📖 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 2026-05-27T01:00:06-04:00.
Suomi T, Kettunen J, Pusa T, Elo LL. Clarifying the scope and capabilities of ROTS in differential expression analysis.
Bioinformatics.
doi:10.1093/bioinformatics/btag335 (22 May 2026)
Galfrè SG, Fantozzi M, Sîrbu A, Testa I, Tolloso M, Alberti A, Priami C, Morandin F. From gene correlations to cell clusters: COTAN improved scRNA-seq analysis.
NAR Genom Bioinform, 8(2), pp. lqag048.
doi:10.1093/nargab/lqag048 (21 May 2026)
Brown EM, Druskat S, Hébert-Dufresne L, Howison J, Mietchen D, Nesbitt A, Pimentel JF, Veytsman B. Biomedical open source software: Crucial packages and hidden heroes.
PLoS Comput Biol, 22(5), pp. e1014260.
doi:10.1371/journal.pcbi.1014260 (13 May 2026)
Landis JT, Love MI. Efficient and Tidy Manipulation of Annotated Matrix Data with plyxp.
bioRxiv.
doi:10.64898/2026.05.06.721669 (11 May 2026)
Deconinck L, Zappia L, Cannoodt R, Morgan M, Core S, Virshup I, Sang-Aram C, Bredikhin D, Schilder B, Seurinck R, Saeys Y. anndataR improves interoperability between R and Python in single-cell transcriptomics.
Bioinformatics.
doi:10.1093/bioinformatics/btag288 (9 May 2026)
Zhu Z, Hu J, Li L. Exploring the mechanism of saffron in treating viral myocarditis using network pharmacology and molecular docking.
Medicine (Baltimore), 105(19), pp. e48736.
doi:10.1097/MD.0000000000048736 (8 May 2026)
Hummel JI, Zauner R, Gruner S, Dorfer S, Ablinger M, Walch V, Barone C, Laimer M, Guttmann-Gruber C, Piñón Hofbauer J, Koller U, Bauer JW, Wally V. Long-term cytokine exposure remodels the methylome and transcriptome of recessive dystrophic epidermolysis bullosa keratinocytes - a bioinformatic analysis.
Front Cell Dev Biol, 14, pp. 1810599.
doi:10.3389/fcell.2026.1810599 (7 May 2026)
Ruz Jurado M, Rodriguez Morales D, Zanders L, Genetzakis E, Dimmeler S, John D. DoTools: a cross platform framework to streamline common single cell workflows.
Bioinform Adv, 6(1), pp. vbag098.
doi:10.1093/bioadv/vbag098 (29 April 2026)
Salah A, Zahnreich S, Marini F. DoReMiTra: an R/Bioconductor data package for orchestrating the analysis of radiation transcriptomic studies.
Bioinform Adv, 6(1), pp. vbag092.
doi:10.1093/bioadv/vbag092 (28 March 2026)
Long K, Gravel-Pucillo K, Waldron L, Davis S, Oh S. Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.
Database (Oxford), 2026.
doi:10.1093/database/baag027 (15 January 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
