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Browsing by Subject "Bioinformatics"
Now showing items 1-20 of 106
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A Bayesian Model for Nucleosome Positioning Using DNase-seq Data
(2015)As fundamental structural units of the chromatin, nucleosomes are involved in virtually all aspects of genome function. Different methods have been developed to map genome-wide nucleosome positions, including MNase-seq and ... -
A Cloud-Based Infrastructure for Cancer Genomics
(2020)The advent of new genomic approaches, particularly next generation sequencing (NGS) has resulted in explosive growth of biological data. As the size of biological data keeps growing at exponential rates, new methods for ... -
A Computational Synthesis of Genes, Behavior, and Evolution Provides Insights into the Molecular Basis of Vocal Learning
(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 example ... -
A Genomic Definition of Centromeres in Complex Genomes
(2011)Centromeres, or sites of chromosomal spindle attachment during mitosis and meiosis, are non-randomly distributed in complex genomes and are largely associated with expansive, near-identical satellite DNA arrays. While the ... -
A Geometric Approach to Biomedical Time Series Analysis
(2020)Biomedical time series are non-invasive windows through which we may observe human systems. Although a vast amount of information is hidden in the medical field's growing collection of long-term, high-resolution, and multi-modal ... -
A Phylogenetic, Ecological, and Functional Characterization of Non-Photoautotrophic Bacteria in the Lichen Microbiome
(2011)Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria ... -
A Semi-Supervised Predictive Model to Link Regulatory Regions to Their Target Genes
(2015)Next generation sequencing technologies have provided us with a wealth of data profiling a diverse range of biological processes. In an effort to better understand the process of gene regulation, two predictive machine learning ... -
A Systems Level Analysis of Temperature-Dependent Sex Determination in the Red-Eared Slider Turtle Trachemys Scripta Elegans.
(2016)Sex determination is a critical biological process for all sexually reproducing animals. Despite its significance, evolution has provided a vast array of mechanisms by which sexual phenotype is determined and elaborated ... -
Application of Phylogenetic Analysis in Cancer Evolution
(2018)Cancer is a major threat to human health and results in 1 in 6 deaths globally. Despite an extraordinary amount of effort and money spent, eradication or control of advanced disease has not yet been achieved. Understanding ... -
Bayesian meta-analysis models for heterogeneous genomics data
(2013)The accumulation of high-throughput data from vast sources has drawn a lot attentions to develop methods for extracting meaningful information out of the massive data. More interesting questions arise from how to combine ... -
Bayesian Modeling for Identifying Selection in B cell Maturation
(2023)This thesis focuses on modeling the selection effects on B cell antibody mutations to identify amino acids under strong selection. Site-wise selection coefficients are parameterized by the fitnesses of amino acids. First, ... -
Bayesian modeling of microbial physiology
(2017)Microbial population growth measurements are widespread in the study of microorganisms, providing insight into areas including genetics, physiology, and engineering. The most common models of microbial population growth ... -
Bayesian Multivariate Count Models for the Analysis of Microbiome Studies
(2019)Advances in high-throughput DNA sequencing allow for rapid and affordable surveys of thousands of bacterial taxa across thousands of samples. The exploding availability of sequencing data has poised microbiota research to ... -
Bayesian Statistical Models of Cell-Cycle Progression at Single-Cell and Population Levels
(2014)Cell division is a biological process fundamental to all life. One aspect of the process that is still under investigation is whether or not cells in a lineage are correlated in their cell-cycle progression. Data on cell-cycle ... -
Bioinformatics and Molecular Approaches for the Construction of Biological Artificial Cartilage
(2018)Osteoarthritis (OA) is one of the leading causes of disability in the United States, afflicting over 27 million Americans and imposing an economic burden of more than $128 billion each year (1, 2). OA is characterized by ... -
Characterization of Gene-by-Age Interaction and Gene-by-Gene Interaction In Coronary Artery Disease
(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 among ... -
Characterization of Influenza A Virus Infection through Analysis of Intrahost Viral Evolution and Within-host Infection Dynamics
(2016)Influenza A virus is a major source of morbidity and mortality, annually resulting in over 9000 deaths in the United States alone. As a segmented, RNA virus, influenza has a high mutation rate, facilitating its evolution ... -
Characterizing Genetic Drivers of Lymphoma through High-Throughput Sequencing
(2016)The advent of next-generation sequencing, now nearing a decade in age, has enabled, among other capabilities, measurement of genome-wide sequence features at unprecedented scale and resolution. In this dissertation, I describe ... -
Chromatin Accessibility Dynamics Underlying Development and Disease
(2015)Despite a largely static DNA sequence, our genomes are incredibly malleable. Comparative studies of chromatin features between different cell types, tissues, and species have revealed tremendous differences in how the genome ... -
Chromatin Determinants of the Eukaryotic DNA Replication Program
(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 checkpoints ...
