I joined Kat Holt’s lab at the University of Melbourne in June 2016 as a McKenzie Postdoctoral Fellow and I am also affiliated to the PRISM^2 NHMRC Centre (Policy Relevant Infectious Disease Simulation and Mathematical Modelling). I am based at the Bio21 Institute. My research consists in evolutionary analyses of infectious pathogen genomes, particularly bacteria and viruses. I develop computational and statistical approaches to estimate evolutionary rates and timescales in these organisms. These estimates are useful to infer the timing of infectious outbreaks and the long-term interactions between pathogens and their hosts.
I completed my PhD at the University of Sydney in 2015, supervised by Prof Simon Ho. I then moved to the Charles Perkins Centre, also at the University of Sydney, to do postdoctoral research with Prof Edward Holmes. My PhD thesis and postdoctoral work in Sydney investigated the factors that determine why some viruses evolve faster than others.
- Phylogenomic methods: These methods are commonly used to infer the evolutionary history of organisms. For example, it is possible to determine the time and location of origin of infectious outbreaks. Much of my research consists in improving these approaches, particularly to improve estimates of the time of origin of infectious outbreaks
- Phylodynamics: Many viral and bacterial pathogens evolve orders of magnitude faster than multicellular organisms. As such, epidemiological processes often leave a signature in their genomes. Phylodynamic methods take advantage of such genomic information to reconstruct transmission dynamics. For example, a few molecular samples from an infectious pathogen, such as Ebola, are sufficient to estimate their transmission rate, incubation period, and pandemic potential. I am currently developing statistical methods to select phylodynamic models for a range of pathogens.
- Duchene S and Holmes ECH (2018) Estimating evolutionary rates in giant viruses using ancient genomes. Virus Evolution, 4(1). ve006.
Workshops and seminars
- Phyloseminar on model adequacy in phylodynamics
- Taming the BEAST.
- I run regular phylogenetics workshop at the University of Melbourne:
- 2017 – Introduction to Pathogen Phylogenetic Analysis – University of Melbourne.
- 2016 – Introduction to Pathogen Phylogenetics – University of Melbourne.
My PhD supervisor, Simon Ho, also runs an annual phylogenetics workshop in Sydney.
- 2019 – 2021 ARC Discovery Early Career Research Award. Phylogenetic methods for genome surveillance of microbial pathogens.
- 2019 – 2021 NHMRC project grant (co-investigator). A statistical framework to exploit routine pathogen genomics data for public health.
- 2015 – McKenzie Postdoctoral Fellowship (2016 – 2018) University of Melbourne, Australia (salary for three years and 25,000 AUD of research funding).
Awards and honours in the past five years
- 2016 – D.G. Catcheside Prize from the Genetics Society of Australasia, Gold Coast, Australia.
- 2014 – Faculty of Science Postgraduate Research Prize for Outstanding Academic, Achievement, University of Sydney, Australia.