📖 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 2025-11-19T17:00:08-05:00.
Türei D, Schaul J, Palacio-Escat N, Bohár B, Bai Y, Ceccarelli F, Çevrim E, Daley M, Darcan M, Dimitrov D, Doğan T, Domingo-Fernández D, Dugourd A, Gábor A, Gul L, Hall BA, Hoyt CT, Ivanova O, Klein M, Lawrence T, Mañanes D, Módos D, Müller-Dott S, Ölbei M, Schmidt C, Şen B, Theis FJ, Ünlü A, Ulusoy E, Valdeolivas A, Korcsmáros T, Saez-Rodriguez J. OmniPath: integrated knowledgebase for multi-omics analysis.
Nucleic Acids Res.
doi:10.1093/nar/gkaf1126 (18 November 2025)
Lopez-Blanch L, Rodríguez-Marin C, Mantica F, Iñiguez LP, Permanyer J, Kita EM, Mackensen T, Codina-Tobias M, Romero-Ferrero F, Fernandez-Albert J, Cuadrado M, Bustelo XR, de Polavieja G, Irimia M. Phenotypic impact of individual conserved neuronal microexons and their master regulators in zebrafish
eLife, 13, pp. RP104275.
doi:10.7554/eLife.104275 (18 November 2025)
Dingwall HL, Grinstein M, Peterson B, Capellini TD, Galloway JL. Dynamic transcriptional and epigenetic changes define postnatal tendon growth
PLoS Genet, 21(11), pp. e1011902.
doi:10.1371/journal.pgen.1011902 (18 November 2025)
Li Y, Jiang Y, Zhu B, Zhang Y, Liu X, Ge L, Hu T, Wang M. Unveiling the potential targets and mechanisms of DEHP/BPA exposure on PCOS: insights from network toxicology and molecular docking
J Ovarian Res, 18, pp. 268.
doi:10.1186/s13048-025-01866-1 (18 November 2025)
Song JH, Agake SI, Tanabata S, Cui Y, Su L, Montes-Luz B, Xu D, Stacey G. Phloem-specific translational regulation of soybean nodulation: Insights from a phloem-targeted TRAP-seq approach
Plant Physiol, 199(3), pp. kiaf570.
doi:10.1093/plphys/kiaf570 (15 November 2025)
Lee JY, Holt JR, Zhao X, Hoadley KA, Hayes DN, Choi HY. ELViS: An R Package for Estimating Copy Number Levels of Viral Genomic Segments at Base-Resolution.
Bioinformatics.
doi:10.1093/bioinformatics/btaf622 (12 November 2025)
Al Ajami A, Schuck J, Marini F, Imkeller K. Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.
NAR Genom Bioinform, 7(4), pp. lqaf149.
doi:10.1093/nargab/lqaf149 (11 November 2025)
Duran GA, Kiraz Y, Baykara D. LEP and FOXO1 genes, as a proposed tumor suppressor autophagic cell death related genes, can be targeted by antidiabetic therapy in nondiabetic breast cancer patients.
Discov Oncol, 16(1), pp. 2072.
doi:10.1007/s12672-025-03903-3 (10 November 2025)
Mihajlovic L, Hofacker LM, Lindner F, Jayakumar P, Diepold A, Huwiler SG. A molecular toolbox to modulate gene expression and protein secretion in the bacterial predator Bdellovibrio bacteriovorus
PLoS Genet, 21(11), pp. e1011935.
doi:10.1371/journal.pgen.1011935 (10 November 2025)
Zhao L, Lv X, Chen W, Li X, Zhou J, Ai Q, Tuo Q. Athero-oncology perspective: identifying hub genes for atherosclerosis diagnosis using machine learning
Front Immunol, 16, pp. 1616096.
doi:10.3389/fimmu.2025.1616096 (4 November 2025)
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
