Justin Chu

Research Topic

High Performance Computational Tools for Nucleic Acid Sequence Classification, Assembly and Analysis

Research Group

Bioinformatics Technology Lab

Research Description

As the cost of DNA sequencing continues to decrease, so does the cost of analyzing this data. Currently, the rate that DNA sequencing improves exceeds the rate of improvement of computational power, necessitating the development of more efficient computational tools for processing of this type of data. My research focuses on the development of novel, computationally efficient, algorithms to close the gap between our ability to generate data to our ability analyze this data. My research focuses on developing methods and tools centered around the novel use of succinct and probabilistic data structures to perform a variety of tasks such as sequence classification, de novo assembly, and targeted assembly. To guide my efforts, I focus on the following goals: to reduce the time and memory costs of existing methods, to improve specificity and sensitivity of algorithms, to adapt to advancements in sequencing technologies, and to better harmonize with other data analysis and processing methods.

Why did you decide to study at UBC?

Vancouver is home to one of most productive genomics research environments in Canada, with leading research institutes like the Centre for High Through-put Biology (CHiBi), the Genome Sciences Centre (GSC) at the BC Cancer Agency, and the Michael Smith Laboratories (MSL). I entered UBC within the CIHR strategic training program in bioinformatics hosted at the GSC. This competitive graduate training program has arrangements in place to allow one to work with many different research labs, not just in Vancouver, but all over the world, broadening students’ knowledge of the field of bioinformatics. The program has since ended, but UBC's bioinformatics program still exists, and new programs such as the NSERC CREATE training program in high-dimensional bioinformatics have taken its place, offering great learning experiences for those looking to get into the field of bioinformatics.

 

Why did you decide to pursue a graduate degree?

My overarching goals in my career are to contribute as much as I can to the field of bioinformatics as a whole, given my interests, strengths, and education. These goals are not only driven by innate curiosity, but by my desire to contribute in the global knowledge so that it may be used to help the public as a whole. After working for a year in the field of bioinformatics as a computational biologist, I realized that it made sense that if I wanted to fulfill these aspects to my full potential, I should pursue a graduate degree.

 

After working for a year in the field of bioinformatics as a computational biologist, I realized that if I wanted to [reach] my full potential, I should pursue a graduate degree.