📖 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 2024-09-16T03:00:08-04:00.
Kitanovski S, Cao Y, Ttoouli D, Farahpour F, Wang J, Hoffmann D. scBubbletree: computational approach for visualization of single cell RNA-seq data.
BMC Bioinformatics, 25(1), pp. 302.
doi:10.1186/s12859-024-05927-y (13 September 2024)
Capraz T, Huber W. Feature selection by replicate reproducibility and non-redundancy.
Bioinformatics.
doi:10.1093/bioinformatics/btae548 (10 September 2024)
Baker BH, Sathyanarayana S, Szpiro AA, MacDonald JW, Paquette AG. RNAseqCovarImpute: a multiple imputation procedure that outperforms complete case and single imputation differential expression analysis.
Genome Biol, 25(1), pp. 236.
doi:10.1186/s13059-024-03376-7 (3 September 2024)
Zhang H, Jiang W, Jiang Y, Xu N, Nong L, Li T, Liu R. Investigating the therapeutic potential of hesperidin targeting CRISP2 in intervertebral disc degeneration and cancer risk mitigation.
Front Pharmacol, 15, pp. 1447152.
doi:10.3389/fphar.2024.1447152 (29 August 2024)
Sola F, Ayala D, Pulido M, Ayala R, López-Cerero L, Hernández I, Ruiz D. ginmappeR: an unified approach for integrating gene and protein identifiers across biological sequence databases.
Bioinform Adv, 4(1), pp. vbae129.
doi:10.1093/bioadv/vbae129 (29 August 2024)
Die JV. refseqR: an R package for common computational operations with records on RefSeq collection.
Bioinform Adv, 4(1), pp. vbae122.
doi:10.1093/bioadv/vbae122 (21 August 2024)
Ghosh T, Baxter RM, Seal S, Lui VG, Rudra P, Vu T, Hsieh EW, Ghosh D. cytoKernel: Robust kernel embeddings for assessing differential expression of single cell data.
bioRxiv.
doi:10.1101/2024.08.16.608287 (19 August 2024)
Dione MN, Shang S, Zhang Q, Zhao S, Lu X. Non-Thermal Effects of Terahertz Radiation on Gene Expression: Systematic Review and Meta-Analysis.
Genes (Basel), 15(8).
doi:10.3390/genes15081045 (8 August 2024)
Liu H, Hu K, O'Connor K, Kelliher MA, Zhu LJ. CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data.
BioTech (Basel), 13(3).
doi:10.3390/biotech13030030 (3 August 2024)
Yu S, Meng G, Tang W, Ma W, Wang R, Zhu X, Sun X, Feng H. cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment.
Bioinformatics, 40(8).
doi:10.1093/bioinformatics/btae511 (2 August 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
