The space of evolutionary trees in infectious disease epidemiology

Research Opportunity
Masters by Research, Honours
Department
Microbiology and Immunology
Location
Doherty Institute
Primary Supervisor Email Number Webpage
Dr Sebastian Duchene sebastian.duchene@unimelb.edu.au 8344 3971 Personal web page
Co-supervisor Email Number Webpage
Dr Mark Davies mark.davies1@unimelb.edu.au (03) 9035 6519 Personal web page

Summary This project has three main aims; (i) estimating evolutionary parameters for a range of pathogens, such as HIV, influenza, and dengue, (ii) using these parameters to simulate evolutionary trees under different epidemiological models, and (ii) applying machine learning techniques to identify whether epidemiological processes lead to a predictable patterns of evolutionary trees.

Project Details

Infectious disease epidemiology relies on mathematical models that describe epidemiological dynamics. These models typically consider the rate at which individuals are infected and recover from an infection. Because many infectious microbes, such as viruses and bacteria, evolve orders of magnitude faster than their hosts, their genomes have a signature of the transmission process. This project will pinpoint the key differences between evolutionary trees generated under different epidemiological processes. This project has three main aims;

  1. estimating evolutionary parameters for a range of pathogens, such as HIV, influenza, and dengue,
  2. using these parameters to simulate evolutionary trees under different epidemiological models, and
  3. applying machine learning techniques to identify whether epidemiological processes lead to a predictable patterns of evolutionary trees. The outcome will be a framework to classify evolutionary trees from genome surveillance studies, which will contribute to current efforts to couple genomics and epidemiology.


Faculty Research Themes

Infection and Immunology

School Research Themes

Infection & Immunity



Research Opportunities

Masters by Research, Honours
Students who are interested in joining this project will need to consider their elegibility as well as other requirements before contacting the supervisor of this research

Graduate Research application

Honours application

Key Contact

For further information about this research, please contact a supervisor.

Department

Microbiology and Immunology

Research Node

Doherty Institute

MDHS Research library
Explore by researcher, school, project or topic.