Dr. Timothy Vaughan

I completed my undergraduate and doctoral studies in theoretical and computational physics at the University of Queensland, Australia, where in 2008 I completed a PhD under Prof. Peter Drummond and Karen Kheruntsyan focusing on the theory of ultracold atomic gases and Bose-Einstein Condensation in particular. From there, I spent a brief period working as a research assistant under Geoffrey Goodhill at the Queensland Brain Institute (also at the University of Queensland) developing and implementing image processing algorithms to assist in quantification of neural growth cone chemotaxis.  In 2009 I then began a post-doctoral project working with Prof. Peter Drummond at Swinburne University of Technology (Melbourne, Australia) applying computational methods from the field of statistical mechanics to the study of the stochastic within-host viral (HIV in particular) infection dynamics.

In 2012 I began work on a second post-doctoral project under Prof. Alexei Drummond at the University of Auckland (Auckland, New Zealand) and Prof. Nigel French at Massey University (Palmerston North, New Zealand) developing and implementing statistical methods for studying pathogen dynamics from genetic sequence data using Bayesian phylogenetic methods. During the course of this project I developed a number of tools and methods including specialised stochastic population dynamics simulation software, an algorithm and software package for inferring ancestral spatial dynamics of evolving populations, an algorithm and software package for phylogenetic inference of recombining bacterial populations, and an algorithm and software package for inferring epidemic prevalence curves using a combination genomic and traditional epidemiological data such as hospitalization case counts. During this time I also contributed to the ongoing development of the popular BEAST 2 phylogenetic inference software platform.

In mid-July 2017 I moved to Switzerland to begin work as a Senior Scientist in Prof. Tanja Stadler's Computational Evolution research group at the D-BSSE in Basel, where I am continuing my work on developing computational and statistical tools to enable Bayesian phylogenetic and phylogenomic inference.

If you would like to know more about my research, or are interested in collaborating with me or perhaps starting a Master's or PhD thesis, please do not hesitate to contact me directly via email.