I joined Kat Holt’s lab at the University of Melbourne in June 2016 as a McKenzie Postdoctoral Fellow, and I am based at the Centre for Systems Genomics. 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. Please find my contact details here.
- Duchêne, S., Holt, K. E., Weill, F. X., Le Hello, S., Hawkey, J., Edwards, D. J., … & Holmes, E. C. (2016). Genome-scale rates of evolutionary change in bacteria. Microbial Genomics, doi: 10.1099/mgen.0.000094
- Duchêne, S., Duchêne, D.A., Di Giallonardo, F., Eden, J.S., Geoghegan, J.L., Holt, K.E., Ho, S.Y. and Holmes, E.C. (2016). Cross-validation to select Bayesian hierarchical models in phylogenetics. BMC evolutionary biology, 16(1), p.1.
- Duchêne, S., Geoghegan, J. L., Holmes, E. C., and Ho, S. Y. (2016). Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. Bioinformatics, In press.
- Duchêne, S., Di Giallonardo, F., & Holmes, E. C. (2016). Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales. Molecular biology and evolution, 33(1) 255-267.
- Peer-reviewed publications – 33 (full list of publications in GoogleScholar)
- H-index – 12
- Phylogenomic methods: These methods are commonly used to infer the evolutionary history of organisms. For example, these methods are commonly used to determine the time and location of origin of infectious outbreaks. Much of my research consists in improving these approaches, for example, detecting sources of bias and developing statistical tests to improve the reliability of these estimates.
- Phylodynamics: In some organisms, such as viruses and bacteria, epidemiological processes and genetic change occur at a similar timeframe. This is an important reason for why bacterial and viral diseases are so difficult to control. Phylodynamic methods take advantage of the rapid evolution of these pathogens to infer their epidemiological patterns. 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.
- Introduction to Pathogen Phylogenetics – University of Melbourne.
My PhD supervisor, Simon Ho, also runs an annual phylogenetics workshop in Sydney.
Awards and Honours
- 2016 – D.G. Catcheside Prize from the Genetics Society of Australasia, Gold Coast, Australia
- 2015 – McKenzie Postdoctoral Fellowship (2016 – 2018) University of Melbourne, Australia (salary for three years and 25,000 AUD of research funding)
- 2014 – Faculty of Science Postgraduate Research Prize for Outstanding Academic, Achievement, University of Sydney, Australia
- 2012 – Francisco José de Caldas Doctoral Scholarship, Scholarship for Ph.D. studies awarded by the Colombian government.