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 27 for “"Genome architecture"”.
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Methods for Analysis of Prokaryotic Genome Architecture
… been organized around the concept of reference genomes. Reference genomes provide a useful comparative touchstone for closely related organisms. However, they do not necessarily represent the biological diversity in a group of genomes. Currently there are more than 96,000 bacterial genomes …
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New insights into 3D genome architecture through improved genomic methods
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2027-05-01
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Integrative analysis of transcriptional activity and genome architecture changes upon viral infections
To study the interplay between spatial nuclear architecture and transcriptional activity during viral infections, I employed a genome-wide chromosome conformation capture approach (Hi-C) on infected murine and human cells and further enriched those libraries for genomic loci of interest and the …
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Mobile genetic element contribution to the genome architecture of the human parasitic flatworm Schistosoma mansoni
… human host and intermediate snail host. Its genome is repeat-rich, with transposable elements (TEs) comprising approximately 35% and Schistosoma-specific W elements (WEs) an additional 10%. Repetitive elements have a profound impact on host genomes, directly contributing to protein-coding …
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Language like behavior in protein secondary structure and analysis of mitochondrial genomes and transposable elements in Antarctic notothenioid fishes
The organization and evolution of genomes can be shaped by underlying evolutionary principles, particularly adaptive forces that contribute to the structural and functional changes in genome architecture. This thesis explores the evolution of genome architecture in two distinct perspectives. In the …
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From Protein Folds to Chromatin: Topological Data Analysis and Deep Learning at Multiple Scales
… protein folds to the three-dimensional architecture of chromatin—structural organization governs molecular function and regulation. We present two complementary computational frameworks that integrate geometric, topological, and spatial modeling with deep learning to elucidate these …
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3D Chromatin Structure and Gene Regulation: Integrated Genome Structure, Transcriptomics and Epigenetics
The three-dimensional (3D) organization of the genome is essential for regulating gene expression, replication, and stability. Chromatin folding mediates enhancer–promoter communication, but bulk Hi-C data obscure single-cell variability, while sparse single-cell Hi-C limits structural resolution. …
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The role of MLL4 in the chromatin framework: from the epigenome to 3D genome organization
… haploinsufficiency, TrxG members show reduced genome binding, while PcG strengthens its enrichment and genome occupancy. This chromatin state rearrangement is also reflected on a three-dimensional scale. Genome Architecture Mapping (GAM) experiments reveal distinct changes in 3D chromatin …
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Scalable Methods for In Situ Genomics
… remains challenging, and accordingly the role of genome structure and organization in determining cellular function is an open question. Mapping cellular genome organization is difficult because it requires joint measurement of linear DNA sequence and 3D spatial context, however, existing …
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Study of 3D Genome Organisation in Budding Yeast by Heterogeneous Polymer Simulations
… the nucleus has revealed the essential role of genome organisation in controlling genome function. Furthermore, genome architecture is highly dynamic and significant chromatin re-organisation occurs in response to environmental changes. However, the mechanisms that drive the 3D organisation of …
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Genetic and phenotypic analysis of novel South African Avian poxviruses
… and one from proposed subclade E have had their genomes completely sequenced. These genomes have been shown to exhibit typical poxvirus genome characteristics with conserved central regions and more variable terminal regions, however all isolates exhibit major differences in defined central …
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Complex evolution of mitochondrial genomes: lessons from salamanders
This dissertation research on genome evolution focuses on understanding the mechanisms that drive the evolution of mitochondrial genome size, content, and organization in animals. This research uses a combination of empirical and computational approaches to examine the evolution of mitochondrial …
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Genomic diversity of Lactobacillus salivarius
… among the lactobacilli due to its multireplicon genome architecture. The circular megaplasmids harboured by L. salivarius strains encode strain-specific traits for intestinal survival and probiotic activity. L. salivarius strains are increasingly being exploited for their probiotic properties in …
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Genome regulation by long noncoding RNAs
Our genomes encode the molecular information that gives rise to life, yet we are just beginning to unravel how this information is organized, interpreted, and regulated. While the human genome contains -20,000 protein-coding genes, mammalian genomes also produce thousands of long non-coding RNAs …
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Pseudoscorpion Systematics & Phylogenetics: Exploring the Effects of Accelerated Rates of Evolution on Both Ancient and Recent Diversification
… arachnid orders, and evidence of a shared whole genome duplication event uniting pseudoscorpions with the arachnopulmonates. Despite 250 years of systematic attention, there is still a lot that we do not know about the evolutionary history of pseudoscorpions, including the basic phylogenetic …
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Evolutionary Genomics of Dominant Bacterial and Archaeal Lineages in the Ocean
… marine microbial diversity and the evolution of genome architecture. In Chapter 2, I use a comparative framework to get insights into the evolutionary forces driving genome streamlining in the Ca. Marinimicrobia, a clade widely distributed in the ocean. This project shows that differences in the …
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Engineering structural variants with prime editing
… paired prime editing to regions across the genome, thereby identifying essential coding and non-coding sequences. First, I built a predictive model for prime editing insertion efficiencies using experimental data generated in our laboratory. This model, called MinsePIE, forecasts insertion …
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Multiscale Modeling of Genome Organization: Bridging Polymer Physics, Molecular Dynamics, and AI
The human genome is intricately organized within the nucleus, and its spatial arrangement plays a critical role in gene regulation, cellular function, and disease. Recent advances in high- throughput experiments have unveiled the heterogeneous and dynamic nature of chromatin organization at …
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Development Of Single-Cell Transcriptomic & Epigenomic Sequencing Technologies To Assess Cell-Type-Specific Gene Regulatory Programs In Mammalian Brains
… single cell level. Measurements of single-cell genomes, transcriptomes, epigenomes (methylomes/genome architecture) at all stages and states of human existence will be included, and to this end, new technologies are constantly being developed and refined to contribute to this venture. In this …
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Chromosome evolution in Lepidoptera
… to have a fixed number of chromosomes in their genome, chromosome numbers vary widely across the tree of life. Changes in chromosome number occur due to rearrangements, such as the fusion and fission of chromosomes, and have been hypothesised to contribute to speciation and adaptation. However, …
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