đź“– 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 2025-07-18T10:00:07-04:00.
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)
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.
doi:10.1093/bioinformatics/btaf399 (14 July 2025)
Kim SJ, Mura M. shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data.
Bioinformatics.
doi:10.1093/bioinformatics/btaf401 (11 July 2025)
O'Connell TM. Pathway Volcano: an interactive tool for pathway guided visualization of differential expression data.
Bioinformatics, 41(7).
doi:10.1093/bioinformatics/btaf367 (1 July 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)
Abudourexiti G, Zhang J, Abudouxikuer G. UPF1 inhibits cervical cancer cell migration and invasion by regulating nonsense-mediated decay of BMP6 and lncRNA WAKMAR2.
J Gynecol Oncol.
doi:10.3802/jgo.2025.36.e127 (23 June 2025)
BernabĂ©-DĂaz JA, Franco M, Vivo JM, Fernández-Breis JT. Optimizing clustering-based analytical methods with trimmed and sparse clustering.
Comput Biol Med, 194, pp. 110436.
doi:10.1016/j.compbiomed.2025.110436 (16 June 2025)
Ă–stling EM, Baltrunas T, Grootenboer N, Urbonavicius S. Cracking the Kinase Code: Urinary Biomarkers as Early Alarms for AAA Rupture-A Pilot Study.
J Clin Med, 14(11).
doi:10.3390/jcm14113845 (29 May 2025)
Yang Q, Han Y, Liu X, Xue L, Ji Z, Ye H. High intratumoral heterogeneity in clear cell renal cell carcinoma is associated with reduced immune response and survival.
Transl Androl Urol, 14(5), pp. 1190-1203.
doi:10.21037/tau-2024-741 (27 May 2025)
Shah K, Guo B, Hicks SC. Addressing the mean-variance relationship in spatially resolved transcriptomics data with spoon.
Biostatistics, 26(1).
doi:10.1093/biostatistics/kxaf012 (31 December 2024)
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
