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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SFU Undergrad Researcher: Cherlene Emma Chang

Introducing Cherlene Emma Chang of the Department of Biomedical Physiology and Kinesiology!

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Name: Cherlene Emma Chang
Department: Biomedical Physiology and Kinesiology
Year: Third
Supervisor: Dr. Tom Claydon

Q: What do you want to be when you grow up?
A: A bioinformatical and clinical researcher. Computation is an increasingly invaluable skillset in the life sciences to quantify
scientific observations, while clinical relevance engages research with the treatment and management of patients to improve their
quality of life.

Q: How did you get involved in research?
A: I got involved in research through the BPK Co-op Program. Co-op is great for students to explore their career options and gain
valuable experience in their respective fields.

Q: What have you been working on in your research so far?
A: I have modelled the effects on the cardiac action potential as a result of the action of low pH on hERG potassium channels.
Myocardial ischemia occurs when blockage of coronary arteries reduces blood flow, preventing adequate oxygen perfusion. One
major consequence is acidosis, a reduction in local pH, contributing to cardiac arrhythmia. Acidosis profoundly affects hERG
potassium channels which provide a major repolarizing drive in the heart, and may suppress the protective mechanism of hERG
channels in preventing premature heartbeats.

Q: What will you be working on this summer?
A: This summer, my project is on zebrafish (Danio rerio) hearts as an excellent model of human cardiac electrophysiology. I will
use zebrafish hearts to study the action potential duration and cytoplasmic calcium handling using optical mapping techniques. I
aim to assess the effects of acidosis on irregular heartbeats using computer simulations.

Q: What is a typical “day in the life” in the lab for you?
A: I strike a balance between computational analysis and running experiments, where I write code in MATLAB and record ionic
currents in frog eggs (Xenopus laevis oocytes). I find that analyzing the data I collected firsthand enriches my research experience
through offering a well-rounded perspective on how each task fits in the bigger picture.

Q: What’s your favourite course that you have taken so far in your degree?
A: Introduction to Biological Physics (PHYS 347). Specifically, the electric circuit model of action potential propagation along a
neuron offered a fresh quantitative perspective on physiology.

Q: If you were a scientific lab instrument, which one would you be?
A: If I were a scientific lab instrument, I would be a computer. I enjoy modeling experimental data to equations, generating figures
for publications, and preparing powerpoint slides for presentations.

Q: What’s the funniest thing in research that’s happened to you?
A: During the 2017 BPK Research Day, I tripped down the stairs in the auditorium in my three-inch platform boots and spilled water
on myself. I laughed it off. Surprisingly, this incident calmed me down for my upcoming three-minute thesis and poster
presentations.

Q: What scares you the most in research?
A: The uncertainty of the future. Researchers apply for grants to get funded. Oftentimes there are more up-and-coming researchers
than grants available. Nonetheless, I will put my best foot forward in securing future grants.