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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 2024-10-11T00:00:08-04:00.

Pirrotta S, Masatti L, Bortolato A, Corrà A, Pedrini F, Aere M, Esposito G, Martini P, Risso D, Romualdi C, Calura E. Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package. NAR Genom Bioinform, 6(4), pp. lqae138. doi:10.1093/nargab/lqae138 (3 October 2024)

Hou C, Ghazanfar S, Marini F, Morgan M, Hicks SC. HuBMAPR: an R Client for the HuBMAP Data Portal. bioRxiv. doi:10.1101/2024.09.26.615227 (27 September 2024)

Gu Z. simona: a comprehensive R package for semantic similarity analysis on bio-ontologies. BMC Genomics, 25(1), pp. 869. doi:10.1186/s12864-024-10759-4 (16 September 2024)

Blimkie TM, An A, Hancock REW. Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR. PLoS Comput Biol, 20(9), pp. e1012422. doi:10.1371/journal.pcbi.1012422 (16 September 2024)

Kitanovski S, Cao Y, Ttoouli D, Farahpour F, Wang J, Hoffmann D. scBubbletree: computational approach for visualization of single cell RNA-seq data. BMC Bioinformatics, 25(1), pp. 302. doi:10.1186/s12859-024-05927-y (13 September 2024)

Rahmatallah Y, Glazko G. Improving data interpretability with new differential sample variance gene set tests. Res Sq. doi:10.21203/rs.3.rs-4888767/v1 (9 September 2024)

Barrios D, Prieto C. Rvisdiff: An R package for interactive visualization of differential expression. Front Bioinform, 4, pp. 1349205. doi:10.3389/fbinf.2024.1349205 (2 September 2024)

Capraz T, Huber W. Feature selection by replicate reproducibility and non-redundancy. Bioinformatics, 40(9). doi:10.1093/bioinformatics/btae548 (2 September 2024)

Zhang H, Jiang W, Jiang Y, Xu N, Nong L, Li T, Liu R. Investigating the therapeutic potential of hesperidin targeting CRISP2 in intervertebral disc degeneration and cancer risk mitigation. Front Pharmacol, 15, pp. 1447152. doi:10.3389/fphar.2024.1447152 (29 August 2024)

Sola F, Ayala D, Pulido M, Ayala R, López-Cerero L, Hernández I, Ruiz D. ginmappeR: an unified approach for integrating gene and protein identifiers across biological sequence databases. Bioinform Adv, 4(1), pp. vbae129. doi:10.1093/bioadv/vbae129 (29 August 2024)