Initiative on Computational Biology to Tackle Big Picture

Beginning in the 1840s, a brilliant French chemist named Louis Pasteur peered through a microscope and made personal discoveries about crystal structure, fermentation, bacteria, infectious disease, vaccines, and public health. He is now revered as the father of modern microbiology.

Beginning in 1990, researchers started the human genome project, an initiative that's already providing incalculable benefits for biological and medical research. But it took hundreds of scientists in 18 countries working for 13 years to decipher billions of base pairs of DNA. And even at that, the work went quicker than anticipated and the scientists actually finished a little ahead of schedule.

This, in essence, is the changing face of biology.

"There will always be a place for an individual researcher recording data or making a new and important scientific observation," said James Carrington, professor and director of the Center for Gene Research and Biotechnology at Oregon State University.

"But the fact is that the questions we are trying to address today are bigger, the challenges are greater, the available technology is far more complex," Carrington said. "And with the bigger problems you can address, the scientific payoffs are also much larger. But in many cases no one person can do all the work, collect all the data or analyze the entire picture."

That, Carrington said, is why OSU has sponsored the Computational and Genome Biology Initiative as one of six key initiatives the university will support in a five year, $10 million effort to spur scientific research and education in certain fields.

Under this initiative, OSU plans to hire several new faculty with broad expertise in both genome and computational biology - new interdisciplinary fields that combine advances in molecular biology with the most sophisticated computational approaches, to help make sense out of vast amounts of data and the work of teams of researchers. A $1.5 million commitment from the Provost's Initiative Fund will be matched by other support to create about $3.6 million in support for this new venture in coming years.

"We see these new faculty and the facilities they will help create as a type of glue that will hold large research teams together, and really help OSU stay at the forefront of biological research," Carrington said. "In addition, we'll be able to train both undergraduate and graduate students in high-tech biology with diverse sets of skills, which are things that private industry is looking for in the new scientists they employ."

Modern research can now generate thousands of times more data than any one scientist can fully examine and manage. But the evolving areas of bioinformatics and computational biology use information-based or digital systems to help organize these data. This enables researchers to ask more useful questions, and gain insights that would not otherwise be possible.

The use of huge teams of researchers and massive computer systems goes back further in some other areas - the NASA space exploration teams of the 1960s, for instance, or the huge atomic accelerators used in physics research. But modern biology, which is based on principles of genetics and a more intricate knowledge of how the cell works, is much more recent, and some of the technology and approaches that are now essential didn't even exist 10 years ago.

"The science of molecular biology as we know it today is very young, so the important problems to solve still seem very complex," Carrington said. "Investigation and application of genome and computational biology will accelerate progress and help OSU maintain leadership in a range of biological fields. This is what the new initiative is going to help us accomplish."

Some projects at OSU that have attracted more than $8 million in federal research funding in recent years are already heavily dependent on computational biology - and take advantage of OSU biocomputing infrastructure that has increased 100 times in power over the past two years. This includes work to study the genomes of ocean microbes, the improvement of trees in managed forests, and "small RNAs" that control growth and development of plants and animals.

But OSU scientists say all research in the molecular biosciences can benefit from greater expertise and facilities in systems-level biology, which integrates large datasets that describe the dynamic interrelationships among cellular components, and computationally intensive science. Salmon restoration efforts, biofuels research, crop breeding programs, natural products drug discovery, and other advances in fields ranging from evolutional biology to veterinary medicine, pharmacy, agriculture and microbiology all stand to benefit.

New courses and laboratories for student instruction in these fields are also anticipated. And competitive graduate research fellowships with an emphasis in computational genomics will be added.

The new initiative is highly interdisciplinary. It will involve eight colleges at OSU and address several of the key themes identified in the university's strategic plan, including advancing scientific discovery, making fundamental contributions to the life sciences and optimizing the health and well being of the general public. There should also be a synergy with Oregon's growing biotechnology industry, and a major increase in the level of external grant funding and fundraising potential.

"We're trying to look at big questions," Carrington said. "In the old days we might have been more limited, asking what a single protein does, or how a single gene is organized and expressed?"

"But if you're serious about understanding complex biological processes, such as the development of disease, you have to know how an entire system works," he said.

"Let's say a virus invades a particular cell type that controls the immune system."

"This disables part of the immune response, and the infection results in disease. Understanding how disease occurs requires a detailed understanding of how the immune system functions, and then how the virus affects all of the key parts of the system. This means we need to understand the nature and interactions of the genes, proteins and metabolites that function normally, and the consequences of virus infection on the entire system."

"These are the types of processes we can now seek to understand and influence," he said. "These and other big picture problems seem very complicated, but we believe computational and genome-enabled research will help us solve them."