Consorzio per il Centro di Biomedicina Molecolare (CBM) Italy

Leader: Remo Sanges 

Brief description of the organization:

CBM is an SME with public and private shareholders which carries out research and advanced training in the field of molecular biomedicine. It provides services promoting the diffusion of innovation, transfer of technology, and support in the launch of new entrepreneurial initiatives. It avails itself of four integrated laboratories available for shared use by internal and external collaborators. The bioinformatics and functional genomics lab supports the analysis of complex biomedical data deriving from high-throughput technologies such as genomics and proteomics and its verification through molecular biology techniques. The lab conducts research within the realm of non-coding sequences; in particular it is focused on the evolution of chordate enhancers and on the discovery and characterization of non-coding RNAs. Moreover, it specializes on the design, use and analysis of custom microarray chips for expression profiling, genotyping and genome tiling studies. The lab is supported by a 64-CPU linux cluster, several database and web servers, automated backup facility on a dedicated backup network, and dedicated internet bandwith, as well as a wet-lab facility.

Main tasks attributed to the project:
Expression profiling, data management, analysis and integration, expression and network validation experiments, contribution to management, training and dissemination activities.

Previous experience relevant to the tasks:  
Remo Sanges has been involved in an FP6 project (TRANSCODE), that involved 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
  • 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