research projects

• The mission of the PROOF Centre of Excellence for the Prevention of Organ Failures is to develop preventive, diagnostic or prognostic biomarkers to fight against heart, lung and kidney failures. Some of the biomarker panels are currently being validated in an international trial. The expectation is that some of these panels will seek regulatory approval and be deployed in clinicial laboratories in 2012. I am the Chief Informatics Officer, and lead a team of statisticians and computer scientists to develop biomarkers by mining transcriptomics, proteomics, metabolomics and clinical data.  Apart from publications in the medical venues, my team has published several papers focusing on data cleansing, quality control and transformation for transcriptomics and proteomics data.

• BIN is the Business Intelligence Network funded by NSERC, IBM and SAP. Business Intelligence is the commercial term for using information within an organization to make informed decisions and to run operations effectively based on known data. As a research group, this network conducts research revolving around (i) policy and strategy management; (ii) capitalizing on document assests; (iii) adaptive data cleaning; and (iv) business-driven data integration. The network has been funded till 2014. I have been the associate director of the network. My projects within this network focus on text mining and natural language processing. Specifically, together with Giuseppe Carenini, we focus on feature extraction and conversation identification from informal documents such as emails, blogs, and meeting notes. We produce extractive and abstractive summaries of the analysis in natural language, in information visualization style, or a carefully crafted combination of the two. More details can be found in the text summarization group page and the book entitled "Methods for Mining and Summarizing Text Conversations". 

• The project on new generation tools for the assessment of nano-material effects on amphibian wildlife is a NSERC strategic grant project. Amphibian wildlife are sentinels of our environment and are used as indicators of ecosystem health. Due to their distinctive life history, they transition from aquatic to terrestrial environments and are particularly vulnerable to pollutants. Currently, the available impact assessment tools rely upon acute toxicological endpoints such as mortality. However, exposure to sublethal concentrations of deleterious substances at critical life stages can severely impact species survival. The short term objective of this project is to develop sensitive indicators   for the determination of disruption of a critical life stage of a native frog species based upon transcriptomic, proteomic and metabolomic analyses of target tissues in vivo and in vitro. In this study, we focus upon the effects of one of the most extensively used nano-particles, nanosilver, whose environmental impact via intentional and unintentional release is unknown. This project began in 2009 and will end in 2012.

• Finally, I include here the description of three Genome Canada projects in which I was heavily involved, until the projects completed in 2009. This description at least serves to provide some context to the publication section.
• The Biomarkers in Transplantation project focused on developing diagnostic and prognostic biomarkers for acute or chronic rejection of a transplanted organ. Most current methods for detecting rejection require the use of highly invasive and risky procedures, such as tissue biopsies. These expensive procedures cause both emotional and physical discomfort to the patients and their families. In this project, we found biomarkers in the blood, so that monitoring could be administered by blood tests. 

• The Application of Pharmacogenomics for Rational Chemotherapy of Lung Cancer  project focused on the identification of  DNA signatures of resistance and sensitivity of various chemotheraphy regimens of lung cancer. Based on mining data on copy number changes and transcriptomics data, we identified sensitivity or resistance signatures so that a rational selection can be conducted on an individual basis.

• The Development and Validation of CGH Arrays for Clinical Use of Cancer project focused on improving the efficacy and reducing the cost of molecular cytogenetic investigation of cancer. Our primary objective was to further develop a prototype whole genome Comparative Genomic Hybridization (CGH) array for use as a high resolution, high throughput clinical laboratory tool. My specific focuses were on the development of breakpoint detection algorithms for identifying regions of copy number gains and losses, and the detection of cancer-specific genomic alterations for research and clinical applications.

Last updated: 28/12/2011