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 23 for “"Gene models"”.
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Understanding Plant Response to Stress Using Gene Model Quality Evaluation and Transcriptome Analysis
… the protein makeup of the early land plants. The gene model sequence data of two early land plants, <em>Physcomitrella patens</em> (moss) and <em>Chlamydomonas reinhardtii</em>(green algae). We specifically focused on the protein family expansion of protein kinases due to their roles in various …
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Approaches to understanding diversity in rubber and carotenoid synthesis in <i>Hevea brasiliensis </i>latex
… synthesised from isopentenyl diphosphate (IPP) generated from the cytoplasmic mevalonate (MVA) pathway and the plastidic methyl erythritol phosphate pathway (MEP). This study utilised two rubber tree clones (RRIM600 and PB235) that show visibly contrasting levels of yellow carotenoids for the …
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Performance comparison of five RNA-seq alignment tools
… is discrete in nature, therefore with reasonable gene models and comparative metrics RNA-Seq data can be simulated to sufficient accuracy to enable meaningful benchmarking of alignment algorithms. To provide guidance in the choice of alignment algorithms, five different alignment tools for RNA-Seq …
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Recent advances using genetic analyses in waterhemp
… for new management options. Understanding the genetic diversity present within the A. tuberculatus gene pool, including for key traits such as non-target-site herbicide resistance and dioecy, may contribute to the advancement of effective management strategies. Inheritance, segregation, and …
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Improving Dbnsfp
… prediction scores to indel annotation based on gene models, including CADD, SIFT, and PROVEAN. All those scores can be calculated on-the-fly after installing resources locally. A Docker implementing the indel annotation and deleteriousness prediction has been developed and ready to be deployed …
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Chemosensory gene expression analysis in the argentine ant, linepithema humile
… expression patterns of a subset of chemosensory genes, including odorant receptors (Ors) and odorant binding proteins (OBPs), in the invasive Argentine ant, Linepithema humile. Fragments of two Ors were identified from a whole ant EST project, which suggested their potential importance in …
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Decoding DNA: scalable genome annotation software, generative AI, and application to the cactus pear genome
The annotation of protein-coding genes from a raw genome assembly involves identifying the sequence regions that are transcribed into mRNA transcripts, spliced, and ultimately translated into protein. Thus, genome annotation is a fundamental task that critically supports systems level biological …
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Improving the genome assembly and annotation of the white-tailed deer (Odocoileus virginianus borealis)
… of pathogens, host-pathogen interactions, host genetic variation, and behavior. Repetitive elements are ubiquitous within mammalian genomes, and long single-molecule reads produced by third-generation sequencing can span these regions. I present a genome produced with DNA from a single …
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The effects of catalase and kisspeptin overexpression on amyloid peptide toxicity
… Aβ. Kisspeptin (KP) is a product of the KiSS-1 gene and contains an Aβ binding domain, which also interacts with Aβ. The localization of catalase, KP and Aβ in the AD brain plus the effects of catalase and KiSS-1 overexpression in neuronal cells were investigated in the present study. Tissue …
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A Genomic and Proteomic Investigation of the Plant Pathogen Armillaria mellea: Buried Treasure or Hidden Threat?
… to enable new studies, and limited experimental models are available to investigate basidiomycete pathogenicity. Herein it is revealed that the A. mellea genome comprises 58.35 Mb, contains 14473 gene models, of average length 1575 bp (4.72 introns/gene). A novel, large-scale proteomic shotgun …
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Cloning and Characterization of the dominant Inhibitor of Wax 1 (Iw1) gene in polyploid wheat
… map, which is currently 1,200 kb in size. Gene models were predicted in silico and we have begun to test candidate genes using allelic diversity and expression analysis. The results of our physiological experiments clearly show a reduction in light reflectance and a possible increase in …
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Integrative Genomics Reveals a Role for GNA13 in Lymphomagenesis
… data sets is one of the major challenges of next generation sequencing.</p><p>In this dissertation, I have developed several complementary strategies to describe the genetic underpinnings of lymphomas. I begin with developing a better method for RNA sequencing that enables strand-specific total …
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Evolution of the Gr family of gustatory and odorant receptors in mosquitoes
… a total of 114 potential proteins encoded by 79 genes. In the sequenced genome, 23 of these genes and protein isoforms are pseudogenic, leaving 91 putatively functional Grs. Comparison with the set of 76 Grs encoded by 52 genes in the distantly related Anopheles gambiae Giles mosquito revealed 13 …
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Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing
… junctions - splice variants of previously known gene models and potential novel transcription units. An attempt was also made to exploit the data to understand the drought mediated transcriptional events (e.g. alternative splicing). Gene Ontology (GO) enrichment analysis revealed massive …
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Data Mining for Selected Genes of Agronomic Interest from the Oil Palm Genome Using a Comparative Genomics Approach
Data mining of genes related to agronomic traits and transcription factors in plant genomes is essential to provide information on target genes for breeders. Taking advantage of the availability of completed genome sequences and the gene model available in a public database, the comparative genomic …
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Exploring the evolution of social behaviour using genomic data
… in the protein coding regions of brain expressed genes. To this end, we used 454 GS FLX sequencing technology to generate the brain Expressed Sequence Tags (ESTs) of twelve socially diverse bees. The ESTs were assembled into species-specific non-redundant contigs and singletons, which were loaded …
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Genetic studies of phenotypic variants in the woodland strawberry, (Fragaria vesca)
… This thesis represents some of the first forward genetics studies evaluating putative T-DNA insertional mutants in F. vesca. The observed phenotypes include alterations to floral development, anthocyanin pigmentation and leaf structure. The floral development mutant named green petal (gp) was not …
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Exploring Genome Structure and Gene Regulation Related to Virulence in Fungal Phytopathogens Using Next Generation Sequencing Techniques
… largely enabled by the development of next-generation sequencing (NGS) techniques. Applications of NGS include studies of entire genomes, characterization of the entire transcriptome (RNA-Seq), and detection of protein-DNA binding sites (ChIP-Seq). The cost of sequencing a fungal genome, for …
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Analysis of genetic variation in Pediculus humanus and Populus trichocarpa
… reads mapped to the 10,775 draft body louse gene models from the whole genome assembly predicted nine presence/absence differences, but PCR confirmation resulted in a single gene difference. One novel microRNA was predicted in both lice species and 99% of the 544 transcripts from Candidatus …
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Reproductive Genomics in the Stick Insect Clitarchus hookeri
… foliage of the plant on which they feed. Parthenogenesis is common among these insects, with 10% of the taxa scattered in different families being completely or partially parthenogenetic. These insects are poorly studied at the molecular level compared with other insects that are of economic …
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