July 01, 2009

CORVALLIS, Ore. - The Center for Gene Research and Biotechnology at Oregon State University has changed its name and its emphasis and is growing to lead a new era of research in which genetic studies use advanced computing systems to tackle biology's biggest questions and toughest problems.

The center, which was formed in 1983, is now the Center for Genome Research and Biocomputing. More importantly, the new name reflects an ongoing revolution in the biological sciences - the merger of biology with advanced computational science.

"The conversion of biology into an information-based science allows much bigger and more difficult questions to be addressed," said Jim Carrington, professor and director of the center. "In addition to research focusing on single genes and proteins, we're now studying entire genomes and populations of genomes, enabled by powerful advances in technology and computational systems.

"This represents a major forefront in biological research, and the center is a key part of how OSU is building leadership in this area."

This center involves the efforts of more than 80 scientists at OSU, in fields ranging from agriculture to biomedicine, plant biology, mathematics and engineering. It helps foster collaboration among scientists in different colleges and disciplines, provides a wide range of sophisticated instruments and technology platforms, and enables advanced computation through infrastructure and in-house expertise. It also provides key technologies and services to students engaged in biological research.

"All projections are that the role of computation in biological research will become more and more dominant," Carrington said. "To expand its leadership in this area at OSU, the university developed the Computational and Genome Biology Initiative, which recently hired five new faculty."

The new faculty include:

  • Dee Denver, Department of Zoology, an expert on the evolution and adaptation of genomes, using the nematode C. elegans as a research model;
  • Todd Mockler, Department of Botany and Plant Pathology, who uses extensive computational research to study how entire genomes are expressed and regulated in the plant model Arabidopsis;
  • Erica Bakker, Department of Horticulture, an expert in the genomic evolution of Arabidopsis and the genes it uses to confer resistance against pathogens;
  • Michael Freitag, Department of Biochemistry and Biophysics, who studies how DNA and associated proteins are modified to affect gene expression;
  • Jeff Chang, Department of Botany and Plant Pathology, an expert in the molecular basis of disease caused by bacteria.

    This new initiative and the changes taking place in the Center for Genome Research and Biocomputing are resulting in a renovated curriculum, new educational programs for graduate students, major new facilities, enhanced fund raising, intriguing research and large grants.

    In another part of these efforts, renovation of the OSU curriculum in molecular and cellular biology is already under way, although it will take up to five years to be fully transformed. Three new courses in computational and genome biology will be created and others upgraded.

    The new developments have begun to attract a new cadre of graduate students in this field, and to enhance and relocate some computational infrastructure at OSU.

    Although closer ties with the Oregon biotechnology industry are anticipated, bigger benefits will arise from basic research, which often underpins advances in the private sector. The goal is to have the university recognized as a research leader in this field, a destination for leading graduate students and a center of high-impact scientific discoveries.

    In essence, computational biology is the effort to use computers, mathematics, modeling and other quantitative approaches to understand complex biological problems. Perhaps the most obvious example is the human genome project - an effort that took hundreds of scientists in 18 countries working for 13 years to decipher billions of base pairs of DNA. Although the actual data collection was a major feat, it is the use of computation that is providing meaning to the genome sequence, Carrington says.

    The craft of combining biology with advanced computing is evolving rapidly, researchers say. According to Steve Giovannoni, a professor of microbiology at OSU, dramatic declines in the cost of DNA sequencing have shifted the advantage to biological scientists who work with computers and huge amounts of genome sequence data.

    "The biology departments of the future will be much more mathematical and computational than in the past," said Steve Giovannoni, a co-director of the initiative. "This will bring biology much closer to disciplines like engineering and physics."

    Some projects at OSU are already heavily dependent on computation - studies of ocean microbe genomes and populations, the genetic improvement of trees in managed forests, the "small RNAs" that control growth and development of plants and animals. These studies have already attracted millions in federal research funding. Projects of this type should only expand, officials say, with the new faculty, graduate students and facilities made possible by the university's new initiative and the changing role of the Center for Genome Research and Biocomputing. Fields ranging from evolutionary biology to applied veterinary medicine all stand to benefit.

    "The pace of discovery using computational biology is really accelerating," Carrington said. "And OSU has a big role to play."

    About the Center for Genome Research and Biocomputing: The Center for Genome Research and Biocomputing at OSU is helping to lead a revolution in the biological science by combining collaboration and service in genome-enabled and computationally intensive science.

    • Source: 

    James Carrington, 541-737-3347

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