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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 2025-05-24T15:00:09-04:00.

Nixon MP, Gloor GB, Silverman JD. Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization. Genome Biol, 26(1), pp. 139. doi:10.1186/s13059-025-03609-3 (22 May 2025)

Wang X, Harper K, Sinha P, Johnson WE, Patil P. Analysis of the cross-study replicability of tuberculosis gene signatures using 49 curated human transcriptomic datasets. Tuberculosis (Edinb), 153, pp. 102649. doi:10.1016/j.tube.2025.102649 (8 May 2025)

Benedetti G, Seraidarian E, Pralas T, Jeba A, Borman T, Lahti L. iSEEtree: interactive explorer for hierarchical data. Bioinform Adv, 5(1), pp. vbaf107. doi:10.1093/bioadv/vbaf107 (6 May 2025)

Arend L, Adamowicz K, Schmidt JR, Burankova Y, Zolotareva O, Tsoy O, Pauling JK, Kalkhof S, Baumbach J, List M, Laske T. Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE. Brief Bioinform, 26(3). doi:10.1093/bib/bbaf201 (1 May 2025)

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. BMC Genomics, 26(1), pp. 433. doi:10.1186/s12864-025-11508-x (1 May 2025)

Huang YP, Harmon L, Deering-Gardner E, Ma X, Harsh J, Xue Z, Wen H, Ramos M, Davis S, Triche TJ Jr. bamSliceR: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis. Bioinform Adv, 5(1), pp. vbaf098. doi:10.1093/bioadv/vbaf098 (28 April 2025)

Nguyen TN, Lee T, Turaga N, Gentleman R, Geistlinger L, Morgan M. AlphaMissenseR: an integrated framework for investigating missense mutations in human protein-coding genes. Bioinform Adv, 5(1), pp. vbaf093. doi:10.1093/bioadv/vbaf093 (23 April 2025)

Dong Z, Zhao K, Gu H, Yang W, Zhang X. Profiling of Circulating Cell-free DNA Methylation Patterns Identifies Aberrant Methylated CTBP1 Promotor Sites for Prediction of Alzheimer's Disease. J Integr Neurosci, 24(4), pp. 36527. doi:10.31083/JIN36527 (23 April 2025)

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)

Cerveira RA, Lenart K, Martin M, Hinchcliff MJ, Hellgren F, Ye K, Geraldo JA, Kreslavsky T, Ols S, Loré K. Scifer: An R/Bioconductor package for large-scale integration of Sanger sequencing and flow cytometry data of index-sorted single cells. Immunoinformatics (Amst), 16, pp. 100046. doi:10.1016/j.immuno.2024.100046 (29 October 2024)