Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 23 for “"human genomes"”.
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Patterns of Archaic Hominin DNA in Modern Human Genomes
… populations. In 15 African hunter-gatherer genomes, I identify signatures of introgression from an unknown archaic hominin with an apparent divergence time with modern humans that is similar to the divergence time of Neanderthals. In a sample of 379 European and 279 East Asian genomes, I …
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Statistical analysis of short template switch mutations in human genomes
Many complex rearrangements arise in human genomes through template switch mutations, which occur during DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. These variants are routinely captured at kilobase-to-megabase scales in …
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Structural variant calling by assembly in whole human genomes: Applications in hypoplastic left heart syndrome
… alignment of short sequencing reads to the human reference genome. SNPs and small indels (variants less than 50 nucleotides) are the most common types of variants detected from alignments. Structural variation can be more difficult to detect from short-read alignments, and thus many software …
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The human molecular clock and mutation process : a characterization using microsatellite DNA
In the past decade, thousands of human genomes have been catalogued, either by whole-genome sequencing or by targeted genotyping. The variability between human genomes encodes invaluable information about human traits and genetic diseases, as well as human migration patterns and population …
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Algorithms for genomics and genetics : compression-accelerated search and admixture analysis
… with data sets at the scale of thousands of human genomes fast becoming the norm. These technological leaps promise to enable corresponding advances in biology and medicine, but the deluge of raw data poses substantial mathematical, computational and statistical challenges that must first be …
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Detection and Characterization of Multilevel Genomic Patterns
… structural changes, and gene expressions of human genomes. Detection and characterization of multilevel, high-throughput microarray genomic data pose new challenges to statistical pattern recognition and machine learning research. In this dissertation, we propose novel computational methods …
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Complete computational sequence characterization of mobile element variations in the human genome using meta-personal genome data
… for insertional structural variants in the human genomes via local de novo sequence assembly or progressive assembly using discordant and concordant read pairs and split-reads. An essential component of our approach involves utilizing all personal genome data available in the public domain …
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Insertionally polymorphic human endogenous retroviruses and their potential role in cancer
… youngest endogenous retrovirus family known in humans, with some of its members being insertionally polymorphic in modern human populations. There have been numerous reports of HERV-K(HML-2) members being present in cancer samples. Here, a robust analysis of the state of HERV-K(HML-2) family in …
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Regulation of the ETn/MusD family of active mouse long terminal repeat retrotransposons
… account for approximately 10% of mouse and 8% of human genomes and may play a role in modifying gene expression. Many species harbor retrotransposon families encompassing both autonomous and non-autonomous members. Specifically, the mouse Early Transposon (ETn) family members lack all retroviral …
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DNA methylation analysis and identification of a novel antisense transcript in the Peg3 imprinted domain
… islands in this region of the mouse, cow, and human genomes. We identified two previously unreported differentially methylated regions (DMR): one in the promoter region of mouse Zim3 and another in the promoter region of human USP29. The PEG3-CpG island is the only DMR that is conserved among …
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Enhancing genomic data quality through deep learning methods
… DNA sequence to the traits we observe, from human disease risk to agricultural performance. Phenotype prediction lies at the heart of this effort, with applications in precision medicine, where it informs genetic risk models and polygenic scores; in agriculture, where it guides breeding for …
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An Ancient Genomic Perspective of Kinship, Disease and Environment
… in Eurasia. An analysis of the 13 victims' genomes substantially reframes this: one young boy is identi ied as the offspring of a local hunter-gatherer mother and a Steppe pastoralist father. Crucially, this plausibly links the violence to external contemporary pastoralists – for the irst …
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Locus-specific proteomics identifies novel repressors of Epstein-Barr virus reactivation
The Epstein Barr virus (EBV) is a human gammaherpesvirus which infects the majority of the global population and is associated with the development of cancer and autoimmune disease. Infection with EBV is lifelong, as the virus enters a latent state in B-cells which persists until an appropriate …
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Computational Insights into Evolutionary Dynamics of Human and Primate Genes
… species is a subject of research interest. For human genes, there is a particular focus on investigating the possible origins of genes. However, there has been limited research on the development process from an evolutionary perspective. Additionally, most previous studies have focused on model …
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Engineering of transcription activator-like effector nucleases (TALENs) for targeted genome editing
… traits in crop plants and livestock, treating human diseases, etc. This thesis describes my efforts on engineering transcription activator-like effector (TALE) nucleases (TALENs) as an efficient tool for targeted genome editing. Targeted genome engineering relies on the introduction of a …
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Long read mapping at scale: Algorithms and applications
… they narrow the scale gap between sizes of genomes and sizes of sequenced reads, with the promise of avoiding assembly errors and repeat resolution challenges that plague short read assemblers. However, long reads themselves sport error rates in the vicinity of 10-15%, compared to the high …
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The Contribution of Structural Variants to 2,095 Molecular Phenotypes in 12,354 European Ancestry Individuals
… the majority of nucleotide variation among human genomes by number of basepairs and have been linked to various diseases and traits including schizophrenia, autism and obesity. In this thesis whole genome sequence data at 15X coverage were generated using 12,354 samples from the INTERVAL …
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Exploring new methodologies to identify disease-associated variants in African populations through the integration of patient genotype data and clinical phenotypes derived from routine health data: A case study for Type 2 Diabetes Mellitus in patients in the Western Cape Province, South Africa
… this is largely driven by the limited data for human genomes from sub-Saharan Africa. While the costs of generating human genomic data have gone down significantly, they are still a barrier to generating large scale African genomic data. This project is therefore a proof-of-concept pilot study …
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