The research question address in this study is, “To what extent will the use of hands-on activities for introducing concepts in bioinformatics promote student engagement in after-school STEM club settings?” It is hypothesized that high school students' engagement in hands-on bioinformatics activities promotes their awareness of, and interest in, STEM...
Gene regulation is a complex mechanism that controls the spatial and temporal expression of genes in a living cell. My dissertation studies focus on two problems. First, tissue-specific gene expression prediction from DNA sequence and chromatin state, and second, the accurate discovery of small over-represented regulatory circuits in gene regulatory...
Rhizopogon vesiculosus is a common ectomycorrhizal (EM) symbiont of Pseudotusga menziesii (Douglas-fir) in the coast range of the Pacific Northwest. The species has been studied for its systematics, genet size, population structure, and competitive ability in several field and experimental studies. This thesis seeks to provide a more thorough characterization...
Hop (Humulus lupulus L. var lupulus) is a plant of great cultural significance, used as a medicinal herb for thousands of years, and for flavor and as a preservative in brewing beer. Studies of the medicinal effects of the unique compounds produced by hop have led to interest from the...
The computational identification of gene Transcription Start Sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are...
Within the past several years the technology of high-throughput sequencing has transformed the study of biology by offering unprecedented access to life's fundamental building block, DNA. With this transformation's potential a host of brand-new challenges have emerged, many of which lend themselves to being solved through computational methods. From de...