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Real-time Phylogenetics for Food-borne Outbreak Surveillance


$27,596 (2019 rate, indexed) per annum, plus an additional $10,000 top-up

3 years, with the possibility of a 1 session extension. 





The project aims to introduce, for the first time, real time evolutionary analysis of agricultural pathogens so that outbreaks affecting crops and the food supply can be managed precisely and rapidly. An interdisciplinary team will implement a large-scale data analytics framework in user-friendly software that integrates Australian infectious disease genomics data with global data. Underpinning this work are new theory and algorithms that apply Sequential Monte Carlo to update phylogenetic analyses continuously as new data arrives.

To demonstrate this technique with real-world datasets, the student will analyse the genomes of significant Xanthomonas species that are threats to fruit, vegetable, grain and fibre crops and bacterial diseases important to production animal health. The student will work closely with research staff at the NSW Department of Primary Industries to achieve this aim. They will also further analyse sequencing data to improve understanding of bacterial disease structure in the Australian context and correlate relationships elucidated by genome sequencing with epidemiological, genotypical and phenotypical data.

Expected outcomes include new knowledge of statistical algorithms for evolutionary analysis, relevant to biological disciplines beyond infectious disease; knowledge to support the management of diseases that reduce food production and enhanced capacity for infectious disease analysis.

Who is eligible?

This scholarship is open to Australian Permanent Residents and New Zealand Citizens. 

Applicants must hold either:

  • Honours with First Class or Second Class Div 2; or
  • MSc with a research thesis of at least 6 months; or
  • An international equivalent degree. 

Selection process


  • Basic experience in microbiology and molecular biology
  • Experience with Linux-based computing and/or biological sequence data analysis


  • Experience with at least one general-purpose programming (or command) language (e.g. Bash, R, Python, Perl, etc.)

Applications closed

Closed 31 August 2019.

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Other information

The student will be primarily based at Elizabeth Macarthur Agricultural Institute, the NSW Department of Primary Industries Centre of Excellence for Plant and Animal Health, and will work closely with experts in Biosecurity and Food Safety. This scholarship offers valuable experience for students looking for careers in government research.