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📖 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 2025-06-29T19:00:07-04:00.

Bernabé-Díaz 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)

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)

Le Nézet L, Sinnwell J, Letko A, André C, Quignon P. Pedixplorer: a Bioconductor package to streamline pedigree design and visualization. Bioinformatics, 41(6). doi:10.1093/bioinformatics/btaf329 (2 June 2025)

Stachelek K, Bhat B, Cobrinik D. Chevreul: An R Bioconductor Package for Exploratory Analysis of Full-Length Single Cell Sequencing. bioRxiv. doi:10.1101/2025.05.27.656486 (1 June 2025)

Östling 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)

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)

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)

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)