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 14 of 14 for “"gene annotations"”.
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Assembling improved gene annotations in Clostridium acetobutylicum with RNA sequencing
… minimized false positive error and determined gene boundaries, in some cases, to the exact basepair of prior studies. Curation of the pSOL1 megaplasmid reconciled transcriptome assembly statistics with findings from E. coli . The resulting annotation can be readily explored and downloaded …
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Comparative gene identification in mammalian, fly, and fungal genomes
… is the accurate identification of protein-coding genes. One approach to gene identification is comparative analysis of the genomes of several related species, to find genes that have been conserved by natural selection over millions of years of evolution. I develop general computational methods …
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Computational Methods for Accelerated Discovery and Characterization of Genes in Emerging Model Organisms
… underlying cause of a recently emerging class of genetic diseases collectively referred to as ciliopathies. The function and structure of cilia are conserved across all organisms with cilia. One of the most influential model systems used to study ciliopathies has been the ciliated green alga …
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Building a robust clinical diagnosis support system for childhood cancer using data mining methods
… to single nucleotide polymorphism (SNP) and gene expression data. This research thesis focuses on three different types of data: gene-annotations, gene expression and single nucleotide polymorphisms. Genetic association studies have led to the discovery of single genetic variants associated …
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Discovery of Function in the Enolase Superfamily
… sequences is valuable, the correctness of the gene annotations poses a problem--approximately one-half of the deposited sequences are incorrectly annotated. We are using the enolase superfamily as a model system to try to solve that problem. To date, >4000 members have been identified in the …
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Discovery of function in the enolase superfamily
… sequences is valuable, the correctness of the gene annotations poses a problem--approximately one- half of the deposited sequences are incorrectly annotated. We are using the enolase superfamily as a model system to try to solve that problem. To date, >4000 members have been identified in the …
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Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models
… comparative genomics analysis of protein-coding genes using phylogenetic codon models, in pursuit of two main lines of biological investigation: First, we develop PhyloCSF, an algorithm based on empirical phylogenetic codon models to distinguish protein-coding and non-coding regions in …
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Transcription analysis of virulent strains of Mycobacterium tuberculosis
… that allowed for the mapping of gene annotations between isolates. This allowed for the mapping of reads to a more suitable Beijing family reference while interpreting the results with annotations from the H37Rv reference. We generated expression and target profiles for the known …
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High-throughput sequencing of RNA 5'- and 3'-termini yields insights into viral and vertebrate gene expression
Next-generation sequencing techniques are unparalleled in their resolution and dynamic range, but are limited by read depletion at transcript ends. Protocols that specifically target these ends overcome this limitation and enable the study of biological phenomena that would otherwise prove …
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Dissecting the genetic basis of wheat yellow rust resistance in the NIAB Elite MAGIC population
… seen the rise of Pst populations that are more genetically diverse, more aggressive and that have adapted to warmer temperatures. These features, likely further aided by increased international travel, have led to important epidemic outbreaks and have jeopardised wheat yellow rust resistance …
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Identification of Quorum Sensing Genes in Halococcus Hamelinensis SP. Nov. 100Na1
… in order to control and regulate specific gene expression. The process of cell-to-cell communication is termed quorum sensing (QS). According to cell density, if a specific threshold concentration of autoinducers is reached, the neighboring cells are able to detect and respond to the …
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Exploration of Cell Cycle-Specific Essential Gene Functions in the Microbial Plant Chlamydomonas Reinhardtii
… followed a candidate strategy based on reverse genetics. These studies have a provided insights into plant cell cycle control, but are generally dependent upon sequence conservation between plant and opisthokont genes. This thesis presents work from an ongoing screen to identify critical …
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Computer-assisted generation and curation of genome-scale metabolic models with case studies in the methanogen genus Methanosarcina
… deal of interest in understanding how methanogenesis works. A wide array of tools has been developed for studying methanogen metabolism, including genetic manipulation tools and efficient culturing techniques. These tools are especially well developed in model methanogens such as Methanococcus …
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Detecting Phenotype-Specific Interactions Between Biological Processes From Microarray Data And Annotations
… biological interpretation of the voluminous data generated by these technologies, however, remains a challenging problem. A commonly used approach in interpreting the results of such high throughput experiments is to map the list of differentially expressed (DE) genes to gene ontology (GO) terms, …