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.
Results
Showing 1 to 20 of 38 for “"Insertions and deletions"”.
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Ruler arrays detect genomic insertions and deletions
… the distance between a set of microarray probes and a set of experimentally defined locations in a nucleic acid, offering new possibilities for locating and characterizing changes in the nucleic acid sequence. Despite the known relevance of genomic changes to pathogens, cancer, development, and …
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In Vitro Evolution of Antibody Affinity using Libraries with Insertions and Deletions
… (SHM) leads to antibodies with improved affinity and specificity. Sequence diversification by SHM is mainly achieved by introduction of point substitutions and a small percentage of insertions/deletions (indels). Although the percentage of indels in affinity matured antibodies is low, probably due …
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Thermodynamics of neutral sets and sequence length changes in the genotype-phenotype map of RNA secondary structure
… RNA secondary structure connects RNA sequences and the corresponding folded molecular structures. This relationship is required for modelling the evolution of functional RNA structures. In this thesis, we fill two gaps in the understanding of the RNA GP map: we analyse neutral sets, i.e. groups …
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Sequence and structural analysis of antibodies
… in this thesis focusses on the sequence and structural analysis of antibodies and has fallen into three main areas. First I developed a method to assess how typical an antibody sequence is of the expressed human antibody repertoire. My hypothesis was that the more \humanlike" an antibody …
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Statistical analysis of short template switch mutations in human genomes
… structural variant calling. However, the genomic and evolutionary consequences of replication-based rearrangements remain poorly characterised at smaller scales, where they are usually interpreted as complex clusters of independent substitutions, insertions and deletions. In this thesis, I …
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Risk prediction with genomic data
… Nucleotide Polymorphism (SNP) genotype data and a novel approach of disease risk prediction with whole exome sequencing data, namely Whole Exome Wide Association Study (WEWAS). It further applies a discriminating machine learning algorithm, namely a Support Vector Machine (SVM) with different …
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Predicting the Functional Effects of Human Short Variations Using Hidden Markov Models
… the development of sequencing technologies, more and more sequence variants are available for investigation. Different types of variants in the human genome have been identified, including single nucleotide polymorphisms (SNPs), short insertions and deletions (indels), and large structural …
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Sequence Detection and Comparative Analysis of the Hv1 and Hv2 Control Regions of Human Mitochondrial DNA by Denaturing High-Performance Liquid Chromatography
… objective of this research was the evaluation and forensic validation of Denaturing High-Performance Liquid Chromatography (DHPLC) as a sequencingindependent means of detecting the presence of sequence differences in pair-wise mixtures of non-concordant amplicons of human mitochondrial DNA …
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Cache-oblivious dynamic search trees
… lookup, as well as efficient amortized insertion and deletion. Efficient implementation of a B-tree requires understanding the cache-line size and page size and is optimized for a specific memory hierarchy. In contrast, the COB-Tree contains no machine-dependent variables, performs well on any …
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Parallel Batch-Dynamic Graph Algorithms: Coreness Decomposition and Spanners
… graph algorithms for coreness decomposition and spanners, as well as a number of other related problems. The first class of problems we consider involves approximating coreness decomposition and several closely related concepts, such as (subgraph) density estimation, arboricity estimation, …
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GRAND-assisted Optimal Modulation
For Gaussian channels with peak and average power constraints the optimal modulation (OM) schemes are known to have nonuniform probability distributions over the signal points. An established way to obtain these distributions is assigning different number of bits to different constellation points. …
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Applications of a Novel Sampling Technique to Fully Dynamic Graph Algorithms
… sampling technique to building fully-dynamic randomized graph algorithms. We present the following results: \begin{enumerate} \item A randomized algorithm to estimate the size of a cut in an undirected graph $G = (V, E)$ where $V$ is the set of nodes and $E$ is the set of edges and $n = |V|$ …
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Isolation and engineering of a high affinity antibody against P-selectin glycoprotein ligand-1 (PSGL-1)
… results in the need for frequent administration and large doses in order to obtain inhibition. High affinity antagonists are desirable because they can be administered in smaller amounts thus reducing the risk of harmful side effects and reducing production costs. Our approach for developing high …
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Keep it secret, keep it safe : privacy, security, and robustness in an adversarial world
… actors. This thesis introduces algorithms and definitions for a series of problems concerning robustness, security, and privacy in the many-party setting. We describe protocols for maintaining a stable configuration despite adversarial perturbations, for cryptographic tasks involving secure …
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Investigating the role of chromatin modifications in CRISPR/Cas9 gene editing
Precisely positioned nucleosomes and heterochromatin have been shown to impede CRISPR/Cas9 editing efficiency. Conversely, Cas9 can open previously inaccessible regions of DNA, and transcriptionally silent targets can usually be edited without difficulty. In order to address this paradox, we have …
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Genetic diversity of the HvFT1 flowering gene in Nordic spring barley (Hordeum vulgare L.)
… for signals of the vernalization, photoperiod and circadian clock pathways and promotes flowering. This is of interest for barley breeders on Iceland, who aim to produce early maturing cultivars. The main objective of this project is to study the genetic diversity of the HvFT1 gene in Nordic …
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Precision Gene Editing for Muscle Diseases
Muscle, comprising both skeletal muscle and cardiac muscle, is integral to the human experience, allowing us to do the many incredible things. Consequently, genetic mutations that cause muscle disease can have a profound effect on the afflicted individual. Gene editing tools like base editors and …
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Next-Generation Sequencing of vlsE Recombinational Switching in the Lyme Spirochete
Borrelia burgdorferi and other spirochetes that cause Lyme disease effectively evade the acquired immune response through antigenic variation. The VlsE antigen is expressed on the spirochete surface during mammalian infection. Virtually unlimited numbers of variants are generated through segmental …
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Probabilistic Model-Based Approach to Evolutionary Analysis of Non-Coding Sequences
… involved in the regulation of gene expression and (ii) they are essential for the study of genome structure and evolution. The availability of genome sequences of closely related species has provided opportunities to analyze non-coding sequences by comparing multiple genomes from different …
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Characterizing phonetic transformations and fine-grained acoustic differences across dialects
… is motivated by the gaps between speech science and technology in analyzing dialects. In speech science, investigating phonetic rules is usually manually laborious and time consuming, limiting the amount of data analyzed. Without sufficient data, the analysis could potentially overlook or …
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