Engineering at Nebraska, Spring 2007
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faculty profile:
Longtime Professor is a Student Again:

When you’re used to getting an immediate reaction from an experiment—even if it’s smoke—getting used to working with colorless, shapeless materials is an adjustment.

“It’s really weird for me,” said Khalid Sayood, who holds the Henson College Professorship in Engineering, Communication and Information Sciences.

Khalid Sayood studies chemistry, biology and genetics to become a better engineer and teacher.Winning a National Institutes of Health Research Career Development Award (K25) has allowed Sayood to take his knowledge in communications and data compression a step further. The award allows Sayood to spend five years learning about chemistry, biology and genetics by taking courses and working with other scientists so he can use his background in communications and information theory to solve biological problems.

It’s not as big of a leap as one might think, Sayood said. Many of his research projects have dealt with studying data patterns and how information is organized. His science courses are teaching him how to interpret data from a biological standpoint.

“There are computer scientists and engineers, people like me, who want to work with biological data but neither know the capabilities or the challenges of acquiring that data,” Sayood said. “This program provides people like me the opportunity to see the other side.”

Biochemistry professor Charles Wood has been one of Sayood’s K25 mentors. Together, they are looking at how HIV evolves as it’s transmitted. Sayood is developing algorithms to detect patterns in genetic sequences.Understanding these sequences could help biologists discover more effective ways to treat, or even prevent, HIV.

“We’re hoping his method will replace more cumbersome, time consuming methods used traditionally to detect sequences and match them up,” Wood said.

One of the biggest challenges of the partnership has been learning to understand each other’s expertise, Wood said, but it’s also been one of the benefits.

Sayood also spends two days a week with Dr. Steve Hinrichs at the University of Nebraska Medical Center, his primary collaborator, developing algorithms to determine patterns specific to bacterial genomes. The fundamental problem in treating infections, Sayood said, is figuring out how to kill the bacteria without harming the patient. Scientists must look for patterns and processes that occur in bacterial cells but not in humans. One of Sayood’s algorithms predicts the origin of replication in bacteria. To validate the prediction of the origin in staphylococcus aureus bacterium, Sayood copies the region of the DNA of S. aureus where his algorithm predicts the origin should be, inserts it into an E. coli plasmid, and then inserts the plas-mid into S. aureus.

Theoretically, Sayood said, the E. coli plasmid shouldn’t replicate in S. aureus. If it contains an origin of replication, however, it might. That would validate the algorithm.

“I’ll never be a biologist but if you are working on research and want certain data it’s good to know how it’s derived,” Sayood said.

Winning a K25 award has given him the time he needed to study bioinformatics, which he said was hard to come by when he held other research grants. The UNL Office of Research was instrumental in helping Sayood write his proposal and find mentors in the biological sciences. Sayood said he’s lost track of how much time he spends studying. “The T.A. wasn’t so sure about an old guy taking his tests,”

Sayood said. “I told him that I had probably taken my last test before he was born.”

Although he isn’t pursuing another degree, Sayood is taking his courses for credit instead of auditing them. “The threat of embarrassing myself is a motivation to thoroughly learn the material,” he said.

Sayood said seeing the classroom from a student’s perspective would make him a better teacher. The next time he teaches Introduction to Bioinformatics, he plans to approach the subject differently based on what he’s learned in science courses.

“I understand the subject matter much better, but I won’t change my teaching style. That’s one area where I think I do okay.”

—Ashley Washburn