Evolutionary dynamics of infectious diseases, Bioinformatics, Mathematical models, Statistical inference of biologically relevant quantities.
Fields of Research (FoR)Infectious Diseases, Immunology, Biological Mathematics, Evolutionary Biology, Bioinformatics, Biostatistics
I was trained as theoretical physicist (Masters), theoretical biologist (PhD 2006 from the Humboldt University of Berlin (Germany)). My research interests include adaptive immune responses against pathogen infections, computational models for studying host-pathogen interactions, and bioinformatics analysis of high throughput next generation sequencing data.Research is one of the things I love the most, along with teaching and sports. Our...view more
I was trained as theoretical physicist (Masters), theoretical biologist (PhD 2006 from the Humboldt University of Berlin (Germany)). My research interests include adaptive immune responses against pathogen infections, computational models for studying host-pathogen interactions, and bioinformatics analysis of high throughput next generation sequencing data.Research is one of the things I love the most, along with teaching and sports. Our research group in Systems Medicine, is an interdisciplinary team with skills in Immunology, Mathematical Modelling, Statistics and Bioinformatics to study immune responses, specifically T cells. This research contributes to better understanding of immune protection against viral infections, but also of immunological tolerance and how autoimmunity arise.
In my interdisciplinary team we also develop bioinformatics and statistical tools for analysis of genomics and immunology high throughput data. The rapid advancement in high-throughput technologies, such as single cell analysis and next generation sequencing, has lead to complex large data-sets, which demand for quantitative skills to interpret data. We have established a unique combination of these new methodologies and systems analyses to address key questions that classical immune-virology experimental approaches alone could not resolve. I have developed novel computational models to analysis viral genomes using next-generation deep sequencing, which led to novel insights on HCV infections, as well as on the translational application of these technologies in terms of monitoring outbreak, drug resistance
I have experience in applying mathematical modelling statistics and bioinformatics to understand infectious diseases, focussing on transmission dynamics of drug resistant mycobacterium tuberculosis, and the transmission of hepatitis C virus among injecting drug users. I made several contributions in how HCV infect a new host and the role of T cell mediated responses using next generation sequencing technologies, flow cytometry and statistical modelling. More recently, he has moved into single cell genomics and systems immunology approaches to understand T cell dynamics.
Please visit also my personal web page (LINK to be provided)
- 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.
- Bioinformatics software We have experience in software tools to study pathogen genomics, immune cells and we also develop workflows for integrated analyses across genomic, immunological and clinical data sets.
- T cell responses in influenza virus We 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
- Analysis of single cell multiomics in the context of Coeliac disease. This project is a collaboration with Prof Chris Goodnow's team at the Garvan Institute.
- 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 New York.
- 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.
Occasions where my research has been picked up by the media:
- Scientists warn of drug-resistant TB, Sydney Morning Herald, August 2009
- New TB strains a spreading danger, The Canberra Times, August 2009
- New drug-resistant TB strains could become widespread says new study, UNSW Science News, August 2009
My Research Activities
My research focusses on understanding Immune responses and specifically T cells in the context of viral infections, but also in autoimmune conditions where these responses go "rogue" and cause harm to our body and mind.
As a theoretical physicist by training, I utilise an interdisciplinary approach to understand these responses. In particular, a major goal in my research is to develop novel technologies and computational biology methdos that can be applied to asnwer key questions of how adaptive immune responses defeat viral infections and how these natural mechansims can be utilised to modern immunotherapies.
My Research Supervision
Areas of supervision
Students: Honours, ILP, MSc, PhD, Post Doctoral Students
We are always open to receive applications for PHD and Honours students. The areas we cover are both computational and experimental.
If you are passionate in an of these disciplines, such as Bioinformatics, Statistics, Data Science, but also Immunology and Genomics please email me
ORCID as entered in ROShttps://orcid.org/0000-0003-0666-6324
We are an interdisciplinary group interested in understanding how viruses evolve under the host immune response.
We take advantage of next generation sequencing technologies to study viral populations including low frequency variants.
Also, we are interested in studying immune escape variants.
In our computational analyses we take advantage of experimental data generated in our lab.
Project 1: Mathematical modelling of T cell trafficking in the liver
This project aims to design a mathematical model to study the trafficking of CD8 T cells in the full body of mice in the absence or presence of antigen.
By taking advantage of ad hoc experimental data we aim at estimating key parameters that regulate T cell trafficking and the subsequent T cell response against antigens presented in lymphoid and non-lymphoid organs. In particular, we are interested in the liver, as this is the only non-lymphoid organ capable of antigen presentation. …