📖 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 2025-06-12T05:00:08-04:00.
Le Nézet L, Sinnwell J, Letko A, André C, Quignon P. Pedixplorer: a Bioconductor package to streamline pedigree design and visualization.
Bioinformatics.
doi:10.1093/bioinformatics/btaf329 (3 June 2025)
Muley VY. Functional Insights Through Gene Ontology, Disease Ontology, and KEGG Pathway Enrichment.
Methods Mol Biol, 2927, pp. 75-98.
doi:10.1007/978-1-0716-4546-8_4 (2 June 2025)
Le HTT, Ahamad I, Muley VY. Deciphering Host Differential Gene Expression in Viral Infections Through Public RNA-Seq Data from NCBI GEO.
Methods Mol Biol, 2927, pp. 51-74.
doi:10.1007/978-1-0716-4546-8_3 (2 June 2025)
Guo X, Sulaiman M, Neumann A, Zheng SC, Cecil CAM, Teschendorff AE, Heijmans BT. Unified high-resolution immune cell fraction estimation in blood tissue from birth to old age.
Genome Med, 17(1), pp. 63.
doi:10.1186/s13073-025-01489-7 (27 May 2025)
Nixon MP, Gloor GB, Silverman JD. Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization.
Genome Biol, 26(1), pp. 139.
doi:10.1186/s13059-025-03609-3 (22 May 2025)
Wang X, Harper K, Sinha P, Johnson WE, Patil P. Analysis of the cross-study replicability of tuberculosis gene signatures using 49 curated human transcriptomic datasets.
Tuberculosis (Edinb), 153, pp. 102649.
doi:10.1016/j.tube.2025.102649 (8 May 2025)
Hu R, Li S, Stackpole ML, Li Q, Zhou XJ, Li W. cfTools: an R/Bioconductor package for deconvolving cell-free DNA via methylation analysis.
Bioinform Adv, 5(1), pp. vbaf108.
doi:10.1093/bioadv/vbaf108 (6 May 2025)
Benedetti G, Seraidarian E, Pralas T, Jeba A, Borman T, Lahti L. iSEEtree: interactive explorer for hierarchical data.
Bioinform Adv, 5(1), pp. vbaf107.
doi:10.1093/bioadv/vbaf107 (6 May 2025)
Arend L, Adamowicz K, Schmidt JR, Burankova Y, Zolotareva O, Tsoy O, Pauling JK, Kalkhof S, Baumbach J, List M, Laske T. Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE.
Brief Bioinform, 26(3).
doi:10.1093/bib/bbaf201 (1 May 2025)
Huang YP, Harmon L, Deering-Gardner E, Ma X, Harsh J, Xue Z, Wen H, Ramos M, Davis S, Triche TJ Jr. bamSliceR: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis.
Bioinform Adv, 5(1), pp. vbaf098.
doi:10.1093/bioadv/vbaf098 (28 April 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
