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UCSD computer scientist wins Young Investigator Award, research on snake venom proteins highlighted

Nuno Bandeira, a computer science and engineering Ph.D. candidate at UC San Diego's Jacobs School of Engineering has won the 2006 Human Proteome Organization's Young Investigator Award for work on snake venom proteins. The award-winning protein analysis technique is expected to aid drug development efforts, help scientists better understand cancer proteins and, perhaps, let scientists dive into dinosaur genetics.

Modified snake venom proteins have been used in the past to create blood thickening and thinning drugs and powerful pain killers -- but there is much more to learn about proteins from snake venom and Bandeira's research provides a new and improved way to study them. In fact, the technique should be useful in studying a wide range of highly modified proteins that researchers have had trouble studying in the past, due to technical limitations.

The award-winning protein analysis technique gives scientists two new technical capabilities: the ability to glean amino acid sequences from mixtures of unidentified proteins and identify the specific ways in which proteins have been modified. Bandeira and colleagues present their improved protein sequencing technique with an analysis of venom proteins from western diamondback rattlesnakes.

Nuno Bandeira performed this research with his Ph.D. advisor -- UCSD computer science and engineering professor Pavel Pevzner, and Karl Clauser from the Broad Institute of MIT and Harvard. Pevzner is also the director of the newly-established Center for Algorithmic and Systems Biology (CASB) at the UCSD Division of Calit2.

In the language of biology, the new technique can be described as "shotgun protein sequencing of post-translationally modified proteins."

"Shotgun" refers to the process of "blowing" the proteins to small pieces. After several interim steps, scientists then put the pieces back together and reconstruct the original proteins, using the weights of amino acids as o
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Contact: Daniel Kane
dbkane@ucsd.edu
858-534-3262
University of California - San Diego
13-Nov-2006


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