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Pioneers of Discovery: Computer science drives Capra’s biomedical research

Oct. 3, 2013, 10:00 AM

Tony Capra, Ph.D., is using the tools of computer science to address problems in genetics, evolution and biomedicine. (photo by Susan Urmy)

Computers have captivated Tony Capra, Ph.D., since his childhood days in Memphis — long before the devices were commonplace. He started playing games on his mother’s home business computer and gradually figured out how it worked, and how to code his own games.

By the mid-1990s, he was an early user of the Internet.

“I had a couple of other nerdy friends, and we would write programs to send messages to each other — sort of like instant messaging before that became an everyday thing,” Capra said.

His computer skills landed him a summer job during high school in the genetics laboratory of a friend’s father at the University of Tennessee, Memphis. It was there — developing Web-based tools for scientists to access biologic information — that Capra got his “first taste of how computer science and biology and genetics can interact and do interesting things.”

He was hooked.

Today, Capra can be found in his Light Hall office, writing computer algorithms to integrate the reams of genomic and protein data sitting in databases around the world. He joined the Vanderbilt faculty in February as an assistant professor of Biomedical Informatics and investigator in the Center for Human Genetics Research.

Capra’s goal is to use the tools of computer science to address problems in genetics, evolution and biomedicine.

“Over the past five years or so, we’ve gotten really good at using genomewide association studies (GWAS) to identify regions of our genome that are associated with certain characteristics or diseases,” Capra said. “In many cases, we know there’s an association, but we don’t know why.”

Capra has been steadily building his computer science toolkit.

He earned degrees in Computer Science and Mathematics from Columbia University before heading to graduate school in Computer Science at Princeton University. There, he dove into bioinformatics and computational biology, writing computer programs to analyze and understand proteins, based on 3-dimensional information and evolutionary comparisons to proteins in other species.

During his postdoctoral fellowship at the University of California, San Francisco, he used computer science to study recent human evolution and what makes us human from a genetics standpoint. Capra and his colleagues wrote algorithms to compare the entire human genome to the genomes of the great apes and other mammals. They identified nearly 800 “human accelerated regions” — stretches of DNA that are conserved among the great apes and are different in humans.

They found that more than 90 percent of these regions do not code for proteins. In further computational and functional analyses, Capra and his colleagues demonstrated that some of these regions regulate gene expression in the brain.

Capra will now be applying the tools he’s developed to understanding the parts of our genome that distinguish one individual from another and that contribute to disease risk.

“There’s all kinds of genomewide functional and experimental information available. We have thousands of human genomes and functional data from many contexts. Now we need algorithms that are smart enough to integrate all these different sources of data,” Capra said. “It’s a really exciting time.”

His advice for today’s computer savvy high schoolers: “Download some genomes and play with them. Who knows what you might find?”

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