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 71 for “"genomic sequence"”.
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The Genomic Sequence and Annotation of Bacteriophage HK239
… T4rII. To learn more about HK239, the genome was sequenced and annotated. The genome is 41,538 bp in length and there are 71 open reading frames. It has a genomic organization similar to other lambda phage and is most closely related to bacteriophage HK022. No additional genes that share homology …
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Accelerating genomic sequence alignment using high performance reconfigurable computers
… of reconfigurable computers to accelerate genomic sequence alignment specifically for genome sequencing applications. We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2) reconfigurable computer, allowing a single …
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The Role of Genomic Sequence in the Spatial and Temporal Propagation of Heterochromatin
<p>Characterizing how genomic sequence interacts with trans-acting regulatory factors to implement a program of gene expression in eukaryotic organisms is critical to our understanding of genome function. One means by which patterns of gene expression are achieved is through the differential …
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Retrotransposon-mediated instability in the human genome
… human genome that have the potential to create genomic instability either during the insertion of new elements or through ectopic recombination. However, recent in vitro analyses have demonstrated that these elements also repair DNA double-strand breaks, hence contributing to the maintenance of …
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Predicting genomic interactions using deep learning
… a deep learning model, Deep3DGenome, to predict genomic interactions using both genomic sequence data and chromatin features. We find that a machine learning model that has anchor specific modules and uses rich chromatin features outperforms previous approaches at predicting 3D interactions.
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Comparative genomics of nematodes: Caenorhabditis elegans as a tool to study the Haemonchus contortus genome
… of small ruminants Haemonchus contortus is being sequenced at the Pathogen Sequencing Unit of the Wellcome Trust Sanger Institute, Cambridge, UK. Currently, in excess of 800 Mb of genomic sequence is available for this on-going project (http://www.sanger.ac.uk/Projects/H_contortus/). Once …
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Mechanism of Pathogenesis and Replication of an Avian Strain of the Hepatitis E Virus in a Chicken Model
… sites, to determine and analyze the complete genomic sequence of the avirulent strain of avian HEV, and to study the compartive pathogenesis of the two isolates of avian HEV, the prototype pathogenic and avirulent strains of avian HEV. We attempted to experimentally infect …
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Genetic analysis of Ximenia Americana under natural conditions
… probe-pairs that hybridised to the X. americana genomic DNA on the basis of the perfect-match (PM) probe signal were selected and analysed using a cel file parser script to generate a new high density probe mask files. These files effectively represent the first ever X. americana DNA-DNA …
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Retrotransposon mediated genomic fluidity in the human and chimpanzee lineages
… are associated with human genetic variation and genomic rearrangement. Although they are abundant throughout primate genomes, their propagation strategy remains poorly understood. The recently released human and chimpanzee draft genome sequences provide the opportunity to compare the human genome …
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Molecular Characterization of Animal Strains of Hepatitis E Virus (HEV): Avian HEV and Swine HEV
… non-human primates, to determine the full-length genomic sequence and genome organization, and to construct an infectious cDNA clone of avian HEV. The prevalence of swine HEV infections in US swine herds and the heterogeneity of swine HEV isolates from different geographic regions of the United …
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Computational genomics : mapping, comparison, and annotation of genomes
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in …
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On the use of locality aware distributed hash tables for homology searches over voluminous biological sequence data
Rapid advances in genomic sequencing technology have resulted in a data deluge in biology and bioinformatics. This increase in data volumes has introduced computational challenges for frequently performed sequence analytics routines such as DNA and protein homology searches; these must also …
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A comparison of two methods of template amplification for next generation sequencing: Implications of polyclonal formation on DNA sequence for several cancer tissues
… effective treatments for cancer patients using genomic sequence data, including the detection of oncogenes (genes involved in cancer development). Simultaneous amplification of multiple DNA templates (referred to as polyclonal formation) is a primary disadvantage when preparing templates for NGS …
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Risk prediction with genomic data
… is the use of insertions and deletions in the genomic sequence (INDEL) together with SNPs as a feature for prediction. A substantial improvement in the prediction accuracy is achieved using the latter approach. The success of the approach of using NSG data shows that it contains valuable …
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Physical and genetical investigation of the Xp11.3 region on the short arm of the human X-chromosome
… high frequency of rearrangements occurring. DNA sequences between DXS8237E, UBE1, PCTKl and the distal gene, UHX1, have been investigated with regard to LINEI elements, which are thought to playa role in X-inactivation. The results obtained strongly suggest a link between LINE1 elements and X …
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Isolation and sequencing of a genomic clone of ESI28 : an early salt-stress induced gene of the salt-tolerant wild wheatgrass Lophopyrum elongatum
A genomic sequence corresponding to a putative actin-depolymerizing factor (ADF) was isolated from a wheat (Lophopyrum elongatum) genomic library. The genomic clone, designated ESI28-G-5, codes for the ESI28 gene (early salt-stress induced). The 5$\sp\prime$-upstream sequence contains a putative …
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A novel genomics and bioinformatics approach to assess immunoglobulin and T cell receptor rearrangements and somatic hypermutation in lymphoproliferative disorders
… mutations are intentionally inserted into the genomic sequence to marginally alter the confirmation of immunoglobulin (Ig) receptors. SHM is part of normal B cell development and is primarily restricted to germinal centres (GC). SHM has therefore been reported in lymphoproliferative disorders …
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Platyrrhine Phylogenetics With A Focus On Callitrichine Life History Adaptations
… phylogeny is universal to any comparative genomic study. Here we have constructed a reliable phylogenetic framework from which reproductive strategy could be studied in callitrichines. First, to determine the most recent common ancestor of Anthropoid primates we took a phylogenomic …
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Chemogenomic approaches to drug design : docking-based virtual screening of nematode GPCRs for potential anthelmintic agents
… the physiology of helminths. The published genomic sequence of nematode Caenorrhabdtis elegans as well the primary sequence of the FLP18R1 G-Protein Coupled Receptor are available. GPCRs play a significant role as targets for therapeutics and are responsible for signal transduction in cells. …
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Motifs, binding, and expression : computational studies of transcriptional regulation
… address three key challenges in the analysis of genomic sequence, protein localization, and expression data: (1) learning representations of the specific binding interactions that determine connectivity in regulatory networks, (2) developing physically grounded models describing these …
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