SimMLST: simulation of multi-locus sequence typing data under a neutral model. - Xavier Didelot; Daniel J. Lawson; Daniel Falush (Bioinform., 2009)

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. - Thibaut Jombart; Anne Cori; Xavier Didelot; Simon Cauchemez; Christophe Fraser; Neil M. Ferguson (PLoS Comput. Biol., 2014)

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. - Xavier Didelot; Daniel J. Wilson 001 (PLoS Comput. Biol., 2015)

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. - Don Klinkenberg; Jantien A. Backer; Xavier Didelot; Caroline Colijn; Jacco Wallinga (PLoS Comput. Biol., 2017)

outbreaker2: a modular platform for outbreak reconstruction. - Finlay Campbell; Xavier Didelot; Richard G. FitzJohn; Neil M. Ferguson; Anne Cori; Thibaut Jombart (BMC Bioinform., 2018)

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination. - Caitlin Collins; Xavier Didelot (PLoS Comput. Biol., 2018)

A dynamic power-law sexual network model of gonorrhoea outbreaks. - Lilith K. Whittles; Peter J. White; Xavier Didelot (PLoS Comput. Biol., 2019)

SARS-CoV-2 transmissibility compared between variants of concern and vaccination status. - Liang Wang; Xavier Didelot; Yuhai Bi; George F. Gao (Briefings Bioinform., 2022)

Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease. - Xavier Didelot; David Helekal; Michelle Kendall; Paolo Ribeca (Bioinform., 2023)

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model. - Ian Roberts; Richard G. Everitt; Jere Koskela; Xavier Didelot (PLoS Comput. Biol., 2025)