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 93 for “"epigenomic"”.
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Correlation-based Linking of Epigenomic Regions to Target Genes in Bulk and Single Cell Epigenomic Data
… that employs peak-gene linking to integrate epigenomic data, thereby translating it into transcriptomic data. This integration facilitates comprehensive secondary analyses on meta-cells and sub-cell types. Crucially, our methodology enables swift computation of modules from any single-cell …
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Computational algorithm development for epigenomic analysis
Multiple computational algorithms were developed for analyzing ChIP-seq datasets of histone modifications. For basic ChIP-seq data processing, the problems of ambiguous short sequence read mapping and broad peak calling of diffuse ChIP-seq signals were solved by novel statistical methods. Their …
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Modeling transcriptomic dynamics and epigenomic conservation
… expression patterns and comparative analysis of epigenomic contributions to gene expressions across biological processes or across species evolutionarily. We presented a comparative model for different biological process based on a new model of clustering of temporal gene expression patterns. …
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Microfluidic Technology for Low-Input Epigenomic Analysis
… to enable low input and high through epigenomics profiling. First, I examined RNA polymerase II transcriptional regulation with microfluidic chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) assays. Second, I probed the temporal dynamics in the DNA …
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Dissecting the genomic and epigenomic alterations underlying glioblastoma
Glioblastoma (GBM) is the most common intrinsic primary brain tumour, characterised by structural complexity, tumoural heterogeneity and poor prognosis. GBM tumours reactivate neurodevelopmental programmes and they are driven by GBM stem-like cells (GSCs), displaying phenotypic similarities to …
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Epigenomic and Transcriptomic Changes in the Onset of Disease
… mutation may facilitate eventual breast cancer. Epigenomic changes in breast cells suggest that cells in the basal compartment may differentiate into a different cell type, and perhaps become the source of breast cancer. Next, we compared the epigenome and genome of murine immune cells under …
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Statistical and computational approaches for the analysis of high-throughput epigenomic data /
… strategy that converts primary TOP-seq epigenomic data into a CG position coverage signal. In the development section, we propose and integrate three signal transformations that enhance the signaling of enrichment-based epigenomic methods. Finally, we present several cases where the …
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Epigenomic and Transcriptional Regulation of Hepatic Metabolism by REV-ERB and Hdac3
… REV-ERBs, HDAC3 and potentially RORα mediate the epigenomic and transcriptional regulation of liver metabolism by the circadian clock.
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Microfluidics for Low Input Epigenomic Analysis and Its Application to Brain Neuroscience
… has improved the sensitivity and resolution of epigenomic analysis due to its outstanding ability to manipulate nanoliter-scale liquid volumes. In this thesis, I report three projects focusing on low-input, cell-type-specific and spatially resolved histone modification profiling on microfluidic …
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Microfluidics for low input epigenomic analysis and application to oncology and brain neuroscience
… neocortex in a similar fashion. We generated an epigenomic tomography that demonstrated the molecular state of the brain in 3D. Lastly, we developed a microfluidic version of the ChIRP-seq process which successfully conducted the assay using only 500K cells. This improvement makes ChIRP-seq in …
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CHARACTERIZATION OF THE EPIGENOMIC PROFILE SHAPING HUMAN FOXP3+ REGULATORY T CELL IDENTITY IN THE TUMOR MICROENVIRONMENT
… immunotherapy approaches. Here, we focus on epigenomic rewiring as a key process that orchestrates Treg adaptation and the acquisition of a tumor-promoting phenotype. The integration of external signals dynamically alters various layers of epigenomic regulation, mediating the establishment of …
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Development Of Single-Cell Transcriptomic & Epigenomic Sequencing Technologies To Assess Cell-Type-Specific Gene Regulatory Programs In Mammalian Brains
… repertoire of single-cell transcriptomics/epigenomics. First, we identified significant challenges associated with single-cell isolation and dissociation from complex adult tissues. Chemical or enzymatic dissociation of complex tissues elicits stress response pathways and ectopic …
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Multiomic Analyses Reveal Epigenomic Alterations and New Targets of Polycomb Repressive Complex 2 in Schwann Lineage Cells and Malignant Peripheral Nerve Sheath Tumors
… PRC2 dysfunction may induce significant epigenomic and gene expression alterations. Our research aimed to understand mechanisms underlying benign-to-malignant tumor transformation for improved diagnosis and treatment of MPNSTs.Our first objective was to functionally validate newly defined …
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Bioinformatic methods for analyses of epigenome and RNA interactome
… on non-coding RNAs and regulatory sequences. Epigenomic modifications and variations were considered to contribute to the diversity of functions found across different cell types, play key roles in the establishment and maintenance of cellular identity during development. Here, we propose to …
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New Microfluidic Technologies for Studying Histone Modifications and Long Non-Coding RNA Bindings
… novel microfluidic technologies to study epigenomic regulations, including 1) profiling epigenomic changes associated with LPS-induced murine monocytes for immunotherapy, 2) examining cell-type-specific epigenomic changes associated with BRCA1 mutation in breast tissues for breast cancer …
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Statistical mechanical modeling of eukaryotic gene regulation
… model to systematically analyze the epigenomic functions in modulating transcription factor-DNA binding. We discovered preferences of TFs for specific combinations of epigenomic modifications, termed as epigenomic motifs. Epigenomic motifs explain why some TFs appear to have different …
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Deciphering genetic associations using genome-wide epigenomics approaches
… genome. In particular, we focus on using epigenomic signatures to characterize non-coding transcriptional regulatory elements and predict regulatory segments of DNA disrupted by genetic variants. In Chapter 2, we describe how genome-wide maps of epigenomic modifications can be used to …
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