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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 2024-07-21T06:00:08-04:00.

Xu S, Hu E, Cai Y, Xie Z, Luo X, Zhan L, Tang W, Wang Q, Liu B, Wang R, Xie W, Wu T, Xie L, Yu G. Using clusterProfiler to characterize multiomics data. Nat Protoc. doi:10.1038/s41596-024-01020-z (17 July 2024)
Özay B, Tükel EY, Ayna Duran G, Kiraz Y. Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening. Anal Biochem, 694, pp. 115619. doi:10.1016/j.ab.2024.115619 (16 July 2024)
Chepeleva M, Kaoma T, Zinovyev A, Toth R, Nazarov PV. consICA: an R package for robust reference-free deconvolution of multi-omics data. Bioinform Adv, 4(1), pp. vbae102. doi:10.1093/bioadv/vbae102 (13 July 2024)
Coetzee SG, Hazelett DJ. MotifbreakR v2: extended capability and database integration. ArXiv. doi: (3 July 2024)
Chen BH, Zhou W. mLiftOver: harmonizing data across Infinium DNA methylation platforms. Bioinformatics, 40(7). doi:10.1093/bioinformatics/btae423 (1 July 2024)
Zhao K, Oualkacha K, Zeng Y, Shen C, Klein K, Lakhal-Chaieb L, Labbe A, Pastinen T, Hudson M, Colmegna I, Bernatsky S, Greenwood CMT. Addressing dispersion in mis-measured multivariate binomial outcomes: A novel statistical approach for detecting differentially methylated regions in bisulfite sequencing data. Stat Med. doi:10.1002/sim.10149 (26 June 2024)
Liu P, Page D, Ahlquist P, Ong IM, Gitter A. MPAC: a computational framework for inferring cancer pathway activities from multi-omic data. bioRxiv. doi:10.1101/2024.06.15.599113 (17 June 2024)
Bollon J, Shortreed MR, Jordan BT, Miller R, Jeffery E, Cavalli A, Smith LM, Dewey C, Sheynkman GM, Tiberi S. IsoBayes: a Bayesian approach for single-isoform proteomics inference. bioRxiv. doi:10.1101/2024.06.10.598223 (11 June 2024)
Liu Z, Ruan Z, Long H, Zhao R, Zhu Y, Lin Z, Chen P, Zhao S. Identification of ceRNA networks in type H and L vascular endothelial cells through integrated bioinformatics methods. Zhong Nan Da Xue Xue Bao Yi Xue Ban, 49(4), pp. 562-577. doi:10.11817/j.issn.1672-7347.2024.230343 (28 April 2024)
Kariotis S, Tan PF, Lu H, Rhodes CJ, Wilkins MR, Lawrie A, Wang D. Omada: robust clustering of transcriptomes through multiple testing. Gigascience, 13. doi:10.1093/gigascience/giae039 (2 January 2024)

Bioconductor Project Papers

Bioconductor key papers and technical reports.
Papers
Huber et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 2015, 12:115-121.
Initial Bioconductor Technical Reports
Bioconductor Core (November 2002) Bioconductor: Assessment of Current Progress


Books

A selection of Bioconductor releated books, book chapters, and online books.


Books
Landmark Bioconductor Book     R Programming for Bioinformatics     Bioconductor Case Studies


Book Chapters
Analyzing biological data using R: methods for graphs and networks


Online Books


Other

F1000 Research Channel