Gerry Tonkin-Hill lab

The Computational Microbiology group, led by Gerry Tonkin-Hill, works closely with clinical and wet-lab collaborators to improve our understanding of how microbes evolve, transmit between and interact with their hosts.

These microbial interactions play a critical role in our health and can have profound impacts on the treatment of both infectious and non-infectious diseases, including cancer. Accurate models of these interactions will help to create optimal microbiome-targeted therapies and mitigate the impact of infectious disease.

Current projects

Microbial evolution and host-microbe interactions

The human microbiome consists of microorganisms, including pathogens and beneficial organisms, that mutate billions of times daily within each person. Our research investigates how these mutations influence human health, including effects on the immune system, nutrient and drug metabolism, infection prevention, and transmission between people and the environment. Key areas of interest include:

Within-host evolution in immunocompromised patients
Interactions between medications and the microbiome
Antibiotic resistance
Bacterial population genetics

Computational and statistical methods

The size of microbial genomics and metagenomic datasets is rapidly increasing. We develop highly scalable statistical and machine learning algorithms to analyse these datasets efficiently. Key areas of interest include:

Linking genotype to phenotype
Pangenomics
Gene prediction, protein annotation and clustering
Transmission inference
Phylodynamics and microbial population structure

Lab members

Sudaraka Mallawaarachchi
Qing Siaw

Gerry Tonkin-Hill

Gerry Tonkin-Hill lab