Data for the greater good
Ben Litterer (’22 data science) uses big data to study proteins with Distinguished Professor Robert Jernigan in the Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology.
Big data and biology
I work in Dr. Robert Jernigan’s lab, where we are interested in using the insights and abilities of powerful computational tools in computer science, statistics and data science to answer fundamental biological questions. Using statistical techniques, my research looks at the functions of proteins and tries to make predictions or improve the understanding of what a particular protein does in your body. Recently, I focused on protein function related to HIV.
Through genome sequencing, scientists have lots of information about protein functions. So, if we have a protein that we know less about, we could find a similar protein and make a statistical estimate on how likely it is to have the same function. We’re mining this huge expanse of knowledge. The more information you have though, the harder it is to look through all of it. It’s like trying to find one particular word at the Iowa State library. I know it’s there, but I don’t know which book to open.
One thing I'm interested in learning about is called embeddings. For example, how do you translate a word into a mathematical representation so you can do math with that word in a sentence? Now do that with proteins. Imagine if you have 1,000 proteins and you could treat them like numbers. You could ask, “How far is one protein from another?” and then just subtract them. There are ways of using machine learning to represent proteins as numbers, and I think that is really cool. Once we can do that fundamental thing well, it will solve all these problems about function and structure.
When I do research
I start by reading. Reading and brainstorming are exciting for me, but it’s a small portion of the time. I also spend a lot of time programming and thinking about the logistical details of implementation, with so much data to process.
The creativity is the most fun part of research for me. I feel very privileged to be taken seriously in my lab. I remember the first time I shared an idea in a lab meeting about a particular protein function. Some of the graduate students said, “That is a smart idea. You’re getting a knack for what it means to do research.” In the future, I’m excited to be part of the conversation in a community of scientists.
A supportive lab
I’m so grateful for the support from postdocs, graduate students and Dr. Jernigan. It’s the number one thing that’s allowed me to have any success in research. Dr. Jernigan never tells me what to do. He encourages me to keep trying what seems like the right idea. That is incredibly helpful for an undergraduate.
I think it’s important ...
That computation is used responsibly. Rather than using these powerful tools to maximize profit, how can we use them to maximize well-being?
"I think it's important that computation is used responsibly. Rather than using these powerful tools to maximize profit, how can we use them to maximize well-being?" - Ben Litterer
from LINK - THE MAGAZINE FOR THE COLLEGE OF LIBERAL ARTS AND SCIENCES AT
IOWA STATE UNIVERSITY