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 28 for “"de novo assembly"”.
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Engineering of tools for De Novo Assembly of Human Cells
… the shortage will likely become exacerbated. For decades, the field of tissue engineering has developed innovative methods to generate model tissues de novo. Top-down approaches, such as microfluidics and 3D bioprinting, provide spatial control by patterning cell types with high resolution, but …
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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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De novo assembly of transcriptome and genome data from the Asia I mtCOI genetic clade of Bemisia tabaci
… required urgently within whitefly community to define genetic differences across distinct populations and to facilitate the development of more effective insecticides to help farmers. In this thesis, the process of de novo assembly and characterizing transcriptome and genome data of an Asia I …
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De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus
The nematode Panagrolaimus superbus can survive for extended peri- ods of time in a desiccated state (anhydrobiosis) and is also freezing tol- erant (cryobiotic). These adaptations make it an interesting candidate for genome and transcriptome sequencing using second generation high through- put …
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Genetic variation within the Daphnia pulex genome
… pulex genome was examined using a high quality de novo assembly and shotgun reads from two distinct D. pulex clones. Patterns of variation and divergence at single nucleotides were examined in physical and functional regions of the genome using comparative assembly output and available …
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Polyploidy inference across time scales in the charismatic carnivorous plant genus Drosera L. (Droseraceae, Caryophyllales)
… dissertation I sought to evaluate methods for detecting chromosome number changes of different types and ages, and to develop Drosera as a system for chromosome evolution. This was achieved by using chromosome evolution models to test different rates of chromosome evolution between different …
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Towards cloning of a novel SCN resistance locus using de novo genome assembly and fosmid screening
… contains a resistance QTL to soybean cyst nematode (SCN) Heterodera glycines, a devastating pest of soybean. This resistance QTL has been fine mapped in PI 468916 to a distance of 147kb. Through the use of whole genome sequencing with de novo assembly we were able to gain information about the …
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Evaluation and annotation of Bemisia tabaci transcriptome data using paired-end RNA sequencing
… crops, transmits more than 100 plant viruses. Despite its global importance as one of the world’s top 100 invasive species, limited genomic resources are available in public domains. In this study, transcriptomic datasets from cassava and non-cassava colonizing B. tabaci populations were used …
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Tiger: tiled iterative genome assembler and approximate multi-genome aligner
Sequence assembly and alignments are two important stepping stones for comparative genomics. With the fast adoption of the next-generation sequencing (NGS) technologies and the coming of the third-generation sequencing (TGS) technologies, genomics has provided us with an unprecedented opportunity …
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An investigation of the microbial population in aquarium water, using next generation sequencing
… clinic, antibiotic resistant genes (ARG) are widely transferred among bacterial communities. As a result, superbugs possessing several antibiotic resistant genes are a significant threat to public health. Antibiotic resistant pathogens in drinking water or wastewater could therefore influence …
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Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph
… displacement</p> <p>amplification (MDA), has made it possible to sequence and assemble bacterial</p> <p>genomes from a single cell. However, the quality of single cell genome assembly has</p> <p>not yet reached the quality of normal multi-cell genome assembly due to the coverage</p> <p>bias …
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Genic copy number variation associated with abiotic/biotic stress among a set of progenitors of contemporary maize germplasm
… fiber, and fuel crop that also serves as a model genetic organism. Although sequence variation is most commonly associated with single nucleotide polymorphisms, it is estimated that a greater portion of the genome is affected by structural variation (SV). This is a broad phenomenon that …
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Recovery and quality estimation of metagenomic assembled genomes of eukaryotes
… 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), which provide …
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Landscape genomics of tropical high altitude plant species
Changes to species distributions involve demographic processes that occur over generations and affect allele frequencies within populations, leading to patterns of genetic restructuring. The specific genetic structuring patterns that will be observed as a consequence depend on explicit geographical …
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Computational Analysis of Viruses in Metagenomic Data
… step towards analyzing metagenomic data is to identify and quantify viruses present in the data. In order to answer this question, we developed a computational pipeline, FastViromeExplorer. FastViromeExplorer leverages a pseudoalignment based approach, which is faster than the traditional …
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Massive Exchange of mRNA between a Parasitic Plant and its Hosts
… pentagona is an obligate parasitic plant that hinders production of crops throughout the world. Parasitic plants have unique morphological and physiological features, the most prominent being the haustorium, a specialized organ that functions to connect them with their host's vascular system. The …
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Analysis of the effect of genetic heterogeneity on de novo genome assembly using Xylocopa virginica as a model.
… genomic and genetic research, and as a result, de novo genome sequencing and assembly for non-model organisms has now become a common task in genome research. However, the integral properties of a genome such as ploidy, mutations, and repeat content impose issues for current genome assemblers. …
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Tracking the In Vivo Dynamics of Antigenic Variation in the African Trypanosome
… and nagana in animals, constantly changes its dense variant surface glycoprotein (VSG) coat to avoid elimination by the immune system of its mammalian host, using an extensive repertoire of dedicated genes. Although this process, referred to as antigenic variation, is the major mechanism of …
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The metabolism of iron-sulfur clusters during hydrogen peroxide stress in escherichia coli
… coli strain that cannot scavenge hydrogen peroxide has been used to identify the cell processes that are most sensitive to this oxidant. Low micromolar concentrations of H2O2 completely blocked the biosynthesis of leucine. The defect was tracked to the inactivation of isopropylmalate isomerase. …
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