Dr John and Anne Chong Lab for Functional Genomics

Functional genomics

Our lab is focused on the systematic functional annotation of the genome. The long-term objective of our research is to identify genes and coding mutations that participate in major age-related and neurological diseases. Our overall research strategy is to combine human population genomics (GWAS or sequencing) data with high throughput functional validation in fruit flies and mammalian systems to identify new genes that contribute to human disease.

We have developed novel functional genomics strategies that we use to identify genes involved in various normal or disease states. Currently we have projects that relate to heart function, pain perception, neurodegeneration, lifespan and metabolic disorders, kidney function, and cancer. In the end our goal is to rapidly improve patient treatment, and many of the new genes we have identified appear to be viable drug targets.

Gene x environment interactions

While our genetics certainly influence what diseases we may be susceptible to, many major human diseases are increasing at a rate faster than genetics alone can explain. Thus an emerging research interest in our lab is what environmental factors are contributing to human disease, and how do our genes interact with these factors to cause disease in some but not others.

I completed my PhD in human immunology at the University of Calgary, Canada and went on to train in conserved functional genomics with Josef Penninger in Vienna, Austria. Since 2011, I have been running a lab in Sydney Australia using conserved functional genomics approaches to find novel human disease genes and pathways. My main interest is in age-related diseases involving the nervous system, including pain, neurodegeneration, and strategies to extend lifespan while preserving overall health.

We currently have several honors or PhD projects available in the lab.

Genes and neural circuits controling pain perception

Summary: This project involves combining human genomics data for chronic pain disease with high throughput behavioural genomics techniques in fruit fly in order to better understand how chronic pain develops after injury.

It involves using high throughput genetics and genomics approaches to better understand how animals become sensitised to pain after injury. The project will involve use of fruit fly behavioural genetics techniques, and potentially bioinformatics, transgenic mice or human stem cells, and the successful applicant will be trained in these techniques.

Lifespan extension

Summary: This project will combine human genomics with behavioural genetic and molecular biology in order to characterise new pathways that can extend lifespan and preserve cognitive function with age.

It involves testing human genomics data on longevity to find new genes that can extend lifespan in the fruit fly. We focus on genes that when targeted specifically in the brain, can extend lifespan while also preserve cognitive function with age. We have identified 40 new targets that can extend lifespan, and the project will involve working on some of these new lifespan extending genes. Project will involve lifespan assays, behavioural genetics, molecular biology, and electrophysiology, and the successful candidate will be trained in all of these techniques.

Whole genome CRISPR screening

Summary: This project will involve new whole genome CRISPR editing strategies, coupled with bioinformatics analysis, to identify the complete molecular mechanism of action for relevant human drugs or disease genes.

Recently CRISPR-based approaches have revolutionised functional genomics techniques. We have set up new whole genome CRISPR screening, and using this technique we have defined the molecular mechanism of action for over 20 relevant human drugs or venoms from deadly Australian creatures. This project involves working with our functional genomics team to continue these efforts. The successful candidate will learn state of the art whole genome CRISPR screening, as well as advanced molecular biology and potentially also basic bioinformatics analysis.

Browse our postgraduate research opportunities and connect with potential supervisors.

• Professor Greg Neely, Charles Perkins Centre, Project lead
• Dr Lipin Loo, Group Leader, RNA Therapies
• Dr Arjun Muralidharan, Group Leader, Neurobiology of Chronic Pain
• Dr Cesar Moreno, Research Fellow
• Dr Christopher Denes, Research Fellow
• Dr Maria Bergamasco, Postdoctoral Research Associate
• Dr Kazuma Fujikake, Research Fellow
• Dr Willie Lin, Charles Perkins Centre, Fruit Fly Facility Manager
• Teleri Clark, PhD student
• Matthew Waller, PhD student
• Sophie Trabish, PhD student
• Tian Du, PhD student
• Mezzalina Vankan, PhD student
• Jasmine Kaur, PhD student
• Geng Li, Masters student
• James Rawson, Research Assistant
• Miriam Puehl, Research Assistant