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 1271 for “"genomes"”.
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Untangling Genomes from Metagenomes
… tools to investigate and assemble two metagenomes sampled from Puget Sound during autumn and spring. Community taxonomic classification and quantification revealed a diverse and changing assemblage of Bacteria and Archaea, including enigmatic members of the uncultured marine Euryarchaeota. …
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Events that shape genomes
… opened up new possibilities for exploring the genomes of non-model organisms. For this thesis, a diverse range of non-model species from both plants and animals were used to identify and answer questions of evolutionary interest in four case studies. In doing so, a wide assortment of …
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Annotation of Non-Model Species’ Genomes
<p>The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered …
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Understanding Genomes Through Engineered Structural Variation
… for recombinases at high throughput to engineer genomes at an unprecedented scale. In the process, I made discoveries about the biology of genome engineering, structural variation, and gene regulation. I first outlined the determinants of short sequence insertion using prime editing by …
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OperomeDB: database of condition specific transcription in prokaryotic genomes and genomic insights of convergent transcription in bacterial genomes
… sequencing datasets for bacterial genomes. 2) Genomics and mechanistic insights of convergent transcription in bacterial genomes. In the first project we developed a database for the prediction of operons for bacterial genomes using RNA-seq datasets, we predicted operons for …
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Structural determinants of mutability across cancer genomes
Cancer is a group of diseases which are characterised and actuated by somatic mutations. In cancer the distribution of mutations across the genome is inhomogeneous, with genomic and epigenomic features influencing mutational patterns. Previous studies have indicated that chromatin organization and …
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Complex evolution of mitochondrial genomes: lessons from salamanders
… to examine the evolution of mitochondrial genomes in vertebrates, focusing on salamanders as an exemplar clade. Chapter One analyzes mitochondrial genome sequences of vertebrate lineages that differ in metabolic rates. Salamanders, which have the lowest metabolic requirements among …
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Probabilistic Modelling of Replication Fidelity in Eukaryotic Genomes
… that optimise complete DNA replication in genomes of different size scales (10 Megabases to 10 Gigabases), spanning the whole eukaryota. We show in yeasts (genome size ~10 Megabases) that the replication origins (sites on DNA where replication can be initiated) are biased towards equal …
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The structure and evolution of breast cancer genomes
… a structural survey of breast cancer cell line genomes in order to find genes that were disrupted by chromosome aberrations in “typical” breast cancers. I investigated three breast cancer cell lines, HCC1187, VP229 and VP267 using data from array painting, SNP6 array CGH, molecular cytogenetics …
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Computational genomics : mapping, comparison, and annotation of genomes
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in …
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Bioinformatics and Next Generation Sequencing: Applications of Arthropod Genomes
… studies: (1) by sequencing and analyzing the genomes of three Tetranychus spider mites with three completely different feeding behaviors, we uncovered genomic signature variations and indicative of pest adaptations; (2) we sequenced, assembled and annotated five Brevipalpus flat mite genomes …
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Efficient algorithms for gene cluster detection in prokaryotic genomes
… and the availability of completely sequenced genomes continuously increases due to the use of semi-automatic sequencing machines. Also these sequences, mostly prokaryotic ones, are well annotated, which means that the positions of their genes and parts of their regulatory or metabolic pathways …
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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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Computational Techniques Applied to RNA Structures and Bacterial Genomes
Modern molecular biology studies increasingly require customized computation support. This is especially true for studies associated with atomic resolution structures and/or NextGen sequencing. In this dissertation, three separate studies are described in which modern computational methodologies …
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The role of mobile elements in recent primate genomes
… (MEs), which constitute ~50% of the primate genomes, have contributed to both genome evolution and gene function as demonstrated by ample evidence discovered over the last few decades. The three studies in this thesis aims to provide a better understanding of the evolutionary profile and …
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Algorithms for analyzing complex structural variations in cancer genomes
Analysis of somatic alterations in cancer genomes has been accelerated through the rapid growth of the quantity, quality and depth of data generated by next-generation sequencing (NGS). Previously most of cancer genome studies were focusing on single nucleotide variations (SNVs), small insertions …
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Comparative gene identification in mammalian, fly, and fungal genomes
… identification is comparative analysis of the genomes of several related species, to find genes that have been conserved by natural selection over millions of years of evolution. I develop general computational methods that combine statistical analysis of genome sequence alignments with …
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Ecology and adaptation of denitrifiers across genomes and environments
Although nitrogen comprises 78% of the Earth’s atmosphere, this N2 gas is largely inaccessible to most living organisms, limiting the supply of bioavailable (i.e. fixed) nitrogen to many marine, terrestrial, and aquatic environments. Microbes primarily mediate the many steps of the nitrogen cycle, …
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Optimization of Cytogenetic and Physical mapping of Culicinae genomes
… highly repetitive nature of the Aedes and Culex genomes, the structure of their polytene chromosomes is damaged by ectopic contacts that make the analysis difficult. Mitotic chromosomes from imaginal discs of 4th instar larvae of Aedes aegypti were tested as a source for the physical genome …
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