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 27 for “"Shotgun sequencing"”.
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De Novo Assembly of Genomes in Microbiomes: From Amplicons to Whole-Genome Shotgun Sequencing
In recent decades, the rapid progress of DNA sequencing technologies has greatly propelled metagenomics research. However, a critical bottleneck in current bioinformatics investigations is the assembly of metagenome at the strain-level resolution. This is indispensable for gaining profound insights …
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Novel Algorithms for Structural Alignment of Non-coding RNAs
… for fragmentary data, such as found in direct shotgun sequencing and metagenomic surveys. A separate and alternative model of local alignment is used as the basis for a structural search filter. This is combined with other filtering techniques and high-performance implementations to increase …
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Information theoretic limits of metagenomic binning
… communities, typically using high-throughput shotgun sequencing. In the metagenomic binning problem, we observe random substrings (called contigs) from a mixture of genomes and want to cluster them according to their genome of origin. Based on the empirical observation that genomes of …
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Construction and phenotypic screening of mid-size insert marine microbial environmental genomic libraries
… approach for both functional screening and shotgun sequencing of environmental genomic libraries.
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The effect of tylosin exposure or exclusion on liver abscess prevalence, fecal pathogen populations, and the microflora of finished beef products from feedlot cattle
… and finished beef products through 16S rRNA gene sequencing and shotgun sequencing from feedlot cattle with and without exposure to tylosin. Overall, liver abscess rates were lower among cattle exposed to tylosin. However, there were no differences among treatment groups for any of the sample …
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Addressing geometric abnormalities and algorithmic shortcomings in metagenomic analysis.
… analysis methods, making maximal use of sequencing data output to accurately represent sample relationships in a microbiome dataset. We introduce LMdist, a dimensionality reduction method for adjusting pairwise distances to more accurately represent distances along a sampling gradient. …
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Leveraging community-based sequencing approaches to characterise the dairy microbiome
… microorganisms, advances in high-throughput DNA sequencing have enabled the study of entire microbial communities in food or food-related samples. In this thesis, shotgun metagenomic sequencing was employed to investigate microbial communities in bulk tank milk. First, shotgun sequencing was used …
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Rarity, cause or consequence: comparative landscape genomics of six lichenized fungi with contrasting range sizes, life histories, and morphologies
… 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 for this research advances established workflows for assessing …
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Host Immune-Microbial Interactions in Inflammatory States
… profiles were constructed from metagenomic shotgun sequencing of stool, differential abundance analysis of microbial species, and functional annotation of the taxonomic profile, yielding 12 microbial species and 79 metabolic pathways that were significantly differentially abundant in …
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Effects Of Diet And Parasites On The Gut Microbiota Of Diverse Sub-Saharan Africans
… African populations using metagenomic sequencing, we can better understand differential response to diseases and environmental factors in producing physiological adaptations. Furthermore, by extending microbiome sampling across a range of traditional African populations in multiple …
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Microbiological, genomic and transcriptomic analyses of human tuberculosis lung cavities
… testing, strain-type determination, whole-genome sequencing, and whole-transcriptome shotgun sequencing was conducted. RESULTS: Samples were obtained from 2 MDR-TB, 1 pre-XDR-TB and 12 XDR-TB patients, and 10 non- TB controls. There was considerable heterogeneity between sputum and the cavity with …
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A demographic and dietary history of ancient dogs in the Americas using ancient DNA
… American Bottom using both stable isotopes and shotgun sequencing of dog coprolites, and used the findings about dog diet to infer human diet during the Late Woodland and Mississippian periods. We found that dogs (and humans) ate no maize during the Late Woodland Period, but were consuming large …
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Metagenomic Analyses of the Human Gut Virome
… microbiota of five humans from the first study. Shotgun sequencing of DNA isolated from the input human VLP preparation, cecal and fecal samples collected over time from these gnotobiotic mice, and VLPs recovered from their fecal samples, revealed a ordered and reproducible sequence of phage …
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Phylogenetic and functional characterization of human microbiome intra-species diversity and tracking of early-life transmission
… its bacteria. The amount of publicly available shotgun sequencing data as well as development of computational tools allowed to reach strain-level resolution in metagenomic analysis. In this thesis, I present systematic approaches to study the strain-level variation using complementary …
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Understanding the evolution of cymothoid isopod parasites using comparative genomics and geometric morphometrics
… museum specimens using a low-coverage shotgun sequencing approach, and usethese data to reconstruct cymothoid phylogeny.We show that, after accounting for shared ancestry, attachment morphology is stronglyinfluenced by parasitic strategy. Whole mitogenome sequences are not suitable …
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Using Museomics to Investigate Extinction and Decline in British Butterflies
… trends. This was achieved using whole genome shotgun sequencing of both historical museum samples and modern samples, and using these sequences for population genomic analysis. As A. crataegi drew closer to extinction in Great Britain, it showed marked increases in inbreeding compared to …
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The integration of fine-scale DNA-DNA associations by inclusion of Hi-C DNA cross-linking information into metagenomic community analysis
… The technical limitations of present-day sequencing technologies have meant, however, that in achieving culture-independence, traditional shotgun metagenomic sequencing experiments make a considerable sacrifice. That sacrifice comes in the form of information loss where, in preparing DNA …
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Characterization of cochlear transcription, translation and energy extraction in aging and noise-induced pathology
… part of this thesis employs whole transcriptome shotgun sequencing to study murine inner ear transcriptional activity in young, healthy animals as well as changes associated with organ aging and noise-induced auditory neuropathy, an important mechanism of hearing impairment in humans. Knowledge …
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Dating the emergence of the divaricate habit in the New Zealand flora
… at no marginal cost, from Next Generation Sequencing shotgun sequencing data of DNA samples enriched for a specific set of markers, and (2) developing a guide to using a piece of phylogenetic reconstruction software (treePL), which was missing from the literature and needed by users. On the …
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Novel insights into fibre and lipid substrates on the microbiome
Since the turn of the millennium, advances in sequencing technology have uncovered a plethora of microorganisms that live with and inside us. There are some indications that a considerable part of the environmental influence on human health and disease is mediated by this microbial community and it …
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