SFU Undergrad Researcher: Matthew Nguyen

Introducing Matthew Nguyen of the School of Computing Science and the Department of Molecular Biology and Biochemistry!

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Name: Matthew Nguyen
Faculty: Computing Science & Molecular Biology and Biochemistry
Year of Study: 3rd
Supervisor: Dr. Leonid Chindelevitch of the Department of Computing Science

Q: How did you get involved in research?
A: Back then, I was just an MBB major with some programming interests. At the end of my 2nd year, I decided to email some bioinformatics prof whose research I was interested in. I had only taken 3 CMPT courses, but Dr. Chindelevitch still took me in. Since I lacked the background, I had to do a lot of self-learning but I’m loving it. Working in the lab pretty much solidified my decision to transfer to the joint major, and now here I am!

Q: What have you been working on in your research so far? (What is your research about?)
A: I am finishing up a large scale project to create a computational framework for the classification of pathogens into epidemiologically related groups using genomic data. Specifically, we are combining data from single nucleotide polymorphisms (SNP), multilocus sequence typing (MLST) and copy number variations (CNVs) to cluster different samples of a pathogen in order to understand their relatedness. Currently, I am working on the implementation and analysis of various clustering algorithms to establish the best one. Upon completion, the project will be integrated into an open-source platform (IRIDA) to help public health authorities analyze epidemics.
With the end in sight, I am also starting up a new project: the use of machine learning methods in order to predict antibiotic resistance in tuberculosis.

Q: What is a typical “day in the life” in the lab for you?
A: I technically don’t need to be in the lab to do any work. Since all of my work is done on the servers at the BC Genomes Science Center, I can work from anywhere with internet, even at home or on my phone! But I still enjoy being in the lab as it is useful: I can seek assistance or bounce ideas off of my supervisor or the other members of my lab. I’ve also got a sweet setup of dual monitors (I want a third…) and a mechanical keyboard. My work usually consists of writing or debugging code (Python or BASH), running different software and algorithms, analyzing the results (maybe run some statistical analyses with R) and writing documentation.

Q: What’s your favorite course that you have taken so far in your degree?
A: CMPT 310 with Dr. Maxwell Libbrecht: Artificial Intelligence Survey. AI is one of THE buzzwords right now. Although this is just a survey course, it is a fascinating introduction to a growing field in computing science, a field which became my main research interest. Machine learning is huge in bioinformatics right now, and although I still lack the in-depth knowledge, this course was a refreshing intro to how it all works. I started self-teaching a lot of machine learning after this great intro.

Q: What scares you the most in the lab or the field?
A: Unexpected results that make no sense are horrible to deal with, especially when I have to use someone else’s program in my pipeline. Did I do something wrong? Is the program I’m using just bad? Maybe if I run it again without changing anything it’ll work…

Q: What is your favorite science joke or meme from your field?
A: I may or may not look at memes too much… I can thank Reddit for that. Shameless plug for /r/programmerhumor.

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