Biological Networks: Evolution, Interaction and Computation

June 14 - June 21, Lipari Island, 2008

Logo06 Aim and scope: The theme of the school, Biological Networks: Evolution, Interaction and Computation, falls within the areas of Bioinformatics & Systems Biology, and deals specifically with bioinformatics aspects of systems biology. There are four lecture series, each of three hours, and six tutorials, each of one hour. The lectures will cover fundamental aspects relating to the evolution of biomolecular systems and their various levels of interaction. Two series of lectures are devoted to molecular evolution in viruses and more complex genomes, while the other two are devoted to mathematical and computational methods needed to infer networks both for evolutionary and functional studies. We note that detection of similarity and comparison of biological sequences and structures remains a fundamental task; in particular, although methods based on sequence alignments alone seem no longer adequate. Moreover, the comparison of biological networks, in order to infer common features, is a particularly important, yet largely unexplored, computational topic. The tutorials will cover the most recent advances in computational methods to establish similarity among biological structures: sequences, protein structures, networks and graphs. Moreover, they will also highlight recent additional results on protein-protein and protein-DNA interactions. Thus they nicely complement the main lectures. As is clear from the enclosed bibliography, the selected themes have received attention in the scholarly literature that ranges from Nature to BMC Bioinformatics and Bioinformatics. In its entirety the planned summer school will allow young researchers interested in bioinformatics and systems biology to be exposed to cutting edge results in the increasingly important area of network inference and analysis in biology.

List of Speakers

  • Lecture Series One (3 Hours)
    Making Viruses, in Vivo and in Vitro [abstract]
    Bill Gelbart, UCLA, Los Angeles, California, USA

  • Lecture Series Two (3 Hours)
    Biomolecular Network Evolution [abstract]
    Sarah Teichmann, MRC Laboratory of Molecular Biology, Cambridge, UK

  • Lecture Series Three (3 Hours)
    Phylogenetic Networks [abstract]
    Gabriel Valiente, Technical University of Catalonia, Barcelona, Spain

  • Lecture Series Four (3 Hours)
    Comparative Analysis of Protein Networks [abstract]
    Roded Sharan, Tel Aviv University, Tel Aviv, Israel


  • Tutorial One (1 Hour)
    Sequence Alignment Algorithms [abstract]
    Alfredo Pulvirenti, University of Catania, Catania, Italy

  • Tutorial Two (1 Hour)
    Methods for Structural Alignment and their Application to Linking Protein Folds [abstract]
    Michael Levitt, Stanford University, Stanford, USA

  • Tutorial Three (1 Hour)
    Alignment-free Classification and Comparison of Biological Sequences and Structures [abstract]
    Raffaele Giancarlo, University of Palermo, Palermo, Italy

  • Tutorial Four (1 Hour)
    Fast Heuristics for Matching and Comparison of Biological Networks [abstract]
    Rosalba Giugno, University of Catania, Catania, Italy

  • Tutorial Five (1 Hour)
    Protein-DNA Interaction [abstract]
    Jon Widom, Northwestern University, Chicago, USA.

  • Tutorial Six (1 Hour)
    Methods for Comparing Protein Surfaces and their Application to Binding Site Recognition [abstract]
    Concettina Guerra, Georgia Tech, USA, and U. of Padova, Italy

School Directors

  • Prof. Alfredo Ferro (University of Catania)
  • Prof. Raffaele Giancarlo (University of Palermo)
  • Prof. Concettina Guerra (University of Padova and Georgia Tech.)
  • Prof. Michael Levitt, (Stanford University)