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 16 of 16 for “"Read mapping"”.
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Long read mapping at scale: Algorithms and applications
… due to the development of long and ultra-long read sequencing technologies by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). Long reads are attractive because they narrow the scale gap between sizes of genomes and sizes of sequenced reads, with the promise of avoiding …
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Mapping Bisulfite-Treated Short DNA Reads
… with bisulfite treatment. Once the short read is mapped, the identity of 5-methylcytosine or 5-hydroxymethylcytosine can be determined by comparing the mapped read to the aligned reference genome. Bisulfite DNA read mapping is characterized by mapping performance as low as 40%. This …
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A Quantitative Exploration of Causes of False Positive Single Nucleotide Polymorphisms in Next-Generation Sequencing Data
… approach to SNP discovery is based on mapping reads to a reference sequence. Apart from sequencing errors, which vary in pattern and rate depending on the sequencing platform, the short read lengths that prevail in NGS, together with the repetitive nature of the genomes of many …
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Minimizer-space computation
… biological tasks, such as genome assembly and read mapping, can be significantly accelerated over state-of-the-art methods.
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Scalable methods for storage, processing and analysis of sequencing datasets
… amounts of next-generation sequencing (NGS) reads generated from sequencing machines around the world have revolutionized biotechnology enabling wide-scale disease and variation studies, personalized medicine and helping us understand our evolutionary history. However, the amount of …
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Computational algorithm development for epigenomic analysis
… the problems of ambiguous short sequence read mapping and broad peak calling of diffuse ChIP-seq signals were solved by novel statistical methods. Their performance was systematically evaluated compared with existing approaches. The potential utility of finding meaningful biological …
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Compressive algorithms for search and storage in biological data
… also for next-generation sequencing (NGS) read mapping. By pairing together a clustered grouping over similar reads and a homology table for similarities in the human genome, our CORA framework can accelerate all-mapping by several orders of magnitude. Additionally, we also present work on …
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Scalable sketching and indexing algorithms for large biological datasets
… continues to progress towards longer sequencing reads with increasingly lower error rates. In order to efficiently process the ever-growing collections of sequencing data, there is a crucial need for more time- and memory-efficient algorithms and data structures. In this thesis, we propose …
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Identification of common and unique stress responsive genes of Arabidopsis thaliana under different abiotic stress through RNA-Seq meta-analysis
… which performs data downloading, preprocessing, read mapping, read counting and differential expression analyses for RNA-Seq data. We found that 5729 and 5062 genes are induced or repressed by only one type of abiotic stresses. There are only 18 and 12 genes that are induced or repressed by all …
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Characterizing Human Transfer RNAs by Hydro-tRNAseq and PAR-CLIP
… gene multiplicity, complicate sequencing and read mapping efforts. To address these issues, I developed hydro-tRNAseq, a method based on partial alkaline RNA hydrolysis that generates fragments amenable for sequencing. To identify transcribed tRNA genes, I further complemented this approach …
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High-Performance Computational Genomics
… or C++. Seq allows for shorter, simpler code, is readily usable by a novice programmer, and obtains significant performance improvements over existing languages and frameworks. Seq is showcased and evaluated by implementing a range of standard, widely-used applications from all stages of the …
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COMPARATIVE GENOMICS AND FUNCTIONAL ANALYSIS OF BIFIDOBACTERIUM CARBOHYDRATE ACTIVE ENZYMES IN HUMAN MILK OLIGOSACCHARIDES UTILIZATION
… reactions to GH subtypes. Lastly, metagenomic reads were mapped against selected Bifidobacterium strains and GH subtype genes. Although B. infantis is associated with a reduced asthma risk, I observed that this strain was also abundant in some subjects with an asthma phenotype. Overall, our …
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Novel methods in transcriptome analysis using RNA-seq
… gene fusion transcripts. Due to the limited read length of NGS data, it is extremely challenging to accurately map RNA-seq reads to SJs, which is important for the analysis of alternative splicing and isoform construction. In this thesis, we describe a novel method, called TrueSight, that …
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Genome-graph based genotyping with applications to highly variable genes in P. falciparum
… regions of the genome, where sample sequencing reads, differing too substantially from the reference, fail to map. This ‘bias against diversity’, due to using a single reference, naturally affects genomic regions under pressure to diversify: this includes the human MHC, a motivating example for …
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Translation-Mediated Stress Responses: Mining of Ribosome Profiling Data
… alignments. I also examined the challenge of mapping footprints to repetitive sequences in the genome and propose ways to mitigate the associated problems. I performed differential expression analyses on data from coronavirus-infected murine cells, retrovirus-infected human cells and …