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Carnegie Mellon U. transforms DNA microarrays with standard Internet communications tool

A standard Internet protocol that checks errors made during email transmissions has now inspired a revolutionary method to transform DNA microarray analysis, a common technology used to understand gene activation. The new method, which blends experiment and computation, strengthens DNA microarray analysis, according to its Carnegie Mellon University inventor, who is publishing his findings in the December issue of Nature Biotechnology with collaborators at the Hebrew University in Israel.

The innovative method combines a new experimental procedure and a new algorithm to identify gene activation captured by DNA microarray analysis with greater sensitivity and specificity. The work holds great promise for vastly improving research on health and disease, according to Ziv Bar-Joseph, assistant professor of computer science and biological sciences at Carnegie Mellon.

"We are very excited about introducing this versatile, powerful method to the research community because it can be used to study a wide range of complex, dynamic systems more comprehensively," said Bar-Joseph, who also is a member of the Center for Automated Learning and Discovery at the School of Computer Science. "Such systems under study include stress and drug response, cancer and embryo development."

DNA microarray analysis -- a multimillion-dollar-a-year industry -- identifies gene activation in living, complex biological systems. DNA microarrays monitor the behavior of thousands of genes over time by detecting changes in the expression of as many as 30,000 different genes on one small chip. The technique has been used to study some of the most important biological systems, including how cells normally divide (the cell cycle) and immune responses to disease and infection.

"Ultimately, we think that the addition of this method to standard DNA microarray analysis will make it more accurate and cost-effective," Bar-Joseph added.

"While DNA microarrays are very powerf
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Source:Carnegie Mellon University


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