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HPC Supporting Research in Genomic Architecture and Expression
Jack Chen is an Associate Professor in the Department of Molecular Biology and Biochemistry at Simon Fraser University, a Michael Smith Foundation for Health Research Scholar, and a Canadian Institutes of Health Research New Investigator. We chatted with Chen to learn more about how he is using WestGrid’s Bugaboo system for his research in genomic architecture and expression.
Q1: Can you describe your research project that makes use of WestGrid? What are the goals of this project?
My research group uses WestGrid facilities for a few projects, all of which involve genome analysis. The goal is to identify critical genomic differences that may underlie functional differences between various individuals or species. In one project, we aim to identify genomic differences that are responsible for the virulence of malaria parasites, which will facilitate the identification of drug targets and subsequent drug design. In another project, we aim to identify genomic differences in worms, which will be analyzed in molecular biology studies for their role in defining the adaptation of worms in different environments. This effort will shed light on worm speciation and, more importantly, the impact of environmental factors on the fitness of worms. We are also working towards the identification of genomic factors that drive the formation of cancer cells.
Q2: What long-term impacts could this research have on the way Canadians live, work or play?
Malaria parasites are no longer a major threat to Canadians, but they can emerge as a threat if our living environment deteriorates. However, malaria continues to be a major threat to lives in developing countries in Africa and Asia. Access to WestGrid facilities has enabled us to investigate this disease as well as others that have an effect on human life. This includes a collaborative project involving liver cancer genomics research.
Q3: How important is the WestGrid infrastructure to your research?
WestGrid is critical to our research on genomics, as thevolume of genomic sequences is large, and beyond the power of normal computers or computer clusters to process. We canno longer host, manage, or analyze genomics data using small lab computer clusters. Additionally, our access to WestGridresources has enabled us to expand the scope of our research and initiate collaborative work with scientists in China.
Q4: What drew you to this field of research?
Genomics is an interesting and dynamic field. It has the potential to solve major puzzles in biology and medicine.
Q5: What do you find to be the most exciting part of your work?
My work has a dynamic and unpredictable nature, as well as the chance to have an important impact on medicine.