What is Bioinformatics?

The definition of bioinformatics is currently controversial, but bioinformatics can be loosely defined as the use of computers and computer science to study biological questions. It forms the intersection between molecular biology (and related biological disciplines) and computing science. This interdisciplinary field involves researchers who work at many different points on the computer science-biology spectrum: From those who are developing new relevant algorithms, to those who are developing and using computational applications to study biological phenomena, gain new insight into the life sciences, identify new drug targets etc. This field is currently evolving, but one point is agreed upon: Bioinformatics is a blossoming field within which there remain many significant discoveries to be made.

Overview of Research and Facilities

Simon Fraser University has a strong interest and long history in Bioinformatics Training and Bioinformatics Research. Dr. David Baillie, a CRC Chair in Genomics in the Department of Molecular Biology and Biochemistry (MBB), was a pioneer in this field. He and others in the Department of Molecular Biology and Biochemistry, trained researchers that have since gone on to leadership roles at genome sequence centres, international pharmaceutical companies, or have become coordinators of Genbank or the Canadian Bioinformatics Workshop.

Training is expanding at SFU, as a new graduate program has been initiated that offers M.Sc. and Ph.D. degrees, or a graduate certificate in Bioinformatics.* A new undergraduate program has recently been approved that leads to an B.Sc. Joint Major in Computing Science and Molecular Biology and Biochemistry. This undergraduate program provides suitable training for a bioinformatics career, while leaving the door open for other career options in the computing or biological sciences. Research is also expanding as new faculty in Bioinformatics have been recently hired. Faculty include Dr. Fiona Brinkman, listed by MIT Technology Reviews as one of the worlds "top young innovators", and involved in a number of microbial pathogen bioinformatics projects. Dr. Frederic Pio, who is using bioinformatics and structural biochemistry to identify new protein-protein and protein-DNA interaction complexes involved in cancer and apoptosis. Dr. Arvind Gupta, the Scientific Director of MITACS (Mathematics of Information Technology and Complex Systems, involving 230 scientists across Canada). Dr. Mark Paetzel, a Michael Smith Foundation for Health Research Scholar and new faculty member in structural biochemistry, and Drs Martin Ester and Ke Wang in computing science who share an interest in data mining algorithms relevant to bioinformatics problems. At SFU, researchers interested in bioinformatics are in a range of computing science, molecular biology, biochemistry, biophysics, information technology, and statistics fields, facilitating stimulating and diverse interactions across disciplines.

Research Interests

Research interests in bioinformatics at SFU are generally in the following areas. In addition, a number of other faculty with some bioinformatics interests have research programs in catalytic RNA, structural biochemistry, biophysics, computational linguistics, and artificial intelligence:

• Comparative Genomics (Baillie, Brinkman)
• Complexity Theory and Optimization (Gupta)
• Computationally predicting protein subcellular localization (Brinkman)
• Databases and data mining (Ester, Wang, Brinkman, Pio)
• Eukaryotic and human genetics and genomics (Baillie, Davidson)
• Genome Annotation (Brinkman, Baillie)
• Membrane and DNA Biophysics (Biophysics Research Group)
• Microbial Pathogenomics (Brinkman)
• Phylogenetics and Evolutionary Genomics (Smith, Brinkman)
• Statistical Genetics and Epidemiology (McNeney, Graham, Davidson)
• Structural Proteomics (Paetzel, Pio)
• 3D visualization (Weise)

Some current Genome Canada Projects at SFU

• C. elegans: Expression Profiles of Cells and Tissues (Baillie, Principle Investigator)
• Functional Pathogenomics of Mucosal Immunity (Brinkman, Director of Bioinformatics)
• Genomics Research on Atlantic Salmon (Davidson, Principle Investigator)

Facilities

Bioinformaticists at SFU have access to notable resources, such as SFU's "Bugaboos" Beowulf Computing Cluster and the "Cave" for 3D visualization at SFU-Surrey. Two of the five project leaders for the large WestGrid project are at SFU. WestGrid is an ambitious project involving the development of a shared grid of high performance computing facilities involving eight institutions across western Canada, and a significant component of these facilties will be housed at SFU.

In addition, bioinformaticists at SFU have access to a range of complementary laboratory facilities and faculty, for collaboration on projects involving laboratory verification of computational results, or gathering of laboratory data for a given bioinformatics experiment.

Simon Fraser University is located atop Burnaby Mountain in Greater Vancouver, British Columbia, Canada, approximately 5 km from the edge of the city of Vancouver (and a three hour drive north of Seattle, Washington, in the U.S.). For an overview of SFU, including its innovative cross-disciplinary and flexible program philosophy, see the information for New Applicants (focused primarily on undergraduates, but relevant to anyone wishing to learn more about SFU).

* Subject to final Senate approval