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A Bioinformatic Framework to Assess the Genomic Response of Species to Environmental Toxins

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Title: A Bioinformatic Framework to Assess the Genomic Response of Species to Environmental Toxins
Author: Nazari, Siavash
Department: Department of Integrative Biology
Program: Bioinformatics
Advisor: Hajibabaei, MehrdadGolding, Brian
Abstract: The current ecotoxicological methods of identifying sites of biological cannot indicate the presence of hazardous chemicals before significant environmental damage has already occurred. In this thesis, I hypothesize that essential pathways and genes are conserved across the taxa and present a bioinformatic pipeline that uses genomic data for environmental monitoring. This pipeline mines chemical-gene interaction data from publicly available databases, retrieves the corresponding protein sequences and performs homology-based searches in the genome of target organisms. Afterwards, it clusters these protein sequences to obtain groups of orthologous sequences, retrieves related biological pathways and learns a Bayesian Network to show meaningful correlations between them and input chemicals. To demonstrate this pipeline, I ran a test dataset consisting of a group of phylogenetically distant taxa on it. The shared affected pathways suggested by this pipeline correspond with findings from previous studies on the toxic effects of target chemicals.
URI: http://hdl.handle.net/10214/14263
Date: 2018-08-31
Rights: Attribution-NonCommercial-NoDerivs 2.5 Canada
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Attribution-NonCommercial-NoDerivs 2.5 Canada Except where otherwise noted, this item's license is described as Attribution-NonCommercial-NoDerivs 2.5 Canada