This study investigates methods of multivariate regression analysis and their applications to biological data. It provides an overview of methods of reduced rank regression and sparse multivariate regression, including their motivations, methods, and applications. It also implements a form of sparse regression known as Regularized Multivariate Regression for Identifying Master...
Agent-based models (ABM) are widely used in network data analysis, and due to their simple structures and sophisticated outcomes, they serve as good tools in understanding the dynamics in networks. In this thesis, we develop an agent-based dynamic network model, and show that it can replicate the expected degree distribution...
In many scientific settings, investigators are interested in the effect of a new treatment. To have a point of comparison data is collected from patients before treatment groups are assigned. When seeking to test the presence of a significant treatment effect it may be unclear how baseline measurements should be...
Diatoms play a major role in ocean biogeochemical cycles and are important tools in bioengineering for natural products and nanotechnology. Diatoms and other algae growing at varying resource-limited growth rates allocate carbon to different metabolic pathways to optimize growth; however, the molecular mechanisms controlling these pathway gating strategies are not...
Hazelnut is one of the most important nuts in worldwide production and the European hazelnut (Corylus avellana L.) is the most economically important of the 11 recognized hazelnut species. Development of new cultivars is continuous, with emphasis on better nut quality, high yield and disease resistance. Hazelnuts are highly heterozygous,...
Copper is the most common ingredient in waterborne preservatives and provides excellent activity against most fungi and insects. However, issues associated with copper migration from treated wood have created increasing concerns about potential risks to non-target organisms in surrounding environments, especially those in sensitive aquatic environments. Various Best Management Practices...
In areas such as spatial analysis and time series analysis, it is essential to understand and quantify spatial or temporal heterogeneity. In this dissertation, we focus on a spatially varying coefficient model, in which spatial heterogeneity is accommodated by allowing the regression coefficients to vary in a given spatial domain....
Differential expression (DE) analysis is a key task in gene expression study, because it uncovers the association between expression levels of a gene and the covariates of interest. This dissertation pertains to two particular aspects of DE analysis—identifying stably expressed genes for count normalization and accounting for correlation between DE...
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...
Coniferous trees are a major North American crop that has been intensively managed for its commercial value, while also serving as critical habitat for abundant wildlife and as carbon sinks. Having diverse functions, North American temperate coniferous forests have become a research hotspot for numerous scientific studies aiming to integrate...