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Browsing Electronic Theses and Dissertations by Duke Department

Browsing Electronic Theses and Dissertations by Duke Department "Computational Biology and Bioinformatics"

Now showing items 1-20 of 27

Analysis and Error Correction in Structures of Macromolecular Interiors and Interfaces

Headd, Jeffrey John (2009)

As of late 2009, the Protein Data Bank (PDB) has grown to contain over 70,000 models. This recent increase in the amount of structural data allows for more extensive explication of the governing principles of macromolecular ...
Automated Microscopy and High Throughput Image Analysis in Arabidopsis and Drosophila

Mace, Daniel L. (2009)

Development of a single cell into an adult organism is accomplished through an elaborate and complex cascade of spatiotemporal gene expression. While methods exist for capturing spatiotemporal expression patterns---in ...
A Bayesian Hierarchical Model with SNP-level Functional Priors Applied to a Pathway-wide Association Study.

Huang, Weizi (2010)

Tremendous effort has been put into study of the etiology of complexdiseases including the breast cancer, type 2 diabetes,cardiovascular diseases, and prostate cancers. Despite large numbers of reported ...
Characterization of Gene-by-Age Interaction and Gene-by-Gene Interaction In Coronary Artery Disease

Zhao, Yi (2012)

The success of genome-wide association studies (GWAS) has been limited by missing heritability and lack of biological relevance of identified variants. We sought to address these issues by characterizing interaction ...
Characterization of Gene Interaction and Assessment of Ld Matrix Measures for the Analysis of Biological Pathway Association

Crosslin, David Russell (2009)

Leukotrienes are arachidonic acid derivatives long known for their inflammatory properties and their involvement with a number of human diseases, most notably asthma. Recently, leukotriene-based inflammation has also ...
Chromatin Determinants of the Eukaryotic DNA Replication Program

Eaton, Matthew Lucas (2011)

The accurate and timely replication of eukaryotic DNA during S-phase is of critical importance for the cell and for the inheritance of genetic information. Missteps in the replication program can activate cell cycle ...
Computational Methods For Functional Motif Identification and Approximate Dimension Reduction in Genomic Data

Georgiev, Stoyan (2011)

Uncovering the DNA regulatory logic in complex organisms has been one of the important goals of modern biology in the post-genomic era. The sequencing of multiple genomes in combination with the advent of DNA microarrays ...
Computational Methods for Investigating Dendritic Cell Biology

de Oliveira Sales, Ana Paula (2011)

The immune system is constantly faced with the daunting task of protecting the host from a large number of ever-evolving pathogens. In vertebrates, the immune response results from the interplay of two cellular systems: ...
Computational Methods to Study Diversification in Pathogens, and Invertebrate and Vertebrate Immune Systems

Munshaw, Supriya Shaunak (2010)

Pathogens and host immune systems use strikingly similar methods of diversification. Mechanisms such as point mutations and recombination help pathogens escape the host immune system and similar mechanisms help the host ...
A Computational Synthesis of Genes, Behavior, and Evolution Provides Insights into the Molecular Basis of Vocal Learning

Pfenning, Andreas R. (2012)

Vocal learning is the ability modify vocal output based on auditory input and is the basis of human speech acquisition. It is shared by few distantly related bird and mammal orders, and is thus very likely to be an ...
Dissecting the Genetic Basis of Convergent Complex Traits Based on Molecular Homoplasy

Wang, Rui (2011)

The goal of my thesis is to understand the genetics of a complex behavioral trait, vocal learning, which serves as a critical substrate for human spoken language. With the available genomes of 23 mammals, I developed a ...
Genome-wide Analysis of Chromatin Structure across Diverse Human Cell Types

Winter, Deborah R. (2013)

Chromatin structure plays an important role in gene regulation, especially in differentiating the diverse cell types in humans. In this dissertation, we analyze the nucleosome positioning and open chromatin profiles ...
The Geometry of Cancer

Guinney, Justin (2009)

Cancer is a complex, multifaceted disease that operates through dynamic changes in the genome. Cancer is best understood through the process that generates it -- random mutations operated on by natural selection -- and ...
Imputation of Microsatellite Markers With Tag SNPs

Knodt, Annchen (2012)

Of the two most common forms of genetic variation in the human genome, Single Nucleotide Polymorphisms (SNPs) and Variable Number Tandem Repeat Polymorphisms (VNTRs), SNPs are much more easily and inexpensively assayed ...
Integrative Genomic Modeling of Complex Traits using Pathway Analysis

Bennett, Brian D. (2012)

Understanding the root molecular causes driving complex traits is a fundamental challenge in genomics and genetics. Numerous studies have used variation in gene expression to understand complex traits, but the underlying ...
Localized Correlation Analysis and Genetic Association with Cardiovascular Disease

Ou, Chern-Han (2010)

Variations in gene expression are potential risk factors for atherosclerosis, which is one of the most common forms of cardiovascular disease. We performed a localized Pearson correlation test in 372 individuals from ...
Mechanistic and Genetic Biases in Human Immunoglobulin Heavy Chain Development

Volpe, Joseph M (2008-04-23)

Broadly neutralizing antibodies against HIV are rare; most patients never develop them at detectable levels. The discovery of four such antibodies therefore warrants research into their origins and their presumed unique ...
Mechanistic Modeling and Experiments on Cell Fate Specification in the Sea Urchin Embryo

Cheng, Xianrui (2012)

During embryogenesis, a single zygote gives rise to a multicellular embryo with distinct spatial territories marked by differential gene expression. How is this patterning process organized? How robust is this function ...
MicroRNA Target Prediction via Duplex Formation Features and Direct Binding Evidence

Lekprasert, Parawee (2012)

MicroRNAs (miRNAs) are small RNAs that have important roles in post-transcriptional gene regulation in a wide range of species. This regulation is controlled by having miRNAs directly bind to a target messenger RNA ...
Modeling Cancer Progression on the Pathway Level

Edelman, Elena Jane (2008-12-11)

Over the past several decades, many genes have been discovered that govern important functions in the development of a variety of diﬀerent cancers. However, biological insight from the list of genes is still limited and ...