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Student Spotlights

Elizabeth Vance

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Major: Bioinformatics
Semester/Term: Spring 2018
Organization: Lewis Lab--University of California, San Diego
Position: Research intern
State/Country: California

What did you do at your internship?

I interned in the Lewis Lab at UCSD in order to learn more about Systems Biology. I worked on two different projects. First, I was asked to debug and run a variant calling pipeline using Python. Second, I was asked to mentor a potential grad student (who didn’t have experience in bioinformatics), clean and organize VCF files and then perform analyses on the data in order to find the genotype/phenotypic correlations in Autism.

Obviously, these projects are part of larger projects that will continue for months and years to come. However, the data we analyzed from the VCF files could potentially lead to some neat discoveries in Autism Spectrum Disorder (ASD) research. As of right now, it appears that there are no single genes that directly contribute to ASD. However, it is hypothesized that the network connections and pathways between genes could be significantly associated with this disorder. So far, we have the data we’ve worked with shows common genes that are found in ASD patients. Next, we are going to study the pathways in which these genes are present, and see if we can find associations there.

The grad student I am working with is hoping to submit a paper with our findings for publication by the end of the summer.

What was the most useful thing you learned from your internship?

A lot of my learning here has been self-regulated and self-motivated. There was a post-doc in the lab who was assigned to mentor me. He would give me specific principles and tutorials to study on my own, and then I’d use what I learned to perform the tasks necessary to help the grad student. I was able to become familiar with specific tools, like Genemania, to study genetic pathways and interactions…however, I think the most useful thing I learned was the R programming language. I already knew a little bit, but using this language every day for two months has allowed it to become a comfortable part of my toolset now. With a good foundation in Python and now R, I feel more prepared to face more advanced programming challenges.

How did your courses and your major prepare you for your internship?

I think that the Computer Science courses obviously gave me a solid foundation in how to computer program. But honestly, C++ is rarely used in bioinformatics. I think my jobs with the DNA sequencing center and as a research assistant for Dr. Kauwe are what really prepared me for this internship. I think it would be more valuable if Python and R were more widely used in the Life Science courses. Other than Intro to Bioinformatics, I’ve yet to use those skills in my classes. I think it would be beneficial if our biology, MMBio, and genetic classes incorporated more sections on data analysis.

What professional skills did you develop in your internship?

I think communication was a skill I definitely had to cultivate. Because I was asked to mentor another student, I was forced to not only learn the skills for myself, but then explain simply the things I was doing to someone else. This was especially difficult because this student had absolutely no background in bioinformatics. It really helped me become aware of the things I REALLY knew. The more confident I was in a subject, the better I was at explaining it.

Would you recommend this internship to other students? Why?

Yes, I would recommend this internship to other students. It’s definitely not your typical internship program. Honestly, there’s not much direction, and it is mainly self-motivated. However, I like that I didn’t have someone hovering over my shoulder all the time. It allowed me to experiment and learn things from trial and error (which, ultimately, is usually more effective for my style of learning). I think it also allows you to witness firsthand what a graduate school research lab looks like.

Is there anything else you would like to say regarding your internship?

Nate Lewis, the professor over the lab, is an incredible guy. He's willing to give advice on everything--not just for the projects you're working on. We've discussed work-life balance, grad school vs industry, PhD programs, marriage (I just got engaged), etc. It's obvious he cares about the people in his lab.

Rank your internship: 1 being terrible, 5 being AWESOME

Professional Advancement: 4

Applicability to Major and Courses: 5

Professional Skills Development: 4

Overall Rating of Internship: 4

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Elizabeth Vance at Lewis Lab building at the University of California, San Diego