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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 15 of 15 for “"Computational Genomics"”.
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High-Performance Computational Genomics
… domain-specific language for bioinformatics and genomics that combines the power and usability of high-level languages like Python with the performance of low-level languages like C or C++. Seq allows for shorter, simpler code, is readily usable by a novice programmer, and obtains significant …
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Two Problems in Computational Genomics
… addresses two novel problems in the field of computational genomics. The first is whole genome alignment and the second is inferring horizontal gene transfer using posets. We define these two problems and present algorithmic approaches for solving them. For the whole genome alignment, we …
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Computational genomics : mapping, comparison, and annotation of genomes
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in …
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GPU acceleration of advanced K-mer counting for computational genomics
… k-mer counting. In this work, we leverage the computational power of the GPU to accelerate KMC2. Our goal is to reduce the overall runtime of many genome analysis tasks that use k-mer counting as an essential step. We achieved 4.03x speedup using one GTX 1080 Ti with one CPU (Xeon E5-2603) …
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The development of a new genetic test for grapevine cultivars using a computational genomics approach
… rich grapevine genomic resources. Using a computational genomics approach, a total of 13 top performing STR markers were selected based on their discrimination power for 304 grapevine cultivars. A Polymerase Chain Reaction (PCR) based test was designed to group these 13 STR markers into 5 …
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Towards unified biomedical modeling with subgraph mining and factorization algorithms
… narrative text, ICU physiologic time series and computational genomics. These algorithms aims to build clinical models that improve both prediction accuracy and interpretability, by exploring relational information in different biomedical data modalities including clinical narratives, physiologic …
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Applications of Machine Learning in Source Attribution and Gene Function Prediction
… application of machine learning techniques in computational genomics across two distinct domains: (1) the predicting the source of bacterial pathogen using whole genome sequencing data, and (2) the functional annotation of genes using single- cell RNA sequencing data. This work proposes the …
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Bioflow: A web based workflow management system for design and execution of genomics pipelines
… of the advancements in the field of functional genomics. Computational genomics, which analyses these sequences, has seen a similar growth. The multitude of sequencing technologies has resulted in various formats for storing the sequences. This has resulted in the creation of many tools for DNA …
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Elucidating the role of Gremlin1 in colorectal cancer
… demonstrate GREM1-mediated VEGFR2 activation. Computational genomics was used to compare gene expression changes in the intestines of wild-type versus Villin1-Grem1 transgenic mice. Our results predicted a variety of cell signalling relationships and pathways, with an emphasis on GREM1-mediated …
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Comprehensive evaluation of error correction methods for high-throughput sequencing data
… has significantly revolutionized the study of genomics and molecular biology. Development of high-throughput sequencing technologies have brought about a quick and cheaper way to sequence genomes. Different technologies use different underlying methods for sequencing and are prone to different …
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Investigating the genomic, transcriptomic and metabolic landscape of Chlamydomonas reinhardtii in the context of vitamin B12 availability
… multi-omics with targeted metabolite analysis, computational genomics and classical molecular biology approaches. First, I present the global transcriptomic and one- carbon cycle related metabolite alterations in response to vitamin B12 scarcity in a B12 auxotroph and its B12-independent …
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Improved GPU implementations of the Pair-HMM forward algorithm for DNA sequence alignment
The student, Enliang Li, accepted the attached license on 2021-04-30 at 13:30.
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Hardware acceleration of the SAMtools variant caller
… their execution revealed that the single most computationally intensive part of the algorithm is the function bcf_call_combine, which is responsible for 23.63% of the execution time of samtools mpileup. In addition, the various functions used for output in samtools mpileup are responsible for a …
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Leveraging genomic and molecular variations to understand the regulatory landscape in human cancers and differentiating stem cells
… cause and consequence. In this thesis, I use computational modelling to detect and understand biologically meaningful associations between genetic variation and gene expression alterations. First, we use data across 27 human cancer types to probe associations between different genetic factors …
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Hardware acceleration of the pair HMM algorithm for DNA variant calling
Made available in DSpace on 2017-08-10T19:16:15Z (GMT). No. of bitstreams: 2 HUANG-THESIS-2017.pdf: 3198752 bytes, checksum: 355bc51ce749cb631e269cc6116f3c3f (MD5) LICENSE.txt: 4208 bytes, checksum: 29aa487d1a5b8c7beed523d9c3a35801 (MD5) Previous issue date: 2017-04-26