Joint PhD Scholarship with Defence Science and Technology (DST)

Population Genetic Signatures in Ricinus communis (Ricin) :

Defence has an increasing focus on the use of Next Generation Sequencing technologies for detection and identification of viruses and bacteria, forensic genotyping and RNA responses to chemical and biological challenges. This PhD program offers a special opportunity to contribute to an International Defence Intelligence Program in collaboration with leading bioinformatics researchers.

A PhD scholarship of $43,000 AUD per annum, for a period of 3½ years is being offered by Defence. The candidate will be enrolled at The University of Melbourne, be based at Melbourne Bioinformatics within the Faculty of Medicine, Dentistry and Health Sciences and will meet regularly with DST and present in Defence forums when appropriate.

Ricin is a potent cytotoxic protein of significant interest to Defence as it has been linked to poisonings in both animals and humans. Famously, ricin was involved in the murder of Bulgarian journalist Georgi Markov in London in 1978 after he was shot with a small platinum-iridium pellet containing the toxin. While there is a continued risk of ricin use in criminal and terrorist activity, there is also concern for its potential use as a mass-scale weapon. This is plausible because the source – the castor oil plant (Ricinus communis) – is readily available around the world and, once established, can spread quickly. There are extensive references to crude ricin extraction methods on the Internet but, importantly, these techniques leave behind DNA signatures. This research program aims to exploit this information to identify the source of ricin under investigation.

DST has already curated a large collection of castor bean seeds and corresponding short-read sequencing information from a range of sources and this will form the primary data source for the research.

This research aims to identify a set of genetic markers in Ricinus communis that enables forensic attribution to:

• link a toxin preparation to plant material
• assign plant materials to their closest-matching genotypic clusters
• infer the likelihoods of geographical origins of plant materials (continent, country, region).

This project represents an exciting opportunity to work with world leading bioinformaticians at the University and to contribute to a larger International Genomics program of relevance to the Defence Intelligence community.

The successful candidate will need to have Australian citizenship, skills and experience in bioinformatics data analytics and a desire to pursue world-leading research in plant genomics with critical application to national security.

Join us as lead developer of the Janis “Portable Pipelines Project”, an exciting system that simplifies the specification of complex analysis workflows and their deployment on HPC and Cloud systems (https://janis.readthedocs.io/en/latest/).

Janis is making a difference now – already, thousands of cancer samples have had their genomes analysed using this system. We believe there is potential for Janis to make a much bigger difference – by further facilitating translation between different workflow specifications, such as Common Workflow Language (CWL), Workflow Definition Language (WDL), Nextflow and the widely-used Galaxy platform.

The role will initially collaborate with leading experts in cancer genomics, situated within a world-leading biomedical precinct, providing a rare opportunity to develop experience in big data analytics for biomedical science.  The role reports to the Academic Lead, Melbourne Bioinformatics, with significant supervision from the project lead at the PeterMac, and in collaboration with other research software engineers from WEHI.