Computability in Europe 2006
Logical Approaches to Computational Barriers

Special Session Talk:
Genome synthesis and genomic functional cores

Speaker: Alessandra Carbone
Author(s): A.Carbone


The project of synthesizing a bacterial genome which can survive in the
laboratory and can realize desired metabolic cycles, has been announced three
years ago by Venter, Smith and Hutchison. It asks for clearing out certain
basic biological mechanisms of living cells. The problem demands to search for
the minimal set of genes that are essential to the life of a microbial
organism. Laboratory experiments realized on specific bacteria allowed to
propose some minimal gene set. Independently, comparative genomics also
proposed some minimal set of genes. But both these "solutions" present
some intrinsic problem.

We shall present some simple mathematical ideas based on Gibbs sampling, 
that allow to detect genomic signatures for sets of genes and sets of
organisms, and to predict genomic functional cores which are specific to
different microbes. Within these sets, one finds many of the genes 
characterized with experiments and genome comparison, but also genes which
might be non-orthologous or whose function might not be characterized yet. More
generally, our computational approach  leads to characterize essential metabolic
pathways through a purely  statistical analysis of complete genomes which is
independent from biological assumptions. 

websites: Arnold Beckmann 2008-03-15