Symbiose Project Team  INRIA/Irisa © 2007  2008
Written by Anne SIEGEL

Hints on research activities
My research program is to
identify and take benefit of properties of dynamical systems in several
domains of mathematics, computer sciences and biology where dynamics
appears, even if somehow hidden. My work consists in identifying
questions related to systems trajectories, then making use of the
properties of these trajectories together with algorithmic computations
in order to answer to questions in the domain where the dynamics was
exhibited.
In theoretical computer science, this approach
allowed characterizing some properties of expansions of real number in
noninteger basis (betanumeration and DumontThomas substitution
system). This also allowed us to propose a strategy of generation for
discrete plane. Underlying dynamics are additions modulo 1 (toral
additions) and fractal geometry.
In bioinformatics, I am first
working on biological network construction, inducing a strong reflexion
on representation abstractions. I also have conducted works on a
constraintbased formalism in order to perform confrontations between
largescale data from molecular biology (transcriptomic, chipchip,
CGH) and knowledge models. Our methodology allows us to introduce
dynamical (actually steady states comparisons) in data analysis, by
mimic automatic reasoning over variational data.
Main results can be summarized as
 Constraintsbased formalism to perform variationlike automatic reasoning over largescale data from molecular biology.
 Construction
of model hierarchies for data interpretations (fatty acid metabolism
regulation, initiation of seaurchin translation).
 Graph
description of fractal boundaries and topological properties.
Application to Markov partitions for toral automorphisms and purely
periodic betaexpansions.
 Combinatorial rules to iterately build discrete plane by making use of Z^{2} action.
Additional links
 French summary of activites pdf
 Paper abstracts in systems biology
 Paper abstracts in numeration and symbolic dynamical systems Overview of work and paper abstracts
 Sofware : Bioquali (analysis
of compatibilities between an interaction graph and microarray data)
Web access

http://www.irisa.fr/symbiose 
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