University College London (UCL) United Kingdom

UCL-logo_small.jpg  Leader: Elia Stupka

Brief description of the organisation:

University College London (UCL) is one of the world’s premier universities, recently ranked 4th worldwide in the Times Higher Education-QS World University Rankings. Importantly for this project UCL’s Biomedical & Life Sciences departments were ranked first in the UK and have significantly outstripped their closest competitors in the 2008 UK Research Assessment Exercise (RAE). UCL provides an ideal setting for the bioinformatics tasks in this project owing to its extensive existing research computing infrastructure comprising of a 2,560 CPU cluster. UCL Genomics provides a central coordinated facility for genomics work within UCL, allowing access to several, complementary technologies in a quality-controlled and cost-efficient environment. The facility comprises of several microarray technologies (Affymetrix, Illumina, Agilent), next-generation sequencing technologies (Illumina GAIIx, ABI Solid and Roche 454) as well as all the accessory hardware which is required to make best use of these technologies, such as fragmentation (using Covaris  S2) and quantity/quality control of input DNA/RNA.

Previous experience relevant to the tasks:
Elia Stupka is the coordinator of an FP6 project (TRANSCODE), a project involved in the comparative genomics analysis of non-coding regions of chordate genomes. Of particular interest to the this project is the competence in the analysis of microarray data (Ferg, Sanges et al. 2007), and in the discovery and characterization of novel genes (Roma, Cobellis et al. 2007) as well as discovery of novel enhancer sequences (Sanges, Kalmar et al. 2006).

Selected recent publications:

  • M.Ferg, R.Sanges, J.Gehrig, J.Kiss, M.Bauer, A.Lovas, M. Szabo, L.Yang, U. Straehle, M.J. Pankratz, F.Olasz, E.Stupka, F.Müller, The TATA binding protein regulates maternal mRNA degradation and differential zygotic transcription in zebrafish, EMBO J, (2007) 26, 3945 3956
  • Roma G., Cobellis G., Claudiani P., Maione F., Cruz P., Tripoli G., Sardiello M., Peluso I. Stupka E. A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells, Genome Research 17:1051-1060, 2007
  • Sanges R, Kalmar E., Claudiani P., D'Amato M., Müller F, Stupka E, Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage Genome Biology 2006, 7:R56
  • The FANTOM Consortium, The transcriptional landscape of the mammalian genome, Science 2005; 309:1559-1563
  • Aparicio S., Chapman J., Stupka E. et al. Whole genome shotgun assembly and analysis of the genome of Fugu rubripes Science 2002; 297(5585) 1301-10
  • The International Genome Consortium, "Initial sequencing and analysis of the human genome", Nature 2001; 409, 860-921