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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 2025-01-24T12:00:08-05:00.

Li D, Xie Z, Shaikh SB, Rahman I. Altered expression profile of plasma exosomal microRNAs in exclusive electronic cigarette adult users. Sci Rep, 15(1), pp. 2714. doi:10.1038/s41598-025-85373-9 (21 January 2025)

Mattessich M, Reyna J, Aron E, Ay F, Kilmer M, Kleinstein SH, Konstorum A. nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares. Bioinformatics. doi:10.1093/bioinformatics/btaf015 (12 January 2025)

Chen Y, Chen L, Lun ATL, Baldoni PL, Smyth GK. edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets. Nucleic Acids Res, 53(2). doi:10.1093/nar/gkaf018 (11 January 2025)

Matsuzawa R, Kawahara D, Kashima M, Hirata H, Ozaki H. tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography. PLoS One, 20(1), pp. e0311296. doi:10.1371/journal.pone.0311296 (8 January 2025)

Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs improve discovery of DNA methylation associations with complex traits. Nat Commun, 16(1), pp. 368. doi:10.1038/s41467-024-55698-6 (3 January 2025)

Pan C, Chen Y. Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective. BMC Bioinformatics, 25(1), pp. 382. doi:10.1186/s12859-024-05996-z (18 December 2024)

Ou J, Liu H, Park S, Green MR, Zhu LJ. InPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data. Front Biosci (Schol Ed), 16(4), pp. 21. doi:10.31083/j.fbs1604021 (17 December 2024)

Wang N, Tang L, Duan R, Shu Y. Investigating the Mechanism of Hedysarum Multijugum Maxim in the Treatment of Liver Cancer through Network Pharmacology and Molecular Docking Validation. Oncology, pp. 1-24. doi:10.1159/000542990 (16 December 2024)

Maurizio A, Tascini AS, Morelli MJ. SurfR: Riding the wave of RNA-seq data with a comprehensive bioconductor package to identify surface protein-coding genes. Bioinform Adv, 5(1), pp. vbae201. doi:10.1093/bioadv/vbae201 (14 December 2024)

Ortega-Legarreta A, Palomino-Echeverria S, Huergo E, Lagani V, Kiani NA, Rautou PE, Picola NP, Tegner J, Gomez-Cabrero D. ClustAll: An R package for patient stratification in complex diseases. PLoS Comput Biol, 20(12), pp. e1012656. doi:10.1371/journal.pcbi.1012656 (13 December 2024)