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đź“– 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 2024-04-19T02:00:08-04:00.

Ruiz-Arenas C, Marín-Goñi I, Wang L, Ochoa I, Pérez-Jurado LA, Hernaez M. NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders. Nucleic Acids Res. doi:10.1093/nar/gkae197 (10 April 2024)
Maden SK, Huuki-Myers LA, Kwon SH, Collado-Torres L, Maynard KR, Hicks SC. lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression. bioRxiv. doi:10.1101/2024.04.04.588105 (6 April 2024)
Lyu Y, Wu C, Sun W, Li Z. Regional analysis to delineate intrasample heterogeneity with RegionalST. Bioinformatics, 40(4). doi:10.1093/bioinformatics/btae186 (29 March 2024)
Choudhary S, Khan S, Rustagi S, Rajpal VR, Khan NS, Kumar N, Thomas G, Pandey A, Hamurcu M, Gezgin S, Zargar SM, Khan MK. Immunomodulatory Effect of Phytoactive Compounds on Human Health: A Narrative Review Integrated with Bioinformatics Approach. Curr Top Med Chem. doi:10.2174/0115680266274272240321065039 (27 March 2024)
Yuan L, Liu Y, Fan L, Sun C, Ran S, Huang K, Shen Y. Identification of Potential Hub Genes Related to Acute Pancreatitis and Chronic Pancreatitis via Integrated Bioinformatics Analysis and In Vitro Analysis. Mol Biotechnol. doi:10.1007/s12033-024-01118-5 (23 March 2024)
Alessandri S, Ratto ML, Rabellino S, Piacenti G, Contaldo SG, Pernice S, Beccuti M, Calogero RA, Alessandri L. CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications. BMC Bioinformatics, 25(1), pp. 110. doi:10.1186/s12859-024-05695-9 (12 March 2024)
Hossain MN, Gao Y, Hatfield MJ, de Avila JM, McClure MC, Du M. Cold exposure impacts DNA methylation patterns in cattle sperm. Front Genet, 15, pp. 1346150. doi:10.3389/fgene.2024.1346150 (20 February 2024)
Rheinnecker M, Fröhlich M, Rübsam M, Paramasivam N, Heilig CE, Fröhling S, Schlenk RF, Hutter B, Hübschmann D. ZygosityPredictor. Bioinform Adv, 4(1), pp. vbae017. doi:10.1093/bioadv/vbae017 (6 February 2024)
Cordoba-Caballero J, Perkins JR, García-Criado F, Gallego D, Navarro-Sánchez A, Moreno-Estellés M, Garcés C, Bonet F, Romá-Mateo C, Toro R, Perez B, Sanz P, Kohl M, Rojano E, Seoane P, Ranea JAG. Exploring miRNA-target gene pair detection in disease with coRmiT. Brief Bioinform, 25(2). doi:10.1093/bib/bbae060 (22 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