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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 2025-12-28T20:00:07-05:00.

Li L, Chen H, Zhou F, Shi Y. Integrated analysis of single-cell and bulk RNA-seq reveals MAGEA3/6-associated immune subtypes and key immune genes in gastric cancer PLoS One, 20(12), pp. e0338705. doi:10.1371/journal.pone.0338705 (26 December 2025)

Mandrycky CJ, Ishida T, Merkel T, Rayner SG, Heck AM, Hadland B, Zheng Y. Under pressure: integrated endothelial cell response to hydrostatic and shear stresses Vasc Biol, 7(1), pp. e250015. doi:10.1530/VB-25-0015 (23 December 2025)

Schalck T, Katyal M, De Graeve S, Roba L, Baldoma JV, Swings T, Van den Bergh B, Michiels J. Reprogramming the EnvZ-OmpR two-component system confers ethanol tolerance in Escherichia coli by stabilizing the outer membrane and altering ferric homeostasis PLoS Genet, 21(12), pp. e1011707. doi:10.1371/journal.pgen.1011707 (17 December 2025)

Zhang L, Ye X, Sun S, Zhang L, Gu Y, Cao S, Zhou M, Sun W, Fu C, Zhang Q, Li M, Xu Z, Miao W, Xu Q, Zhu S. Transcriptomic Insights Reveal PRTFDC1 as a Novel Regulator of Myogenic Differentiation in Sujiang Pig Satellite Cells Vet Sci, 12(12), pp. 1197. doi:10.3390/vetsci12121197 (14 December 2025)

Rouina H, Singh D, Arlt C, Malekian B, Schreiber L, Stich B, Marshall-Colon A. Regulatory analysis of root architectural and anatomical adaptation to nitrate and ammonium in Brachypodium distachyon Front Plant Sci, 16, pp. 1708928. doi:10.3389/fpls.2025.1708928 (12 December 2025)

Pedersen EM, Steinbach J, Pedersen CB, Schork AJ, Krebs MD, Vilhjálmsson BJ, Privé F. Automatic detection of n-degree family members Front Genet, 16, pp. 1708315. doi:10.3389/fgene.2025.1708315 (12 December 2025)

Lee S, Vijayalingam S, Klotz E, Dedert C, Xu F, Chinnadurai G, Ezekiel UR. Isogenic iPSC-derived CTBP1 mutant neuronal cells exhibit neurodevelopmental defects Front Neurosci, 19, pp. 1695464. doi:10.3389/fnins.2025.1695464 (12 December 2025)

Du L, Pan J, Xu N, Yan F, Tian W, Li Q. Integrative bulk and single-cell transcriptome analyses reveal integrated stress response-related biomarkers in periodontitis with experimental validation Front Immunol, 16, pp. 1705047. doi:10.3389/fimmu.2025.1705047 (11 December 2025)

Yang L, Yang R, Wang Y, Asad MA, Wang Y, Chang Z, Miao T, Yang S, Wei Y, Wu S, Bao J, Wu M, Ye J, Zhai R, Ye S, Zhang X, Zeng F, Yu F. Integrative genomic and transcriptomic approaches decipher pre-harvest sprouting resistance in rice Front Plant Sci, 16, pp. 1692942. doi:10.3389/fpls.2025.1692942 (11 December 2025)

Piltti KM, Lakatos A, Benavente-Perez F, Elrachid ZH, Nava AA, Addonizio NT, Nguyen V, Zahedi A, Song WA, Chen X, David J, Portillo A, Manughian-Peter AO, Rodriguez AN, Anzalone A, Cahill CM, Anderson AJ. C1q drives neural stem cell quiescence by regulating cell cycle and metabolism through BAI1 Nat Commun, 16, pp. 11386. doi:10.1038/s41467-025-66185-x (11 December 2025)