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Functional Genomics and Proteomics
 
Global inspection of pathogens' genome:

The availability of the genomic sequences of human pathogens, together with the development of computational tools for data mining, analysis and processing, allow for characterization of the complete protein repertoire an organism can express. The research at the IIBR bioinformatics unit focuses on microbial genomes, aims at gene selection (e.g. genes potentially encoding for virulence factors, secreted or membrane-associated proteins, regulatory elements, species specific genes) from various pathogens. The application of advanced methodologies together with high-power computer capabilities, enable the researchers to perform a state-of-the-art, large-scale genomic analysis, which includes: 		 
 
  • DNA and protein sequence analysis
  • Sequence similarity searches
  • Motif, domain and structure prediction
  • Database mining and functional assignments
  • Database construction, integration and management
  • Cross-genome analysis and comparative genomics studies
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      This systematic computational whole genome screen may be applied to diverse R&D areas, such as vaccine development, drug discovery, pathogen characterization and diagnostics.

    The in-silico identified potential antigenic proteins are assayed by classical or high throughput functional in-vitro and in-vivo screening, employing immuno-PCR expression elements and DNA and polypeptide vaccine approaches.    		  
     
    Global inspection of the pathogen's proteome:

    The potential coding ability of the pathogen's genome, determined by bioinformatic studies, is tested for the actual expression of various genes, by proteomics analysis.
    The proteomic capability at IIBR allows for establishing
    protein maps and direct identification of proteins. Hundreds of cellular proteins from cultured pathogens are separated by high-resolution 2-dimensional electrophoresis, establishing a protein signature characteristic of the particular biological sample analyzed. MALDI-TOF mass spectrometry analysis of individual protein "spots", which generates a fingerprint spectrum, serves for identification of the proteins in annotated ORFs genomic databank. This approach is exploited for the selection of proteins possibly involved in the interaction of pathogenic bacteria with their host, as well as for identification of vaccine candidate antigens and strain specific antigens for development of diagnostic tools.    		  
    Bioinformatics analysis
     
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