LeishCyc: a biochemical pathways database for Leishmania major. - Maria A. Doyle; James I. MacRae; David P. De Souza; Eleanor C. Saunders; Malcolm J. McConville; Vladimir A. Likic (BMC Syst. Biol., 2009)

Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens. - María P. Magariños; John P. Overington; Santiago J. Carmona; Dhanasekaran Shanmugam; Maria A. Doyle; Stuart A. Ralph; Gregory J. Crowther; Christiane Hertz-Fowler; Solomon Nwaka; Matthew Berriman; David S. Roos; Wesley C. Van Voorhis; et al. (BMC Bioinform., 2010)

An integrative bioinformatic predictor of protein sub-cellular localisation in malaria. - Ben J. Woodcroft; Robert Radloff; Lee M. Yeoh; Kristie-Lee Scanlon; Maria A. Doyle; Giel G. van Dooren; Geoffrey I. McFadden; Christopher J. Tonkin; Terence P. Speed; Stuart A. Ralph (BMC Bioinform., 2011)

CONTRA: copy number analysis for targeted resequencing. - Jason Li 002; Richard Lupat; Kaushalya C. Amarasinghe; Ella R. Thompson; Maria A. Doyle; Georgina L. Ryland; Richard W. Tothill; Saman K. Halgamuge; Ian G. Campbell; Kylie L. Gorringe (Bioinform., 2012)

The RNA workbench 2.0: next generation RNA data analysis. - Jörg Fallmann; Pavankumar Videm; Andrea Bagnacani; Bérénice Batut; Maria A. Doyle; Tomas Klingström; Florian Eggenhofer; Peter F. Stadler; Rolf Backofen; Björn A. Grüning (Nucleic Acids Res., 2019)

Interfacing Seurat with the R tidy universe. - Stefano Mangiola; Maria A. Doyle; Anthony T. Papenfuss (Bioinform., 2021)

Galaxy Training: A powerful framework for teaching! - Saskia D. Hiltemann; Helena Rasche; Simon L. Gladman; Hans-Rudolf Hotz; Delphine Larivière; Daniel J. Blankenberg; Pratik D. Jagtap; Thomas Wollmann; Anthony Bretaudeau; Nadia Goué; Timothy J. Griffin; Coline Royaux; et al. (PLoS Comput. Biol., 2023)

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)