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Inference of epigenetic subnetworks and expression-based analysis using a breast cancer dataset
DownloadFall 2018
Changes in gene expression have been thought to play a crucial role in various types of cancer. With the advance of high-throughput experimental techniques, many genome-wide studies are underway to analyze underlying mechanisms that may drive the changes in gene expression. It has been observed...
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Investigation of Causal Mutations in Livestock and Companion Animals Using Whole-Genome Sequencing (WGS) and Bioinformatics
DownloadSpring 2024
In this thesis project, three studies were conducted, aimed at identifying the causal variants responsible for phenotypic/genotypic sex discordance in cattle, copper toxicosis in Dalmatian dogs, and low fertility/infertility in cattle. In all three studies, whole-genome sequencing (WGS) and...
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2003
Greiner, Russell, Wishart, David, Eisner, Roman, Lu, Z., Lu, Paul, Macdonell, Cam, Poulin, B., Szafron, Duane, Anvik, J.
Technical report TR03-14. Identifying the destination or localization of proteins is key to understanding their function and facilitating their purification. A number of existing computational prediction methods are based on sequence analysis. However, these methods are limited in scope, accuracy...
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Fall 2016
The field of biomedicine is reeling from “information overload”. Indeed, biomedical researchers find it almost impossible to stay current with published literature due to the vast amounts of data being generated and published. As a result, they are turning to text mining. Over the past two...
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Single-nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle-associated symbiotic fungus, using whole-genome resequencing
Download2014-01-01
Ojeda, Dario I., Dhillon, Braham, Tsui, Clement K. M., Hamelin, Richard C.
Single-nucleotide polymorphisms (SNPs) are rapidly becoming the standard markers in population genomics studies; however, their use in nonmodel organisms is limited due to the lack of cost-effective approaches to uncover genome-wide variation, and the large number of individuals needed in the...
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Fall 2015
Researchers conduct association studies to discover biomarkers in order to gain new biological insight on complex diseases and phenotypes. Although most researchers have intuitions about what defines a biomarker and how to assess the results of an association study, there is neither a formal...
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2013
Abou-Moustafa, Karim T., Kozyrskyj, Anita, Guttman, David, Scott, James, Yasui, Yutaka
Entropy measures of probability distributions are widely used measures in ecology, biology, genetics, and in other fields, to quantify species diversity of a community. Unfortunately, entropy–based diversity indices, or diversity indices for short, suffer from three problems. First, when...