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

epicontacts: Handling, visualisation and analysis of epidemiological contacts. - V. P. Nagraj; Nistara Randhawa; Finlay Campbell; Thomas Crellen; Bertrand Sudre; Thibaut Jombart (F1000Research, 2018)

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data. - Finlay Campbell; Anne Cori; Neil M. Ferguson; Thibaut Jombart (PLoS Comput. Biol., 2019)