Gov. George Pataki's recent proposal to designate Buffalo as the site for a world-class Center of Excellence in Bioinformatics was only fitting.

Bioinformatics, strictly speaking, refers to the use of advanced computational technologies to interpret the vast amounts of data found through the Human Genome Project, as well as the genome, the total of all genes, of other species.

The majority of the DNA used in the project came from volunteers in Western New York, courtesy of Roswell Park Cancer Institute's proficiency in creating DNA libraries.

But making Buffalo a center for bioinformatics also is a natural progression of the pioneering work that the center's four partner institutions-UB, Roswell Park (RPCI), Hauptman-Woodward Medical Research Institute (HWI) and Kaleida Health-have been doing for years.

"Buffalo is uniquely positioned to make this happen," said Bruce Holm, senior associate dean in the School of Medicine and Biomedical Sciences.

According to Holm and others who will be involved with the center, some of the scientific areas in which Buffalo excels will be critical ingredients in the bioinformatics revolution:

n Supercomputing: UB is home to the Center for Computational Research (CCR), one of the nation's leading academic supercomputing centers, with the large-scale computing and visualization capabilities, and the staff expertise necessary for tackling the massive computational problems presented by the data in the human genome.

CCR already serves as the computational backbone for research under a $25 million National Institutes of Health grant in structural genomics to a consortium of nine institutions, including UB and HWI.

- Visualization: Also at UB is the New York State Center for Engineering Design and Industrial Innovation (NYSCEDII), which has the virtual-reality capabilities to allow scientists to visualize and interact with three-dimensional molecular structures in large, immersive environments.

- Structural Biology, Genomics and Proteomics: During the past five years, more than $17 million in key scientific awards has been received by the UB medical school, RPCI and HWI to study genomics, proteomics (the study of protein structures as related to furthering drug design), structural biology and neuroimaging as they pertain to disease modeling and drug discovery.

- Generation of DNA Microarrays: The DNA microarray facility, jointly operated by UB and RPCI, allows scientists to detect thousands of genes simultaneously and analyze their expression. By creating custom gene “chips,” each of which can contain up to 20,000 genes, the facility provides a boon to researchers investigating which of the 100,000 human genes are active in a given cell or tissue.

- Pharmaceutical Science: Pioneering work in the School of Pharmacy and Pharmaceutical Sciences led to the development of the field of pharmacodynamics, which is the study of how drugs affect cells and tissues as a function of time and concentration. Continued work by the same researchers has resulted in new techniques using gene arrays to find markers of pharmacological effect that can be used to optimize new drugs and therapies.

At the same time, HWI and UB are home to the developers of SnB, the molecular structure-determination software based on the algorithm developed by Nobel Laureate Herbert Hauptman, now HWI president, and the shake-and-bake algorithm developed by George DeTitta, HWI executive director; Charles Weeks, senior HWI research scientist, and Russ Miller, director of CCR and professor of computer science and engineering.

“We have the right collection of institutions, individuals and facilities to make this happen,” said Miller, “Many of us have been working collaboratively for years.”

As one of the top 10 U.S. academic supercomputing centers, CCR provides the computing power that is essential for any successful bioinformatics initiative.

“Without CCR, we wouldn’t even be in the game,” said Holm. “There was a reason and vision for developing CCR—it was to recognize how important supercomputing was going to be, both to academic science and to economic development.”

And while it is very early, the business community already is starting to respond. A major firm with strong ties to the area and an interest in bioinformatics has stated that it is considering an additional significant investment in resources in Buffalo, now that a Center of Excellence in Bioinformatics has been proposed.

Holm added that because Buffalo is a very low-overhead place to locate a business, he expects to see more firms become interested in the area as the center gets going.

“Heads are turned by this kind of investment,” he said.

That’s also likely to be the response from federal funding agencies, according to Jaylan Turkkan, UB vice president for research.

“The federal government wants to see that a state supports a university’s activities,” she said.

“When we can show them that we already have a coherent plan for this center, that we have space identified and major support from Albany, all of these things will make us that much more competitive,” she said, “especially because they demonstrate to NIH that recruitment of top faculty will be much easier.”

In addition, Turkkan noted, the four participating institutions have long histories of collaboration that include formal memoranda and faculty with joint appointments.

It is the nature of those institutions themselves and the capabilities they posses that also make it possible to exploit bioinformatics in its broadest sense.

According to Holm, the data that came out of the human genome project are merely a starting point for the new discipline.

“All that’s been found is code,” he said. “Now we have to find out what it means, how it’s linked to human disease and how to make links with potential therapeutics.”

To begin with, the incredible amounts of data that are generated need to be stored, then analyzed.

“With thousands and thousands of genes, finding the right patterns of genes that connect with those that can cure diseases is an unbelievably monumental number-crunching task,” said Turkkan.

Proteomics and structural biology also require massive supercomputing capabilities.

“There are 30,000 different ways that proteins can fold,” Turkkan said. “Only with high-end computing are scientists going to be able to model and predict what those folds are going to look like. And when you talk about the three-dimensional structure of molecules, a person almost needs to be immersed in the structure of the molecule to be able to walk around it and manipulate it.”

According to DeTitta, the current setup at NYSCEDII allows scientists to interact with biological data through visual data-mining techniques. But, he said, eventual expansion to a fully developed, six-wall (walls, floor and ceiling) “cave”—a capability now available at only one other institution in the nation—will amplify the amount of information that can be displayed by factors of six at the very least.

“It will literally be possible to ‘walk through’ a compound, evaluate the fit of a series of drug leads to a particular target protein and suggest changes to drug candidates to maximize their potential efficacy,” he said.