Introducing Bioinformatics
July 10, 2007 - Aaron Baca
Jenny Yang wants to know why cells die.
She's not a medical doctor and she's not a biologist. Yang is a biochemistry professor who specializes in researching the role calcium and various proteins play in keeping living cells healthy. For a decade, she has compared how molecules bind together in the gooey innards of cells, searching for clues to tell scientists why calcium helps maintain the vibrancy of some cells, but then prompts others to kill themselves.
It's one of the holy grails of biology: programmed cell death. Yang would like to find the miniscule triggers that throw this death switch. The answers might lead to new drug therapies and treatments that could kill some cancers and degenerative diseases. Some futurists even believe there might be ways to cheat old age itself.
"We know there are answers in calcium," Yang says. "There's something that acts as a sensor (inside the cell). I’m trying to recreate that sensor so we can change it."
Yang, however, is not a mathematician or a computer scientist — two fields whose value to work like hers is growing exponentially. She depends on both fields daily and is able to draw on a talented pool of experts at Georgia State who are combining computer technology and biology to form a new boutique of computer science called bioinformatics. The field has breathed new life into both biology and computer science, and it’s developing a brand image for Georgia State.
"Ah!" exclaims Yi Pan, chair of Georgia State’s computer science department. He half jumps from the chair behind his desk. "Biology, chemistry and computer science! They need us! They need computer science to figure out what’s happening in their labs!"
Such is bioinformatics. It's one of those words that sound weirder each time you say it, but the field is rapidly becoming a scientific commodity. Properly defined, bioinformatics is the use of information management, mathematics, artificial intelligence and chemistry to solve complicated biology problems at a molecular level.
To put it more simply, "It's using computers to model, predict and manage the huge amount of information generated in a biology lab," Pan says.
Although small when compared to the computer science departments of peer universities, the CS department at Georgia State is becoming one of the ranking bioinformatics centers of the Southeast.
In fact, nearly all of the department's 15 faculty members work with researchers in chemistry and biology to devise customized laboratory management systems. It's an edict Pan handed down two years ago after becoming the department's chair.
"I knew we would never be able to compete with Georgia Tech or the University of Georgia if we did computer science like they did," Pan says. "They have more people than us. They have more money than us. …So we chose to be different."
Being different at Georgia State means combining traditional computer research in areas such as software and hardware development and then adapting it to biology, Pan says. The departmentwide effort is paying off in terms of recognition. Pan serves as editor-in-chief of the International Journal of Bioinformatics Research and Applications by Inderscience Publishers. Pan and other faculty also edit the Wiley academic book series on bioinformatics. And this spring, the CS department hosted the Institute of Electrical and Electronics Engineers annual symposium on bioinformatics.
It was only eight years ago that the CS department split from Mathematics to become a standalone department. The doctoral program began in 2000, and the number of Ph.D. graduates coming out of the program has increased consistently every year. Ten students graduated in 2006, and more than a dozen are expected to graduate this year.
A check of graduate employment records in the department shows most doctoral students continue to work in bioinformatics at other institutions.
"Now Georgia State University is a name people know," Pan says. The department's focus on bioinformatics began in 2001 when Robert Harrison was hired as a professor. A Yale-educated computer scientist, Harrison researches computational chemistry and bioinformatics. He has a joint appointment within the biology department. His work includes numerical analysis and algorithm design, as well as the use of supercomputers to answer difficult computational problems.
"We do real computer science, and we attack real problems at Georgia State. I think it’s important to re-emphasize that every day," Harrison told a group of supercomputing experts who recently visited the campus.
Pan credits the department’s work in bioinformatics with new grant and research money, a growing base of computer science students interested in doing interdisciplinary work and the ability to attract talented faculty.
The department has won about $500,000 in research grants for projects directly related to computational biology in the past three years from the National Science Foundation, the National Institutes of Health and the Georgia Research Alliance.
One of the department's newest jobs includes a project with biology professor Paul Katz to develop a Web-based resource for researchers to catalog individual neurons in the human brain.
"Our goal is to become one of the strongest departments on campus," Pan says. "I hope our success will show through continued growth."