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Full-Text Articles in Life Sciences
Applying Unsupervised Multi-Omic Learning To Identify Patterns Of Human Genomic Regulatory Regions With An Emphasis In Characterizing Hervh Loci., Corinne Sexton
UNLV Theses, Dissertations, Professional Papers, and Capstones
With the increase of diverse genomic data types, machine learning provides an opportunity to integrate several omics datasets into one cohesive annotation. In this dissertation, I apply an unsupervised clustering approach to a novel representation of 3D chromosome conformation data and chromatin mark data. Specifically I use this new method to annotate the regulatory function of human endogenous retrovirus H (HERVH). In chapter 1, I propose a synthesized model of HERVH function as an activating lncRNA based on previously published work. As HERVH and transposable elements in general are repetitive due to their methods of retrotransposition, in chapter 2 I …
Contribution Of Retrotransposons To Breast Cancer Malignancy, Isaac D. Raplee
Contribution Of Retrotransposons To Breast Cancer Malignancy, Isaac D. Raplee
USF Tampa Graduate Theses and Dissertations
The components contributing to cancer progression, especially the transition from early to invasive are unknown. Consequently, the biological reasons are unclear as to why some patients diagnosed with atypia and ductal carcinoma in situ (DCIS) never progress into invasive breast cancer. The “one gene at a time” approach does not sufficiently predict progression. To elucidate the early stage progression to invasive ductal cancer, expression signature of transcripts and transposable elements in micropunched samples of formalin-fixed, paraffin embedded (FFPE) tissue was conducted. A bioinformatics pipeline to analyze poor quality, short reads (>36 nts) from RNA-Seq data was created to compare …