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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 2026-11-09T00:00:09-05:00.

Tomita A, Maeda T, Mori-Moriyama N, Nomura Y, Kurita Y, Kashima M, Betsuyaku S, Sato Y, Nagano AJ. Transcriptomic biomarkers reveal jasmonic and salicylic acid states under field herbivory in Arabidopsis thaliana. Commun Biol, 9(1). doi:10.1038/s42003-026-11263-z (6 November 2026)

Zampetakis I, Gkogkou E, Trougakos IP. Recurrent transcriptional signatures of acquired chemoresistance across cancer models. Comput Biol Chem, 126(Pt 2), pp. 109557. doi:10.1016/j.compbiolchem.2026.109557 (4 November 2026)

Su Z, Huang J, Mo W, Li J, Zeng Q, Chen H, Deng S, Xiang X, Xiang K. Circulating miR-26b-5p as a Potential Host-Derived Biomarker for Active Pulmonary Tuberculosis. Infect Drug Resist, 19, pp. 643442. doi:10.2147/IDR.S643442 (3 November 2026)

Appierdo R, Pham G, Yin O, Tang AS, Shao TY, Severance AL, Yilmaz B, Einhaus J, Wong RJ, Vallania F, Gherardini PF, Helmer-Citterich M, Gaudillière B, Oskotsky TT, Stevenson DK, Way SS, Sirota M. Integrative transcriptomic analysis and preclinical validation identify lansoprazole as a therapeutic candidate for preeclampsia. iScience, 29(11), pp. 117963. doi:10.1016/j.isci.2026.117963 (31 October 2026)

Rusnak L, Weber LM. smoothclust: Spatial smoothing and boundary-density summaries for spatial transcriptomics. bioRxiv. doi:10.64898/2026.10.26.761912 (30 October 2026)

Vásquez-Castro F, Sanchez Solis LD, Myers SA. PrEditR: a protein-centric platform for CRISPR-mediated base editor sgRNA design. Bioinform Adv, 6(1), pp. vbag323. doi:10.1093/bioadv/vbag323 (30 October 2026)

Wu X, Rong L, Yu T, Zhou Y, Li J, Li S. A tandem repeat in TCF25 intron 1 is associated with MC1R activation through dual mechanisms of transcriptional derepression and chromatin looping underlying black plumage in chickens. Poult Sci, 105(12), pp. 107987. doi:10.1016/j.psj.2026.107987 (17 October 2026)

Deflandre G, Gibb S, Gatto L. PSMatch: An R/Bioconductor Package to Explore Proteomics Identification Data. Methods Mol Biol, 3071, pp. 81-95. doi:10.1007/978-1-0716-5519-1_5 (15 October 2026)

Rainer J, De Graeve M, Louail P, Gibb S, Gatto L. An Open Infrastructure for Mass Spectrometry Data in R. Methods Mol Biol, 3071, pp. 29-54. doi:10.1007/978-1-0716-5519-1_3 (15 October 2026)

Præstholm SM, Correia JC, Hoyos Justiniano R, da Rocha AL, Leuchtmann AB, Sereiva T, Porsmyr-Palmertz M, Rothamel K, Kaminska D, Sri Ganji R, Potěšil D, Zdráhal Z, Pihlajamäki J, Yeo GW, Ruas JL. Zfp697/ZNF697 is an RNA-binding protein that modulates TGF-β1 signaling and hepatic inflammation in liver disease. Mol Metab, 114, pp. 102457. doi:10.1016/j.molmet.2026.102457 (14 October 2026)