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 2025-08-15T06:00:07-04:00.
Taoka H, Murakawa T, Kawaguchi K, Koizumi M, Kaminishi T, Sakamaki Y, Tanaka K, Harada A, Inoue K, Kanki T, Ohkawa Y, Fujita N. Transcriptional dynamics uncover the role of BNIP3 in mitophagy during muscle remodeling in Drosophila
eLife, 14, pp. RP105834.
doi:10.7554/eLife.105834 (13 August 2025)
Bollon J, Shortreed MR, Jeffery E, Jordan BT, Miller R, Cavalli A, Smith LM, Dewey CN, Sheynkman GM, Tiberi S. IsoBayes: a Bayesian approach for single-isoform proteomics inference.
Bioinformatics.
doi:10.1093/bioinformatics/btaf450 (11 August 2025)
Xiang X, Mei X, Song X, Pan B, Ma K, Tan C, Liu L, Li S, Dong Q, Tang T. High-density lectin microarray uncovers stage-specific plasma glycoprofiling signatures for non-muscle-invasive and muscle-invasive bladder cancer.
Int Urol Nephrol.
doi:10.1007/s11255-025-04708-7 (10 August 2025)
Belleau P, DeschĂŞnes A, Tuveson DA, Krasnitz A. Inference of Genetic Ancestry from Cancer-Derived Molecular Data with RAIDS.
Methods Mol Biol, 2932, pp. 153-176.
doi:10.1007/978-1-0716-4566-6_8 (8 August 2025)
Ramos M, Shepherd L, Sheffield NC, Mahmoud A, Pagès H, Wokaty A, Righelli D, Risso D, Davis S, Oh S, Waldron L, Morgan M, Carey V. Bioconductor's Computational Ecosystem for Genomic Data Science in Cancer.
Methods Mol Biol, 2932, pp. 1-46.
doi:10.1007/978-1-0716-4566-6_1 (8 August 2025)
Gabrilovich S, Devor E, Cardillo N, Bender D, Goodheart M, Gonzalez-Bosquet J. scRNA-seq Can Identify Different Cell Populations in Ovarian Cancer Bulk RNA-seq Experiments
Int J Mol Sci, 26(15), pp. 7512.
doi:10.3390/ijms26157512 (4 August 2025)
Lara-Vega I, Nájera-MartĂnez M, Vega-LĂłpez A. Pentoxifylline and Norcantharidin Synergistically Suppress Melanoma Growth in Mice: A Multi-Modal In Vivo and In Silico Study
Int J Mol Sci, 26(15), pp. 7522.
doi:10.3390/ijms26157522 (4 August 2025)
Bao Y, Ma F, Huo C, Jia H, Li Y, Yang X, Liu J, Gu P, Shi C, Gu M, Zhu L, Wang Y, Liu B, Na R, Zhang W. Single-Nucleus RNA Sequencing and Spatial Transcriptomics Reveal Cellular Heterogeneity and Intercellular Communication Networks in the Hypothalamus–Pituitary–Ovarian Axis of Pregnant Mongolian Cattle
Animals (Basel), 15(15), pp. 2277.
doi:10.3390/ani15152277 (4 August 2025)
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, 41(8).
doi:10.1093/bioinformatics/btaf435 (2 August 2025)
Polio A, Wagner V, Bender DP, Goodheart MJ, Gonzalez Bosquet J. A Natural Language Processing Method Identifies an Association Between Bacterial Communities in the Upper Genital Tract and Ovarian Cancer
Int J Mol Sci, 26(15), pp. 7432.
doi:10.3390/ijms26157432 (1 August 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
