📖 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 2024-05-19T03:00:09-04:00.
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)
Xu Z, Niu L, Kresvich JK, Taylor JA. Methscore: a comprehensive R function for DNA methylation-based health predictors.
Bioinformatics.
doi:10.1093/bioinformatics/btae302 (3 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)
Pan Y, Wang X, Sun J, Liu C, Peng J, Li Q. Multimodal joint deconvolution and integrative signature selection in proteomics.
Commun Biol, 7(1), pp. 493.
doi:10.1038/s42003-024-06155-z (24 April 2024)
Ruiz-Arenas C, MarÃn-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.
doi:10.1093/nar/gkae197 (10 April 2024)
Maden SK, Huuki-Myers LA, Kwon SH, Collado-Torres L, Maynard KR, Hicks SC. lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression.
bioRxiv.
doi:10.1101/2024.04.04.588105 (6 April 2024)
Lyu Y, Wu C, Sun W, Li Z. Regional analysis to delineate intrasample heterogeneity with RegionalST.
Bioinformatics, 40(4).
doi:10.1093/bioinformatics/btae186 (29 March 2024)
Furumo Q, Meyer M. PIPETS: A statistically robust, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing.
bioRxiv.
doi:10.1101/2024.03.18.585559 (20 March 2024)
Özer ME, Özbek Sarica P, Arğa KY. SVM-DO: identification of tumor-discriminating mRNA signatures via support vector machines supported by Disease Ontology.
Turk J Biol, 47(6), pp. 349-365.
doi:10.55730/1300-0152.2670 (14 December 2023)
Bioconductor Project Papers
Bioconductor key papers and technical reports.Papers
Gentleman et al. Bioconductor:
open software development for computation biology and bioinformatics. Genome Biology. 2004, 5:R80.
Huber et al. Orchestrating
high-throughput genomic analysis with Bioconductor. Nature
Methods. 2015, 12:115-121.
Initial Bioconductor Technical Reports
Bioconductor Core (November 2002) An Overview of Projects in
Computing for Genomic Analysis
Bioconductor Core (November 2002) Bioconductor: Assessment of
Current Progress