Medical genomics and bioinformatics
Our group develops methods for interrogating genomic, transcriptomic and proteomic data to develop new biomarkers and rapid diagnostic and prognostic tools. We are currently working in the area of infectious disease and cancer. In the area of infectious disease we are using real-time nanopore sequencing, combined with bacterial cell capture to develop culture-free methods for detection of pathogen and prediction of its antibiotic resistance profile. We are collaborating with clinicians to trial these approaches to detect sepsis, as well as to monitor drug resistance evolution in the airways of cystic fibrosis patients.
In the area of cancer, we have been working on tools for identifying early stage cancer using circulating cell free DNA. We are also interested in cell free DNA as a marker of tissue damage in heart and kidney disease. We also have interests in fundamental bioinformatics challenges such as genome assembly (particularly in the area of metagenomics); identification of genomic structural variation ; identification of multi-clonal structural variants in cancer.
Traineeships, honours and PhD projects include
- Development of algorithms for detection of base modifications in nanopore data
- Detection of aberrant methylation patterns and copy number changes from cell free DNA
- Detection of tissue damage by analysis of cell free RNA
