European Molecular Biology Laboratory (EMBL)
The European Molecular Biology Laboratory (EMBL) is an International Treaty Organisation set up to further European excellence in molecular biology. It is headquartered in Heidelberg, Germany and has sites near Cambridge (EMBL-EBI), Rome, Hamburg and Grenoble. EMBL-EBI is Europe's bioinformatics resource centre, storing the public domain data in protein structures, proteins, DNA (including the human genome) and chemical screens. Both services (such as dataresources) and research occurs at EMBL; the research includes topics such as human epigenetics (ENCODE), metagenomics (METAHIT), Cell Biology, Development and Mouse Biology. EMBL-EBI has one of the largest disk and compute facilities dedicated to biology in Europe.
EMBL-EBI has extensive experience in data pipelines and analysis, in particular being involved in ENCODE (including Chip-seq and RNA-seq) project, the BLUEPRINT FP7 project (in epigenetics), ICGC projects (Breast Cancer and Kidney Cancer). EMBL-EBI's role in these project include both the low level processing and management and the more sophisticated data analysis. In the context of ENCODE for example, the discovery that over 50% of the non-coding regulation can be explained by ENCODE data was performed at the EBI. EMBL-Heidelberg has been heavily involved in metagenomics, in particular the META-HIT project in the data analysis, leading to the discovery of different gut microflora types
Profile of staff members
The following staff members are involved. Dr Ewan Birney, Associate Director of EMBL-EBI, provides overall leadership to WP4. Dr Birney has been involved in genomics since the draft human genome project, contributing to many other projects (Mouse, Chicken etc). His most high profile recent project has been his leadership of the ENCODE project, where the scale up phase finished in 2012. In WP4, Dr Alvis Brazma (expert in transcriptomics), Dr Paul Flicek (expert in epigenomics) and Dr Chris Steinbeck (expert in metabolomics) are also providing expertise. In WP2, Dr Peer Bork, an expert in genomics and metagenomics from EMBL-Heidelberg will participate. Dr Bork was one of the drivers for the EU MetaHit project in determining and analysing human gut microflora
Recent publications relevant to the project
An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.
Enterotypes of the human gut microbiome. Arumugam M etal. Nature. 2011 May 12;473(7346):174-80.
Mouse genomic variation and its effect on phenotypes and gene regulation. Keane etal. Nature. 2011 Sep 14;477(7364):289-94. doi: 10.1038/nature10413.
Efficient storage of high throughput DNA sequencing data using reference-based compression. Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.
Genome Res. 2011 May;21(5):734-40
Heritable individual-specific and allele-specific chromatin signatures in humans. McDaniell R etal. Science. 2010 Apr 9;328(5975):235-9.