📖 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 2026-07-22T18:00:05-04:00.
Broft M, Scheper W, Schubert M. pepitope facilitates TCR-neoantigen screen analysis in the R language.
Bioinformatics.
doi:10.1093/bioinformatics/btag542 (21 July 2026)
Dogu E, Gupta S, Olivella R, Sabido E, Vitek O. MSstatsQC-ML: A Supervised Machine Learning Approach to Monitor System Suitability and Quality Control in Mass Spectrometry-Based Proteomics.
J Proteome Res.
doi:10.1021/acs.jproteome.6c00186 (20 July 2026)
Shah K, Hou C, Thompson JR, Hicks SC. BatchSVG: identifying batch-biased genes in the application of spatially variable gene detection.
Bioinformatics.
doi:10.1093/bioinformatics/btag522 (16 July 2026)
Kitanovski S, Conroy S, Sonneck J, Claas L, Dorsch M, Urban S, Chen J, Kaiser M, Grüner BM, Hoffmann D. Uncertainty-aware quantitative analysis of high-throughput live cell migration data.
PLoS Comput Biol, 22(7), pp. e1014472.
doi:10.1371/journal.pcbi.1014472 (13 July 2026)
Marshal OJ. damidBind: an R/Bioconductor package for differential DamID analysis and data exploration.
Bioinformatics.
doi:10.1093/bioinformatics/btag512 (13 July 2026)
Villemin JP, Giroux P, Maillard M, Colombo PE, Larbouret C, Colinge J. Addressing multiple facets of ligand-receptor network inference including single-cell proteomics.
Nucleic Acids Res, 54(13).
doi:10.1093/nar/gkag690 (3 July 2026)
Alsalihi A, Flight RM, Moseley HNB. The recount3 Python package for programmatic access to uniformly processed RNA-seq data.
bioRxiv.
doi:10.64898/2026.06.17.732943 (19 June 2026)
Chen Y, Yoo S, Ahn S, Imran HZB, Reyes YA, Nguyen DV, Soltani T, Wu D. Mesospace-domain biochar regulates electron transfer to enhance elemental sulfur-driven autotrophic denitrification for low-carbon mariculture wastewater treatment.
Water Res, 303, pp. 126268.
doi:10.1016/j.watres.2026.126268 (8 June 2026)
Fei L, Maksimovic J, Oshlack A. barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.
Bioinformatics, 42(6).
doi:10.1093/bioinformatics/btag397 (1 June 2026)
Bansal A, Barmola H, Yadav S, Rao S. SMTrackR: an R/Bioconductor package for mapping protein binding at individual DNA molecules.
Bioinform Adv, 6(1), pp. vbag091.
doi:10.1093/bioadv/vbag091 (15 May 2026)
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
