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 22 for “"Pan-Genome"”.
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Creating and analysing an African pan-genome
The human reference genome is currently a core resource for understanding the role of genetics in human health, disease, and variation, and has been invaluable in the development of clinical and computational tools for these purposes. However, the limited number of individual genomes used to create …
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A pan-genome wide association study to identify genes associated with invasive Streptococcus pneumoniae
… We tested this hypothesis by applying a pan-genome approach using whole-genome sequencing short reads of 1477 samples from Malawi, including those obtained from the nasopharynx of carriers (825 samples) and from the blood and cerebrospinal fluid of patients (652 samples). In-silico …
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Exploring the Population Structure, Recombination Landscape, and Pan-Genome of the Global Neisseria meningitidis Population
… particularly the ‘meningitis belt’ that spans from West Africa to East Africa, where there is greater disease burden and periodic epidemics which can span the region. Due to difficulties in treatment, the primary method of controlling invasive meningococcal disease is vaccination. …
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Evolution of targets at the host-pathogen interface
… Chapter 2: Protein-coding potential of the Mtb genome <br>Using comparative genomics, I investigate the protein-coding potential of globally-distributed Mtb strains. Previous reports had suggested that the pan-genome (or all unique protein coding sequences among all strains) gets larger with …
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Examining bacterial variation with genome graphs and Nanopore sequencing
… genes found within a given species is called the pan-genome and is generally much larger than the gene repertoire of a single cell. A consequence of this pan-genome is that bacterial genomes are highly adaptable and thus variable. The dominant paradigm for analysing genetic variation relies on a …
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Methods for Analysis of Prokaryotic Genome Architecture
… 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. Currently there are more than 96,000 bacterial genomes …
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Applications of Machine Learning in Source Attribution and Gene Function Prediction
… the source of bacterial pathogen 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 …
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A gene-space de Bruijn graph framework for improved genotyping of antimicrobial resistance genes
… greatly improved the completeness of bacterial genome assemblies, allowing for more accurate detection of AMR. However, even with long-reads, assembly remains imperfect and this can result in the under-detection of genuinely present AMR genes and inaccurate predictions of antimicrobial …
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Novel Micropatterned Substrate for Investigation of Ovarian Cancer Aggregate Formation and Response to Epigenetic Drug Therapy
… cell lines were used in the absence/presence of pan-genome epigenetic drugs such as suberoylanilide hydroxamic acid (SAHA). The micropatterned substrate supported cell proliferation, migration, and aggregate formation while maintaining phenotype and viability. Treating aggregates with SAHA …
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Comparative genomics of Bifidobacteria
… the sequence analysis of 14 bifidobacterial genomes from various species of the genus Bifidobacterium, and the determination of their open pan-genome trend. This analysis first determined the total number of genes to be considered as the reservoir of functions available to representatives of …
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Co-linear Chaining on Graphs With Cycles
… in bioinformatics. As the volume of sequenced genomes grows rapidly, pairwise sequence alignment becomes inefficient for pan-genomic analyses involving multiple sequences. The graph representation of multiple genomes has been an increasingly useful tool in pan-genomics research. Therefore, …
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Unravelling the role of Bacteroides and Phocaeicola in the human gut: exploring evolutionary dynamics, mother-to-infant vertical transmission, and functional characteristics
… different time points were also evaluated. Whole genome sequence (WGS) was carried out and the average nucleotide identity (ANI) was used to determine whether different isolates were the same strain. A blast comparison of the whole genome was also carried out. Metabolomics analyses and …
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Comparative genome analysis of human bifidobacteria with commercial potential
… two newly sequenced B. longum subsp. longum genomes and subsequent comparative analysis with publicly available B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis genomes (Chapter 2). The acquired data revealed a closed pan-genome for this bifidobacterial species and …
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A pan-genomics approach linking genotype and phenotype in the mega-pest, Helicoverpa armigera
… This information enables the application of pan-genomic approaches (which are focused on assessing the large-scale variation within a group) to organisms with large or complex genomes. In this thesis I describe my work on a pan-genomic approach to catalogue significant genetic variation …
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A pan-genomics approach linking genotype and phenotype in the mega-pest, Helicoverpa armigera
… This information enables the application of pan-genomic approaches (which are focused on assessing the large-scale variation within a group) to organisms with large or complex genomes. In this thesis I describe my work on a pan-genomic approach to catalogue significant genetic variation …
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Phenotypic and Genotypic Characteristics for Escherichia coli strains responsible for bacterial bloom events in Australia
… encapsulated, and capsule-negative strains. A pan genome comparison of phylogroup A E. coli revealed that the iron uptake system encoded by fecIRABCDE operon was over-represented among bloom strains (100%) compared to non-bloom E. coli (<39%). Growth assays however showed that the fec operon is …
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Phenotypic and Genotypic Characteristics for Escherichia coli strains responsible for bacterial bloom events in Australia
… encapsulated, and capsule-negative strains. A pan genome comparison of phylogroup A E. coli revealed that the iron uptake system encoded by fecIRABCDE operon was over-represented among bloom strains (100%) compared to non-bloom E. coli (<39%). Growth assays however showed that the fec operon is …
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Genic copy number variation associated with abiotic/biotic stress among a set of progenitors of contemporary maize germplasm
… it is estimated that a greater portion of the genome is affected by structural variation (SV). This is a broad phenomenon that includes copy number variation (CNV), inversions, and translocations that affect an intermediate-scale of genomic sequence. Structural variation has the potential to …
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Redefining gene distributions in K. pneumoniae and E. coli using large public datasets
… which new genetic material is introduced into a genome from an outside source. Drug resistance is most commonly driven by gene acquisition, and it is through the acquisition of virulence genes that K. pneumoniae and E. coli can cause disease. Indeed, HGT has been estimated to occur in high rates …
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Spatial-temporal patterns in evolutionary ecology and fluid turbulence
… and ecosystem stability, leading to a large pan-genome, an accelerated evolutionary timescale, and the emergence of ecotypes that are adapted to the stratified levels of light transmission as a function of ocean depth. The goal of Part 2 is to understand the nature of the transition to …
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