Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2002. / Includes bibliographical references (leaves 175-187). Also available in electronic version. Access restricted to campus users.

Thesis (M. Phil.)--University of Hong Kong, 2009. / Includes bibliographical references (leaves 155-169). Also available in print.

Thesis (M. Sc.)--York University,1998. Graduate Program in Biology. / Typescript. Includes bibliographical references (leaves 76-90). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pMQ27358.

Thesis (Ph. D.)--University of Texas at Austin, 2001. / Vita. Includes bibliographical references (leaves 133-166). Available also in a digital version from Dissertation Abstracts.

Thesis (M. Phil.)--University of Hong Kong, 2002. / Includes bibliographical references (leaves 88-110).

Thesis (Ph. D.)--University of Oregon, 2002. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 210-219). Also available for download via the World Wide Web; free to University of Oregon users.

Not available / text

Not available / text

I have pursued a breadth of research that explored the functional genomic study of eukaryotic transcriptional regulation. I have utilized two model organisms, many experimental methodologies, and have developed a suite of computational resources to study the interaction of transcription factors with regulated targets. In Saccharomyces cerevisiae I worked with my collaborator Dr. Zhanzhi (Mike) Hu to characterize the whole-genome transcriptional response of 263 individual transcription factor deletions. We utilized a sophisticated error model and directed-weighted graphs to model a network of high-confidence targets for each transcription factor profiled. We then used regulatory epistasis to elucidate the true set of primary KO-regulated targets and construct a functional transcriptional regulatory network. This network was analyzed for ontological and sequence motif enrichment in order to gain insight into the biological functions represented by transcription factors studied. Functional validation was performed to evaluate the probability of novel functional characterizations. Significant insight was gained from this study with regard to the nature of regulatory cascades and the inability for DNA binding events to predict regulation. This set of analysis was performed with a novel bioinformatic server called ArrayPlex. ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics including microarray data storage, quality assessments, data visualization, gene annotation retrieval, statistical tests, genomic sequence retrieval and motif analysis. It uses a client-server architecture based on open source components, provides graphical, command-line, as well as programmatic access to all needed resources, and is extensible by virtue of a documented API. Using many of the techniques and computational resources developed, I pursued the study of microRNA transcriptional abundance and targeting in H. sapiens cell cultures. Utilizing custom-fabricated microarrays, I measured the whole-genome response of both mRNAs and microRNAs under serum stimulation, c-Myc overexpression, and c-Myc siRNA-mediated knockdown. I then characterized the regulatory interactions between the sets of regulated microRNAs and coordinately regulated transcription factors. Using analytical methods sensitive to regulatory directionality of both populations I was able to determine high-confidence relationships between transcription factors and regulated microRNAs as well as microRNAs and regulated gene targets.

published_or_final_version / abstract / toc / Zoology / Doctoral / Doctor of Philosophy