Course on System Biology 2007
The course will be held in Dipartimento di Fisica Universita` di Torino, Via Giuria 1, 5th floor room "Fubini".

Upon request of some of you we have decided to have a rather tight schedule: we have squeezed the course in a week. Each day there will be 3 hours of lecture, starting at 9.30:

20, 21 May 2007 - Martin Weigt (ISI Foundation) on Gene Regulation ( ~ 2 x 3 h.)
22 May 2007 - Vittoria Colizza (ISI Foundation) on Complex Networks (~ 3 h.)
25 May 2007 - Martin Weigt statistical inference if biological networks ( ~ 2 h. )
26, 27 May 2007 - Andrea Pagnani (ISI Foundation) on metabolic networks (~ 2 x 3 h.

The (tentative) program is the following:
A) Thermodynamics of gene regulation
1- Basic notations of gene regulation (transcription/translation, promoter region, transcription factors etc.)
2- Basic notations of statistical physics (Boltzmann factor, partition function)
3- Thermodynamics of transcription-factor binding (transcription factor binding sites, mismatch energies, bindingprobability, programmability of TFBSs)
4- Thermodynamics of gene regulation (transcriptional activation and repression, combinatorial control using lactose repressor as example)
5- Physical interpretation of microarray data (Hybridization of complementary DNA/RNA sequences)

B) Introduction to graph theory
1- Basic notions of graphs (vertex, edge, degree, distance, diameter, clustering coefficient, center, connectedness etc.)
2- Graph ensembles (Erdos-Renyi random graphs, small-world networks, scale-free networks)
3- Motif search (null models, statistical over-representation of motifs)
4- Network inference from gene-expression data (co-expression networks, ARACNE algorithm based on pairwise mutual information)
5- A general introduction to Complex Biological Networks.

C) Analysis of metabolic networks
1- Definitions for metabolic networks (metabolites as vertices, reactions as directed edges, extremal pathways)
2- Flux-balance analysis (Flux balance and maximal biomass production, elements of linear programming, FBA)