Uncovering hidden genomic features using computational approaches
Open Access
- Author:
- Chung, Wen-Yu
- Graduate Program:
- Computer Science and Engineering
- Degree:
- Doctor of Philosophy
- Document Type:
- Dissertation
- Date of Defense:
- February 25, 2009
- Committee Members:
- Webb Colby Miller, Dissertation Advisor/Co-Advisor
Webb Colby Miller, Committee Chair/Co-Chair
Anton Nekrutenko, Committee Member
Raj Acharya, Committee Member
Padma Raghavan, Committee Member
Reka Z Albert, Committee Member - Keywords:
- Computational Biology
Bioinformatics
Systems Biology
Molecular Evolution - Abstract:
- Modern genetic studies are heavily dependent on analyses of whole genome sequences that have only become available in the past decade. Technologies such as microarrays and next-generation sequencing can associate quantitive expression patterns of genes to their genomic sequences and allow the study of changes at the genome-wide level or the comparison of multiple genomes. Sequences plus expression information allow us to capture an extensive and realistic overview on any given genome. Novel mathematical and computational methods are essential for managing and mining information from these large-scale data sets. I have undertaken three projects that try to answer the following biological questions using computational approaches: (1) how do duplicate genes diverge in a co-expression network? (2) how many vertebrate genes are there with alternative open reading frames? (3) how can we delineate whole genome expression patterns using new sequencing technology? Within each project, I have developed computational methods and applied these to targeted data sets demonstrating the feasibility and power of these new bioinformatic approaches and addressing questions of biological significance.