Home
Help
Publications

📖 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 2025-11-03T03:00:07-05:00.

Li P, Zhang C, Yang S, Wu Y, Chen H, Ma S, Wu Y, He Z, Wang L, Liu Y, Wang Q. Peripheral blood mononuclear cell DNA methylation biomarkers for prognostic stratification in Chinese lung adenocarcinoma: a genome-wide epigenetic profiling study. Clin Epigenetics, 17(1), pp. 177. doi:10.1186/s13148-025-01992-z (27 October 2025)

Manzoor HB, Acun M, Yasavoli-Sharahi H, Matar C, Mer A, Tsang BK, Asare-Werehene M. Global DNA methylation signatures associated with chemoresistance and poor prognosis of high grade serous ovarian cancer. Sci Rep, 15(1), pp. 36869. doi:10.1038/s41598-025-20827-8 (22 October 2025)

Mohammed FA, Fall EHM, Tune KK, Hammamieh R, Jett M, Muhie S. MultiModalGraphics: an R package for graphical integration of multi-omics datasets. BMC Bioinformatics, 26(1), pp. 259. doi:10.1186/s12859-025-06265-3 (21 October 2025)

Loriot A, Devis J, Gatto L, De Smet C. A survey of human cancer-germline genes: Linking X chromosome localization, DNA methylation and sex-biased expression in early embryos. PLoS Genet, 21(10), pp. e1011734. doi:10.1371/journal.pgen.1011734 (15 October 2025)

Anwara AM, Jeba A, Lahti L, Coffey E. LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis. Bioinformatics. doi:10.1093/bioinformatics/btaf570 (11 October 2025)

Yang Q, Hartman J, Sifakis EG. BreastSubtypeR: a unified R/Bioconductor package for intrinsic molecular subtyping in breast cancer research. NAR Genom Bioinform, 7(4), pp. lqaf131. doi:10.1093/nargab/lqaf131 (7 October 2025)

Angel A, Naom L, Nabet-Levy S, Aran D. xCell 2.0: robust algorithm for cell type proportion estimation predicts response to immune checkpoint blockade. Genome Biol, 26(1), pp. 335. doi:10.1186/s13059-025-03784-3 (3 October 2025)

Liu P, Page D, Ahlquist P, Ong IM, Gitter A. MPAC: a computational framework for inferring pathway activities from multi-omic data. Bioinformatics, 41(10). doi:10.1093/bioinformatics/btaf490 (2 October 2025)

Barzaghi G, Krebs AR, Zaugg JB. FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data. Bioinformatics, 41(10). doi:10.1093/bioinformatics/btaf502 (2 October 2025)

Luo S, Germain PL, von Meyenn F, Robinson MD. On metrics for subpopulation detection in single-cell and spatial omics data. Nucleic Acids Res, 53(18). doi:10.1093/nar/gkaf921 (23 September 2025)