Browsing Genetics by Title
Now showing items 115-134 of 146
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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 ... -
Single-cell Analysis Reveals the Molecular Roadmap of Mouse Embryogenesis
Mammalian embryogenesis is a rapid and complex process that involves the proliferation and diversification of cells. Within a few weeks, a single-cell zygote gives rise to hundreds of millions of cells that express a wide ... -
Some problems in probabilistic modeling of germline and somatic evolutionary processes
Evolutionary processes shape biological systems at all scales, and understanding evolutionary mechanisms requires quantitative frameworks that are matched in sophistication to modern experimental capabilities. This ... -
Species-scale high-throughput functional analysis of natural variants in yeast
The impact of natural genetic variation on phenotype is difficult to measure because we only partially understand how polymorphisms present in a population affect gene function. Understanding the relationship between genetic ... -
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 ... -
Systematic Data Acquisition and Analysis Strategies for Quantitative Proteomics
Mass spectrometry-based proteomics has emerged as a powerful tool to gain insight into biological systems. As biological studies get more complex, there is a pressing need to increase throughput without sacrificing quality ... -
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 ...