Like bacteria, our global talent search has no borders

The Australian Centre for Genomic Epidemiological Microbiology (Ausgem) is looking to recruit a bioinformatics PhD student to join its research program in 2019 .

  • Open to Australia and New Zealand citizens (and international students who can pay international student fees of 26K USD/year).
  • The successful candidates will be awarded $27,082 per annum, indexed, over 3.5 years.
  • Applicants are required to have the equivalent of a BSc Honours or Masters by Research degree.
  • Start your application by filling out the short form at the bottom of this page.

Development of bioinformatic methods for real-time analysis of bacterial and viral outbreaks

Infectious disease outbreak surveillance has been transformed by rapid advance in genomic diagnostics. Samples from infected patients are now routinely whole-genome sequenced by public health labs worldwide, with hundreds of new genome sequences being deposited to public databases every day. In order to use this information for public health investigations it is necessary to analyse the data in real-time.

This project will focus on developing and applying new statistical algorithms for phylogenetic inference on data streams. These work builds upon Sequential Monte Carlo methods, a well known class of statistical inference algorithms for streaming data sets, with applications outside biology in robot control and quantitative finance. There is flexibility in the project to work either on theoretical aspects such as convergence proofs, technical aspects such as software implementations, or applied aspects, analysing actual outbreaks as they occur.

Desirable skills and qualifications:

  • Strong knowledge of a programming language such as Python, R, or C++
  • Knowledge of probabilistic modelling
  • An interest in or knowledge of approximate inference algorithms
  • Driving licence

This project will be supervised by Associate Professor Aaron Darling.
Additional supervision will be provided by Dr Mathieu Fourment (UTS).

The Australian Centre for Genomic Epidemiological Microbiology (Ausgem) was initiated as a collaborative partnership between the New South Wales Department of Primary Industries (DPI) Elizabeth Macarthur Agricultural Institute and the ithree institute at the University of Technology Sydney (UTS) and has now grown to include other UTS researchers. Ausgem also has strong links with major hospitals, primary producers, and other microbiology groups within Australia, as well as active collaborations in the UK and Europe. Ausgem’s research program focuses on the use of DNA technologies to strengthen the State’s capacity to identify and respond to biosecurity threats, manage food safety, and increase agricultural productivity.

Ausgem brings together academic and government researchers who collectively aim to identify and mitigate the risk of infectious disease through the use of DNA sequencing technologies and bioinformatics.

Ausgem’s surveillance techniques for new and emerging diseases will help equip doctors, farmers, and policy makers with better tools to protect our food supply, human and animal health, and the environment: a concept known as One Health.

Our scientists also study the effectiveness of interventions such as prebiotics, probiotics and vaccines in disease management.

PhD Scholarship Expression of Interest

Application timelines can be found here . However, exceptions can be made so please get in touch asap.

To start your application, complete the form below (all fields are compulsory):

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