Integrating whole-genome sequence and functional genomics for polygenic prediction

Advances in whole-genome sequencing (WGS) are enabling the analysis of millions of genetic variants across the full allele-frequency spectrum, including rare variants that are poorly captured by conventional GWAS. 

At the same time, rapidly expanding functional genomic resources provide rich information about the biological consequences of genetic variation. Integrating these data offers an important opportunity to better understand genetic architecture and improve polygenic prediction of complex traits and diseases.

This PhD project will develop new statistical models that integrate WGS variants with functional genomic annotations to improve estimation of genetic effects and polygenic risk scores. 

The project will also explore the use of ancestral recombination graphs (ARGs) to efficiently represent genealogical relationships and linkage disequilibrium among sequence variants, facilitating analysis of large-scale WGS data. Computationally efficient Bayesian algorithms will be developed to enable application to biobank-scale datasets containing tens of millions of variants.

The project will provide interdisciplinary training in statistical genetics, Bayesian modelling, population genetics, functional genomics, and high-performance computing.

You will join a highly collaborative research environment at the Institute for Molecular Bioscience, The University of Queensland, with expertise spanning statistical and population genetics, genomics, computational biology, and complex trait research. 

The project will provide access to large-scale genomic datasets, high-performance computing infrastructure, and established national and international collaborations. 

You will also benefit from regular interaction with researchers working across statistical methodology, human genetics, and functional genomics, providing an excellent environment for interdisciplinary training and career development.

This project is supported by the Research project scholarship.

Learn more about the Research project scholarship.

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 genomic sequence analysis, statistical modelling, and/or evolutionary genetics would be of benefit to someone working on this project.

You will demonstrate academic achievement in the fields of statistical genomics and/or evolutionary genetics and the potential for scholastic success.

A background or knowledge of evolutionary genetics is highly desirable.

You must submit an expression of interest (EOI) by 25 September, 2026 25 September, 2026.

Before you apply

1. Check your eligibility for the Doctor of Philosophy (PhD).
2. Prepare your documentation.
3. If you have any questions about whether the project is suitable for your research interests, contact Dr Jian Zeng (j.zeng@uq.edu.au).

When you apply

To apply, submit an expression of interest (EOI) for the program. You don't need to apply separately for the project or scholarship. How to submit an EOI

In your EOI, complete the ‘Scholarship/Sponsorship’ section with the following details:

1. Are you applying for an advertised project: 'Yes'
2. Project: 'Research project scholarship'
3. Scholarship Code Listed in the Advertisement: GENOME-ZENG
4. Link to Scholarship Advertisement: https://study.uq.edu.au/study-options/phd-mphil-professional-doctorate/projects/integrating-whole-genome-sequence-and-functional-genomics-polygenic-prediction

Submit an EOI