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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 2025-01-02T17:00:08-05:00.

Pan C, Chen Y. Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective. BMC Bioinformatics, 25(1), pp. 382. doi:10.1186/s12859-024-05996-z (18 December 2024)

Ou J, Liu H, Park S, Green MR, Zhu LJ. InPAS: An R/Bioconductor Package for Identifying Novel Polyadenylation Sites and Alternative Polyadenylation from Bulk RNA-seq Data. Front Biosci (Schol Ed), 16(4), pp. 21. doi:10.31083/j.fbs1604021 (17 December 2024)

Wang N, Tang L, Duan R, Shu Y. Investigating the Mechanism of Hedysarum Multijugum Maxim in the Treatment of Liver Cancer through Network Pharmacology and Molecular Docking Validation. Oncology, pp. 1-24. doi:10.1159/000542990 (16 December 2024)

Maurizio A, Tascini AS, Morelli MJ. SurfR: Riding the wave of RNA-seq data with a comprehensive bioconductor package to identify surface protein-coding genes. Bioinform Adv, 5(1), pp. vbae201. doi:10.1093/bioadv/vbae201 (14 December 2024)

Ortega-Legarreta A, Palomino-Echeverria S, Huergo E, Lagani V, Kiani NA, Rautou PE, Picola NP, Tegner J, Gomez-Cabrero D. ClustAll: An R package for patient stratification in complex diseases. PLoS Comput Biol, 20(12), pp. e1012656. doi:10.1371/journal.pcbi.1012656 (13 December 2024)

Jiang Y, Wu W, Xie L, Zhou Y, Yang K, Wu D, Xu W, Fang R, Ge J. Molecular targets and mechanisms of Sijunzi decoction in the treatment of Parkinson's disease: evidence from network pharmacology, molecular docking, molecular dynamics simulation, and experimental validation. Front Pharmacol, 15, pp. 1487474. doi:10.3389/fphar.2024.1487474 (26 November 2024)

Martinez Moreno M, Karambizi D, Hwang H, Fregoso K, Michles MJ, Fajardo E, Fiser A, Tapinos N. Role of the Egr2 Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape. Biomedicines, 12(11). doi:10.3390/biomedicines12112594 (13 November 2024)

Lobato-Fernandez C, Gimeno M, San Martín A, Anorbe A, Rubio A, Ferrer-Bonsoms JA. A Systematic Identification of RNA-Binding Proteins (RBPs) Driving Aberrant Splicing in Cancer. Biomedicines, 12(11). doi:10.3390/biomedicines12112592 (13 November 2024)

Oh S, Gravel-Pucillo K, Ramos M, Schatz MC, Davis S, Carey V, Morgan M, Waldron L. AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines. F1000Res, 13, pp. 1257. doi:10.12688/f1000research.155449.1 (21 October 2024)

Lynch MP, Wang Y, Ho Sui S, Gatto L, Culhane AC. demuxSNP: supervised demultiplexing single-cell RNA sequencing using cell hashing and SNPs. Gigascience, 13. doi:10.1093/gigascience/giae090 (2 January 2024)