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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 2026-04-07T15:00:07-04:00.

Zhang L, Cassol D, Gongol B, Girke T. systemPipeR: a multipurpose workflow management system for reproducible data analysis. NAR Genom Bioinform, 8(2), pp. lqag032. doi:10.1093/nargab/lqag032 (2 April 2026)

Easton CA, Wilmarth PA, Criss M, Kim K, Reddy AP, Tanne S, Boone JQ, Tran KD. Comparison of Transcript and Protein Abundance in Human Donor Retinas Support Extending Postmortem Interval From 12 to 18 Hours to Expand the Donor Pool for Biomedical Research. Invest Ophthalmol Vis Sci, 67(4), pp. 9. doi:10.1167/iovs.67.4.9 (1 April 2026)

Abassi N, Schwarz L, Filippi E, Marini F. DeeDeeExperiment: Building an infrastructure for integrating and managing omics data analysis results in R/Bioconductor. Bioinformatics. doi:10.1093/bioinformatics/btag157 (27 March 2026)

Duan D, Ma W, Tang W, Wu H, Zhang L, Feng H. mist: a hierarchical Bayesian framework for detecting differential DNA methylation dynamics in single-cell data. Nat Commun. doi:10.1038/s41467-026-70523-y (12 March 2026)

Jastrzebski JP, Gawronska M, Babis W, Quaranta M, Czopek D. PMScanR: An R Package for the Large-Scale Identification, Analysis, and Visualization of Protein Motifs. J Comput Biol, 33(3), pp. 379-384. doi:10.1177/15578666261423966 (2 March 2026)

Sevilla-Porras M, Ruiz-Arenas C, Pérez-Jurado LA. UPDhmm: detecting uniparental disomy from NGS trio data. Bioinformatics, 42(3). doi:10.1093/bioinformatics/btag062 (28 February 2026)

Mitchell JT, Stapleton O, Krishnan K, Nagaraj S, Lvovs D, Cherry C, Poissonnier A, Horton W, Adey A, Rao V, Huff A, Zimmerman JW, Kagohara LT, Zaidi N, Coussens LM, Jaffee EM, Elisseeff JH, Fertig EJ. Differential cell signaling testing for cell-cell communication inference from single-cell data by dominoSignal. Bioinformatics, 42(3). doi:10.1093/bioinformatics/btag089 (28 February 2026)

Aalam J, Parveen R. In silico transcriptomic analysis for biomarker discovery in TB and HIV co-infection. Comput Biol Chem, 123, pp. 108954. doi:10.1016/j.compbiolchem.2026.108954 (20 February 2026)

Dash H, Roberts T, Weinert M, Skene N. MotifPeeker: benchmarking epigenomic profiling methods using motifs. Bioinform Adv, 6(1), pp. vbag023. doi:10.1093/bioadv/vbag023 (15 February 2026)

Ronchi J, Foti M. MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases. Bioinform Adv, 6(1), pp. vbag042. doi:10.1093/bioadv/vbag042 (13 February 2026)