Novel workflow for pan-genome-driven gene exploration, functional annotation and metabolic reconstruction

Genome-scale metabolic reconstructions seek to capture the metabolic potential of organisms in a mathematical framework, integrating information from genomics, bioinformatics and systems biology. These reconstructions underpin metabolic modelling, allowing the understanding, prediction and optimisation of cellular metabolism with diverse applications from biotechnology, medicine and environmental science. However, given the time and effort required to generate a high-quality metabolic reconstruction, the number of reconstructions available are orders of magnitude less than the number of genomes sequenced. We are seeking a candidate to develop new bioinformatic approaches to better leverage information within the pan-genome to improve the consistency and accuracy of gene-calling and functional annotation across a genre of organisms and then faithfully capture this information in metabolic reconstructions. Novel metabolic modelling approaches can be further developed to identify missing metabolic funcitonalities from the pan-genomic reconstruction using data from high-throughput phenotype screening technologies.

The University of Queensland's Australian Institute for Bioengineering and Nanotechnology (AIBN) is a dynamic multi-disciplinary research institute dedicated to developing technology to alleviate societal problems in the areas of health, manufacturing and environmental sustainability. AIBN brings together the skills of more than 450 world-class researchers complimented by an extensive suite of integrated facilities, working at the intersection of biology, chemistry, engineering and computer modelling. Witha reputation for delivering translational industry, academia and government. AIBN goes beyond basic research to develop the growth of innovative industries for the benefit of the Queensland and Australian economies.

Our people are our greatest asset. We offer collaborative, inclusive work and study places, which are enriched by the significant diversity of our staff, students and community. We genuinely believe that creativity and innovation flourishes in an environment where people feel supported, valued and empowered. Mutual respect, inclusively and accountability are the cornerstone of UQ's culture.

This project is supported by the Research project scholarship.

Learn more about the Research project scholarship.

You must contact the principal supervisor for this project to discuss your interest. You should only complete the online application after you have reached agreement on supervision.

Always make sure you are approaching your potential supervisor in a professional way. We have provided some guidelines for you on how to contact a supervisor.

Your application will be assessed on a competitive basis.

We take into account your:

• previous academic record
• publication record
• honours and awards
• employment history

A working knowledge of bioinformatics would be of benefit to someone working on this project.

You will demonstrate academic achievement in the field/s of computer programming and the potential for scholastic success.

A background or knowledge of mathematical modelling and pan-genomics is highly desirable.

Before you apply

Before submitting an application you should:

1. check your eligibility for a Doctor of Philosophy (PhD)
2. prepare your documentation
3. contact Dr Tim McCubbin (t.mccubbin@uq.edu.au) to discuss your interest and suitability
4. submit your application by 13 May, 2024 13 May, 2024.

When you apply

You apply for this scholarship when you submit an application for your program. You don’t need to submit a separate scholarship application.

In your application ensure that under the ‘Scholarships and collaborative study’ section you select:

• ‘My higher degree is not collaborative’
• ‘I am applying for, or have been awarded a scholarship or sponsorship'
• ‘Other’, then ‘Research Project Scholarship’ and in the ‘Name of scholarship’ field enter GENE EXPLORATION-MCCUBBIN.

Apply now