📖 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 2024-12-11T21:00:09-05:00.
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)
Jiang Y, Wu W, Xie L, Zhou Y, Yang K, Wu D, Xu W, Fang R, Ge J. Molecular targets and mechanisms of Sijunzi decoction in the treatment of Parkinson's disease: evidence from network pharmacology, molecular docking, molecular dynamics simulation, and experimental validation.
Front Pharmacol, 15, pp. 1487474.
doi:10.3389/fphar.2024.1487474 (26 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 MartÃn 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)
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)
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
Books
A selection of Bioconductor releated books, book chapters, and online books.Books
