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Some of the material in is restricted to members of the community. By logging in, you may be able to gain additional access to certain collections or items. If you have questions about access or logging in, please use the form on the Contact Page.
One of the central goals of evolutionary biology is to understand the evolutionary relationships among organisms by constructing phylogenetic estimates, commonly known as evolutionary trees. The accuracy of phylogenetic estimates can be...
The primary goal of this project was to produce a molecular phylogeny for the sub-family of goby fish Oxudercinae, known as mudskippers. Molecular study of this group, combined with morphological data, could help develop an analogous...
Next generation sequencing can rapidly analyze entire genomes in just hours. However, due to the nature of the sequencing process, errors may arise which limit the accuracy of the reads obtained. Luckily, modern sequencing technologies...
Scientists have used computers to model a plethora of systems since the rise of the computer age. The most common use of modeling is to analyze an existing system. With a complete model of an existing system the parameters can be changed...
Utilizing high throughput gene expression data stored in public archives not only saves research time and cost but also enhances the power of its statistical support. However, gene expression profiling data can be obtained from many...
Controlling spatial-temporal gene expression patterns is a fundamental task for maize growth and development. With the emergence of massively parallel sequencing, genome-wide expression data production has reached an unprecedented level....
Over the past decade, the technologies used to obtain sequencing data from biological tissues have significantly improved. This has resulted in a marked increase in the ability of biological researchers to collect unprecedented...
The DNA in the eukaryotic genome is wrapped in 147--bp segments around an octamer of histone proteins to form the fundamental subunit of chromatin, the nucleosome. Nucleosomes regulate the access of proteins to DNA, thus regulating...
Background: Genomic and epigenomic data analyses has been a popular research area in the 21st century. Common research problems include detecting differentially expressed genes between groups, clustering and classification using genomic...
Over 232, 000 women will be diagnosed with breast cancer in 2014 in the United States, and approximately 40, 000 women will die from this disease. Similarly, it is estimated that 230, 000 men will be diagnosed with prostate cancer in the...
Big data has brought both opportunities and challenges to our research community. Complex models can be built with large volumes of data researchers have never had access before. In this study we explore the structure learning of...
We present two studies incorporating existing biological knowledge into differential gene expression analysis that attempt to place the results within a broader biological context. The studies investigate breast cancer health disparity...
In the United States approximately 17, 000 new spinal cord injury cases occur annually. Even with timely medical interventions, the primary injury is often exacerbated by a period of inflammation and pathological vascular changes that...
Work is presented from two projects, each involving an application of machine learning to precision medicine. The first project was for the Document Triage Task of the BioCreative VI Precision Medicine Track. Teams were asked to build...
Alzheimer’s disease is a progressive neurodegenerative disorder and the most common form of dementia. Like many neurological disorders, Alzheimer’s disease has a sex-biased epidemiological profile, affecting approximately twice as many...
Manual Nuclear Magnetic Resonance (NMR) spectral analysis of proteins is a time intensive effort with methods often specific to each analysis. The method described in this thesis automates the resonance assignment of protein side chains...
Excluding skin cancers, prostate cancer is the most frequently diagnosed cancer in American men. The American Cancer Society estimated 220, 800 new prostate cancer cases would be diagnosed in 2015. Prostate cancer is also the second...
High throughput sequencing data are rich in information and contain many off-target sequences (reads) that are often ignored but may be biologically relevant. Seed extension, a combination of reference and de novo based assembly methods, ...
This dissertation consists of three projects in two research areas: 1) modeling of temporal point process (with one project) and 2) protein design in computational structural biology (with two projects). My research work in these three...
Major hallmarks of cancer include metastasis and evading the immune system. Despite cutting edge treatments developed in an era of extensive cancer research, immunotherapy has not been proven efficient enough in solid tumors, and...
Improving the Accuracy of 3D Chromosome Structure Inference and Analyzing the Organization of Genome in Early Embryogenesis Using Single Cell Hi-C Data
This dissertation summarizes my graduate work on the structure and organization of mouse genome during preimplantation development. My research is divided into three different areas, which I will discuss in turn. To begin, I will discuss...
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