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  • 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
    Full Text:
    degree of Doctor of Philosophy in Molecular and Cellular Biology presented on January 5, 2018. Title

  • Investigating Transcriptional Control of Specialized Gene Expression in Plants

    Creator:
    Fraser, Valerie N.
    Abstract:
    Specialized or secondary metabolism is a collection of pathways and small molecules that, while beneficial to an organism, are not strictly necessary for survival. Plants use secondary metabolites to, among other things, attract pollinators, defend against biotic and abiotic stressors, and form symbioses. Natural products from plants have seen an...
    Resource Type:
    Dissertation
    Full Text:
    . Fraser for the degree of Doctor of Philosophy in Molecular and Cellular Biology presented on August 2

  • Investigating the Mechanisms for the Effects of Nitrate Treatment on Exercise Performance and Energy Metabolism

    Creator:
    Keller, Rosa M.
    Abstract:
    Dietary nitrate (NO3-), consumed primarily from leafy green and root vegetables, lowers blood pressure, improves vascular function and aerobic exercise performance. This performance-enhancing effect of nitrate supplementation is largely attributed to the increased bioavailability of the signaling molecule, nitric oxide (NO). Nitric oxide is a ubiquitous free radical signaling molecule...
    Resource Type:
    Dissertation
    Full Text:
    and tricarboxylic acid cycle intermediates, non-esterified fatty acids, lactate, and ketone bodies

  • Predicting Protein-Protein Interactions in a Cnidarian Model System

    Creator:
    Gregory, Dylan B.
    Abstract:
    The symbiotic sea anemone Exaiptasia diaphana (Aiptasia) is a model organism used to better understand cnidarian-algal symbiosis and coral bleaching (dysbiosis). Many biological processes are hypothesized to be involved in coral dysbiosis, and the innate immunity is a key area of interest. Rab proteins are small proteins with GTPase domains,...
    Resource Type:
    Honors College Thesis
    Full Text:
    regulate symbiotic interactions in Aiptasia. Since molecular and biochemical assays can be resource

  • Impacts of Reduced Tillage and Disturbance on Soil Health and Microbial Community Dynamics in Grass Seed Cropping Systems

    Creator:
    Zamora, Cesar G.
    Abstract:
    In Oregon perennial and annual grass seed cropping systems conservation management practices and their impacts on soil health and soil microbial community is not well understood. There is strong motivation to employ conservation tillage and other conservation practices to curb atmospheric carbon levels and improve soil health. However, the few...
    Resource Type:
    Masters Thesis
    Full Text:
    microbial communities. Using molecular based assays and measuring soil health indicators we aimed to

  • Machine Learning for Precision Medicine: Application to Cancer Chemotherapy Response Prediction and Wound Healing Status Assessment

    Creator:
    Wei, Qi
    Abstract:
    Ph.D. candidate Qi Wei's thesis consists of two projects: Chemotherapy Project: a study based on the research paper "Predicting chemotherapy response of various cancer types using a variational auto-encoder approach" submitted to the bioRxiv preprint archive and accepted by the BMC bioinformatics; and Wound Monitor Project: implementing and assessing analytics...
    Resource Type:
    Dissertation
    Full Text:
    the tumor’s molecular profile [68, 22, 37, 91, 47, 35]. Therefore, gene expression data of tumor

  • Toward a flexible and accurate approach to null network sampling

    Creator:
    Bright, Zachary A.
    Abstract:
    Null networks are a type of random graph that is favored for the analysis of a wide variety of real-world networks, including gene-regulatory networks, food webs, and species co-occurrence matrices. As a hypothesis-generating tool, null networks are invaluable because they can reveal network motifs and unusual large-scale properties of networks...
    Resource Type:
    Masters Thesis