Bioinformatics

Increasingly biomedical research is performed with large-scale data, as new technologies allow scientists to study entire systems in parallel. For instance, the determination of the human genome sequence has now led to methods that allow researchers to study 25,000 genes in a single experiment.

These and other high-throughput analysis methods generate staggering amounts of data that inevitably require tremendous computational resources to process and store. To effectively manage and derive value from this information, one requires knowledge in both the biological and computational fields. This is where bioinformatics steps in as the interdisciplinary field that unites computation, statistics and the life sciences.

Our Research

Our bioinformatics team, headed by Dr. Wyeth Wasserman, is recognized worldwide as a leader in gene regulation research. This group studies the biochemical processes that control when and where genes will be turned on within the body, while working in close partnership with all labs at the CMMT. They depend on collaborators to obtain the biological data needed to develop their mathematical models. In turn, the biology labs gain expertise and powerful computational tools to probe and analyze their data.

Our bioinformatics program is supported by a modern, state-of-the-art computing infrastructure that includes a cluster of IBM Blade Center servers containing over 60 CPUs, a Storage Area Network (SAN) capable of holding over 10 terabytes of data, and more than 10 additional multi-CPU servers to perform a variety of dedicated roles including web, email, database, and development. In addition, a CMMT-wide network provides high-speed intranet access to connect all of the Centre's laboratories, as well as serve as a gateway for internet access via the UBC fibre-optic network.

Recent breakthroughs in the field of bioinformatics realized at the CMMT include the release of JASPAR in 2004 and 2006—a high-quality and open-access database that has become a de-facto standard in the study of gene regulation and used by researchers all over the world—and the development of D-GRIP in 2007, a personalized medicine software designed to predict one's predisposition to disorders like Alzheimer's disease and atherosclerosis by detecting minute mutations in the person's genes.

Publications

Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res. 37(Database issue):D54-60. (2009) PMID 18971253

Andersen MC, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput. Biol. 4(1):e5. (2008) PMID 18208319

Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L, Cui Y. An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Hum. Mol. Genet. 16(11):1381-90. (2007) PMID 17428815

Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res. 35(Database issue):D51-4. (2007) PMID 17099235

Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res. 34(Database issue):D95-7. (2006) PMID 16381983