanslow C, Baybayan P, Belhadj S, Losic B, Harting J, Bluske K, LoTempio J, Al-Kouatly HB, Karam R, Rowell WJ, Xiao C, Vilain E, Berger SI. Identification of de novo variants from parent-proband duos via long-read sequencing. Am J Hum Genet, 113(3), pp. 437-452. doi:10.1016/j.ajhg.2026.02.006 (5 March 2026)

Jastrzebski JP, Gawronska M, Babis W, Quaranta M, Czopek D. PMScanR: An R Package for the Large-Scale Identification, Analysis, and Visualization of Protein Motifs. J Comput Biol, pp. 15578666261423966. doi:10.1177/15578666261423966 (2 March 2026)