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 705 for “"whole genome"”.
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Oligonucleotide Design for Whole Genome Tiling Arrays
… of known and predicted genes, high-density, whole genome tiling arrays probe intensively for sequences that are known to exist in a contiguous region. Current programs for designing oligonucleotides for tiling arrays are not able to produce results that are close to optimal since they allow …
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Estimating telomere length from whole genome sequencing data
… and Parabam, as well as their applications to whole genome sequencing (WGS) data. Telomerecat is a tool for estimating telomere length from WGS data. The strength of Telomerecat lies in its applicability. This applicability is due to a number of advantages over previous attempts to estimate …
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Efficient Algorithms for Prokaryotic Whole Genome Assembly and Finishing
<p>De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) …
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Whole genome regulatory variant evaluation for transcription factor binding
… advent of high-throughput sequencing technology, Genome Wide Association Studies (GWAS) have identified thousands of genetic variants that are associated with disease and complex traits. Many of these variants reside in the non-coding region of the genome, and affect gene expression and downstream …
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Advancing RNA Virus Discovery and Biology with Whole Genome Sequencing
… to define these mechanisms is the lack of whole genome sequences for many of these viruses. To address this specific gap, I developed a versatile amplicon-based whole-genome sequencing (WGS) approach to identify viral genomes of hantaviruses and severe acute respiratory syndrome coronavirus …
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Whole genome doubling confers unique genetic vulnerabilities on tumor cells
Whole genome doubling (WGD) generates genetically unstable tetraploid cells that fuel tumorigenesis. Cells that undergo WGD must acquire adaptive characteristics to accommodate their tetraploid state, and these adaptations may confer unique vulnerabilities that can be exploited therapeutically. We …
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Whole genome approaches to identify genes involved in early meiosis.
… bread wheat, which contains three very similar genomes from slightly diverged progenitors. Despite having homoeologous chromosomes present in the same nucleus, bread wheat displays diploid-like behaviour during meiosis I. Such an involved physical process as meiosis also has complexity reflected …
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COMPREHENSIVE WHOLE GENOME SEQUENCING UNRAVELS THE COMPLEX GENOMIC LANDSCAPE OF NEUROBLASTOMA
… spectrum of clinical outcomes. Although the genome of this tumor has been extensively studied through the last decades, a comprehensive analysis of NBL mutational landscape – which may expain its complexity – is still lacking. Moreover, while the role of germline variants in the …
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Identification of Familial Wilms Tumor Predisposition Genes Using Whole Genome Sequencing
… penetrance, estimated to be 30%.</p> <p>Whole genome sequencing of eleven individuals in three Wilms tumor families was performed to identify the gene(s) responsible for genetic predisposition to Wilms tumor in these families, and to increase our understanding of a genetically …
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Understanding How Whole Genome Duplication in Plants Impacts Herbivore-plant Interactions
… One such prevalent change in plants is whole-genome duplication (WGD), or polyploidy, but we are still learning how WGD affects ecological interactions. In particular, studies of herbivory on polyploids have primarily focused on established polyploid plant populations. Although this …
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Whole genome sequencing to characterize Cutthroat Trout populations across the Continental Divide
… markers representing only a small portion of the genome, such as with ND2 mitochondrial DNA haplotypes, microsatellites, and amplified fragment length polymorphisms (AFLPs), and have not included a comprehensive nuclear DNA assessment from all extant lineages of Cutthroat Trout found in Colorado. …
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Development of computational approaches for whole-genome sequence variation and deep phenotyping
… possible to detect variants in 98% of the human genome. A drop in sequencing costs made it feasible to sequence 10,000 individuals including 1,250 subjects diagnosed with PAH and relatives as part of the NIHR Bioresource – Rare (BR-RD) disease study. This large cohort allows the genome-wide …
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Structure-based realignment of non-coding RNAs in multiple whole genome alignments
Whole genome alignments have become a central tool in biological sequence analysis. A major application is the de novo prediction of non-coding RNAs (ncRNAs) from structural conservation visible in the alignment. However, current methods for constructing genome alignments do so by explicitly …
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DD34E DNA Transposable Elements of Mosquitoes: Whole-Genome Survey, Evolution, and Transposition
… and spreading within, and in some cases, between genomes. I describe a whole-genome analysis of DD34E TEs, which belong to the IS630-Tc1-mariner superfamily of DNA transposable elements, in the African malaria mosquito, Anopheles gambiae. Twenty-six new transposons as well as a new family, gambol, …
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Algorithms for pre-microrna classification and a GPU program for whole genome comparison
… with pre-miRNA-like hairpin can be found in genomes. It is a challenge to distinguish the real pre-miRNAs from other hairpin sequences with similar stem-loops (referred to as pseudo pre-miRNAs). The first part of this dissertation presents a new method, called MirID, for identifying and …
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De Novo Assembly of Genomes in Microbiomes: From Amplicons to Whole-Genome Shotgun Sequencing
… investigations is the assembly of metagenome at the strain-level resolution. This is indispensable for gaining profound insights into microbial communities and addressing pivotal biological inquiries. Despite the availability of existing assembly tools, certain challenges remain …
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Insights into the genomic histories of diverse human populations using whole-genome sequencing analysis.
… 54 human populations which are part of the Human Genome Diversity Project (HGDP-CEPH) panel. Using whole-genome sequences previously produced at the Wellcome Sanger Institute, I generated a comprehensive catalogue of structural variation identifying a total of 126,018 variants, of which 78% are …
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Molecular characterization of microbial communities in small-scale biodigesters using whole genome shotgun metagenomic approach
… those in rural areas. This study employs whole-genome shotgun metagenomics integrating data from metagenomic reads, contigs, and metagenome-assembled genomes (MAGs) can achieve a more comprehensive understanding of microbial taxonomy and functional capabilities in biodigesters. This study …
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4D Ex Vivo Crispr/Cas9 Whole-Genome Screen to Identify Genes Regulating Lung Cancer Metastasis
… performed a proof-of-concept CRISPR/Cas9 whole genome knockout screen in the A549 lung adenocarcinoma cell line and utilized a novel <em>ex vivo 4D </em>lung metastasis model to find gene candidates to test <em>in vitro. </em>I prepared samples and performed next generation sequencing. I …
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