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Wellcome Trust Lectures Show Trend Toward Integrated Systems Approach


HINXTON, UK--The Wellcome Trust Genome Campus was officially opened by HRH Princess Anne last October, but to many, the three-day Inaug ural Symposium held here June 15-17 was the real scientific opening, celebrating the completion of the campus and its achievements to date.

Organized by the Wellcome Trust and the three institutes located on the campus (the Sanger Centre, Medical Research Council Human Genome Mapping Project Resource Centre, and the European Bio inform atics Institute), the symposium was visited by 200 scientists in the fields of bioinformatics, genetics, and molecular biology. Reflect ing the campus's mission, the organizing committee brought together key contributors to the fields of genomics and genetic analysis, new technologies, and ethical and legal implications of genetics.

A "Genomes and Genetics" session, chaired by Fred Sanger, gave an overview of the various sequencing and genome efforts. Almost every sequencing project presented acknowledged major contributions by the Sanger Centre, which has reached a milestone of 100 million base-pairs of finished sequence among its combined sequencing projects.

"To make use of this massive amount of information, we need the skills of bioinformaticians. Those skills are fundamental to our hope to manipulate, manage, and mine this massive amount of biological data, which is already available."

In the case of C. elegans sequencing, as presented by Robert Waterston of Washington Univer sity, the collaboration between the Genome Sequencing Center at the Washington School of Medicine and the Sanger Centre has yielded already finished sequences for 80 percent of the genome. The other 20 Mb expected to be completed at the end of this year.

The Sanger Centre's Bart Barrell gave a whirlwind tour of the sequencing efforts of bacterial and other microbial genomes. The Centre has a large program in microorganisms, funded by the Wellcome Trust and its spinoff, Beowulf Genomics. The latter outsources the sequencing of patho gens of special interest to biomedical research. One major success of the Sanger Centre in this area is the complete genome of M. tuber cu losis, just ahead of a similar effort at TIGR.

Bioinformatics update

During the bioinformatics session, NCBI's Stephen Bryant spoke on the topic of "Structure Neighbors and Identification of Homologous Features." He demonstrated NCBI's effort to make complex information easily accessible to biologists, and exemplified this with Entrez's feature to distinguish look-alike protein structures from those that are really homologous in function.

Terry Gaasterland of the University of Chicago followed with a presentation on the "Automated Assessment of Genomic Properties: from ORF's to Pathways and Processes." Setting up systems that allow for automated real-time genome analysis is important in dealing with the ever-growing influx of biological data, but the take-home message was that all these systems still require human supervision to assess or enforce the decisions made by the system, she said.

In "Discovering Genetics Net works," Gary Stormo of the Uni versity of Colorado outlined ap proaches that combine experimental and computational methods to tackle some of the problems that face bioinformaticists when they look for the regulatory mechanisms and interactions that influence gene expression. He demonstrated this with ongoing work towards defining the specificity of DNA binding proteins.

Chris Sander of the Whitehead Institute/MIT Center for Genome Research and Millennium Pharma ceuticals presented the work of his previous group at the European Bio inform atics Institute on "Map ping the Protein Uni verse," which focused on describing function and structure to proteins of unknown structure by clustering all protein sequenc es in multidimensional space.

All four bioinformatics presentations conveyed strong sentiment in favor of moving away from simple stand-alone applications using a few data sources toward integrated systems that use all available data from genomic and protein sequenc es, protein structure and function, gene expression, and metabolic data to mine information and reach under standing by looking at the known biological data as whole.

Other presentations focused on genetic mechanisms behind diseases and how genetics can be used to improve understanding and create treatments, if not cures. The final day of the symposium was dedicated to presentations discussing ethical and legal issues that arise from genetics and the sequencing of the human genome.

In her closing speech, Dame Bridget Ogilvie, director of the Wellcome Trust, stressed the importance of centers such as the Genome Campus, where data production, collection, and use go hand in hand. "To make use of this massive amount of information, we need the skills of computational biologists, bioinformaticians," she said. "Those skills are fundamental to our hope to manipulate, manage, and mine this massive amount of biological data, which is already available. Realizing that this area of biology is important for the future, the Wellcome Trust has already been told firmly that they have to invest even more money in the training of people in this area," she concluded.

--Jean-Jack M. Riethoven

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