European Bioinformatics Institute

An academic research institute located on the Wellcome Trust Genome Campus in Hinxton near Cambridge (UK), part of the European Molecular Biology Laboratory (EMBL). The EBI's mission has four facets: (i) to provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress (ii) to contribute to the advancement of biology through basic investigator-driven research in bioinformatics (iii) to provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators and (iv) to help disseminate cutting-edge technologies to industry.

The EMBL-EBI operates databases and services in most important domains of bioinformatics, often in collaboration with international partners. For ten years, the EBI has offered access to genome-scale data through Ensembl, a comprehensive system for the integration, analysis, annotation, visualisation and dissemination of such information. Ensembl, developed in partnership with the Wellcome Trust Sanger Institute, is a modular system; components include modules for comparative genomics, and for handling large-scale variation data. Ensembl is focused solely on vertebrate species; but since 2009, has been partnered by five additional sites providing coverage of the remainder of the taxonomic space, including Ensembl Plants and other sites (for invertebrate metazoa, fungi, protists an bacteria) conceptually including many classes of plant pests, symbionts and pathogens. The Ensembl Plants site is built in close collaboration with Gramene, a leading resource for plant genomics based in the United States of America can creating a strong link (and a set of common databases shared) between Europe and and U.S.A. Current activities of particular importance to plants include the storage, analysis and presentation of variation data (currently included from Arabidopsis thaliana, rice and grape); the development of algorithms for the assembly of large genomes from next generation sequencing data; and interactions between host and pathogen genomes.

The project coordinator, Dr. Paul Kersey, has worked on genome-scale data at the EBI for over 10 years, and leads a team developing Ensembl-based resources for non-vertebrate species within the wider nucleotide-centric services of the organisation, run by Dr. Ewan Birney, who has overseen the Ensembl project at EBI since 2000.

Selected publications:
P. J. Kersey et al. Ensembl Genomes: Extending ensembl across the taxonomic space Nucleic Acids Research, Database Issue 2010 38:D563-D569
P. Flicek et al. Ensembl’s 10th year. Nucleic Acids Research, Database Issue 2010 38:D557-D562P. Kersey and R. Apweiler. Linking publication, gene and protein data. Nature Cell Biology 2006 8:1183-9.
P. Kersey et al. Integr8 and Genome Reviews: integrated views of complete genomes and proteomes. Nucleic Acids Research, Database Issue 2005 33:D563-D569
P.J. Kersey et al. The International Protein Index: An integrated database for proteomics experiments. Proteomics 2004 4:1985-1988.

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