51³Ô¹Ïapp

I am a Professor in Systems Immunology and Machine Learning at the School of Medical Sciences at UNSW Sydney, and I am a visiting fellow at the Garvan Institute for Medical Research and at the Weill Cornell College of Medicine NY, USA.Ìý

My research program uses a Systems Immunology approach to study of T cell responses with the ultimate goal to develop and new immunotherapies that can be used against incurable cancer and autoimmune diseases.ÌýÌýI am passionate about Immunology, and of discoveries that are rapidly translating into immunotherapies for uncurable disorders.ÌýTo achieve this goal I have developed a systems immunology program, which is an interdisciplinary approach that combines experimental and computational analyses to translate new molecular and genomics discoveries to Ìýtransform current immunotherapies into successful, precise and accessible solutions for a broader community of individuals.

I have a strong focus on utilising single cell cutting edge technologies genomics and computational biology ML techniques to develop next-generation T cell immunotherapies for cancer and autoimmunity, where I lead discoveries that can then be translated into clinical intervention, such as predicting side effects, identifying new solutions for unmet clinical needs.

Our research group in Systems Immunology and Immunogenomics, is an interdisciplinary team with skills in Immunology, Mathematical Modelling, Statistics and Bioinformatics to study immune responses, specifically T cells.ÌýI haveÌý over 140 peer-reviewed publications where I have made significant contributions describing landmark bioinformatic methods to combine single-cell transcriptome data with antigen receptor sequences, computational models for haplotype reconstruction of genomes from high throughput deep sequencing data. I developed statistical models that allow for the identification of the full distribution of mutating and recombining genomes from a highly diverse sample, as well as mathematical models that have contributed to the design of public health interventions to control viral infection in prison settings. I have also developed experimental techniques for identification of antigen specific T cells from blood samples and utilised high dimensional flow cytometry, mass cytometry, as well as functional assays.

The current major research focus of my laboratory is on the single-cell analyses of immune cells in the context of viral infections, autoimmunity and CAR T cells. I have successfully applied these techniques in autoimmune disease, viral infections and CAR T cells, and applied to both human and mouse samples. My lab has also developed single cell approaches to study rate populations of antigen specific immune cells isolated from cryopreserved human samples (blood or tissue) and developed novel bioinformatics methods to analyse these data to explore how T cell phenotypes and clonotypes change longitudinally over time in the same individual.

During my career I have been successful in obtaining research funds from public and private sector for a total of >20 millions. At UNSW Sydney, I am a Principal Investigator of a recently funded Institute, the UNSW Future Institute of Cellular Genomics, which has planned to invest US$ 4.5 Millions over the next 7 years to deliver cutting edge single cell technologies in cellular genomics. In the last three years, I have successfully obtained research funds from private sector (BD Bioscience) to lead a project on the application of single cell multi-omics to study CAR T cell therapies, and specifically from samples obtained from a clinical trial conducted in Sydney. In this project my laboratory has led the experimental and bioinformatics analyses. ÌýMy track record and skills provide evidence that I am capable to lead the data analyses and contribute to the experimental design in this project.

Ìý

Research Interests

Systems ImmunologyÌý

1. Immune Receptor analysis using Next generation Sequencing Our group is very much interested in the study of T and B cell receptors and how these highly specific proteins determine successful immune responses. We use statistics and bioinformatics to analyse immune receptor data generate din our lab and from collaborators.Ìý
2. Bioinformatics softwareÌýWe have experience in software tools to study pathogen genomics, immune cells and we also develop workflows for integrated analyses across genomic, immunological and clinical dataÌýsets.
3. T cell responses in influenza virus ÌýÌýWe are closely collaborating with professor Katherine Kedzierska (Peter Doherty Institute in Melbourne) on the study of T cell responses that arise during influenza virus infection using single cell genomics

Single Cell Genomics and Multi-Omics

1. Analysis of single cell multiomicsÌýin theÌýcontext of Coeliac disease. ThisÌýproject is a collaboration with Prof Chris Goodnow's team at the Garvan Institute.
2. Understanding CAR T cell therapy response in the context of blood disorders and solid tumors. This is an exciting project in collaboration with clinicians at Westmead Hospital in Sydney, and also with Researchers at Weill Cornell in NewÌýYork.
3. Single cell isolation and Single cell transcriptomics. This is our new interest. We are studying how antigen speciifc T cells change their phenotype upon antigen encounter, and how these cells further develop into protective memory cells.

Ìý