Are We There Yet? Genomic Profiling and Mechanism in Cancer Research. - Paul S. Meltzer; Sean R. Davis; Kristin Baird; Yidong Chen 002 (CSB, 2004)

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. - Steffen Durinck; Yves Moreau; Arek Kasprzyk; Sean R. Davis; Bart De Moor; Alvis Brazma; Wolfgang Huber (Bioinform., 2005)

GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. - Sean R. Davis; Paul S. Meltzer (Bioinform., 2007)

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. - Yuelin Zhu; Sean R. Davis; Robert M. Stephens; Paul S. Meltzer; Yidong Chen 002 (Bioinform., 2008)

RCircos: an R package for Circos 2D track plots. - Hongen Zhang; Paul S. Meltzer; Sean Davis 001 (BMC Bioinform., 2013)

SRAdb: query and use public next-generation sequencing data from within R. - Yuelin Zhu; Robert M. Stephens; Paul S. Meltzer; Sean R. Davis (BMC Bioinform., 2013)

NCBI GEO: archive for functional genomics data sets - update. - Tanya Barrett; Stephen E. Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F. Kim; Maxim Tomashevsky; Kimberly A. Marshall; Katherine H. Phillippy; Patti M. Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; et al. (Nucleic Acids Res., 2013)

Public data and open source tools for multi-assay genomic investigation of disease. - Lavanya Kannan; Marcel Ramos; Angela Re; Nehme Hachem; Zhaleh Safikhani; Deena M. A. Gendoo; Sean Davis 001; David Gomez-Cabrero; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; et al. (Briefings Bioinform., 2016)

caOmicsV: an R package for visualizing multidimensional cancer genomic data. - Hongen Zhang; Paul S. Meltzer; Sean R. Davis (BMC Bioinform., 2016)

Orchestrating a community-developed computational workshop and accompanying training materials. - Sean Davis 001; Marcel Ramos; Lori A. Shepherd; Nitesh Turaga; Ludwig Geistlinger; Martin T. Morgan; Benjamin Haibe-Kains; Levi Waldron (F1000Research, 2018)

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor. - Shweta Gopaulakrishnan; Samuela Pollack; BJ Stubbs; Hervé Pagès; John Readey; Sean Davis 001; Levi Waldron; Martin Morgan; Vincent J. Carey (F1000Research, 2019)

BiocPkgTools: Toolkit for mining the Bioconductor package ecosystem. - Shian Su; Vincent J. Carey; Lori A. Shepherd; Matthew E. Ritchie; Martin T. Morgan; Sean Davis 001 (F1000Research, 2019)

Toward a gold standard for benchmarking gene set enrichment analysis. - Ludwig Geistlinger; Gergely Csaba; Mara Santarelli; Marcel Ramos; Lucas Schiffer; Nitesh Turaga; Charity W. Law; Sean Davis 001; Vincent J. Carey; Martin Morgan; Ralf Zimmer; Levi Waldron (Briefings Bioinform., 2021)

Ten simple rules for large-scale data processing. - Arkarachai Fungtammasan; Alexandra Lee; Jaclyn N. Taroni; Kurt Wheeler; Chen-Shan Chin; Sean Davis 001; Casey S. Greene (PLoS Comput. Biol., 2022)

Learning and teaching biological data science in the Bioconductor community. - Jenny Drnevich; Frederick J. Tan; Fabricio Almeida-Silva; Robert Castelo; Aedín C. Culhane; Sean Davis 001; Maria A. Doyle; Susan P. Holmes; Leo Lahti; Alexandru Mahmoud; Kozo Nishida; Marcel Ramos; et al. (CoRR, 2024)

Learning and teaching biological data science in the Bioconductor community. - Jenny Drnevich; Frederick J. Tan; Fabricio Almeida-Silva; Robert Castelo; Aedín C. Culhane; Sean R. Davis; Maria A. Doyle; Ludwig Geistlinger; Andrew R. Ghazi; Susan P. Holmes; Leo Lahti; Alexandru Mahmoud; et al. (PLoS Comput. Biol., 2025)