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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 2024-02-23T01:00:08-05:00.

Hauchamps P, Bayat B, Delandre S, Hamrouni M, Toussaint M, Temmerman S, Lin D, Gatto L. CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data. BMC Bioinformatics, 25(1), pp. 80. doi:10.1186/s12859-024-05691-z (20 February 2024)
Nishida K, Maruyama J, Kaizu K, Takahashi K, Yugi K. Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks. NPJ Syst Biol Appl, 10(1), pp. 16. doi:10.1038/s41540-024-00342-8 (19 February 2024)
Wu L, Long Y, Qiu J, Dai X, You X, Li T, Chen H. Exploring the mechanism of action of Sparganii Rhizoma-Curcumae Rhizoma for in treating castration-resistant prostate cancer: a network-based pharmacology and experimental validation study. Sci Rep, 14(1), pp. 3099. doi:10.1038/s41598-024-53699-5 (7 February 2024)
Serizay J, Matthey-Doret C, Bignaud A, Baudry L, Koszul R. Orchestrating chromosome conformation capture analysis with Bioconductor. Nat Commun, 15(1), pp. 1072. doi:10.1038/s41467-024-44761-x (5 February 2024)
Zhang J, Zhang L, Gongol B, Hayes J, Borowsky AT, Bailey-Serres J, Girke T. spatialHeatmap: visualizing spatial bulk and single-cell assays in anatomical images. NAR Genom Bioinform, 6(1), pp. lqae006. doi:10.1093/nargab/lqae006 (2 February 2024)
Cai P, Robinson MD, Tiberi S. DESpace: spatially variable gene detection via differential expression testing of spatial clusters. Bioinformatics, 40(2). doi:10.1093/bioinformatics/btae027 (1 February 2024)
Lewinski M, Brüggemann M, Köster T, Reichel M, Bergelt T, Meyer K, König J, Zarnack K, Staiger D. Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2). Nat Protoc. doi:10.1038/s41596-023-00935-3 (26 January 2024)
Li D, Xie Z, Shaikh SB, Rahman I. Abnormal expression profile of plasma exosomal microRNAs in exclusive electronic cigarette adult users. Res Sq. doi:10.21203/rs.3.rs-3877316/v1 (24 January 2024)
Joshi K, Wang DO. epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation. Brief Bioinform, 25(2). doi:10.1093/bib/bbad521 (22 January 2024)
Sadat Kalaki N, Ahmadzadeh M, Najafi M, Mobasheri M, Ajdarkosh H, Karbalaie Niya MH. Systems biology approach to identify biomarkers and therapeutic targets for colorectal cancer. Biochem Biophys Rep, 37, pp. 101633. doi:10.1016/j.bbrep.2023.101633 (12 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