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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 2024-12-02T14:00:08-05:00.

Page CG, Londsdale A, Mitchell KA, Schröder J, Harvey KF, Oshlack A. Damsel: analysis and visualisation of DamID sequencing in R. Bioinformatics, 40(12). doi:10.1093/bioinformatics/btae695 (28 November 2024)

Khleborodova A, Gamboa-Tuz SD, Ramos M, Segata N, Waldron L, Oh S. Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R. Bioinformatics. doi:10.1093/bioinformatics/btae707 (25 November 2024)

Furumo Q, Meyer MM. PIPETS: a statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing. BMC Bioinformatics, 25(1), pp. 363. doi:10.1186/s12859-024-05982-5 (23 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)

Tegenfeldt F, Kuznetsov D, Manni M, Berkeley M, Zdobnov EM, Kriventseva EV. OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Res. doi:10.1093/nar/gkae987 (13 November 2024)

Shah K, Guo B, Hicks SC. Addressing the mean-variance relationship in spatially resolved transcriptomics data with spoon. bioRxiv. doi:10.1101/2024.11.04.621867 (8 November 2024)

Iyer MK, Fletcher A, Shi C, Chen F, Kanu E, Eckhoff AM, Bao M, Frankel TL, Chinnaiyan AM, Nussbaum DP, Allen PJ. Spatial Transcriptomics of IPMN Reveals Divergent Indolent and Malignant Lineages. bioRxiv. doi:10.1101/2024.10.29.620810 (3 November 2024)

Stoneman HR, Price A, Gignoux CR, Hendricks AE. CCAFE: Estimating Case and Control Allele Frequencies from GWAS Summary Statistics. bioRxiv. doi:10.1101/2024.10.24.619530 (29 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)