Publication Date

2017-07-19

Availability

Embargoed

Embargo Period

2019-07-19

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PHD)

Department

Human Genetics and Genomics (Medicine)

Date of Defense

2017-06-26

First Committee Member

Claes Wahlestedt

Second Committee Member

Nicholas Tsinoremas

Third Committee Member

Eden R. Martin

Fourth Committee Member

Mitsunori Ogihara

Fifth Committee Member

Philip D. Harvey

Abstract

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.

Keywords

bioinformatics; ChIP-seq; epigenetics; heatmaps; HPC; genomics

Available for download on Friday, July 19, 2019

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