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.
Results
Showing 1 to 20 of 29 for “"microbial genomes"”.
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Statistical Methods For Assessing Structural Change In Human & Microbial Genomes
<p>Genetic sequencing has been recognized as an effective approach to accurately address biological problems, such as clinical detection of disease, mutation discovery, and targeting specific biomarkers associated with complex diseases. Compared with conventional Sanger sequencing, next-generation …
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Gene finding and the evaluation of synonymous codon usage features in microbial genomes
… phylogenetischen und strukturellen Analysen des Genomes und liefern weiteres, unabhängiges Beweismaterial für den archaebakteriellen Ursprung von Teilen des T. maritima Genoms.
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Probing statistical patterns across the tree of life: Comparative methods for microbial genomes and traits
Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2025-12-01
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Genomic signatures of sex, selection and speciation in the microbial world
Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared …
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Genome-wide microbial phylogeny reconstruction with polytomy identification
… With ever increasing speed of newly sequenced microbial genome deposition, the study of the evolutionary relationships among microbes has becoming more and more imperative. Using complete genome sequences to infer large scale multi-furcating microbial phylogeny without relying on MSA (multiple …
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Collective Evolution of Biological and Physical Systems
… in undercooled liquids, the evolution of microbial communities through diversification fronts propagating along microbial genomes, the evolution of the universality and optimality of the genetic code, and the emergence of genome biases. I present a new phase-field model of solidification …
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Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California
… application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the “genome proxy” microarray, which targeted marine microbial genomes and genome fragments …
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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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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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Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California
… application of a new tool for profiling marine microbial communities. Chapter 1 places the tool in the context of the range of methods used currently. Chapter 2 describes the development and validation of the "genome proxy" microarray, which targeted marine microbial genomes and genome fragments …
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Diverse enzyme reactions in phosphonate natural product biosynthesis
… products have been characterized by mining of microbial genomes. Phosphonates, which are characterized by their hydrolytically stable carbon-phosphorus bond, are prevalent in everyday life, such as in commercially available herbicides and an antibiotic deemed critically important in the clinic. …
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Structure and dynamics of genome-wide diversity in Prochlorococcus
… has its foundation in the diversity of microbial genomes. Here we explore adaptation and diversification through the lens of the marine cyanobacterium Prochlorococcus, which comprises a group of closely-related ecotypes that together perform most of the primary production in low-nutrient …
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A phylogenetic framework for large-scale analysis of microbial communities
… phylogenetics allows researchers to study microbial evolution, resolve strain-level relationships between microbes, and also taxonomically place and characterize novel and unknown microbial genomes. This thesis presents a novel computational phylogenetic approach implemented during my …
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The Heme -Copper Oxidoreductase Superfamily: Genomics and Structural Analyses
… superfamily by analyzing over 1100 microbial genomes (Bacteria and Archaea) and nine microbial environmental metagenomic datasets. Over 2000 new putative members were found which we classify into eight oxygen reductase families (A-, B-, C-, D-, E-, F-, G-, and H-families) and five …
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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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Taxonomic classification of metagenomic sequences
… organisms like animals or plants. Examples are microbial communities in the gut or on the skin of animals and humans, or bacteria that live in symbiosis with plants. The vast majority of such microbes are unculturable and thus cannot be sequenced by means of traditional methods. The recently …
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Gene expression control and antimicrobial peptide production by haute couture bacteria
… DNA synthesis technologies. For example, entire microbial genomes have chemically synthesized and interesting synthetic systems have been built with novel gene expression dynamics. Additionally, cells have been engineered to efficiently produce high value compounds, including a number of …
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Effects Of Diet And Parasites On The Gut Microbiota Of Diverse Sub-Saharan Africans
… amplicon and shotgun sequencing to characterize microbial genomes and annotate their functions. I combined this microbial data with extensive phenotype and ethnographic data. With this dataset, I detected gut microbial taxa associated with subsistence strategy, sex, geography, and host genetics. …
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Evaluating substrate utilisation to target newly identified health-promoting gut bacteria
… 3 through the analysis of publicly available microbial genomes of the same species of interest and, through the creation of metabolic models, predicting the substrates that these microorganisms could consume. Finally, in Chapter 4 we employ an ex vivo model to evaluate, through shotgun …
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De Novo Assembly of Genomes in Microbiomes: From Amplicons to Whole-Genome Shotgun Sequencing
… indispensable for gaining profound insights into microbial communities and addressing pivotal biological inquiries. Despite the availability of existing assembly tools, certain challenges remain unresolved. Within this thesis, I have delineated four crucial research questions: Firstly, do …
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