A retrodictive stochastic simulation algorithm. - Timothy G. Vaughan; Peter D. Drummond; Alexei J. Drummond (J. Comput. Phys., 2010)

Efficient Bayesian inference under the structured coalescent. - Timothy G. Vaughan; Denise Kühnert; Alex Popinga; David Welch 003; Alexei J. Drummond (Bioinform., 2014)

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. - Remco R. Bouckaert; Joseph Heled; Denise Kühnert; Timothy G. Vaughan; Chieh-Hsi Wu; Dong Xie; Marc A. Suchard; Andrew Rambaut; Alexei J. Drummond (PLoS Comput. Biol., 2014)

IcyTree: rapid browser-based visualization for phylogenetic trees and networks. - Timothy G. Vaughan (Bioinform., 2017)

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - Remco R. Bouckaert; Timothy G. Vaughan; Joëlle Barido-Sottani; Sebastián Duchêne; Mathieu Fourment; Alexandra Gavryushkina; Joseph Heled; Graham Jones; Denise Kühnert; Nicola De Maio; Michael Matschiner; Fábio K. Mendes; et al. (PLoS Comput. Biol., 2019)

TreeKnit: Inferring ancestral reassortment graphs of influenza viruses. - Pierre Barrat-Charlaix; Timothy G. Vaughan; Richard A. Neher (PLoS Comput. Biol., 2022)

EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. - Ciara E. Judge; Timothy G. Vaughan; Timothy Russell; Sam Abbott; Louis du Plessis; Tanja Stadler; Oliver Brady; Sarah Hill (PLoS Comput. Biol., 2024)

ReMASTER: improved phylodynamic simulation for BEAST 2.7. - Timothy G. Vaughan (Bioinform., 2024)