Undergraduate Bioinformatics Student Teams Up With CS Professor on Nature Paper

Bonnie Huang ’21 had the opportunity to work with computer science Professor Melissa Gymrek on a paper published Jan. 13 that find tandem repeats, which are also associated with Huntington’s disease, may contribute to Autism Spectrum Disorder 

Why did you choose bioinformatics as a major?

Entering college, I was interested in human health and all areas of STEM, from biology and chemistry to math and computer science. I decided to major in bioinformatics due to its interdisciplinary nature and figured it would be fascinating to be able to apply computer science to solve biological problems in a variety of fields.

Why did you attend UC San Diego?
One of the main factors that drew me to UC San Diego was the Jacobs Scholarship, which gave me the opportunity to pursue my interests and focus on academics and extracurricular activities (such as research and community service) without worrying about the financial burden of college. Another important factor was the top-notch bioengineering/bioinformatics faculty/curriculum as well as the abundant research opportunities available at UC San Diego.

How did you get in touch with Professor Gymrek and become an undergraduate researcher in her lab?

My sophomore year, I took a class with Professor Gymrek (CSE 185 – Advanced Bioinformatics Laboratory) and learned about her lab’s work on the development of computational tools to analyze repetitive DNA regions in the human genome. I found her research extremely interesting, especially since I’ve always wanted to learn more about human genetics and find a way to combine my interests in computer science and biology. We set up a meeting to discuss research opportunities, and I’ve been fortunate to be a part of her lab ever since.

What was it like to be part of her lab and become a coauthor on a paper published in Nature?

Being a part of the Gymrek Lab has been an amazing experience. Professor Gymrek is a fantastic and extremely supportive mentor, and I’ve truly enjoyed working with everyone in the lab. Over the past year, I’ve been developing a novel software tool called SISTR to score short tandem repeat mutations in the human genome based on how likely they are to cause disease. In one part of the paper, we use SISTR to analyze short tandem repeat mutations in individuals with autism and predict which mutations are most likely to be harmful. Overall, I’ve learned a lot from working on SISTR and applying the skills I’ve gained from my computer science, biology, and bioinformatics courses to contribute to medical research.

What are your plans for after graduation? 

I plan to go to medical school and pursue a career in academic medicine, where I would be able to combine my interests in research, teaching and patient care. In the future, my goal is to both treat patients and use my background in bioinformatics to help solve medical problems and improve patient care through the development of new diagnostic tools and personalized treatments.

What would your advice be to an incoming freshman who wants to do research?

One way to find a lab to join is to explore different research groups’ websites/papers and email professors whose research you find interesting. It can also be helpful to go to office hours to talk with professors about their research and ask them questions about your field of interest. Another way to gain experience is through summer research programs, so keep an eye out for applications to those as well.

Paper: Patterns of de novo tandem repeat mutations and their role in autism

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Study finds neglected mutations may play an important role in Autism Spectrum Disorder