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

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dc.contributor.advisor Hajibabaei, Mehrdad
dc.contributor.advisor Golding, Brian Nazari, Siavash 2018-09-05T20:27:08Z 2019-08-21T05:00:27Z 2018-08-31 2018-08-21 2018-09-05
dc.description.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. en_US
dc.language.iso en en_US
dc.rights Attribution-NonCommercial-NoDerivs 2.5 Canada *
dc.rights.uri *
dc.subject Research Subject Categories::NATURAL SCIENCES::Chemistry::Theoretical chemistry::Bioinformatics en_US
dc.subject Research Subject Categories::TECHNOLOGY::Information technology::Computer science::Computer science en_US
dc.subject Research Subject Categories::NATURAL SCIENCES::Chemistry::Biochemistry::Functional genomics en_US
dc.title A Bioinformatic Framework to Assess the Genomic Response of Species to Environmental Toxins en_US
dc.type Thesis en_US Bioinformatics en_US Master of Science en_US Department of Integrative Biology en_US
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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