Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. - Tim Carver; Simon R. Harris; Matthew Berriman; Julian Parkhill; Jacqueline A. McQuillan (Bioinform., 2012)

BamView: visualizing and interpretation of next-generation sequencing read alignments. - Tim Carver; Simon R. Harris; Thomas D. Otto; Matthew Berriman; Julian Parkhill; Jacqueline A. McQuillan (Briefings Bioinform., 2013)

Random projection based clustering for population genomics. - Sotiris K. Tasoulis; Lu Cheng 004; Niko Välimäki; Nicholas J. Croucher; Simon R. Harris; William P. Hanage; Teemu Roos; Jukka Corander (IEEE BigData, 2014)

A national-scale GIS-based system for modelling impacts of land use on water quality. - Alexander H. Elliott; Annette F. Semadeni-Davies; Ude Shankar; John R. Zeldis; David M. Wheeler; David R. Plew; Gerald J. Rys; Simon R. Harris (Environ. Model. Softw., 2016)

Phandango: an interactive viewer for bacterial population genomics. - James Hadfield; Nicholas J. Croucher; Richard J. Goater; Khalil AbuDahab; David M. Aanensen; Simon R. Harris (Bioinform., 2018)

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data. - Allison L. Hicks; Nicole E. Wheeler; Leonor Sánchez-Busó; Jennifer L. Rakeman; Simon R. Harris; Yonatan H. Grad (PLoS Comput. Biol., 2019)

RCandy: an R package for visualizing homologous recombinations in bacterial genomes. - Chrispin Chaguza; Gerry Tonkin-Hill; Stephanie W. Lo; James Hadfield; Nicholas J. Croucher; Simon R. Harris; Stephen D. Bentley (Bioinform., 2022)