Browsing Genetics by Title
Now showing items 34-53 of 65
-
Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana
Our understanding of gene regulation in plants is constrained by our limited knowledge of plant cis-regulatory DNA and its dynamics. One way in which cis-regulatory elements can be delineated is by their characteristic ... -
Massively parallel functional dissection of regulatory elements
(2013-02-25)Massively parallel sequencing has accelerated the cataloging of cis-regulatory elements in mammalian genomes. However, it remains challenging to estimate the functional effects of variation in cis-regulatory elements. The ... -
Mechanisms of buffering of phenotypic variation in A. thaliana: Features of HSP90 and characterization of AGO1 as a new regulator of robustness
Biological systems have molecular mechanisms that allow them to maintain a constant phenotype despite environmental and genetic perturbations. These mechanisms can take the form of master regulator of robustness, gene ... -
Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome
Though invisible to the naked eye, microbes are crucial to life as we know it. These tiny single-celled organisms are found in almost every known environment, helping to maintain balance across a vast array of ecological ... -
Molecular tagging to overcome limitations of massively parallel sequencing
(2013-04-17)Massively parallel technologies have dramatically reduced the cost and increased the throughput of DNA sequencing, transforming the study of patterns of genetic variation in human and model organisms, the genetic basis of ... -
MSY4, a sequence-specific RNA binding protein expressed during mouse spermatogenesis
(2000)Translational control is an important mechanism of gene regulation, especially in gametogenesis and early embryogenesis, where there are periods of time in which there is no transcription. Previously transcribed mRNAs must ... -
Mutation Patterns in Human Cancer and Coexpressed Genes in the Drosophila Genome
(2013-11-14)For my dissertation I focused on two distinct projects. In the first project, I analyzed early cancer exome datasets to identify patterns of mutation that offer insight into somatic mutational processes in humans. This ... -
Mutational Heterogeneity in Cancer
Somatic mutation plays a key role in the formation and progression of cancer. Differences in mutation patterns likely explain much of the heterogeneity seen in prognosis and treatment response among patients. Recent ... -
New methods for haplotyping and de novo assembly of genomes and metagenomes
The study of genomics is made possible by the creation of genome assemblies: strings of sequences that represent the DNA content of a species, or an individual within a species. However, genome assemblies do not spring ... -
New technologies for sequencing and interpreting genomes
(2014-02-24)A central goal of biomedical research is to catalog genetic variation and uncover its causal relationship to phenotype. As humans are diploid organisms with two copies of each chromosome (except for the sex chromosomes in ... -
New tools, targets and approaches for gene, genome and metabolic engineering
Genome engineering tools and DNA sequencing technologies have improved dramatically over the past decade. These technologies are transforming many areas of research ranging from evolutionary biology to human disease. My ... -
Next Generation ABO Genetics and Genomics
Accurately cross matching units of blood based on blood type is essential for successful transfusion therapy. ABO is the most clinically relevant blood group in transfusion therapy due to the presence of naturally occurring ... -
Next Generation Mendelian Genetics
(2013-02-25)The study of Mendelian disorders has been of immense utility in uncovering the genetic and molecular basis of numerous human traits, and has greatly furthered the identification of genes, the annotation of gene function ... -
A novel sequencing method to explore two molecular mechanisms of rapid adaptation
To survive in an ever-changing world, organisms need to rapidly adapt to new environments. In my dissertation, I address two molecular mechanisms that may contribute to rapid adaptation to new environments and help to ... -
Organization and evolution of transcription factor occupancy in the human genome
<italic>Cis</italic>-regulatory DNA encodes the circuitry that enables cell development and differentiation. <italic>Cis</italic>-regulatory DNA is densely populated by recogntition sequences for transcription factors and ... -
Patterns and determinants of variation in functional genomics phenotypes in the yeast Saccharomyces cerevisiae
(2013-04-17)Phenotypic variation among individuals within populations is ubiquitous in the natural world, and a preeminent challenge in biology is understanding the contribution of genetic variation to this phenotypic variation. Despite ... -
Patterns of Archaic Hominin DNA in Modern Human Genomes
In this dissertation I describe the development of a method for identifying introgressed archaic haplotypes. I then present the application of this method to several populations. In 15 African hunter-gatherer genomes, I ... -
Population genomic insights into recent human evolutionary history
(2014-04-30)The advent of large-scale population genomic datasets has enabled detailed inferences regarding human evolutionary history. Demographic changes and positive selection have left their marks on the genome and we can now begin ... -
Positive selection in the human lineage across time scales
Understanding the evolutionary history of humankind has long been a central goal of biology. This history extends over millions of years- beginning with the events that led to our divergence from chimpanzees and other ... -
A practically efficient graph-theoretic approach to protein identification in mass spectrometry
(University of Washington Graduate School, 2011-06)Tandem mass spectrometry has emerged as a powerful tool for the characterization of complex protein samples, an increasingly important problem in biology. The effort to efficiently and accurately perform inference on ...