Browsing Genetics by Title
Now showing items 127-146 of 146
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Tethering distinct molecular profiles of single cells by their lineage histories to investigate sources of cell state heterogeneity
Gene expression heterogeneity is ubiquitous within single cell datasets, even among cells of the same type. Heritable expression differences, defined here as those which persist over multiple cell divisions, are of particular ... -
The Distribution of Neanderthal Ancestry Across Populations And Within Genomes
For many millennia, modern humans overlapped in time and space with archaic humans such as Neanderthals and Denisovans. We now know that modern and archaic humans interbred, and that modern human populations carry some ... -
The evolution of microRNA in primates
MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution within humans and across the primate lineage is largely uncharacterized. A particular miRNA ... -
The protective oocyte envelope of threespine stickleback fish
After the end of the last ice age, ancestrally marine threespine stickleback fish (Gasterosteus aculeatus) have undergone an adaptive radiation into freshwater environments throughout the Northern Hemisphere, creating an ... -
Tools and Analyses for Differential Label-Free Proteomics Using Mass Spectrometry
(2012-08-10)The comparative measurement of protein abundance is a powerful method to detect changes in the biological dynamics of cells and tissues. Shotgun proteomics has proven to be a method where a wide range of proteins can be ... -
Tools and Challenges for the Implementation of Next-Generation Sequencing in Clinical Pharmacogenetics
Understanding the genetic basis of an individual's response to therapeutic drugs (pharmacogenetics) is a unique area of research with significant translational impact for medicine. Known genetic variants with effects on ... -
Toward comprehensive characterization of chromatin state
One of the principal questions in biology is how the genome encodes the information required for producing a multicellular organism. Somehow, the structure of the genome maps to every function in the living organism, from ... -
Transcript cleavage and polyadenylation in plants
Eukaryotic gene expression is finely regulated at the post-transcriptional level by the untranslated regions of mRNA. The coding sequence (CDS) of mRNA is flanked by 5’- and 3’-untranslated regions (UTRs). The end boundary ... -
Transcription of human-specific duplicate genes
In this work, I set out to characterize new genes contained specifically within the human genome but absent from any other, including our closest evolutionary cousins. Our interest in these genes is twofold: First, gene ... -
Transcriptomic profiling of macrophage polarization
Macrophages perform a wide variety of crucial, and sometimes contradictory, functions. While “pro-inflammatory” activities like fighting off infections and “anti-inflammatory” activities like wound-healing traditionally ... -
Translation initiation during influenza virus infection and its role in cellular immunity
There are numerous factors that direct and constrain influenza evolution. On the one hand influenza virus is constrained to encode proteins that allow it to complete the viral life cycle, but the immune system also recognizes ... -
Ultra-large-scale genomics approaches to improve cancer therapeutic response
The advent of low-cost, high-throughput sequencing technologies has elucidated targetable cancer-specific genomic alterations and allowed the development of precision therapies and their deployment into clinical use. ... -
Understanding how mutations shape the evolution of seasonal influenza virus hemagglutinin
Influenza virus hemagglutinin (HA) is under strong selective pressure. These selective forces constrain and drive the evolution of HA in nature. As it evolves, HA rapidly accumulates mutations that can affect its function ... -
Understanding recursive splicing in the human genome
Recursive splicing is a non-canonical splicing mechanism that results in an intron being removed in two or more segments. Identifying recursive splicing presents technical challenges due to the lack of evidence in mRNA and ... -
Understanding SARS-CoV-2 antigenic evolution using complete genotype-to-phenotype maps of the effects of mutations on antibody binding
Since the COVID-19 pandemic began, global sequencing efforts have allowed scientists to follow the evolution of the SARS-CoV-2 virus in real time. The consequences of that evolution, however, are less readily apparent. ... -
Understanding the genetic basis of phenotype variability in individuals with neurocognitive disorders
Individuals with a diagnosis of a neurocognitive disorder, such as an autism spectrum disorder (ASD), can present with a wide range of phenotypes. Some have severe language and cognitive deficiencies while others are only ... -
Using exome sequencing to study adaptive evolution in non-human primates and human populations
(University of Washington Graduate School, 2012)Positive selection promotes the fixation of functional genetic differences. Studying these adaptive differences can provide insights into how species adapt to their environment and develop their unique phenotypes. In this ... -
Using Visual Phenotypes to Dissect Sequence-Function Relationships and Complex Drug Responses
Cellular morphology is a potent indicator of cellular function and dysfunction, but the relationships between morphology, genetic variants, and cellular state remain incompletely understood. In this thesis, I describe a ... -
Variation in germline mutagenesis in humans and other great apes
All heritable variation begins with damage or copying mistakes affecting the DNA of germline, eggs, or embryos. Different DNA motifs and loci can have different mutation rates, and these rates can vary or change over time ... -
Whole organism lineage tracing by combinatorial and cumulative genome editing
Each of us begins life as a single fertilized cell, or zygote. The act of fertilization brings about an endeavored series of cell divisions, ultimately resulting in the forty trillion cells in each adult human. How are ...