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