Browsing Genetics by Title
Now showing items 34-53 of 58
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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 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 ... -
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 ... -
PRIMUS: Pedigree Reconstruction and Identification of a Maximum Unrelated Set
This dissertation describes the methods and algorithms developed to improve human genetic analysis for both genome-wide association studies (GWAS) and pedigree-based analyses. The new algorithms are included in the software ... -
Proteomic identification and evolutionary analysis of primate reproductive proteins
(2013-11-14)Sex and reproduction have long been recognized as drivers of distinct evolutionary phenotypes. Studying the evolution and molecular variation of reproductive proteins can provide insights into how primates have evolved and ... -
Regulatory variation and human disease
(2014-02-24)Non-coding regulatory regions are strongly implicated in human disease via genetic studies. However, it is currently not possible to interpret reliably and systematically the functional consequences of genetic variation ... -
Scalable continuous culture-based approaches for understanding evolution and cancer
Understanding the genetic basis of adaptation in evolution is an area of research that has the potential to characterize the forces that have shaped the evolution of all life. For much of history, it was far easier to see ... -
The sperm proteome of the red abalone, Haliotis rufescens, and the discovery and characterization of an abundant, rapidly evolving acrosome protein
(2014-02-24)Abalone, a broadcast spawning marine mollusk, is an important model for molecular interactions and positive selection in fertilization, but the focus has previously been on only two sperm proteins, lysin and sp18. We have ... -
Study of the Cryptosporidium parvum DHFR-TS in the model system Saccharomyces cerevisiae
(1998)Cryptosporidium parvum is a ubiquitous protozoan that causes severe gastrointestinal disease. The severe diarrhea that results can be life-threatening, particularly for the very young, old, and immune-compromised. Currently ...