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Showing 1 to 12 of 12 for “"Genome Rearrangement"”.
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Genome Rearrangement, Randic Index and Routing Number
… from discrete mathematics are studied:</p> <p>Genome rearrangements are to represent evolusion of genomes as signed or unsigned permutations of genes and compute their distances based on the minimum number of certain operations (evolutionary events) needed to transform one permutation into …
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Patterns of somatic genome rearrangement in human cancer
Cancer development is driven by somatic genome alterations, ranging from single point mutations to larger structural variants (SV) affecting kilobases to megabases of one or more chromosomes. Studies of somatic rearrangement have previously been limited by a paucity of whole genome sequencing data, …
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Plane Permutations and their Applications to Graph Embeddings and Genome Rearrangements
… a powerful framework to study less related genome rearrangement problems. As results, we refine and extend several existing results on enumeration of maps by counting plane permutations filtered by different criteria. In the spirit of the topological, graph theoretical study of graph …
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Robust and Efficient Algorithms for Protein 3-D Structure Alignment and Genome Sequence Comparison
… protein structure alignment and query, and genome sequence related problems including haplotype reconstruction and genome rearrangement. It first presents an algorithm for pairwise protein structure alignment that is tested with structures from the Protein Data Bank (PDB). In many cases it …
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The Extent and Nature Of Chromosomal Rearrangements in B Lymphocytes
<p>Chromosomal rearrangements, including translocations, require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are frequently involved in producing leukemias, lymphomas and sarcomas. Mature B cell lymphomas are unique among tumors in …
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Mechanisms and impact of alternative transposition-induced segmental duplications
… are prevalent in both plant and animal genomes, and have played important roles in genome evolution. The focus of my project is to understand the transposition-mediated mechanisms that lead to the formation of segmental duplications, and the immediate impact of recently generated large …
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Methods for Analysis of Prokaryotic Genome Architecture
… been organized around the concept of reference genomes. Reference genomes provide a useful comparative touchstone for closely related organisms. However, they do not necessarily represent the biological diversity in a group of genomes. Currently there are more than 96,000 bacterial genomes …
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Clinical Significance of Homologous Recombination Deficiency Score Testing In Endometrial Cancer
… the coding regions of 43 genes and 54,091 genome wide single nucleotide polymorphisms (SNPs) developed by Myriad Genetics. The HRD score is the sum of three previously described scores (loss of heterozygosity, telomeric allelic imbalance, and large-scale state transition) that quantitate …
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Novel methods in transcriptome analysis using RNA-seq
… and (ii) coding potential from the reference genome sequences into a unified model that utilizes semi-supervised self-training to precisely identify SJs. Both simulation and real data evaluations showed that TrueSight achieved higher sensitivity and specificity than existing tools. We also …
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The structure and evolution of breast cancer genomes
… among the most complex karyotyes of all cancers. Genome rearrangements are potentially an important source of mutation in breast cancer but little is known about how they might contribute to this disease. My first aim was to carry out a structural survey of breast cancer cell line genomes in order …
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Integrative analysis of transcriptional activity and genome architecture changes upon viral infections
… activity during viral infections, I employed a genome-wide chromosome conformation capture approach (Hi-C) on infected murine and human cells and further enriched those libraries for genomic loci of interest and the viral genomes with biotinylated RNA baits. In parallel, I profiled newly …
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Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase
… to repair, with potential complications from genome rearrangement. To prevent this genetic instability, a cell can utilize a homologous chromosome as a template to accurately repair DSBs. This process is called homologous recombination. Homologous recombination begins when an enzyme complex …