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UMR leaders aim to catch, lead bioinformatics wave

By Matthew Stolle

Post-Bulletin, Rochester MN

The field of bioinformatics gained its growing prominence during efforts in the 1990s to map the human genome.

As the amount of biological information has exploded, researchers have needed new, more powerful computing tools to sort through this data.

That has put a premium on the ability of researchers to develop algorithms to mine large data bases for patterns. The ability of computers to screen molecular compounds also can accelerate the discovery of new drugs and therapies.

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The hope in Rochester is that these discoveries can lead to spin-off companies and new business opportunities.

While the total investment at the University of Minnesota Rochester is less than $1 million, UMR officials said they are spending the dollars they do have with a strategic focus.

The goal is to fund the kind of cutting-edge research that begins to draw federal research grants from the National Science Foundation and attract more state funding, said Dick Westerlund, UMR interim vice chancellor for academic affairs.

With that in mind, UMR is supporting five research projects with $100,000 "seed" grants. Each project is collaborative in nature, with a university student paired with a Mayo Clinic or IBM researcher or both.

UMR also seeks to build momentum by funding the 10 bioinformatics traineeships before formally rolling out a graduate program next year.

Question of funding

One major question for some is whether the state is investing enough to fully capitalize on the opportunities available.

Drew Flaada, director of the IBM/Mayo collaboration and life sciences development team and a member of a Rochester higher education committee, said the university deserves a "ton of credit" for what it has accomplished. Students are being enrolled, research projects are being identified and academic programs are being developed. The big question is whether the program will to continue to receive the kind of state support that will allow the program to move beyond the first stage.

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"Are we on the right path here? The answer is absolutely. But if you look at it in the overall scheme of things, I think we’re kind of on the first steps of this path. And there are others that are investing more aggressively than we are seeing here," Flaada said.

Even with the limited funding, university officials are convinced they can "build rapidly" by taking advantage of the expertise already present in Rochester, said Claudia Neuhauser, director of the Ecology, Evolution and Behavior Department at the University of Minnesota.

Student drawn by computer power

Students like Andrew Norgan would seem to symbolize the educational potential and the collaborative possibilities of studying within a five-mile radius of Mayo, IBM and the university.

As one of 10 trainees in the UMR program, Norgan is using his research in bioinformatics as part of his doctorate studies at Mayo Graduate School. And his work, he hopes, will afford collaborative opportunities with IBM.

What drew him to the bioinformatics field was the power of computers to solve biological problems, he said.

"Computer power has grown immensely. What I can do on my laptop is now more than could have been done on the world’s best computers only a couple of decades ago," Norgan said.

His research is focused on the life cycle of viruses, how they replicate and grow and how therapies might be developed to inhibit their reproduction.

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Norgan said viruses such as Ebola and HIV show certain common characteristics. When a virus infects a body, it finds cells it can attach to, enters it and begins the process of replicating.

When they spread beyond the invaded cell, they take different routes. Some simply explode. Others follow a process called "viral budding." Pushing up against the cell’s membrane, they pinch off a piece of the membrane and leave. An infected cell can conceivably create millions of little buds that can escape the cell to infect more cells.

It is where a cell’s machinery and the virus interact in the budding process that researchers like Norgan are looking to disrupt the virus’s progress. If molecular compounds could be found to interfere with that interaction, the potential exists to find a cure.

Computers allow simulations

Yet the sheer magnitude of the task is daunting. Hundreds of thousands of compounds exist that researchers could test.

Such experiments conducted in a lab would be very expensive and time-consuming, but not with computers and their vast computational power. With their ability to simulate how certain drugs might interact with proteins in a cell, researchers can test hundreds of thousands of small molecules.

"These things just require brute force computation and lots of it," said Norgan, who has clusters of computers testing for the Ebola virus. "The more of them that you have available to do the work, the more quickly it gets done."

The problem is that the vast majority of compounds, even if they were found to work against viruses, are usually toxic or unsuitable for people. So the search continues.

Norgan said he’s realistic about what he hopes to achieve in the program. He does not envision himself being the next Jonas Salk in graduate school.

"My goal is not necessarily to develop a treatment in graduate school. My goal is to contribute to our understanding of how things work in such a way that, hopefully, we can make incremental progress towards (a treatment)," Norgan said.

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