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 12 of 12 for “"Genome Browser"”.
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NextBrowse: An integrated and interactive web-based genome browser for analyzing and interpreting genomic data
… availability of software frameworks such as the Genome Analysis Toolkit, data interpretation and analysis still requires human intervention and refinement. Genome browsers enable developers and users of sequence analysis tools to visualize, compare, and better interpret genomic data such as gene …
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Develpment of soybean knowledge base for systems biology studies
… are visualized under the differential expression browser, which includes volcano plot, gene annotation, Venn diagram and the weighted gene correlation network analysis (WGCNA). These visualization and analytical tools provide soybean scientists an integrated and systematic manner to view their …
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Development of Soybean Knowledge Base (SoyKB), a multi-omics data integration web resource for bridging molecular breeding and translational genomics in Glycine Max
… OF MISSOURI-COLUMBIA AT AUTHOR'S REQUEST.] Many genome-scale data are available in soybean (Glycine Max) including genomics, transcriptomics, proteomics and metabolomics datasets, together with growing knowledge of soybean in gene, microRNAs, pathways, and phenotypes. This represents rich and …
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Tissue-specific classification of alternatively spliced human exons
… the University of California Santa Cruz (UCSC) genome browser were analyzed for tissue-specific skipping. Expressed sequence tags (ESTs) were aligned to exons and their tissue of origin and histology were identified. ACEs were also identified as a subset of the skipped exons. About 18% of the …
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Assembling improved gene annotations in Clostridium acetobutylicum with RNA sequencing
The C. acetobutylicum genome annotation has been markedly improved by integrating bioinformatic predictions with RNA sequencing(RNA-seq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth stages to sample the transcriptome from a range of …
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Functional and computational analysis of RNA-binding proteins and their roles in cancer
… RNA sequencing data and its integration into a genome browser. Appendix C describes a method for clonal analysis of neural stem cell growth and differentiation in culture using live imaging and `microdot' plates, developed as part of the work presented in part one of the thesis.
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Development of a Transposon Based Activation Tagged Mutant Population in Tomato for Functional Genomic Analysis
… molecular and agronomic research. With whole genome sequencing in progress, there is a need to study functional genetics through mutant lines that exceed the practical limitations imposed by the popular research cultivar, Micro-Tom. This project utilized Agrobacterium transformation and the …
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Identification Of Candidate Genes For Self-Compatibility In A Diploid Population Of Potato Derived From Parents Used In Genome Sequencing
… F1 hybrids between two genotypes used in potato genome sequencing, we observed fruit set on many greenhouse-grown plants. Subsequently, after controlled self-pollinations, we confirmed fruit set in 32 of 103 F1 plants. Our goal was to identify genes responsible for self-compatibility in this …
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Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation
… is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet …
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Computational Analysis of High-Replicate RNA-seq Data in <em>Saccharomyces cerevisiae</em>: Searching for New Genomic Features
… to search the <em>Saccharomyces cerevisiae</em> genome for new genomic features. RNA-seq data were aligned to the genome with three successively stringent set of parameters for the STAR aligner (Dobin et al., 2013). The varying levels of stringency elucidated some complexities in the RNA-seq …
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The chromatin landscape of barley: gene expression, evolution and epigenetics
… important crop species with a large diploid genome. Around a half of the barley genome and a fifth of the genes are constrained within a low-recombining pericentromeric (LR-PC) region. I explored the LR-PC gene component with a genomic investigation of gene expression, diversity and …
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The role of neurofilament-light polipeptide (NEFL) in the onset and progression of hepatocellular carcinoma
… we analyze the CpG island described in UCSC Genome browser in the 5’ flanking genomic region of NEFL gene. Analysis of the methylation status of 10 consecutive CpG dinucleotides in 5 HCC and 3 normal rat livers exhibited no differences in the methylation status in HCC and controls. These …