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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 2024-12-10T20:00:09-05:00.

Pressl C, Baffuto M, Darnell P, Wang C, Carroll TS, Heintz N, Mätlik K. Isolation and Molecular Profiling of Nuclei of Specific Neuronal Types from Human Cerebral Cortex and Striatum Curr Protoc, 4(12), pp. e70067. doi:10.1002/cpz1.70067 (9 December 2024)

Luck C, Jacobs KA, Okimoto RA. The Capicua C1 Domain Is Required for Full Activity of the CIC::DUX4 Fusion Oncoprotein Cancer Res Commun, 4(12), pp. 3099-3113. doi:10.1158/2767-9764.CRC-24-0348 (9 December 2024)

Luo W, Wu H, Yang Z, Lan T, Wu L, Huang Y. Machine Learning and Experimental Validation Identified Ferroptosis Signature and Innovative Biomarkers (ESR1 and GSTZ1) in Liver Fibrosis J Inflamm Res, 17, pp. 10313-10332. doi:10.2147/JIR.S490258 (4 December 2024)

Page CG, Londsdale A, Mitchell KA, Schröder J, Harvey KF, Oshlack A. Damsel: analysis and visualisation of DamID sequencing in R. Bioinformatics, 40(12). doi:10.1093/bioinformatics/btae695 (28 November 2024)

Khleborodova A, Gamboa-Tuz SD, Ramos M, Segata N, Waldron L, Oh S. Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R. Bioinformatics. doi:10.1093/bioinformatics/btae707 (25 November 2024)

Furumo Q, Meyer MM. PIPETS: a statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing. BMC Bioinformatics, 25(1), pp. 363. doi:10.1186/s12859-024-05982-5 (23 November 2024)

Lv L, Luo H, Zhang M, Wu C, Jiang Y, Tong W, Li G, Zhou Y, Li Y, Wang Z, Liu C. Comprehensive transcriptomic analysis identifies cholesterol transport pathway as a therapeutic target of porcine epidemic diarrhea coronavirus Virus Res, 350, pp. 199502. doi:10.1016/j.virusres.2024.199502 (23 November 2024)

Jiang L, Lu X, Dai Y, Jiang K, Miao Y, Yu J, Yin L, Wei J. Establishment and analysis of a prognostic model of pancreatic ductal adenocarcinomas based on nerve-cancer crosstalk-related genes Int J Clin Exp Pathol, 17(11), pp. 396-410. doi:10.62347/GHUM8504 (15 November 2024)

Martinez Moreno M, Karambizi D, Hwang H, Fregoso K, Michles MJ, Fajardo E, Fiser A, Tapinos N. Role of the Egr2 Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape. Biomedicines, 12(11). doi:10.3390/biomedicines12112594 (13 November 2024)

Lobato-Fernandez C, Gimeno M, San Martín A, Anorbe A, Rubio A, Ferrer-Bonsoms JA. A Systematic Identification of RNA-Binding Proteins (RBPs) Driving Aberrant Splicing in Cancer. Biomedicines, 12(11). doi:10.3390/biomedicines12112592 (13 November 2024)