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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 2024-05-23T07:00:10-04:00.

Ruiz-Arenas C, Marín-Goñi I, Wang L, Ochoa I, Pérez-Jurado LA, Hernaez M. NetActivity enhances transcriptional signals by combining gene expression into robust gene set activity scores through interpretable autoencoders. Nucleic Acids Res, 52(9), pp. e44. doi:10.1093/nar/gkae197 (22 May 2024)

Murovec U, Accetto T. Transcriptomic analysis of polysaccharide utilization loci reveals substrate preferences in ruminal generalists Segatella bryantii TF1-3 and Xylanibacter ruminicola KHP1 BMC Genomics, 25, pp. 495. doi:10.1186/s12864-024-10421-z (20 May 2024)

Calamari ZT, Flynn JJ. Gene expression supports a single origin of horns and antlers in hoofed mammals Commun Biol, 7, pp. 509. doi:10.1038/s42003-024-06134-4 (20 May 2024)

Steenwyk JL, King N. The promise and pitfalls of synteny in phylogenomics PLoS Biol, 22(5), pp. e3002632. doi:10.1371/journal.pbio.3002632 (20 May 2024)

Kang T, Qin X, Chen Y, Yang Q. Systematic investigation of Radix Salviae for treating diabetic peripheral neuropathy disease based on network Pharmacology. World J Diabetes, 15(5), pp. 945-957. doi:10.4239/wjd.v15.i5.945 (15 May 2024)

Kleverov M, Zenkova D, Kamenev V, Sablina M, Artyomov MN, Sergushichev AA. Phantasus, a web-application for visual and interactive gene expression analysis. Elife, 13. doi:10.7554/eLife.85722 (14 May 2024)

Zhang J, Ye L, Chen Q, Wang F. Response analysis of Pinus sibirica to pine wood nematode infection through transcriptomics and metabolomics study Front Plant Sci, 15, pp. 1383018. doi:10.3389/fpls.2024.1383018 (7 May 2024)

Xu Z, Niu L, Kresovich JK, Taylor JA. methscore: a comprehensive R function for DNA methylation-based health predictors. Bioinformatics, 40(5). doi:10.1093/bioinformatics/btae302 (2 May 2024)

Eulalio T, Sun MW, Gevaert O, Greicius MD, Montine TJ, Nachun D, Montgomery SB. regionalpcs: improved discovery of DNA methylation associations with complex traits. bioRxiv. doi:10.1101/2024.05.01.590171 (1 May 2024)

Meng G, Pan Y, Tang W, Zhang L, Cui Y, Schumacher FR, Wang M, Wang R, He S, Krischer J, Li Q, Feng H. imply: improving cell-type deconvolution accuracy using personalized reference profiles. Genome Med, 16(1), pp. 65. doi:10.1186/s13073-024-01338-z (29 April 2024)