Histone Modification ChIP-seq Algorithm Engineering and High Performance Bioinformatics Graphics and Analysis Software for Computational Epigenetics

Novel algorithm design, implementation, and optimization in histone modification ChIP-seq analysis of broad chromatin mark data is the subject of part I of this dissertation, focusing on data-driven precision medicine computational strategies for mapping ChIP-seq peaks to genomic features (and biological function) as well as coverage island analysis of low-sample size ChIP-seq experiments within individual biological replicates. Part II of this dissertation focuses on novel algorithm design, implementation, and analysis of high performance visualization techniques for histone modification ChIP-seq data using static and interactive biological gene expression heatmaps.