Browsing Genetics by Title
Now showing items 101-120 of 146
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Oncogene-driven post-transcriptional regulation in lung cancer
Lung cancer is often caused by genetic mutations which alter the activity of proteins in the RAS family, with somatic mutation of the KRAS gene occurring in ~30% of lung adenocarcinoma tumors. A gene of the same family, ... -
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 ... -
Powering phosphoproteomics with large scale data analysis and machine learning
Cells are the fundamental biological units of organisms and are constantly changing their internal state in response to external stimuli and stresses. A common way in which they do this is through the addition and subtraction ... -
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 ... -
Proteome-wide amino acid substitution and biochemical selection to understand protein biology
Proteins are important macromolecules that carry out most biological functions and are enabled to do so by the diverse chemistries of the twenty amino acids. Changes in the amino acid sequence of a protein can change ... -
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 ... -
Pseudotyped lentiviral systems for studying viral entry proteins from emerging viruses with pandemic potential
Viral entry proteins facilitate viral entry into host cells through receptor binding and membrane fusion. They play a critical role in the viral life cycle and, as prominent surface proteins, are common targets of the host ... -
Quantifying progeny production from individual influenza virus-infected cells
The distribution of progeny virions produced by virus-infected cells is extremely heterogeneous. This trend has been observed in diverse viruses, including bacteriaphage and pathogenic human viruses. To date, it has been ... -
Quantitative cross-linking mass spectrometry for protein structural stability studies
Mass spectrometry-based methods for protein-ligand identification have expanded classical techniques for the bioanalytical characterization of small molecule target engagement and their modes of action. In the last decade, ... -
Regression models to Detect and Quantify Peptides from Mass Spectra
Data-independent acquisition (DIA) mass spectrometry-based proteomics aims to quantify every peptide and its derivatives in a sample by systematically sampling every ion. However, much of the signal in the resulting spectra ... -
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 ... -
Role of Transcription Factor-MicroRNA Feedback Circuits in the Canalization of Human Regulatory Networks
Complex interactions between hundreds of transcription factors underlie the gene expression profiles that give rise to cellular form and function. However, it is still not entirely understood how organisms faithfully ... -
Root Development & Acquired Thermotolerance Regulatory Targets in Arabidopsis thaliana
In this thesis, I will describe my work in two research topics using Arabidopsis thaliana: root development and acquired thermotolerance. 1. Arabidopsis roots are an excellent model for studying cell development because ... -
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 ... -
Shifting the Paradigm: Peptide-Centric Analysis of Systematically Sampled Mass Spectrometry Data
In mass spectrometry-based shotgun proteomics, data-independent acquisition (DIA) is an emerging technique due to its systematic and unbiased sampling of precursor ions. However, current DIA methods often use wide precursor ...