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 15 of 15 for “"Hi-C data"”.
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Modelling transcription factors diffusion in 3D using Hi-C data
… can upregulate or downregulate the rate at which transcription occurs. Their main mechanism of functioning is described by their ability to interact to DNA, namely, to find their target site and bind to it. In the search mechanism also known as facilitated diffusion, TFs can float freely …
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SCL: A Lattice-Based Approach to Infer Three-Dimensional Chromosome Structures from Single-Cell Hi-C Data
<p>In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.</p> …
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Polymer models of chromosomes
Studies of chromosomes have a long history. Since late XIX century, microscopy studies have revealed that chromosomal organization as seen by light microscopy is different among organisms, cell types, or stages of the cell cycle. However, the internal organization of chromosomes at scales below the …
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Toward sequence-to-structure predictions of chromatin: Generative AI sheds light on genome organization
… environment complicate investigations into this system. This thesis alleviates these challenges and holds the potential to accelerate genome organization research by presenting several methodological advances. An efficient Hi-C inversion algorithm appears first. This technique extracts …
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Modeling Genome Organization in Eukaryotic and Prokaryotic Cells Using Folding Determinant Interactions
… by nuclear landmarks and regulatory factors. In this thesis, I develop polymer-based chain-growth Monte Carlo frameworks to investigate genome folding in both mammalian and bacterial systems. For mammalian cells, I model how lamina-associated domains (LADs) and specific fold interactions (SFIs) …
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3D Chromatin Structure and Gene Regulation: Integrated Genome Structure, Transcriptomics and Epigenetics
… enhancer–promoter communication, but bulk Hi-C data obscure single-cell variability, while sparse single-cell Hi-C limits structural resolution. This dissertation develops computational approaches to reconstruct single-cell chromatin conformations, integrate them with functional genomics, …
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UNCOVERING STRUCTURE-FUNCTION RELATIONSHIPS IN CHROMATIN ARCHITECTURE
… such as gene expression and DNA replication, which are crucial to establishment and maintenance of cell identity in human development. Recent technological advances have enabled the creation of high-resolution maps of chromatin architecture genome-wide from which to test new biological …
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Study of 3D Genome Organisation in Budding Yeast by Heterogeneous Polymer Simulations
… 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 the genome remain largely unknown. To understand the effect of biophysical …
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Linker Histone Medicated Regulation of Mitotic Chromosome Compaction and Individualization
… Here, I investigated the role of the linker histone variant H1.8 in regulating mitotic chromosome structure. I showed that H1.8 suppresses binding of condensins and topo II to mitotic chromatin in Xenopus egg extracts. Using an in vitro reconstitution system, I showed that H1.8 inhibits …
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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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Investigation of transcription factor binding at distal regulatory elements
… remote regulatory elements, termed enhancers, which are brought into contact with promoters via DNA looping. Enhancers typically contain clusters of transcription factor binding sites, and TF recruitment to them is thought to play a key role in transcriptional control. In this thesis I have …
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The role of long non-coding RNA LINC00673 in lung tumorigenesis
… as key regulators of cellular behaviour. This project explores the roles of long non-coding RNA (lncRNA) in the progression of lung adenocarcinoma (LUAD) – the most common type of lung cancer – to improve current understanding of the disease. Using a combination of computational and wet-lab …
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Spatial organisation of the immunoglobulin heavy chain locus and inter-chromosomal gene networks driving B cell development
… to recognize a countless number of antigens. This highly diverse repertoire is produced during B cell development in the bone marrow from the immunoglobulin heavy chain (Igh) and light chain (Igk and Igl) loci. The mouse Igh is a large (~3Mb) multigene locus that contains 195 variable (V), 10 …
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Higher Order Chromosome Organization and Recombination Dynamics of Meiotic Prophase I In Mouse Spermatocytes
… or “hotspots” on parental chromosomes, which are repaired by homologous recombination (HR). HR produces either crossovers, which result in the exchange of flanking markers between homologs, or noncrossovers, which are short regions ofgene conversion to the donor genotype. Crossover …
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Chromosome and Genome Evolution in Culicinae Mosquitoes
… mosquitoes. Two genera, Culex and Aedes, from this subfamily have world-wide distribution and are responsible for transmitting of several deadly diseases including Zika, West Nile fevers, chikungunya, dengue, and Rift Valley fevers. Developing high-quality genome assembly for mosquitoes, …