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 12 of 12 for “"microbial genomics"”.
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Linking sequence to function in microbial genomics
Microbial genomes show high plasticity due to horizontal transfer, large community sizes, and rapid growth paired with adaptive mutations. Despite this mutability of gene content, most studies of microbial communities still rely on bulk, single-gene amplicon sequencing. In this thesis, I present …
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Novel phylogenetic approaches to problems in microbial genomics
Present day microbial genomes are the handiwork of over 3 billion years of evolution. Comparisons between these genomes enable stepping backwards through past evolutionary events, and can be formalized using binary tree models known as phylogenies. In this thesis, I present three new phylogenetic …
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Expanding the limits of Scale and sensitivity in microbial genomics
Sequencing of microbial genomes has enabled new understanding of human health and disease. Certain microbes can support human health through the microbiota, helping to train our immune system or supply essential nutrients. In other cases, microbes may be pathogenic, overwhelming the immune system …
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Bacterial genes and genome dynamics in the environment
One of the most marvelous features of microbial life is its ability to thrive in such diverse and dynamic environments. My scientific interest lies in the variety of modes by which microbial life accomplishes this feat. In the first half of this thesis I present tools to leverage high throughput …
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Methods for Analysis of Prokaryotic Genome Architecture
Research in comparative microbial genomics has largely been organized around the concept of reference genomes. Reference genomes provide a useful comparative touchstone for closely related organisms. However, they do not necessarily represent the biological diversity in a group of genomes. …
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Comparative microbial genome analysis of lactobacilli
… important lactic acid bacteria. Comparative Genomics is becoming increasingly important as a method of investigating the diversity of function and phylogeny of all microbial taxa, including Lactobacillus. In Chapter 1, I give an overview of relevant concepts in comparative microbial genomics, …
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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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Exploring the genomic and phenotypic diversity of the Vibrio cholerae species
Vibrio cholerae is the aetiological agent of cholera, an acute diarrhoeal disease which is estimated to result in up to 143,000 deaths per annum. Cholera is a considerable public health concern because it can spread rapidly in and explosive pandemics. Current pandemic cholera is caused by a …
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Analysis of Salivary Microbiota in Patients with Full-arch Implant Supported Fixed Prostheses
… colonized by a large number of different microbial species that are in a state of equilibrium. Dysbiosis can be caused by either changes in local or systemic conditions and is associated with increased risk of caries, periodontal disease, oral cancer and systemic diseases such as diabetes, …
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Redefining gene distributions in K. pneumoniae and E. coli using large public datasets
The work in this thesis is concerned with characterising genes and their distributions in Escherichia coli and Klebsiella pneumoniae. While both K. pneumoniae and E. coli are found in the guts of healthy individuals, as well as in animals and in the environment, they are particularly relevant …
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Using the Bacterial Plant Pathogen Pseudomonas syringae pv. tomato as a Model to Study the Evolution and Mechanisms of Host Range and Virulence
… do not cause disease in A. thaliana. Comparative genomics revealed candidate effector genes responsible for this host range difference. Effector genes conserved in strains pathogenic in A. thaliana were expressed in T1 to test whether they would allow T1 to growth better in A. thaliana. …
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Structural and biochemical studies on enzymes involved in natural product biosynthesis and cellular respiration
Natural products have recently become an interest in modern research. This is due to their synthesis mainly by living organisms and their natural biosynthesis and abundance. Many of these compounds have been found to have pharmaceutical and industrial applications, and have been used as the basis …