Publication Date

Summer 2022

Degree Type

Master's Project

Degree Name

Master of Science in Bioinformatics (MSBI)


Computer Science

First Advisor

Brandon White

Second Advisor

Wendy Lee


Differential Expression Analysis, Oxford Nanopore Technologies sequencing platform, Notch, Nanopore sequencing.


As the genomics revolution continues, there is constant pressure to make sequencing technology more accessible and practical for a growing series of applications. Existing sequencing technologies are often prohibitively expensive, limiting their use for novel diagnostic and research applications. Additionally, existing technologies are often limited by short read lengths, which may present problems to certain quantitative sequencing applications. One such application is Differential Expression Analysis, in which RNA-Seq is performed in paired samples under different experimental conditions to identify differences in gene expression. In this study, an Oxford Nanopore Technologies sequencing platform was used to conduct a differential expression study to identify Notch targets. Notch is a transcription factor that regulates numerous functions related to cellular growth and development, and misregulations in the Notch pathway can lead to developmental disorders and cancer. Nanopore Sequencing offers a cheaper and potentially more effective way to conduct research on Notch-mediated expression. It was found that while nanopore sequencing offers a cheaper alternative to existing methods, additional development of the technology is required to perform at the same level as current research standard platforms in differential expression.