Home
Help
Publications

📖 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 2026-05-24T23:00:22-04:00.

Brown EM, Druskat S, Hébert-Dufresne L, Howison J, Mietchen D, Nesbitt A, Pimentel JF, Veytsman B. Biomedical open source software: Crucial packages and hidden heroes. PLoS Comput Biol, 22(5), pp. e1014260. doi:10.1371/journal.pcbi.1014260 (13 May 2026)

Deconinck L, Zappia L, Cannoodt R, Morgan M, Core S, Virshup I, Sang-Aram C, Bredikhin D, Schilder B, Seurinck R, Saeys Y. anndataR improves interoperability between R and Python in single-cell transcriptomics. Bioinformatics. doi:10.1093/bioinformatics/btag288 (9 May 2026)

Zhu Z, Hu J, Li L. Exploring the mechanism of saffron in treating viral myocarditis using network pharmacology and molecular docking. Medicine (Baltimore), 105(19), pp. e48736. doi:10.1097/MD.0000000000048736 (8 May 2026)

Cardinali-Rezende J, Silva CAPT, Costa A, Garrido LM, Ferro M, Bacci M Jr, De Souza AO, Araújo WL. Motility and growth Burkholderia two-component: a new regulatory system of Burkholderia seminalis. Appl Microbiol Biotechnol, 110(1). doi:10.1007/s00253-026-13775-4 (7 May 2026)

Perrin-Gilbert N, Amjad N, Fumeron P, Tulli S, Waterfall JJ. Yomix: an interactive tool for the exploration of low-dimensional embeddings in omics data. Bioinformatics, 42(5). doi:10.1093/bioinformatics/btag301 (3 May 2026)

Okamoto AS, Coveney CR, Ganapathee DS, Capellini TD. In Vitro Massively Parallel Screening of Human Regulatory Elements Involved in Postcranial Skeletal Development for Differential Activity Compared to Chimpanzee. Genome Biol Evol, 18(5). doi:10.1093/gbe/evag121 (1 May 2026)

Matralis AN, Stylianaki EA, Ladopoulou EM, Kanellopoulou P, Smyrniotis S, Magkrioti C, Papavasileiou KD, Willems S, Rincon Pabon JP, Nastos D, Galaras A, Moro C, Dedos SG, Kaffe E, Hatzis P, Osman-Ponchet H, Merk D, Politis A, Afantitis A, Tseti I, Antoniou KM, Wells AU, Aidinis V. An aerosolized dual-action autotaxin inhibitor-PPARγ agonist for the treatment of pulmonary fibrosis. Cell Rep Med, 7(5). doi:10.1016/j.xcrm.2026.102778 (30 April 2026)

Ruz Jurado M, Rodriguez Morales D, Zanders L, Genetzakis E, Dimmeler S, John D. DoTools: a cross platform framework to streamline common single cell workflows. Bioinform Adv, 6(1), pp. vbag098. doi:10.1093/bioadv/vbag098 (29 April 2026)

Zhu Y, Berkovska O, Wang L, Yang M, Johansson HJ, Mermelekas G, Zarrineh M, Yin D, Orre LM, Lehtiö J. Differential protein expression analysis of quantitative mass spectrometry data using DEqMS. Nat Protoc. doi:10.1038/s41596-026-01349-7 (22 April 2026)

Pelzer B, Meydan C, Spiegel IM, Karagiannidis I, Xia M, Teater M, Welter EM, Searcy ZE, Hilton LK, Barisic D, Fong A, Fa P, Sethi S, Isgor IS, Fielding JJ, Karbalayghareh A, Burdette CS, Tumuluru S, Debek SM, Lee S, Massoni-Badosa R, Durmaz C, Salataj E, Pararajalingam P, Chen Z, Pelzl RJ, Shah S, Rivas MA, Hoehn KB, Mlynarczyk C, Isles HM, Wang X, Dogan A, Elenitoba-Johnson KSJ, Scott DW, Dreval K, Morin RD, Leslie CS, Puri R, Geri JB, Chin CR, Chadburn A, Mason CE, Reinhardt HC, Anguera MC, Béguelin W, Venturutti L, Melnick AM. SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and therapeutic vulnerabilities. Cancer Discov. doi:10.1158/2159-8290.CD-25-1458 (21 April 2026)