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 259 for “"metagenomic"”.
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Taxonomic classification of metagenomic sequences
… methods. The recently upcoming discipline of metagenomics provides various in vivo- and in silico-tools to overcome this limitation. In particular, high-throughput sequencing techniques like 454 or Solexa-Illumina make it possible to explore those microbes by studying whole natural microbial …
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Microbial profiling using metagenomic assembly
… strategies should allow the relation of metagenomic sequence data to our understanding of microbial taxonomy, while also facilitating the discovery of novel taxa. For eukaryotes, a method has been established that links DNA sequences to the identification of organisms: DNA Barcoding. A …
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Information theoretic limits of metagenomic binning
The goal of metagenomics is to study the composition of microbial 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 …
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Deep learning approach to metagenomic binning
… neural network (CNN) based approach to metagenomic binning that embeds reads into a low-dimensional vector space based on taxonomic classification. We show that our method can get the speed and sensitivity necessary taxonomic classification. Our method was able to achieve 13% accuracy on …
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Optimal clustering techniques for metagenomic sequencing data
Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in the vagina, but results have been inconsistent, possibly due to methodological differences. We …
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Metagenomic Analyses of the Human Gut Virome
… of experimental and computational tools for metagenomic analyses of viruses purified from frozen fecal samples obtained from healthy adult monozygotic twin pairs and their mothers living in the USA, over the course of a year. The virome in this population was dominated by phages and exhibited …
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A Metagenomic Study of The Tick Midgut
<strong>A Metagenomic Study of the Tick Midgut<br></strong> Daniel Yuan, B.S.<br> Supervisory Professor : Steven J. Norris, Ph.D.<br> Southern tick–associated rash illness (STARI) or Master’s disease is a Lyme-like illness that occurs following bites by <em>Amblyomma americanum</em>, the lone-star …
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Computational Analysis of Viruses in Metagenomic Data
… and regulating many key ecosystem processes. As metagenomic data can contain many microbiomes including many viruses, by analyzing metagenomic data we can analyze many viruses at the same time. The first step towards analyzing metagenomic data is to identify and quantify viruses present in the …
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Matrix Factorization for Learning Metagenomic Pathways and Species
… called Operational Taxonomical Units (OTUs) from metagenomic data. The methods are based on Nonnegative Matrix Factorization (NMF). The rows of our data matrix correspond to metagenomic samples and columns correspond to chemical reactions present in the samples. In order to learn both pathways and …
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Shotgun metagenomic analysis of antimicrobial resistance in wastewater
… they relate to AMR indicators identified through metagenomic sequencing. Through monitoring of local WWTPs, it was found that AMR indicators shifted over time and in relation to human behavior that changed due to the COVID-19 pandemic. Hospital wastewater did not measurably impact the microbiome …
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Metagenomic Data Analysis Using Extremely Randomized Tree Algorithm
… this issue using molecular techniques such as metagenomic sequencing and metagenomic data analysis. Such analyses compare the broad spectrum of ARGs in water and wastewater samples, but these studies use comparisons which are limited to similarity/dissimilarity analyses. However, in such …
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Addressing geometric abnormalities and algorithmic shortcomings in metagenomic analysis.
Our work aims to identify shortcomings in microbiome 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 …
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Natural Products From Functional Screening of Soil Metagenomic Libraries
… a strategy that eludes 99% of the microbiome. Metagenomics offers a route to study uncultured bacteria by extracting DNA present in environmental samples and cloning this eDNA into a vector to make metagenomic libraries. Libraries can then be screened in various ways to find natural products …
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Dairy-Met: compositional metagenomic analysis of milk and cheeses
Unpasteurised milk and many cheeses contain a diverse microbiological population. These microorganisms play important roles in dairy foods and can, for example, contribute to the development of flavours and aromas, determine safety, cause spoilage or enhance the health of the consumer. It is thus …
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Computational Tools for Annotating Antibiotic Resistance in Metagenomic Data
Metagenomics has become a reliable tool for the analysis of the microbial diversity and the molecular mechanisms carried out by microbial communities. By the use of next generation sequencing, metagenomic studies can generate millions of short sequencing reads that are processed by computational …
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Functional metagenomic discovery and characterisation of CAZymes by microfluidic methods
… future. With the emergence of large-scale metagenomic sequencing projects, the number of protein sequences in databases has grown exponentially in recent years. This abundance of recorded sequence data, though, stands in contrast to the small number of experimentally verified functional …
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Recovery and quality estimation of metagenomic assembled genomes of eukaryotes
… communities (e.g on the human skin). Shotgun metagenomics can provide access to the combined genetic information of a community in a culture independent manner. Using de novo assembly and post processing methods, it can lead to the generation of so called metagenomic assembled genomes (MAGs), …
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Pure culture and metagenomic approaches to investigate cellulose and xylan degradation
… from novel actinomycete isolates and the use of metagenomics to uncover previously unidentified cellulase genes was undertaken. Actinomycetes were cultivated from soil samples and the isolate with the best cellulase and xylanase activity was subjected to strain improvement through protoplast …
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Metagenomic Characterization of Microbial Communities in Groundwater Associated with Contaminated Land
… ahydrocarbon plume. To achieve this, a joint metagenomic study of the virusesand bacteria populating an old gasworks site was carried for one year. Theviral, bacterial and functional gene diversities found were influenced by thepH of the groundwater. Both potential hydrocarbon degraders and …
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