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 2024-11-18T04:00:08-05:00.

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)

Eagles NJ, Bach SV, Tippani M, Ravichandran P, Du Y, Miller RA, Hyde TM, Page SC, Martinowich K, Collado-Torres L. Integrating gene expression and imaging data across Visium capture areas with visiumStitched. BMC Genomics, 25(1), pp. 1077. doi:10.1186/s12864-024-10991-y (13 November 2024)

Wang M, Fontaine S, Jiang H, Li G. ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models. Bioinformatics. doi:10.1093/bioinformatics/btae661 (7 November 2024)

McIlwain SJ, Hoefges A, Erbe AK, Sondel PM, Ong IM. Ranking Antibody Binding Epitopes and Proteins Across Samples from Whole Proteome Tiled Linear Peptides. Bioinformatics. doi:10.1093/bioinformatics/btae637 (5 November 2024)

Coetzee SG, Hazelett DJ. motifbreakR v2: expanded variant analysis including indels and integrated evidence from transcription factor binding databases. Bioinform Adv, 4(1), pp. vbae162. doi:10.1093/bioadv/vbae162 (23 October 2024)

Banovic F, Blubaugh A. Epicutaneous house dust mite (HDM)-induced skin lesions feature early activation of T helper 2 inflammatory and pruritogenic pathways in HDM-nonsensitised dogs. Vet Dermatol. doi:10.1111/vde.13307 (23 October 2024)

Alkhateeb MA, Aljarba NH, Yousafi Q, Anwar F, Biswas P. Elucidating gastric cancer mechanisms and therapeutic potential of Adociaquinone A targeting EGFR: A genomic analysis and Computer Aided Drug Design (CADD) approach. J Cell Mol Med, 28(20), pp. e70133. doi:10.1111/jcmm.70133 (22 October 2024)

Turek C, Ölbei M, Stirling T, Fekete G, Tasnádi E, Gul L, Bohár B, Papp B, Jurkowski W, Ari E. mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate. BMC Bioinformatics, 25(1), pp. 334. doi:10.1186/s12859-024-05948-7 (18 October 2024)

Paparozzi V, Nardini C. tidysbml: R/Bioconductor package for SBML extraction into dataframes. Bioinform Adv, 4(1), pp. vbae148. doi:10.1093/bioadv/vbae148 (3 October 2024)

Yan J, Zhou X, Yang H. TGF-β signaling-related signature for predicting prognosis and therapeutic response in lower-grade glioma. Transl Cancer Res, 13(9), pp. 4985-5002. doi:10.21037/tcr-24-144 (9 September 2024)