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Alexis Thornton: Graduate Student

What are you researching right now?

I work with a method called EVIP, which stands for expression-based variant-impact phenotyping, and basically what that means is we use expression data, like RNA-Seq, to predict the function of different mutations that happen in cancer. This is important because right now when people try to understand the impact of mutations, basically they do one experiment to learn about one mutation, and with expression profiling methods like what we’re working on, we can learn about hundreds of mutations at once which is important because there are millions of mutations that have been identified but not studied. With this method we’ll be able to characterize more of them and it could lead to understanding how to treat them in patients.

For example, there are two frameshift mutations that happen in colorectal cancer and we found that, although people might expect them to have the same effect since they’re in the same gene, they’re actually not having the same effect. We found that the frameshift that was longer and closer to being a full protein was actually causing a change of function instead of causing the protein to lose its function. It just caused it to do something different, which is interesting. So in clinical trials now, they might not group patients that have those two mutations together. They’ll acknowledge that they are having different effects on the cell.

I’m also working on my thesis proposal, the creation of a database of isoform signatures, which is important because nothing like that really exists right now. There’s no open source resource where if you want to know what this isoform is associated with, to look at. Everything is mostly done at the gene level right now even though isoforms of the same gene are shown to have different functions. So we want to aid in that.

What drew you to this research?

What motivated me to start doing research was that I wanted to study alzheimer's because my grandma had alzheimers, so I joined the alzheimer's lab at the University of Florida and did a lot of research I thought was really interesting. But I wanted to try to see what bioinformatics was and how I could incorporate that, so I started with that which is what led me to UC Santa Cruz where I now study cancer, also something that hits close to home for me.

How did you get interested in bioinformatics?

I wasn’t taught about bioinformatics as an undergrad and had never even heard of it until after graduating and so I was used to thinking about solving biological questions in certain ways and when I found out that you could do it in a way other than being in the lab and pipetting, I was really interested in that since I didn’t really like being in the wetlab. Being able to solve biological questions through engineering software and analyzing data was interesting to me.

What do you like about UC Santa Cruz?

I like the environment here. It’s very different than where I grew up in Florida. We don’t have redwood trees or mountains or anything. It’s beautiful. And as far as the research going on, it’s really interesting and there’s a lot of experts in our field that you get the chance to collaborate with and learn from. Working with Angela Brooks is great. She’s a great advisor and mentor and always patient but pushing you to be better and get good research done and ask good questions. I chose the biomolecular engineering and bioinformatics program here is because my background was mostly in biology and I wanted to get into the bioinformatics side of things and this is a great place to get into that.

I also enjoy  the sense of community and the fact that it’s a small environment but there’s so much good research going on and so many experts in the field that it’s a really great place to be and you really feel like you can collaborate with people.

Biomolecular Engineering
Degree Program: 
Ph.D., Biomolecular engineering and bioinformatics
Place of Birth: 
Undergraduate Institution: 
University of Florida
Graduate Institution: 
UC Santa Cruz
Angela Brooks