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)

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)

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)

Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates. - Alessandra Løchen; James Truscott; Nicholas J. Croucher (PLoS Comput. Biol., 2022)