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 195 for “"ChIP-seq"”.
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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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Statistical methods for ChIP-seq and microbiome studies using next-generation DNA sequencing data
… 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 of microbiome features on …
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Miniaturised epigenome and interactome screening : development and application of microfluidic ChIP-seq and AP-MS
Contains fulltext : 213664.pdf (Publisher’s version ) (Open Access)
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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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Development And Application Of Next Generation Sequencing Pipelines In Arabidopsis
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used assay to uncover the function of proteins of interest by generating a snapshot of the protein’s binding sites in an organism at a certain stage given specific conditions. Previous publications provide recommendations …
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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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Microfluidic Technology for Low-Input Epigenomic Analysis
… tumorigenesis. Chromatin immunoprecipitation (ChIP) is the technique of choice for examining in vivo DNA-protein interactions and has been a great tool for studying epigenetic mechanisms. However, conventional ChIP assays require millions of cells for tests and are not practical for examination …
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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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Functional analysis of tcf21 and tbx20 in zebrafish
… network, scientists use a technique called ChIP-seq that can determine where in the genome these transcription factors bind. Nearby genes are potential targets of their regulation, and we can validate these enhancers by testing differences in expression using a fluorescent protein reporter …
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Non-Parametric Analyses of the Regulatory Roles of LINE-1 Retrotransposons during Motor Neuron Differentiation
… despite the advancements in next-generation sequencing due to difficulty in establishing the identities of specific elements involved in a biological process of interest, e.g. transcription factor (TF) binding, from functional data modalities such as ChIP-seq and ChIA-PET. Results: First, I …
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Characterizing the Nuclear Function of the Cell Adhesion Molecule Fat and Chromatin Regulation by the Inner Nuclear Membrane Protein Speg
… binds to specific genomic loci in vivo. Through ChIP-seq, I characterized the genome-wide DNA binding profile of Ft in vivo. ChIP-seq results suggested that nuclear Ft binds mostly open chromatin. Interestingly, the ChIP-seq profile of Ft is highly correlated with that of the Hippo pathway …
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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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Whole genome regulatory variant evaluation for transcription factor binding
With the advent of high-throughput sequencing technology, Genome Wide Association Studies (GWAS) have identified thousands of genetic variants that are associated with disease and complex traits. Many of these variants reside in the non-coding region of the genome, and affect gene expression and …
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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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Bayesian Integration and Modeling for Next-generation Sequencing Data Analysis
… from large-scale genomic data. Next-generation Sequencing (NGS) can now produce high quality data at DNA and RNA levels. However, in cells there exist a lot of non-specific (background) signals that affect the detection accuracy of true (foreground) signals. In this dissertation work, under …
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Statistical methods for variant discovery and functional genomic analysis using next-generation sequencing data
… development of high-throughput next-generation sequencing (NGS) techniques produces massive amount of data, allowing the identification of biomarkers in early disease diagnosis and driving the transformation of most disciplines in biology and medicine. A greater concentration is needed in …
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Placental co-transcriptional activator Vestigial-like 1 (VGLL1) drives tumorigenesis via increasing transcription of proliferation and invasion genes
… in cellular invasion and proliferation, and ChIP-seq and RNA-seq assays were performed to identify VGLL1 target genes and potential impact using pathway analysis. ChIP-seq analysis identified eight transcription factors with a VGLL1-binding motif that were common between all three cell types, …
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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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AN INVESTIGATION OF THE MECHANISMS OF GROUCHO MEDIATED TRANSCRIPTIONAL REPRESSION
… repression. Recent studies that used Gro ChIP-seq data from Drosophila cells and embryos indicated that Gro could mediate transcriptional repression by promoting Pol II promoter-proximal pausing. In this work, I took three different approaches to test this model, and gain understanding of …
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