The Univeristy of Melbourne The Royal Melbourne Hopspital

A joint venture between The University of Melbourne and The Royal Melbourne Hospital


Research Projects

Project: Integrative infectious disease phylodynamics

Davies Group

Recent advances in sequencing technologies have dramatically increased the amount of genome data available for many organisms. Because many microbial pathogens, such as viruses and bacteria, such genome data are informative about their transmission dynamics, a field known as infectious disease phylodynamics. A key challenge in phylodynamics is coupling genome sequence data with other sources of information, such as epidemiology, drug resistance profiles, and geographic location. Ideally, these different sources of information will improve the range of inferences in phylodynamics. These inferences are particularly important for genome surveillance initiatives, where genome sequences and associated metadata are routinely generated to understand the evolution of infectious pathogens in near-real time.

This project has two broad aims; (i) to develop Bayesian hierarchical models to integrate different types of data in phylodynamic analyses, and (ii) to leverage these frameworks for genome surveillance where computational speed and assessing statistical power are essential. This project has a strong methodological component, but it will capitalise on existing data of influenza viruses, HIV, and outbreak-causing bacteria generated at the Doherty Institute and through a network of external collaborators (University of Sydney and University of New South Wales). There are ample opportunities with international collaborators (ETH Zurich, Institut Pasteur and University of Auckland), including leading developers of Bayesian phylogenetic methods, such as BEAST. A good understanding of phylogenetics and Bayesian statistics is essential, and programming skills in at least one scripting language (e.g. R or Python) are highly desirable. There are opportunities for a PhD stipend or top-up for highly motivated candidates.

Contact project supervisor for further
information and application enquiries

Project Supervisor

Dr Sebastian Duchene

Project availability

Davies Group

[email protected]

3 vacancies

Antimicrobial Resistance and Healthcare Associated Infections
Host Pathogens Interactions
Cross Cutting Disciplines
Discovery Research
Indigenous Health
Public Health

The Davies group aims to apply genome sequencing methodologies and bioinformatics approaches to understand the evolution and transmission of bacterial pathogens. This knowledge can help facilitate a global understanding of pathogen evolution, in addition to informing public health intervention to reduce the disease burden associated with bacterial pathogens. Current projects address key research questions such as: is there a genetic difference between strains causing different disease manifestations? What is driving the emergence and dissemination of bacterial pathogens? Do host immune factors govern disease severity? Our research closely aligns with key international collaborators including the Wellcome Trust Sanger Institute in the United Kingdom.