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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 2025-04-23T15:00:08-04:00.

Drnevich J, Tan FJ, Almeida-Silva F, Castelo R, Culhane AC, Davis S, Doyle MA, Geistlinger L, Ghazi AR, Holmes S, Lahti L, Mahmoud A, Nishida K, Ramos M, Rue-Albrecht K, Shih DJH, Gatto L, Soneson C. Learning and teaching biological data science in the Bioconductor community. PLoS Comput Biol, 21(4), pp. e1012925. doi:10.1371/journal.pcbi.1012925 (22 April 2025)

Fievet G, Broséus J, Meyre D, Hergalant S. adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks. Bioinformatics. doi:10.1093/bioinformatics/btaf168 (15 April 2025)

Rahmatallah Y, Glazko G. Improving data interpretability with new differential sample variance gene set tests. BMC Bioinformatics, 26(1), pp. 103. doi:10.1186/s12859-025-06117-0 (14 April 2025)

Ben Aribi H, Dixon I, Abassi N, Awe OI. Efficient and easy gene expression and genetic variation data analysis and visualization using exvar. Sci Rep, 15(1), pp. 12264. doi:10.1038/s41598-025-93067-5 (10 April 2025)

Huuki-Myers LA, Montgomery KD, Kwon SH, Cinquemani S, Eagles NJ, Gonzalez-Padilla D, Maden SK, Kleinman JE, Hyde TM, Hicks SC, Maynard KR, Collado-Torres L. Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex. Genome Biol, 26(1), pp. 88. doi:10.1186/s13059-025-03552-3 (7 April 2025)

Li W, Xu K, Chen F. Gene expression study in retinoblastoma patients with different anaplasias and lateralities. Sci Rep, 15(1), pp. 9925. doi:10.1038/s41598-025-94225-5 (22 March 2025)

Waury K, Kvartsberg H, Zetterberg H, Blennow K, Teunissen CE, Abeln S. Data-driven evaluation of suitable immunogens for improved antibody selection. Protein Sci, 34(4), pp. e70100. doi:10.1002/pro.70100 (21 March 2025)

Hou C, Ghazanfar S, Marini F, Morgan M, Hicks SC. HuBMAPR: an R client for the HuBMAP data portal. Bioinform Adv, 5(1), pp. vbaf048. doi:10.1093/bioadv/vbaf048 (10 March 2025)

Yang H, Fu H, Zhang M, Liu Y, He YO, Wang C, Cheng L. EnrichDO: a global weighted model for Disease Ontology enrichment analysis. Gigascience, 14. doi:10.1093/gigascience/giaf021 (6 January 2025)