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 25 for “"massively parallel sequencing"”.
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Dynamics of faecal bacterial populations in early infancy as determined by massively parallel sequencing
… using quality controlled Illumina MiSeq sequencing data. Methods: We sampled infant meconium and maternal faecal specimens at birth, as well as two subsets of infant faecal specimens at 4-12 and 20-28 weeks of life. We extracted nucleic acid from faecal specimens using the automated …
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Investigation into implementing a massively parallel sequencing workflow for forensic human identification in South Africa
… ForenSeqTM DNA Signature Prep kit was the first massively parallel sequencing (MPS) workflow validated on the MiSeq FGxTM system, addressing several challenges identified in CE-based methods. With forensic laboratories in developing regions showing proclivity towards a seemingly impossible …
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Investigation into implementing a massively parallel sequencing workflow for forensic human identification in South Africa
… ForenSeqTM DNA Signature Prep kit was the first massively parallel sequencing (MPS) workflow validated on the MiSeq FGxTM system, addressing several challenges identified in CE-based methods. With forensic laboratories in developing regions showing proclivity towards a seemingly impossible …
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Evolution's footsteps : reconstructing in vitro and in vivo evolutionary trajectories via massively parallel sequencing and profiling
… genetics or microarray mapping followed by sequencing, and many relevant genes may remain undetected. The recent development of technologies for cost-effective whole-genome resequencing offers the opportunity to comprehensively study evolution in action. Here, I present a combined …
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The use of massively parallel sequencing to study the virome, epigenome and genome of canine and feline cancers
The remarkable advancements in sequencing technologies have allowed the entire mutational landscape of hundreds of different types of human cancers to be defined. This knowledge gives patients two new categories of treatment options, small molecule inhibitors and targeted immunotherapy. Veterinary …
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The Intra-Tumour Heterogeneity Landscape of Human Cancers
… Somatic mutations can be measured through massively parallel sequencing, where mutations that are supporting incomplete expansions will appear as subclonal. These mutations can be used as a marker of the existence of the expansion and allow for a window into the clonal and subclonal …
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REPSA Directed Assessment of Native Cleavage Resistance of DNA to Type IIS Restriction Endonucleases and Modification of REPSA for High Temperature Application
… cleavage resistant species arose after 7 rounds. Massively parallel sequencing of the selected DNAs and bioinformatics analysis yielded a consensus binding sequence of 5'-GA(t/c)TGACC(c/a)GC(t/g)GGTCA(g/a)TC, a 20base pair palindromic site comparable to that described in the literature. Taken …
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Scaling short read de novo DNA sequence assembly to gigabase genomes
The recent advent of massively parallel sequencing technologies has drastically reduced the cost of sequencing, sparking a revolution in whole genome de novo sequencing. However, these new technologies sample much shorter segments of DNA, called short reads, than conventional but more costly long …
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Principled Methods and Models for Deep Learning Based Functional Genomics
… more broadly can be attributed to the rise of massively parallel sequencing technology and its derivatives. As the volume of sequencing and other high-throughput experimental data increases exponentially, so does the need for computational methods to analyze and condense these vast amounts of …
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A Statistical Model to Determine Multiple Binding Sites of a Transcription Factor on DNA Using ChIP-seq Data
… Chromatin Immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology that can reveal protein binding sites in genome with superior accuracy. Although many methods have been proposed to find binding sites for ChIP-seq data, they can find only one binding …
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Statistical methods for testing differential gene expression in bulk and single-cell RNA sequencing data
… factors, such as disease and development. RNA sequencing (RNA-seq) uses massively parallel sequencing technologies to profile the transcriptome. Among others, the objective of many RNA-seq studies is to identify features of the transcriptome (such as genes) that are deferentially expressed (DE) …
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Optimisation of sample preparation for DNA extraction from formalin fixed paraffin embedded tissues of unresolved sudden unexpected death cases
… analyses, indicating that genotyping or sequencing assays need to be designed to target amplicons less than 400 bp in size. The degraded nature of the FFPET samples also suggests that massively parallel sequencing might be suited for downstream molecular analysis for determining cause of …
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Evaluation of small extracellular vesicular microRNAs as biomarkersfor exposure of nicotine and E-liquids on human lung cells
… was measured by qPCR using the 2^ΔΔCt method. Massively parallel sequencing of small RNA was performed to identify sEV miRNA as novel biomarker. TEM, NTA, fNTA and western blot – all confirmed the successful isolation and processing of small EVs.From C14MC, differential expression of sEV miRNA …
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Discovery of a DNA-binding Consensus and Potential Genomic Regulatory Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359
… sequences that TTHA1359 preferentially binds, massively parallel sequencing to acquire the sequence information of these selections, and bioinformatics to discover TTHA1359-binding motifs from the acquired sequence information. TTHA1359-binding to the identified consensus was biophysically …
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Diagnosi prenatale non invasiva di malattie monogeniche attraverso la ricerca e l'isolamento di cellule e DNA fetale nel sangue materno
… further refinements the isolation procedure. In parallel we have developed a protocol for non invasive fetal sexing from cffDNA. This method appears to be highly accurate showing 100% sensitivity and 96% specificity. In the next future we are planning to analyze cffDNA both for monogenic diseases …
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Tumor Antigens Revealed by Exome Seqeuncing Drive Editing of Tumor Immunogenicity
… mechanisms remain poorly defined. We used massively parallel sequencing to characterize the expressed mutations in a highly immunogenic sarcoma, d42m1, and identified mutant spectrin-β2 as the major rejection antigen. Moreover, we demonstrate that editing of d42m1 tumor cells occurs via a T …
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Identifying New Genes for Inherited Breast Cancer by Exome Sequencing
… identify additional breast cancer genes by exome sequencing. In order to select families for gene discovery, we first screened families for mutations in all known breast cancer genes using targeted capture and massively parallel sequencing (BROCA). Families that remained unsolved after screening …
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The evolution of freeze tolerance in a historically tropical snail
… of the temperate zone by Melampus. Using massively parallel sequencing, I have isolated > 500,000 expressed sequence tags and assembled these into ~20, 000 seasonally expressed transcripts. A comparison of these transcripts has revealed 2 candidate markers to test for their association …
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Studying sequence effects of mRNA 5' cap juxtapositions on translation initiation rate using randomization strategy of the extreme 5' end of mRNA
… frequencies in E5S of the original library using massively parallel sequencing. The second position of E5S was found to have a markedly higher influence on translation initiation than positions further downstream (for technical reasons it was not possible to estimate the influence of the first …
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Development of Bioinformatic Methods for Data-Driven Forensic Short Tandem Repeat Analyses
… role in the forensic DNA typing. The arrival of massively parallel sequencing platforms (MPS) in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual …
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