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Bioinformatics Journal
SIGSIM: Systems Biology of E.coli

Keynote Speaker - Dr. James Kent, University of California, Santa Cruz, 2003 Overton Prize Winner

Patching and Painting the Human Genome
Authors: W James Kent, Terry Furey, Charles Sugnet, Matt Schwartz, Angie Hinrichs, Ryan Weber, Krishna Roskin, Robert Baertsch, Mark Diekhans, Heather Trumbower, Fan Hsu, Donna Karolchik, and David Haussler
The web site is one of the key public portals to the human genome. This talk will describe the development of the first public assemblies of the human genome, and the continued evolution of the UCSC Genome Browser. The initial assembly algorithm was deliberately kept simple because it had to be developed in an exceedingly tight time frame and run on relatively modest computer hardware. Over 8 public releases (and 25 internal release) the program grew more sophisticated and used an increasingly wide array of input data. Once the assembly was available it became possible to annotate the genome in earnest. Our annotations at first focused on mapping mRNAs and ESTs to the genome. Because of the volume of data involved this required the development of a new algorithm, BLAT. We created a genome browser to display these annotations on the web, focusing on simplicity of user interface and a fast response time. The Genome Browser became very popular among researchers. Many other parties also produced high quality gene predictions and other annotations, and we worked to make it very easy for them to put these into the Genome Browser as well. Last week the browser displayed Annotations from a dozen different groups on three mammalian genomes and serviced over one million requests for information. Currently much of our research focuses on fully exploiting comparative genomics and whole genome microarray data. We also are making it easier to navigate the browser when very large amounts of annotations are available.