Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data. - Ricardo Ramirez-Gonzalez; Mario Cáccamo; Daniel MacLean (Bioinform., 2011)

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. - Raoul Jean Pierre Bonnal; Jan Aerts; George Githinji; Naohisa Goto; Daniel MacLean; Chase A. Miller; Hiroyuki Mishima; Massimiliano Pagani; Ricardo Ramirez-Gonzalez; Geert Smant; Francesco Strozzi; Rob Syme; et al. (Bioinform., 2012)

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. - Ricardo Ramirez-Gonzalez; Raoul Jean Pierre Bonnal; Mario Cáccamo; Daniel MacLean (Source Code Biol. Medicine, 2012)

StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics. - Ricardo H. Ramirez-Gonzalez; Richard M. Leggett; Darren Waite; Anil S. Thanki; Nizar Drou; Mario Cáccamo; Robert P. Davey (F1000Research, 2013)

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby. - Graham J. Etherington; Ricardo H. Ramirez-Gonzalez; Dan MacLean (Bioinform., 2015)

PolyMarker: A fast polyploid primer design pipeline. - Ricardo H. Ramirez-Gonzalez; Cristobal Uauy; Mario Cáccamo (Bioinform., 2015)

BrAPI - an application programming interface for plant breeding applications. - Peter Selby; Rafael Abbeloos; Jan Erik Backlund; Martin Basterrechea Salido; Guillaume Bauchet; Omar E. Benites-Alfaro; Clayton L. Birkett; Viana C. Calaminos; Pierre Carceller; Guillaume Cornut; Bruno Vasques Costa; Jeremy D. Edwards; et al. (Bioinform., 2019)

An online database for einkorn wheat to aid in gene discovery and functional genomics studies. - Parva Kumar Sharma; Hanin Ibrahim Ahmed; Matthias Heuberger; Dal-Hoe Koo; Jesus Quiroz-Chavez; Laxman Adhikari; John Raupp; Stéphane Cauet; Nathalie Rodde; Charlotte Cravero; Caroline Callot; Inderjit Singh Yadav; et al. (Database J. Biol. Databases Curation, 2023)