Enhancer discovery in crossbred cattle using CAGE-seq

This is a dry lab project that focuses on the functional genomics assay CAGE-seq (Cap Analysis of Gene Expression sequencing) to identify enhancers and transcription start sites (TSSs) and to quantify gene expression in a single tissue from more than 300 animals. The long-term goal is to leverage these regulatory and expression data to elucidate relationships between genomic variation and phenotype. We expect the outcomes will inform and improve genomic selection for key traits in beef cattle, and identify candidate regulatory targets for potential cis-genome editing to achieve favourable phenotypic changes.

Two positions are available (related project themes, different primary supervisors). Please also see the project ENHANCER-NGUYEN.

The project will be undertaken in a high-quality, particularly well-suited research environment. The Queensland Alliance for Agriculture and Food Innovation (QAAFI) is recognised as a world-leading institute for tropical and sub-tropical agriculture and food research, especially in the areas of genetics and other biotechnologies. The Centre for Animal Science at QAAFI delivers world-class research to Australia's livestock industries.

Excellent computing facilities are already available and used by the research team, which is especially important given the high computational requirements for the proposed project. UQ has multiple high-performance supercomputing facilities that the project team will have access to. The Bunya high-performance computing cluster from Dell EMC Technologies Australia features ~6000 AMD EPYC Milan series cores with 96 physical cores per node running a current generation RHEL-type Linux distribution.

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 Linux/HPC computing environments, reproducible bioinformatics workflows, and/or statistical analysis in R and/or Python would be of benefit to someone working on this project.

You will demonstrate academic achievement in the fields of bioinformatics, computational biology, and/or genetics/genomics and the potential for scholastic success.

A background or knowledge of regulatory genomics, CAGE-seq data analysis and/or comparative genomics is highly desirable.

You must submit an expression of interest (EOI) by 2 March, 2026 2 March, 2026.

Before you apply

1. Check your eligibility for the Master of Philosophy (MPhil).
2. Prepare your documentation.
3. If you have any questions about whether the project is suitable for your research interests, contact Associate Professor Elizabeth Ross (e.ross@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: ENHANCER-ROSS
4. Link to Scholarship Advertisement: https://study.uq.edu.au/study-options/phd-mphil-professional-doctorate/projects/enhancer-discovery-crossbred-cattle-using-cage-seq

Submit an EOI