Evolutionary dynamics of infectious diseases, Bioinformatics, Mathematical models, Statistical inference of biologically relevant quantities.
Field of Research (FoR)
I am a theoretical physicist with a PhD in Theoretical Biology and Biophysics (Humboldt Univeristy of Berlin, Germany). 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 human viral infections. This research contributes to better understanding of transmission...view more
I am a theoretical physicist with a PhD in Theoretical Biology and Biophysics (Humboldt Univeristy of Berlin, Germany). 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 human viral infections. This research contributes to better understanding of transmission of viral infections, immune responses against hepatitis viruses and influenza, as well as in developing 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
Please visit also these School of Medical Sciences pages:
I am interested in Evolutionary dynamics of infectious diseases, Bioinformatics, Mathematical models, Statistical inference of biologically relevant quantities.
In our lab we are always interested in new talented PhD and Master students. Please email me if interested.
- Next generation Sequencing Our group is very much interested in Next Generation Sequencing (NGS) applied to HCV viral dynamics. This technique allows the detection of rare species of the virus and therefore allows a detailed quantification of viral evolution. We are using NGS to also detect escape mutants that avoid immune responses causing chronic infections.
- 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.
- Bioinformatics software Please, contact me for more information and for few computer programs that I developed with my collaborators.
- Hepatitis C virus and its evolutionary dynamics I am interested in modeling of Hepatitis C virus dynamics. HCV is a rapidly mutating virus with fascinating dynamics. It can evolve very quickly within a host and escape immune responses. My interest is in the population dynamics and epidemiology of HCV infections and in understanding the role of host heterogeneity in driving viral evolution. For instance, I am working on the role of MHC frequency distribution and its effect in determining the probability of escape mutants.
- T cell dynamics and Antigen presentation I am interested in the mechanisms behind antigen processing and presentation in the context of MHC class I response. I am working on a project in collaboration with Ass Prof Katherine Kedzierska (Peter Doherty Institute in Melbourne) on the dynamical evolution of immunodominance in T cell responses against influenza virus.
- T cell trafficking in the liver We are also interested in T cell trafficking and in the T cell driven immune response in the liver. This project is in collaboration with Dr Patrick Bertolino and Dr David Bowen at the Centenary Institute (University of Sydney).
- Statistical analyses of hepatitis C virus in injecting drug users Epidemiological and statistical analyses of a large cohort of HCV infected subjects in NSW prisons, the Hepatitis C Incidence and Transmission Study (HITS). Currently, I am responsible for the statistical analyses of a large epidemiological, virological and immunological dataset on early evolution of the virus in these subjects, see my publications.
- Molecular Epidemiology A great application of mathematical models of infectious diseases is the study of transmission dynamics of complex pathogens, such as bacteria. Given their complex genomes, it is often hard to study directly changes in the DNA sequence of these organisms. Therefore scientists have come up with few typing scheme.
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
as a theoretical biologists I suffer from a sort of disease, which is to be interested in lots of things. Genarally I am deeply involved in understanding immune responses against viral infections. 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.
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.