Frank Cai

Publication Date

Fall 2023

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)


Computer Science

First Advisor

Leonard Wesley

Second Advisor

Wendy Lee

Third Advisor

William Andreopoulos


Amyloid-Beta and Tau; Alzheimer's disease; significant single nucleotide polymorphisms; epigenetic interactions; biomarker; pipeline.


Alzheimer's Disease (AD) and other forms of Mild Cognitive Impairment (MCI) affect millions of people around the world. The buildup of Amyloid-Beta (Aβ) and Tau proteins in the brain produced by amyloid precursor protein (APP) has been identified as an important cofactor in the onset and progression of AD. However, although patients diagnosed with AD exhibit Aβ and Tau buildup, about 40% of the subjects with Aβ and Tau buildup are not diagnosed with AD. In this project, we hypothesize the involvement of other epigenetic interactions between APP and related genes in addition to the buildup of Aβ and Tau that might explain the onset and progression of AD. A robust and systematic methodology is applied to identify potential epigenetic biomarkers of AD. Single Nucleotide Polymorphisms (SNP) mutated proteins are considered in this study. A novel integrated epigenetic computational pipeline is implemented for SNP protein sequence generation, protein structural-functional change prediction, statistical analysis, and identification of significant SNPs associated with AD. These significant SNPs warrant further investigation as potential biomarkers linked to AD.