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Full-Text Articles in Bioinformatics
Computational Modelling Of Human Transcriptional Regulation By An Information Theory-Based Approach, Ruipeng Lu
Computational Modelling Of Human Transcriptional Regulation By An Information Theory-Based Approach, Ruipeng Lu
Electronic Thesis and Dissertation Repository
ChIP-seq experiments can identify the genome-wide binding site motifs of a transcription factor (TF) and determine its sequence specificity. Multiple algorithms were developed to derive TF binding site (TFBS) motifs from ChIP-seq data, including the entropy minimization-based Bipad that can derive both contiguous and bipartite motifs. Prior studies applying these algorithms to ChIP-seq data only analyzed a small number of top peaks with the highest signal strengths, biasing their resultant position weight matrices (PWMs) towards consensus-like, strong binding sites; nor did they derive bipartite motifs, disabling the accurate modelling of binding behavior of dimeric TFs.
This thesis presents a novel …
Characterization Of Urinary Microbiome And Their Association With Health And Disease, Yige Bao
Characterization Of Urinary Microbiome And Their Association With Health And Disease, Yige Bao
Electronic Thesis and Dissertation Repository
There has been a growing interest in human microbiome studies in the past decade, with the development of high-throughput sequencing techniques. These microorganisms interact and respond to the host as an entity, and are involved in various homeostatic functions including nutrition digestion, immune response, metabolism and endocrine regulation. The urinary microbiome, however, remains relatively under-investigated.
One of the technical challenges of urinary microbiome studies is the samples usually contain a large number of host cells and low microbial biomass. These samples with the high host, low microbial abundance (“high-low” samples) are associated with increased risk of compromised quality of …