📖 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 2025-08-03T19:00:06-04:00.
Mullen DJ, Wu Z, Nelson-Moore E, Cao H, Han L, Offringa IA, Rhie SK. Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.
Bioinformatics.
doi:10.1093/bioinformatics/btaf435 (1 August 2025)
Lynskey SJ, Moody C, Ziemann M, Gill SD, McGee SL, Page RS. From Tear to Repair: Transcriptomic Signatures Related to Rotator Cuff Tendon Healing Outcomes: A Prospective Clinical and Laboratory Study.
J Shoulder Elbow Surg.
doi:10.1016/j.jse.2025.06.004 (28 July 2025)
Xu Z, Motsinger-Reif AA, Niu L. Efficient gene set analysis for DNA methylation addressing probe dependency and bias.
Bioinformatics.
doi:10.1093/bioinformatics/btaf422 (24 July 2025)
Iyengar SS, Qin AR, Robertson N, Harman AN, Patrick E. SpatioMark: Quantifying the impact of spatial proximity on cell phenotype.
Bioinformatics.
doi:10.1093/bioinformatics/btaf409 (17 July 2025)
Wang X, Jiang T, Shen A, Chen Y, Zhou Y, Liu J, Zhao S, Chen S, Ren J, Zhao Q. CaMutQC: An R package for integrative quality control and filtration of cancer somatic mutations.
Comput Struct Biotechnol J, 27, pp. 3147-3154.
doi:10.1016/j.csbj.2025.07.011 (16 July 2025)
Sarwal R, Tarca V, Dubin C, Kalavros N, Bhatti G, Bhattacharya S, Butte A, Romero R, Stolovitzky G, Oskotsky TT, Tarca AL, Sirota M. Benchmarking Large Language Models for Predictive Modeling in Biomedical Research With a Focus on Reproductive Health.
bioRxiv.
doi:10.1101/2025.07.07.663529 (10 July 2025)
Ghosh T, Baxter RM, Seal S, Lui VG, Rudra P, Vu T, Hsieh EWY, Ghosh D. cytoKernel: robust kernel embeddings for assessing differential expression of single-cell data.
Bioinformatics, 41(7).
doi:10.1093/bioinformatics/btaf399 (1 July 2025)
Barth J, Reynolds AW. EpipwR: efficient power analysis for EWAS with continuous outcomes.
Bioinform Adv, 5(1), pp. vbaf150.
doi:10.1093/bioadv/vbaf150 (25 June 2025)
Taridalu S, Sista Kameshwar AK, Suzuki M. ERSAtool: A User-Friendly R/Shiny Comprehensive Transcriptomic Analysis Interface Suitable for Education.
bioRxiv.
doi:10.1101/2025.06.20.660710 (24 June 2025)
Wu X, Huang X, Chen P, Kang J, Yang J, Huang Z, Xu S. scQTLtools: An R/Bioconductor Package for Comprehensive Identification and Visualization of Single-Cell eQTLs.
Biology (Basel), 14(7).
doi:10.3390/biology14070743 (23 June 2025)
Bioconductor Project Papers
Bioconductor key papers and technical reports.Papers
Gentleman et al. Bioconductor:
open software development for computation biology and bioinformatics. Genome Biology. 2004, 5:R80.
Huber et al. Orchestrating
high-throughput genomic analysis with Bioconductor. Nature
Methods. 2015, 12:115-121.
Initial Bioconductor Technical Reports
Bioconductor Core (November 2002) An Overview of Projects in
Computing for Genomic Analysis
Bioconductor Core (November 2002) Bioconductor: Assessment of
Current Progress
Books
A selection of Bioconductor releated books, book chapters, and online books.Books
