Index Catalog // ScholarsArchive@OSU

Bioinformatics applied to freshwater cyanobacterial blooms and cyanophage

Creator:: Schwartz, Andrew D.
Abstract:: Freshwater cyanobacterial blooms are a nuisance and health threat in the Pacific Northwest. The accepted methods of characterizing these blooms by microscopic cell counts cannot differentiate between toxic and non-toxic strains of the cyanobacterium Microcystis. Also, there is limited understanding of freshwater cyanophage that may control bloom dynamics. In order...
Resource Type:: Masters Thesis
Full Text:: : BIOINFORMATICS APPLIED TO FRESHWATER CYANOBACTERIAL BLOOMS AND CYANOPHAGE! Abstract approved: Theo W

Genome Organization in the Ectomycorrhizal Truffle Rhizopogon vesiculosus

Creator:: Lu, Dabao Sun
Abstract:: 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...
Resource Type:: Masters Thesis
Full Text:: to provide a more thorough characterization of the genome of R. vesiculosus using bioinformatic

From fossils to phylogenies

Creator:: Goodwin, Baylee N., Besser, August D., and Ramsey, Stephen A.
Abstract:: 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...
Resource Type:: Learning Object and Presentation
Full Text:: . What is Bioinformatics? Why is it important? Bioinformatics is a field of science that blends biology

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

Creator:: Tilton, Susan C., Tal, Tamara L., Scroggins, Sheena M., Franzosa, Jill A., Peterson, Elena S., Tanguay, Robert L., and Waters, Katrina M.
Abstract:: Background: MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput...
Resource Type:: Article

Prediction of gene transcription start sites and initiation patterns from DNA sequence content

Creator:: Morton, Taj H.
Abstract:: 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...
Resource Type:: Masters Thesis

Walking tree heuristics for biological string alignment, gene location, and phylogenies

Creator:: Oregon State University. Dept. of Computer Science, Cull, Paul, 1943-, Holloway, James Lee, and Cavener, Jeffrey Douglas
Abstract:: Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids (proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and aligning strings brings out their shared characteristics. Although string matching is well-understood in the edit-distance model, biological strings...
Resource Type:: Research Paper

Identification and Functional Characterization of Genes that Regulate Biomass Production, Floral Development, and Leaf Senescence in Populus Species using Genetic Engineering and Bioinformatics Tools

Creator:: Lu, Haiwei
Abstract:: This dissertation is comprised of four studies on different elements of Populus biotechnology and genomic science: 1) growth improvement by recombinant DNA (rDNA) modification of gibberellin (GA) metabolism; 2) gene editing using zinc-finger nucleases (ZFNs); 3) induction of floral sterility by RNA interference (RNAi) of AGAMOUS (AG) gene homologs; and...
Resource Type:: Dissertation
Full Text:: , and Leaf Senescence in Populus Species using Genetic Engineering and Bioinformatics Tools

Computational Approaches for Understanding Combinatorial Gene Regulation

Creator:: Ansariola, Mitra
Abstract:: 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...
Resource Type:: Dissertation

Algorithms for massive biological datasets

Creator:: Bryant, Douglas W. (Douglas Wesley)
Abstract:: 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...
Resource Type:: Dissertation

Statistical analysis of RNA sequencing count data

Creator:: Mi, Gu
Abstract:: RNA-Sequencing (RNA-Seq) has rapidly become the de facto technique in transcriptome studies. However, established statistical methods for analyzing experimental and observational microarray studies need to be revised or completely re-invented to accommodate RNA-Seq data's unique characteristics. In this dissertation, we focus on statistical analyses performed at two particular stages in...
Resource Type:: Dissertation
Full Text:: collaborators at the Center for Genome Research and Biocomputing (CGRB) and members of the Bioinformatics Users

ScholarsArchive@OSU

Bioinformatics applied to freshwater cyanobacterial blooms and cyanophage

Genome Organization in the Ectomycorrhizal Truffle Rhizopogon vesiculosus

From fossils to phylogenies

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

Prediction of gene transcription start sites and initiation patterns from DNA sequence content

Walking tree heuristics for biological string alignment, gene location, and phylogenies

Identification and Functional Characterization of Genes that Regulate Biomass Production, Floral Development, and Leaf Senescence in Populus Species using Genetic Engineering and Bioinformatics Tools

Computational Approaches for Understanding Combinatorial Gene Regulation

Algorithms for massive biological datasets

Statistical analysis of RNA sequencing count data

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