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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 about 17 hours ago.

Chen J, Mohamed A, Bhuva DD, Davis MJ, Tan CW. mastR: An R Ppackage for Automated Identification of Tissue-Specific Gene Signatures in Multi-Group Differential Expression Analysis. Bioinformatics. doi:10.1093/bioinformatics/btaf114 (17 March 2025)

Hauchamps P, Delandre S, Temmerman ST, Lin D, Gatto L. Visual Quality Control With CytoMDS, a Bioconductor Package for Low Dimensional Representation of Cytometry Sample Distances. Cytometry A. doi:10.1002/cyto.a.24921 (4 March 2025)

Huang J, Li J, Li X, Guo H, Chen S. Identification of FZD7 as a potential ferroptosis-related diagnostic gene in endometriosis by bioinformatics analysis. Sci Rep, 15(1), pp. 7172. doi:10.1038/s41598-025-90803-9 (28 February 2025)

Moses L, Huseynov A, Rich JM, Pachter L. Geospatially informed representation of spatial genomics data with SpatialFeatureExperiment. bioRxiv. doi:10.1101/2025.02.24.640007 (27 February 2025)

Su S, Xiao L, Lancaster J, Cameron T, Breslin K, Hickey PF, Blewitt ME, Gouil Q, Ritchie ME. A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor. F1000Res, 13, pp. 1243. doi:10.12688/f1000research.155204.2 (24 February 2025)

Iyer MK, Fletcher A, Okoye JO, Shi C, Chen F, Kanu E, Eckhoff AM, Bao M, Pasca di Magliano M, Frankel TL, Chinnaiyan AM, Nussbaum DP, Allen PJ. Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms Reveals Divergent Indolent and Malignant States. Clin Cancer Res. doi:10.1158/1078-0432.CCR-24-1529 (19 February 2025)

Chee TM, Zahra CJ, Fong KM, Yang IA, Bowman RV. Potential utility of miRNAs derived from pleural fluid extracellular vesicles to differentiate between benign and malignant pleural effusions. Transl Lung Cancer Res, 14(1), pp. 124-138. doi:10.21037/tlcr-24-945 (22 January 2025)

Lewis MJ, Wang S. locuszoomr: an R package for visualizing publication-ready regional gene locus plots. Bioinform Adv, 5(1), pp. vbaf006. doi:10.1093/bioadv/vbaf006 (16 January 2025)

Sun W, van Ginneken D, Perié L. scMitoMut for calling mitochondrial lineage-related mutations in single cells. Brief Bioinform, 26(1). doi:10.1093/bib/bbaf072 (22 November 2024)

Flores JP, Davis E, Kramer N, Love MI, Phanstiel DH. A Bioconductor/R Workflow for the Detection and Visualization of Differential Chromatin Loops. F1000Res, 13, pp. 1346. doi:10.12688/f1000research.153949.1 (11 November 2024)