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.
Results
Showing 1 to 20 of 38 for “"ChIP-seq data"”.
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Spatial and temporal coupling models for the discovery of binding events in ChIP-Seq data
… two methods for identifying binding events in ChIP-Seq data. The motivation of this venture is to propose a complete read generating process under a probabilistic graphical model framework which will determine more accurately binding event locations and enforce alignment of events across …
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A Statistical Model to Determine Multiple Binding Sites of a Transcription Factor on DNA Using ChIP-seq Data
… followed by massively parallel sequencing (ChIP-seq) is a new technology that can reveal protein binding sites in genome with superior accuracy. Although many methods have been proposed to find binding sites for ChIP-seq data, they can find only one binding site within a short …
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Statistical methods for ChIP-seq and microbiome studies using next-generation DNA sequencing data
… dissertation, we studied two different types of data generated by next-generation sequencing technologies. Chapter 2 is about analysis of ChIP-seq data with biological replicates to identify protein-binding sites. Chapters 3-4 are about analysis of microbiome data to estimate the causal effects …
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Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution
… at high spatial resolution from noisy ChIP-Seq data. I first present the genome positioning system (GPS) algorithm which predicts protein-DNA interaction events from ChIP-Seq data using a single-base resolution generative probabilistic model. Using synthetic and actual ChIP-Seq data, I …
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Zero-Inflated Models to Identify Transcription Factor Binding Sites in ChIP-seq Experiments
… immunoprecipitation followed by highthroughput sequencing (ChIP-seq) is considered the gold standard in locating these binding sites and programs use to identify DNA-transcription factor binding sites are known as peak-callers. ChIP-seq data are known to exhibit considerable background noise and …
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Identifying chromatin interactions at high spatial resolution
… at high spatial resolution from ChIA-PET data. We introduce SPROUT which is a hierarchical probabilistic model that discovers high confidence interactions between binding events that it accurately locates. We apply SPROUT to CTCF ChIA-PET data from mouse embryonic stem cells and …
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The Novel Regulation of Histone Modification In Cancer Development
… histone acetyltransferase (HAT) GCN5 for subsequent H3 acetylation. Genome-wide analysis of chromatin immunoprecipitation followed by sequencing (ChIP-seq) data sets reveals that NEDD4 regulates glucose-induced H3K9 acetylation at transcription starting site (TSS) and enhancer regions. …
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Role of Histone Lysine Demethylase, KDM1B, in Trophoblast Stem Cell Self-Renewal and Differentiation
… in vitro differentiation from transcriptomics data as its expression is markedly induced at the onset of differentiation. Furthermore, Kdm1b had been implicated in mouse development and placentation, via directing DNA methylation of maternal imprints in the oocyte. KDM1B is a histone lysine …
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Bayesian analysis for mixtures of discrete distributions with a non-parametric component
… false non-discovery rate in the case of discrete data. Moreover, it does not incur the label-switching problem. An application of the method to data generated by ChIP-sequencing experiments is shown. A one-dimensional Markov random field model is proposed, which accounts for the spatial …
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Computational algorithm development for epigenomic analysis
… 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 performance was …
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Characterization of Gene-by-Age Interaction and Gene-by-Gene Interaction In Coronary Artery Disease
… marginal main effects were detected. Open access ChIP-seq data was available for comparison with the statistical model, and to relate GWAS findings with biological mechanisms. The agreement between the statistical and biological models was very limited.</p>
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Bayesian Integration and Modeling for Next-generation Sequencing Data Analysis
… biology currently faces challenges in a big data world with thousands of data samples across multiple disease types including cancer. The challenging problem is how to extract biologically meaningful information from large-scale genomic data. Next-generation Sequencing (NGS) can now produce …
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Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework
… conserved sites, and rely heavily upon multiple sequence alignments. However, sequence conservation based approaches have limited ability to detect lineage-specific elements that could contribute to species-specific traits. In this thesis, we describe a novel framework that utilizes a birth-death …
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Functional analysis of low grade glioma genetic variants using statistics and physics-inspired deep learning methods
… and the lack of relevant types of experimental data in the brain. Based on statistical methods and physics-inspired deep learning methods, this work presents a comprehensive computational framework for performing functional analysis of LGG GWAS loci. We hypothesized that GWAS loci contain causal …
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Computational Methods for the Measurement of Protein-DNA Interactions
… effect their gene regulatory function. For many sequence specific DNA binding proteins we plan to predict the location of their action by having a model of their affinity to short DNA sequences. Existing and new models of protein sequence specificty are investigated and their ability to predict …
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Integrating biclustering techniques with de novo gene regulatory network discovery using RNA-seq from skeletal tissues
… of these skeletal tissues using RNA-seq technology was performed using differential expression, clustering and biclustering algorithms, to detect similarly expressed genes, which provides evidence for genes potentially interacting together to produce a particular phenotype. …
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Autonomous and non-autonomous regulation of chromatin structure during cellular senescence
… high-mobility group A (HMGA). Using ATAC-sequencing (assay for transposase accessible chromatin) we demonstrate that nucleosome positioning is substantially altered in RIS and that this re-distribution is also antagonised by NOTCH1, resulting in a distinct chromatin landscape. Importantly, …
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The novel roles of BCL6 and BATF3 in regulating human CD8⁺ T cell dysfunction
… in dysfunctional CD8⁺ T cells, with ATAC-seq demonstrating enhanced chromatin accessibility at their gene loci. Transcription factor footprinting shows increased BATF3 motif occupancy in chronically stimulated cells and integrative multi-omic analysis combining footprints, open chromatin …
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Transcriptional Regulation by DAX-1 in Pluripotent and Differentiated Cells
… in knock-down and knock in experiments through ChIP experiments. These findings emphasize a significant role of DAX-1 in moderating apoptosis in a breast cancer cell line.</p> <p>In the context of undifferentiated mouse embryonic stem cells, Dax-1 is highly expressed and has been shown to be an …
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Harnessing transcriptomic data to better understand gene regulatory mechanisms of neurodevelopmental disorders
… neurodevelopment and NDDs —using transcriptomic data.. To assess the role of NMD, I first create a novel framework which utilises a data-driven approach to identify in silico NMD targets using steady-state RNA-seq data. I then apply the data-driven NMD (DD-NMD) framework to study NMD roles of the …
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