Section: New Results
Systems biology
Participants : Jérémie Bourdon, Jean Coquet, Victorien Delannée, Jacques Nicolas, Anne Siegel, Nathalie Théret, Pierre Vignet.
Representation of symbolic dynamical systems generated by a substitution. Iterated morphisms are combinatorial processes which are related to several classes of dynamical systems appearing in several fields of computer sciences and mathematics: numeration, ergodic theory, discrete geometry. They may be associated to fractal sets called "Rauzy fractals" whose topological properties are linked to the properties of the underlying dynamical system. We have introduced a generic algorithm framework to check such topological properties within a complete family of iterated morphism. This makes efficient the verification of conjectures on several families of substitutions related to multi-dimensional continued fraction algorithms. [A. Siegel] [14]
Identification of logical models for signaling pathways. Logical models of signaling pathways are a promising way of building effective in silico functional models of a cell. The automated learning of Boolean logic models describing signaling pathways can be achieved by training to phosphoproteomics data. In our work, combinatorial optimization methods based on recent logic programming paradigm allow to enumerate, and discriminate the family of logical models explaining data. Together, these approaches enable a robust understanding of the system response. The results are implemented in the caspo software. The main weakness of ASP-based learning algorithm is that they focus on the comparison of two time-points and assumes that the system has reached an early steady state. We have generalized such a learning procedure in order to discriminate Boolean networks according to their transient dynamics. To that goal, we exhibit a necessary condition that must be satisfied by a Boolean network dynamics to be consistent with a discretized time series trace. [A. Siegel] [23], [28]
Model of the Delayed Translation of Cyclin B Maternal mRNA After Sea Urchin Fertilization. An extended model of the numerical model introduced in [74] was developed to have a better understanding of the role of cyclin B in protein synthesis within minutes after fertilization of sea urchin eggs. The model confirms that regulation of cyclin B biosynthesis is an example of a select protein whose translation is controlled by pathways that are distinct from housekeeping proteins, even though both involve the same cap-dependent initia- tion pathway. Therefore, this model should help provide insight to the signaling utilized for the biosynthesis of cyclin B and other select proteins. [J. Bourdon, A. Siegel] [24]
Deciphering pathways involved in TGF-