UMR professor’s statistical tools help DNA researchers

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On October 26, 2005

A researcher at the University of Missouri-Rolla is on the forefront of developing new statistical tools, ones that will help biologists and other scientists sort through massive amounts of data to find disease-causing genes.

For the past three years, Dr. Gary Gadbury, assistant professor of mathematics and statistics at UMR, has worked with a team of researchers from the University of Alabama at Birmingham to develop methods to analyze “microarray” data. Microarray research is an emerging field that allows researchers to take thousands of measurements on a few items to obtain a massive data set. Researchers then may simultaneously study the expressions of thousands of genes on a few items to see how certain factors affect gene expression.

“Microarray experiments are part of discovery-oriented research,” Gadbury says. “Scientists don’t always know what they’re looking for in such high-dimensional investigations.”

Gadbury says his research, which involves the development of new computer programs, is part of the genomic experiments that are currently being done on both plants and animals. “These projects are designed to identify genes that are affected by certain conditions,” he says.

Research in this field explores disruptions or changes in gene expression that may be responsible for many diseases, including heart disease, high blood pressure, diabetes and Alzheimer’s disease.

Microarray research differs from more traditional approaches. Typically, researchers take fewer measurements on each item than the total number of items in the experiment. Because microarray research generates such massive amounts of data, a challenge arises in how to store and analyze the data. Gadbury worked with UAB researchers to develop new computer software, HDBStat!, which is a solution for researchers and educators alike.

“This type of research will become more common in the coming years, making it important to have new tools and techniques for analyzing and interpreting resulting data,” Gadbury says.

HDBStat! is free to academic institutions and non-profit organizations.

Gadbury’s research is funded by a four-year grant from the National Science Foundation that totals $192,306. The funding will last through September 2006.

In addition to Gadbury’s work on computer software, the grant has provided funding for Qinfang Xiang, a doctoral student from Rolla who is in the UMR mathematics and statistics department, to assist with Gadbury’s research. Xiang has co-authored a book chapter with Gadbury, and he recently submitted his first paper as the lead author.

The grant has also allowed Gadbury to speak at several conferences throughout the nation. In August 2005, Gadbury spoke at the National Statistical Meetings in Minneapolis, Minn., along with two graduate students from his department. Other recent talks were at conferences in Portland, Maine, and Austin, Texas, and at an annual research meeting near New Palz, N.Y.

Gadbury is currently joining UAB researchers in applying for renewal of the NSF grant so he can continue this research with microarry data. His current research includes analyzing the false discovery rate (FDR) of microarray experiments.

“If you do an experiment, you may look at 20,000 genes, and 200 appear to be differentially expressed as a result of the treatment,” Gadbury says. He says some of the genes look “interesting” or significant at first, but they may not truly be affected by the treatment. FDR methods help researchers avoid falsely calling too many genes significant. Gadbury says that the goal when designing experiments is to keep the FDR low.

Gadbury says microarray research is only one category under the big umbrella of bioinformatics, or solving biological problems using computational methods.

“There is a growing interest in bioinformatics at UMR,” Gadbury says. “I am hoping to apply things I learned from working with UAB to things that originate at UMR.”

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On October 26, 2005. Posted in Research