RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). - Socorro Gama-Castro; Heladia Salgado; Martín Peralta-Gil; Alberto Santos-Zavaleta; Luis Muñiz-Rascado; Hilda Solano-Lira; Verónica Jiménez-Jacinto; Verena Weiss; Jair S. García-Sotelo; Alejandra López-Fuentes; Liliana Porrón-Sotelo; Shirley Alquicira-Hernández; et al. (Nucleic Acids Res., 2011)

regionReport: Interactive reports for region-based analyses. - Leonardo Collado-Torres; Andrew E. Jaffe; Jeffrey T. Leek (F1000Research, 2015)

Rail-RNA: scalable analysis of RNA-seq splicing and coverage. - Abhinav Nellore; Leonardo Collado-Torres; Andrew E. Jaffe; José Alquicira-Hernández; Christopher Wilks; Jacob Pritt; James Morton; Jeffrey T. Leek; Ben Langmead (Bioinform., 2017)

Programmatic access to bacterial regulatory networks with regutools. - Joselyn Chávez; Carmina Barberena-Jonas; Jesus E. Sotelo-Fonseca; José Alquicira-Hernández; Heladia Salgado; Leonardo Collado-Torres; Alejandro Reyes (Bioinform., 2020)

Megadepth: efficient coverage quantification for BigWigs and BAMs. - Christopher Wilks; Omar Y. Ahmed; Daniel N. Baker; David Zhang; Leonardo Collado-Torres; Ben Langmead (Bioinform., 2021)

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. - Nicholas J. Eagles; Emily E. Burke; Jacob Leonard; Brianna K. Barry; Joshua M. Stolz; Louise Huuki; BaDoi N. Phan; Violeta Larios Serrato; Everardo Gutiérrez-Millán; Israel Aguilar-Ordoñez; Andrew E. Jaffe; Leonardo Collado-Torres (BMC Bioinform., 2021)

Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. - Nicholas J. Eagles; Emily E. Burke; Jacob Leonard; Brianna K. Barry; Joshua M. Stolz; Louise Huuki; BaDoi N. Phan; Violeta Larios Serrato; Everardo Gutiérrez-Millán; Israel Aguilar-Ordoñez; Andrew E. Jaffe; Leonardo Collado-Torres (BMC Bioinform., 2021)

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. - Dario Righelli; Lukas M. Weber; Helena L. Crowell; Brenda Pardo; Leonardo Collado-Torres; Shila Ghazanfar; Aaron T. L. Lun; Stephanie C. Hicks; Davide Risso (Bioinform., 2022)

IntroVerse: a comprehensive database of introns across human tissues. - Sonia García-Ruíz; Emil K. Gustavsson; David Zhang; Regina H. Reynolds; Zhongbo Chen; Aine Fairbrother-Browne; Ana Luisa Gil-Martínez; Juan A. Botía; Leonardo Collado-Torres; Mina Ryten (Nucleic Acids Res., 2023)

BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data. - Nicholas J. Eagles; Richard Wilton; Andrew E. Jaffe; Leonardo Collado-Torres (BMC Bioinform., 2023)