Magpie Laboratory of Computational Genomics

The Laboratory of Computational Genomics aims to create and use new software tools to explore the unfolding world of genomes. Our tools aim to integrate, analyze, and visualize the output of high throughput molecular biology experiments in the context of complete genome sequence data. Projects in the laboratory focus on the automated annotation of eukaryotic and microbial genome sequence data (genomes, chromosomes, contigs, and cDNA clones), the semi-automated annotation of gene expression data, and the integration of gene expression and genome sequence analysis. We apply these tools to specific biological questions in collaboration with experimental biologists and to the problem of structural genomics target selection.

  Current News

Sea Urchin Genome Published
The genome of the California Purple Sea Urchin, Strongylocentrotus purpuratus, was published on November 10, 2006. Visit the Sea Urchin Genome Project for more information.

  Current Research

Developing systems to extend and expedite genome annotation including areas such as transcription analysis, automated functional annotation of genes and extending links between genes and groups of genes to integrate the gene by gene view into an over-arching genome level view.

Scripps Genome Center
Mammalian Alternative Splicing Databases | Other Alternative Splicing Databases
  In the Lab

Members MAGPIE Output Gene chip
Shuba Gopal works on HERON, an automated genome annotation system, and annotations of E.coli, T.brucei and D.melanogaster with HERON prototype. Partial Magpie view of genomic DNA showing three reading frames on one strand of a genome. Gene chips enable researchers to detect expressions of a large number of genes at once. They are small glass wafers that resemble computer chips, but their surfaces are studded with bits of DNA rather than transistors.
Gaasterland Bio/CV Current Research in the Lab Publications: Abstracts and Links Lab Members Computational Resources