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 249 for “"Illumina"”.
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Design and characterization of novel immunogens for AIDS vaccine development and evaluation of a sample inference method for NGS Illumina amplicon data
… the appropriate neutralizing epitopes.</p> <p>Illumina amplicon sequencing is an important tool for the identification and quantification of species or variants in metagenomics studies, but sequencing errors make it challenging to correctly identify the authentic differences. Many denoising …
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Development of new tools and applications for high-throughput sequencing of microbiomes in environmental or clinical samples
… and diversity. Sequencing platforms like the Illumina Genome Analyzer II (GAI1) and the Applied Biosystems SOLiD enable experiments that were previously too expensive or time-consuming by providing a very large number of short reads at a significantly lower cost per base pair (bp) than …
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Genome-wide analyses using bead-based microarrays
… the BeadArray microarray technology developed by Illumina. The design of this technology is unique and gives rise to many computational and statistical challenges. However, I show how knowledge from other microarray technologies can be used to our advantage. I describe the beadarray software …
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FPGA acceleration of DNA error correction
… error-correction methods have been proposed for Illumina reads, their throughput is not high enough to process data from large genomes. The thesis describes the first FPGA-based error-correction tool, which is designed to improve the throughput of DNA error correction for Illumina reads. The base …
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Droplet digital PCR detection and next-generation sequencing of HIV-1 in breastmilk of breastfeeding women on antiretroviral treatment
… sequencing of viral variants in breastmilk using Illumina MiSeq next generation sequencing to inform transmission risk and efficacy of maternal ART clinical trials. HIV-negative breastmilk samples were spiked with 8E5 cells (a cell line where each cell contains one replication-defective HIV …
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Genetic basis of human disorders of gonadal development
… created. Following sample preparation using the Illumina library preparation kit, sequencing was accomplished using paired-end sequencing technology on an Illumina HiSeq2000 sequencer. The data from the Illumina sequencers was analyzed first using the Illumina sequencing data analysis pipeline …
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Host and pathogen genomics: the molecular repertoire of soybean and Sclerotinia interactions
… in the microarrays to deep sequencing using the Illumina/Solexa SBS platform. These studies allowed for the identification of a set of genes that may play important roles during pathogenicity, including several known defense-related genes. The data also suggested the possible involvement of iron …
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Metagenomic Analysis of Antibiotic Resistance Genes in the Fecal Microbiome Following Therapeutic and Prophylactic Antibiotic Administration in Dairy Cows
… and subjected to DNA extraction followed by Illumina paired-end HiSeq sequencing and quantitative polymerase chain reaction (qPCR). Illumina sequences were analyzed using MG-RAST and the Antibiotic Resistance Gene Database (ARDB) via BLAST. Abundance of ampC, ermB, tetO, tetW, and 16S rRNA …
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Análisis Metagenómico del Viroma Intestinal en Pacientes Intrahospitalarios y de Unidad de Cuidados Intensivos de Bogotá, Colombia
… por Oxford Nanopore Technologies (ONT) e Illumina. En promedio, se obtuvo 161,855 lecturas por muestra usando secuenciación por ONT, de las cuales cerca del 0,03% correspondió a lecturas virales. Para el caso de Illumina, se obtuvo alrededor de 20.286.589 lecturas por muestra, donde …
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Development of Genomic Resources for the Evaluation of Red Snapper, an Emerging Species Candidate for Marine Aquaculture and Stock Enhancement
… markers were developed through screening of Illumina paired-end sequencing reads. Microsatellite loci and Single Nucleotide Polymorphisms (SNPs) generated through Restriction Site Associated DNA (RAD) sequencing were assayed in 5 outbred full-sib families to construct a high-density linkage …
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Preference and affiliation refines the neurotranscriptome pathway for mate preference
… the brains of each female were sequenced (Illumina RNA-seq) directly following the behavioral assay.
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Characterization of Small Non-Coding RNAs in the Seminal Plasma of Beef Bulls with Predicted High and Low Fertility
… Sequence libraries were prepared using the Illumina TruSeq Small RNA preparation kit and sequenced on an Illumina MiSeq. Using the NCBI database of known human, porcine, mouse, and bovine miRNAs and known human piRNAs, expressed sequences were identified and mapped to the Bovine genome …
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De novo sequencing, assembly and analysis of the genome and transcriptome of the nematode Panagrolaimus superbus
… methods along with 50 bp and 100 bp paired end Illumina reads. Eight different gDNA assemblies were prepared, generating predicted genome sizes ranging from 87.9 kilobases to 159.7 kilobases. The longest contigs were obtained from the 454 genomic DNA assembly and the assemblies of the Illumina …
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Characterizing the Microbiome of Scottish Freshwater Pearl Mussels (Margaritifera margaritifera): A Metabarcoding Analysis using Next-Generation Sequencing
… Technology) for full-length amplicons and MiSeq (Illumina) for short amplicons, enabling a comparative analysis of platform performance at the species level. Results revealed that the mussel microbiome was distinct from that of river water, with significant differences even at high taxonomic …
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Ribosomal protein mutants and their effects on plant growth and development
… was non-mitochondrial and probably cytosolic. Illumina sequencing of two r-protein mutant transcriptomes, pfl1 (rps18a) and pfl2 (rps13a), identified a novel set of up and down regulated genes, previously unknown or linked to r-protein mutants. The 20 genes identified were classified into four …
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High Throughput Sequencing of SARS-CoV-2
… comparing two sequencing platforms, MinION and Illumina, we determined that the Illumina platform was the preferred method based on error rates, sequencing read depth, and multiplexing compatibility. Using our pipeline, we calculated the mutation rate of SARS-CoV-2 in twelve individuals who were …
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Through the layers of the Ethiopian genome: a survey of human genetic variation based on genome-wide genotyping and re-sequencing data
… 80 extant Ethiopian populations were typed on an Illumina Omni 1M SNP array. The results showed a good concordance between genetic and linguistic stratification and, overall, a complex population structure placing the Ethiopians in between North and Sub Saharan Africans, due to the recent non …
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Genetic characterization of Rhodococcus rhodochrous ATCC BAA-870 with emphasis on nitrile hydrolysing enzymes
… was sequenced using Solexa technology and an Illumina Genome Analyzer. The Solexa sequencing output data was analysed using the Solexa Data Analysis Pipeline and a total of 5,643,967 reads, 36-bp in length, were obtained providing 4,273,289 unique sequences. The genome sequence data was …
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Analysis of cellular responses to microwave irradiation in E. coli and change of oxygen level and culture medium in human cancer cell lines using RNA-seq based transcriptomic profiling
… objective. Among the NGS technologies, the Illumina platforms are the current standard for RNA-seq analysis for their best cost efficiency and sequencing accuracy. In this study, we employed Illumina-based RNA-seq to examine the gene expression profile change in E. coli cells after exposure …
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