Bioinformatics and Computational Biology Takes Research Centre-Stage

CROSS-DISCIPLINARY STUDIES ABOUNDING IN ONTARIO

The Terrence Donnelly Centre for Cellular and Biomolecular Research (Donnelly CCBR) at the University of Toronto will be the first of its kind in Canada, allowing scientists from a wide range of disciplines to collaborate as they explore the roles that genes play in health and disease. Scheduled to open next September, the Centre will bring together researchers from the faculties of medicine, pharmacy, and science and applied engineering. Many projects will involve bioinformatics and computational biology, which are helping to advance genetic research and are leading to new companies and education programs in Ontario.

“The need to use computers in biology has increased within the past five years as the sequencing of human genes has provided a huge mountain of information and has led to other investigations that also are producing reams of information,” says Dr. Jim Friesen, Professor Emeritus in the university’s Banting and Best Department of Medical Research and a former co-director of the Donnelly CCBR.

For example, studies are trying to find out the role of genes in cells, how they make proteins, how many proteins, under what circumstances, what the proteins interact with, and a host of other details that eventually may help pinpoint the causes of diseases and help with prevention, diagnosis or treatment. This type of approach may be used in the study of almost any disease.

Bioinformatics and computational biology help to organize and make sense of the data coming out of the studies. “They are sort of two interlinked fields, bioinformatics being more shaded toward assembling the initial data, and computation aimed at using those assemblages of data to make sense of it and to get patterns out of it,” says Dr. Friesen.

“Mathematicians, statisticians, biologists, even physicists and chemists, people who have a quantitative viewpoint of the world are now building into all of this biological information. They’re trying to make sense of it, organizing it, collating it, looking at the interactions. From that eventually, and in fact it’s even starting, people will be able to make certain predictions about how biological systems work.”

For example, cancer researchers already are using a lot of this type of information to look at different kinds of cancers and to try to identify people who have a disposition for certain kinds of cancers, which then would allow the clinician to zero in on the most appropriate dosages for chemotherapy.

Years ago, researchers looked at just one gene at a time but now they look at hundreds or thousands of genes at a time with the help of computers, using them to put information from studies into organized databases and then to examine the data. Computer scientists, mathematicians, statisticians and other researchers are devising many computer tools to work with the data, including specific sets of software to try to wrinkle out the patterns and knowledge coming from all the data.

The Donnelly CCBR and MaRS are planning to have a joint symposium on bioinformatics and computational biology in the fall of 2005. “MaRS offers a really fantastic opportunity for us to try to bring together some of the computational biology and bioinformatics that kind of bridges the gap between the very basic kind of research and the more applied and clinical research,” says Dr. Friesen. “For example, The Hospital for Sick Children will have its computational biology group at the MaRS Centre, and there is a possibility that others will be there too. We hope there can be a kind of access between MaRS and the Donnelly CCBR that will provide at least the conceptual backbone for bioinformatics and computational biology studies in the city.”

Where does Ontario stand in these fields? “We do have some strengths for sure,” says Dr. Friesen. “For example, at Mount Sinai Hospital there is the Blueprint research program headed by Christopher Hogue, which has one of the world’s best databases for the interaction of proteins.”

“I would say that Ontario probably has the best overall setup in Canada and that a year or two from now we will be by far the best in Canada. I think in a couple of years we are aiming to be one of the world locations for computational biology.”

Bioinformatics Solutions Inc., founded in Waterloo, Ont., in 2000, develops software that has attracted customers from Europe, Japan and the United States, as well as Canada. Its products include PEAKS software for protein and peptide analysis and RAPTOR, a protein structure prediction program that received a top ranking in the international Critical Assessment of Fully Automated Structure Prediction competition in 2002.

“The world of biology is sort of transforming itself from a wet science to a dry science, moving out of the labs and into the computer world because they have to analyze so much information,” says Dr. Ming Li, a computer scientist who is one of the company founders and a professor at the University of Waterloo.
The University of Waterloo’s undergraduate program in bioinformatics was one of the first of its kind in North America, and graduated its first students in 2004.

In Kingston, Ont., Queen’s University will be graduating its first class of biomedical computing students in April, says Dr. Janice Glasgow, a professor and Queen’s Research Chair in Biomedical Computing at the School of Computing. Graduates of the four-year program will have studied the fundamentals of mathematics, statistics, chemistry, biology, molecular biology and physiology. As well as possessing advanced programming skills, they are well versed in areas such as software design, database management, artificial intelligence, computational biology and medical informatics.

“In the first class we have about 20, and in the following year there will be about 40, so it’s a growing area of interest for students,” Dr. Glasgow says. “They’re getting a good grounding in the life sciences. They do all the basics, including biology, chemistry, biochemistry, some physiology, anatomy and genetics. They’re also getting a very computational background.”

“The idea is that they will have the tools and the ability to create the new software that is needed in individualized development, whether it be in research labs, pharmaceutical companies, biotech or bioinformatics companies.”

The collaborative nature of bioinformatics and computational biology in Canada is also attracting researchers such as Dr. Miguel Andrade, a biochemist with a PhD in computational biology. He came to the Ottawa Health Research Institute last year after working in Germany and is now part of a stem cell research project. His group includes people with various backgrounds, such as biochemistry, biology, physics and software development.

Dr. Andrade says that when he worked in a bioinformatics group in Germany it was so large that collaboration with biologists was not a regular part of the work. “I like it here because we are working more in close collaboration with biological groups, and that’s more rewarding.”

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