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 48 for “"Bioinformatic tools"”.
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Bioinformatic tools for single-cell data analysis in clinical studies
… parallel efforts to develop and apply new bioinformatic techniques to generate robust findings from single-cell data The advances are especially pertinent for small clinical studies in which low sample numbers are limiting In the first part of the thesis, two classes of methods are …
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Development of Bioinformatic Tools and Procedures to Computationally Support DNA Barcoding
… roughly the same for the standalone alignment tools tested, and for the matK gene the results were better than the standalone alignment tools but not as good as the manually edited version of the matK alignment.<br/><br/>From the development of the new metabarcoding analysis pipeline, the …
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Developing bioinformatic tools for phosphorylation site co-regulation and correlation: The plant Cellulose Synthase Complex as a case study
Cellulose is the most abundant biopolymer on the planet, and this paracrystalline polysaccharide has a variety of industrial applications ranging from textiles to biofuel production. Regulation and polymerization of cellulose in plant cell walls are complex pathways consisting of many proteins with …
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Production, characterization and evaluation of anti-diabetes peptides from proteins of improved common bean (Phaseolus vulgaris L.) cultivars using bioinformatic tools, enzymatic systems, and in vitro and in vivo models
… bean protein and determined their efficacy using bioinformatics tools, enzymatic systems, in vitro and in vivo models. Our research started with the selection and characterization of proteins, peptide profile, protein inhibitors, α-amylase inhibitors, phenolic compounds and anthocyanins of …
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Characterization of protein secretion in Mycobacterium leprae using phoA fusions in Escherichia coli and Mycobacterium smegmatis
… with known MT secreted proteins; 2) to apply bioinformatic tools designed to assess proteins for secretion, to proteins selected in objective 1 with the goal of improving the likelihood that selected proteins are secreted by M. leprae, 3) to validate secretion of selected ML proteins through …
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The Majority of the Diaphragm Immune Transcriptome Profile Rescued in Mdx Mice by Microdystrophin Gene Therapy was maintained by Voluntary Wheel Running
… were analyzed with Microsoft Excel, R, and bioinformatic tools such as KEGG and DAVID to explain immune system adaptations in response to combined microdystrophin treatment and running in mdx mice. Two major inflammatory signaling pathways, the IL-6/JAK/STAT and NF-kB signaling pathways …
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Evaluation of Genetic Variants Influencing Susceptibility to Type 2 Diabetes Associated End-Stage Kidney Disease and Associated Phenotypes
… including whole exome sequencing and bioinformatic tools, in an effort to further elucidate the genetic architecture of T2D-ESKD and non-T2D ESKD in several samples of African Americans, and to a lesser extent, in European Americans.
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Engineering antimicrobial strains of saccharomyces cerevisiae as industrial platform for non-sterile bioprocesses
… and their amino acid sequence was analyzed using bioinformatic tools. AlphaFold, Clustal Omega, and SNAP2 were used to predict AMP tertiary structures, construct a phylogenetic tree, and analyse mutation effects, respectively.
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Evolutionary and ecological genomics in deep-sea organisms
… methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. These tools are then applied to test global- and regional-scale biogeographic hypotheses …
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Novel hypothalamic G protein-coupled receptors involved in the control of reproduction
… dysfunctions. Using six different online tools, the compound heterozygous (L282V+E339K) mutation identified in OXTR and the double heterozygous (V40M/L287P) mutation identified in NPY4R were examined for prediction of deleterious effects. These mutant GPCRs were then cloned into a …
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Using Tumour Evolution to Understand the Epigenetic and Transcriptional Adaptations of Cancer to Host Immunity
… escape *in vivo*. Finally, a collection of bioinformatic tools were developed to perform process-based analysis of The Cancer Genome Atlas. These tools can suggest hypotheses of gene function and regulatory mechanisms and explore the pathological significance of gene expression signatures in …
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Elucidation of Jasmonate-Responsive Promoter Elements in the Calmodulin-Like Gene CML39 in Arabidopsis
… hormone jasmonic acid (JA) in Arabidopsis. Bioinformatic tools predict a large number of putative JA-responsive cis-elements within the CML39 promoter. Deletion analysis of CML39 promoter fragments in planta reveals that some cis-elements respond in a tissue-specific manner. Analysis of …
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Genomic studies of motif enrichment and conservation in the regulation of gene expression in the brain
Several bioinformatic tools will be brought to bear in this thesis to identify specific genomic loci that serve as regulatory gateways of gene expression in brain. These "motifs" are short nucleotide patterns that occur in promoters and 5' or 3' untranslated regions of genes. Occurrences of motifs …
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Utilising Single-Cell Technology to Investigate Gene Regulation
… with adapted protocols and specialised bioinformatic tools now enabling analysis far beyond gene expression profiling. In addition to measuring expression, emerging methods can quantify the result of some of the molecular mechanisms previously mentioned. Explicitly, single-cell …
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Comparative Whole-genome and Phenotype Analyses of Virulence Factors and Lethality in Nematode Challenge Assay among Aeromonas isolates
… among the 46 isolates was mapped using several bioinformatic tools. Isolates with similar virulence factor and antibiotic resistance genetic markers tended to originate from similar hosts or the environment, indicating common selective pressure. Challenge of <em>Caenorhabditis elegans </em>with …
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Cell Signalling and MicroRNAs: Regulation and Evolution
… regulation through the incorporation of several bioinformatic tools. The results of this work show that microRNA-mediated regulation in signalling networks is particularly important onreceptors. In addition, the evolutionary analysis shows that rodents and humans microRNA-mediated regulation of …
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Rarity, cause or consequence: comparative landscape genomics of six lichenized fungi with contrasting range sizes, life histories, and morphologies
… fungi produced to date. Using a suite of bioinformatic tools, short-read sequences produced using whole-genome shotgun sequencing (WGS) were aligned to reference genomes, assembled from long-read sequencing, and filtered for quality before downstream analyses. The novel pipeline developed …
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Antibody production with synthetic peptides against human Coronavirus-NL63 ORF3 protein
… Open Reading Frame 3 (ORF3) protein. Firstly, bioinformatic tools were used to assist in identifying antigenic determinants and antigenic epitopes were used to generate peptides of ORF3 protein. Thereafter, the ORF3 protein was characterized using various molecular techniques across the …
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Effect of Different Growth Conditions on Cell Growth Using Biphenyl as a Sole Carbon Source by the Bacteria Isolated from Soil Samples Collected from San Jacinto River, Texas
… any known bph genes to break down biphenyl. Bioinformatic tools such as BUSCO, BRAKER, PROKKA, RAST, Roary, KEGG Map, and ghostKoala were employed to investigate and verify the presence of pathways potentially capable of producing novel biphenyl’s derived secondary metabolite. Annotation …
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Characterizing neural tissues with mass spectrometry imaging via enhanced computational approaches
… in planarian regeneration. In addition, several bioinformatic tools are developed to predict final neuropeptide structures and associated masses that can be compared to experimental MSI data in order to make assignments of neuropeptide identities. The integration of computational approaches into …
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