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 68 for “"Functional Annotation"”.
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PROTEIN SURFACE SIMILARITIES EVALUATION FOR FUNCTIONAL ANNOTATION STUDIES
… This process can be applied in the field of functional annotation, through the identification of similarities between surfaces of homologous proteins, and in study of interaction between proteins, through the identification of complementary areas between interacting proteins. The whole …
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Novel Lineage Specific Genes Expressed in Cattle Placenta: Discovery, Functional Annotation and Evolution
… play important roles in the morphological and functional adaptations of the ruminant placenta.
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First survey and functional annotation of prohormone and convertase genes in the pig
… and convertase genes that were identified were functionally annotated. As a result, 95 unique prohormone genes, 2 alternative calcitonin-related sequences, 7 prohormone convertases and 1 cleavage facilitator were identified in the pig genome 10.2 assembly and trace archives. The genome search …
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CLASSIFYING PEROXIREDOXIN SUBGROUPS AND IDENTIFYING DISCRIMINATING MOTIFS VIA MACHINE LEARNING
Accurate and automated functional annotation is a pressing open problem, with functional characterizations lagging far behind the exponential growth in biological sequence databases. In this thesis, I present our recent development of machine learning methods for high-throughput, accurate, …
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Comparing organisms on the level of metabolism
… has become an extremely powerful tool to uncover functional properties of these molecules. In general, however, the biological function is a result of many interacting molecules forming large interaction networks such as regulatory networks or metabolic pathways. To improve our understanding of …
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Aromatic hydrocarbon metabolism by Rhodococcus sp. I24 : computational, biochemical and transcriptional analysis
… were selected for microarray analysis based on functional annotation assignments made by the Consensus Annotation by Phylogeny Anchored Sequence Alignment (CAPASA) program, a high throughput system for automated functional annotation assignment of DNA sequence similarity search results. CAPASA …
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Harnessing Deep Learning with Protein Language Models to Unveil Microbial Enzyme Function in Health and Disease
In microbial genomics, accurate annotations of the biological functions of enzymes are critical, as these proteins have important roles in catalysing essential biochemical reactions with high specificity and efficiency. Historically, functional annotation tools have relied on hidden Markov models …
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Functional and cross-trait genetic architecture of common diseases and complex traits
… a method for partitioning heritability by functional annotation from genome-wide association summary statistics, and I apply it to 17 diseases and traits and many different functional annotations. Next, I show how to apply this method to use gene expression data to identify diseaserelevant …
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Domain-based approaches to understanding phylogeny and orthology
… are used in phylogenetic reconstruction and functional identification. Two groups of ionotropic glutamate receptors (iGluR’s) were identified with the topology of the binding core and pore-loop of the eukaryotic iGluR’s. Group 1 has a potassium-like selectivity filter and Group 2 is most …
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Genome-wide analysis of transcriptional expression programs, regulatory networks and Cis-regulatory sequences in Saccharomyces cerevisiae
… regulators. Such studies not only allow for the functional annotation of both genes and regulators, but can also provide clues about the identity of the regulatory regions within DNA, the structure of global regulatory networks and the regulation of DNA-binding proteins. These and other insights …
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Applications of Machine Learning in Source Attribution and Gene Function Prediction
… using whole genome sequencing data, and (2) the functional annotation of genes using single- cell RNA sequencing data. This work proposes the development of a bioinformatics pipeline tailored for identifying genomic variants, including gene presence/absence and single nu- cleotide polymorphism. …
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Dual-omics approach for 3,4-dihydroisocoumarin characterisation from Hydrangea serrata and isolation of polyketide synthases for heterologous expression in Pseudomonas putida KT2440
… assembly of leaves and roots alongside with functional annotation was generated and examined in two ways. The aim of this work was to isolate new polyketide synthase homologues from H. serrata with prospective of heterologous expression in the bacterial host Pseudomonas putida KT2440. The …
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Integrative high-throughput study of arsenic hyper-accumulation in Pteris vittata
… and Trinity <em>de novo</em> assembly. Functional annotation of the transcriptome was performed in terms of blast search, Gene Ontology term assignment, Eukaryotic Orthologous Groups (KOG) classification, and pathway analysis. Differentially expressed genes induced by arsenic stress were …
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Computational discovery of gene modules, regulatory networks and expression programs
… rapamycin, and cell-cycle module networks. I use functional annotation databases, independent biological experiments and DNA-motif information to validate the discovered networks, and to show that they yield new biological insights. Second, I present GeneProgram, a framework based on Hierarchical …
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Computational methods for functional interpretation of diverse omics data
… transcriptomic, proteomic, and metagenomic data. Functional interpretation of these data is key to elucidating the potential role of different molecular levels (e.g., genome, transcriptome, proteome, metagenome) in human health and disease. However, the massive size and heterogeneity of raw data …
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Unbiased global proteomic profiling of patient-derived meningiomas of all grades to identify molecular signatures of differentially expressed proteins and phosphoproteins.
… performed differential expression analyses and functional annotation studies to identify commonly upregulated proteins and phosphoproteins in all grades of meningioma compared to meningeal tissue as well as grade-specific candidates relevant for tumour progression. Top candidates were validated …
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Towards Understanding the Genetic Basis of Virulence in Pseudomonas aeruginosa
… these, 280 were genes that do not currently have functional annotations. Functional enrichment analysis of genes highlighted the importance of amino acid biosynthesis and metabolism, nucleotide biosynthesis and metabolism, and biogenesis of motility related structures. This study has laid the …
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Influence of landscape-variation in geochemistry on taxonomic and functional composition of microbial mat communities in the McMurdo Dry Valleys, Antarctica
… Here we report on work investigating the functional diversity of microbial mat and underlying soil communities in the McMurdo Dry Valleys of Antarctica across a gradient of phosphorus availability on glacial tills of distinct age and mineral composition in Taylor Valley, Antarctica. …
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