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Pathogenic bacteria, which are the causative agents for anthrax, plague, and tularemia, to name a few, are important from both forensic and pathological aspects. Although a number of DNA sequences have been generated and a great deal of additional information has been gleaned, there are no comprehensive data repositories from which to draw global conclusions. My research at TGen focuses on developing computational tools to create large knowledge bases for these data and to assist in discovery of new knowledge about the identity, distribution, and pathology of these organisms through the development of relevance networks.
Rapid identification is critical in determining whether outbreaks of these diseases are natural or caused by biological weapons. I am developing tools to quickly identify and discriminate between individual strains of bacteria using a limited subset of single-nucleotide polymorphisms (SNPs), which can be developed into an assay for rapid identification. I am also studying the incidence, distribution and function of long, non-tandem, repeating DNA subunits in anthrax, plague and tularemia bacterial strains. For the development of the pathogenic bacterial knowledge bases, I am developing the databases on our super-computer cluster, residing on the campus of Arizona State University, as well as web-scavenging robots, in conjunction with Dr. Curtis Jamison of George Mason University, to scour the web for relevant resources and automatically populate the databases as necessary.
As a future direction, I am interested in elucidating the structure and function of non-coding regions of DNA, both within and between genes, in eukaryotic genomes, with a special emphasis on conserved regions among taxa at different levels.
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