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November 3, 2003

Engineering school offers graduate degrees in bioinformatics

UCSC is one of just seven universities in the nation to offer all three degrees in bioinformatics

By Tim Stephens

The Baskin School of Engineering has received formal approval to begin offering graduate degrees in bioinformatics, an interdisciplinary field that uses information technology and computer science to solve complex problems in biology.

A number of students who plan to earn graduate degrees in bioinformatics are already enrolled at UCSC.

The engineering school now has programs leading to M.S. and Ph.D. degrees in bioinformatics, in addition to the B.S. degree that has been available for undergraduates since 2001.

UCSC is now the only UC campus and one of just seven universities in the country to offer all three degrees in bioinformatics (B.S, M.S., and Ph.D.). A number of students who plan to earn graduate degrees in bioinformatics are already enrolled at UCSC. There are currently 20 graduate students in computer science who will transfer into the new graduate program in bioinformatics.

"We had 170 applicants for the bioinformatics graduate program last year, before it was formally approved," said Kevin Karplus, professor of computer engineering.. "It is a very competitive program. Our acceptance rate for domestic students was 15 percent, and for foreign students it was 3 percent."

UCSC has developed one of the top bioinformatics research programs in the country under the leadership of Karplus, David Haussler, professor of computer science and director of UCSC's Center for Biomolecular Science and Engineering (CBSE), and professor of computer engineering Richard Hughey. The CBSE has spearheaded the development of collaborative research and education programs in bioinformatics and other areas, bringing together faculty from different disciplines in engineering and the physical and biological sciences.

Karplus said the graduate program in bioinformatics is looking for students with at least some background in both computer programming and biology.

Programming experience is especially valuable, because it is not an easily acquired skill, he said.

UCSC's bioinformatics program focuses on tool building--creating new software programs and methods for analyzing and organizing data generated by research in molecular biology and biochemistry. The increasing use of "high-throughput" techniques in these fields is generating vast amounts of data, and advanced computational techniques are needed to extract useful information from such huge datasets.

"Our focus is on producing the tools that are needed to answer interesting questions in biology," Karplus said.

In the past, graduate students at UCSC who were interested in bioinformatics have earned degrees in related fields, such as computer science. Several UCSC alumni have been highly successful in the field. David Kulp, for example, who studied computer science under Haussler, helped start a biotechnology company based on software initially developed at UCSC for finding genes within genome sequences.

The company, Neomorphic, was later acquired by Affymetrix, and Kulp is now on the faculty of the University of Massachusetts - Amherst.

The UCSC Genome Browser is one of the world's most popular bioinformatics tools, providing a web-based portal for the scientific exploration of the human genome sequence and the genomes of a growing number of other organisms. The browser was developed by James Kent, now a CBSE research scientist, while he was a graduate student in molecular, cell, and developmental biology at UCSC. The genome browser web server at UCSC now receives about 140,000 page requests a day from scientists in dozens of countries.

"Our current strengths are in the areas of comparative genomics, gene finding, DNA microarrays, and protein structure prediction. We expect to continue to grow and expand, but we're not trying to do everything," Karplus said.

The engineering school is currently in the process of establishing a new Department of Biomolecular Engineering, which will administer the bioinformatics program once the new department is approved.

Additional information about the bioinformatics graduate program at UCSC is available online.

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