Anne Siegel, Research director, computer science, CNRS 

Contact 
IRISA (CNRS & Univ Rennes 1), Inria Rennes
Dyliss team.
Bat 12. Campus de Beaulieu.
35042 Rennes cedex
France
Tel: (33) (0) 2 99 84 74 48 Email: anne.siegel [[{at}]] irisa.fr 
Research 

Research field 
Qualitative dynamical systems in computer science, biology and discrete mathematics.

Publications 

Responsibilities 

CV  to be updated [pdf] 
Recent papers 


Research activities 

Participationtoresearch programs 

Supervising 

Dissemination 

Teaching 

Meeting organization 

Short Bio 

Short Bio 
I am a former student in mathematics at Ecole Normale Supérieure de Lyon (199498). I succeeded at the Agregation de mathematics in 1997. I received my PhD thesis in 2000 at the math lab (IML) of Université de la Méditerannée in Marseille. My thesis was focused on combinatorial and numbertheoretic descriptions of substitutive dynamical systems, supervised by P. Arnoux. In september 2001, I was proposed an assistant professor position (McF) at the laboratory of mathematics in Rennes (IRMAR). Four months later, in 2002, the CNRS offered me a position of research scientist (CR2) at the computer science laboratory of Rennes (IRISA). I joined the bioinformatics group, named the Symbiose team. Since then, I have been conducting researches in both symbolic dynamics (focusing on applications in numeration and discrete geometry) and systems biology. Since 2008, I have been in charge of the subgroup of the symbiose team focused on biological systems . I received my habilitation thesis in mathematics and computer science in 2008 at the university of Rennes 1. I was promoted as a research director at CNRS in fall 2010 (concours DR 2010, interdisciplinaire 43/02). Since 2012, I am the leader of the Dyliss team, a spinoff of the former symbiose team. The domain of the team is bioinformatics and systems biology. The team develops qualitative formal systems for a better understanding of key actors of nonmodeled species when they are challenged by their environment, such as algae which have to adapt to tide or bacteria which survive in highly sulfured mines. 
Miscellaneous 

Hints on research activities 
My research program mainly consists in identifying and taking benefit of properties of dynamical systems in several domains of mathematics, computer sciences and biology where dynamics appears, even (mainly) if somehow hidden. My job is first to identify questions related to systems trajectories, second to make use of the properties of these trajectories together with algorithmic computations in order to provides new insights to the domain where the dynamics was exhibited. In theoretical computer science, this approach allowed me characterizing some properties of expansions of real number in noninteger basis (betanumeration and DumontThomas substitution system). This also allowed proposing a strategy of generation for discrete plane. Underlying dynamics are additions modulo 1 (toral additions and automorphisms) and fractal geometry. In bioinformatics, I have been first dealing with biological networks construction, inducing a strong thought on the level of abstraction required to properly modelling biological systems with respect to available data. 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. This provides tools for network/influence graphs diagnosis, correction and prediction.

Collaborations and coauthors (to be updated...) 
B. Adamczeswki (numeration systems), S. Akiyama (betanumeration), P. Arnoux (tilings and discrete geometry), T. Baumuratova (analysis of EWSFLI1 signalling network), R. Bellé (seaurchin translation), V. Berthé (discrete geometry and numeration systems), S. Blachon (analysis of CGH data), P. Blavy (regulation of fatty acids metabolism), J. Bourdon (dynamics of biological systems), D. Eveillard (systems biology), C. Frougny (numeration systems), C. Guziolowski (study of largescale networks with constraintsbased approaches), A. Hilion (free group automorphisms), S. Lagarrigue (regulations of fatty acids metabolisms), S. Lemosquet (mammary cow lactary diets and metabolic networks), M. Le Borgne (depedency diagrams for constraints based resolution), J. van Milgen (nutrition and metabolic networks), S. Prigent (Sea urchin translation, algae metabolism), O. Radulescu (model construction, constraints over the dynamics of systems), T. Schaub (constraint resolution with answer set programming), W. Steiner (numeration systems and fractals), G. Stoll (EWSFLI1 signalling network), J. Thuswaldner (topology of fractals), T. Tonon (algae metabolism), P. Veber (constraints for biological networks). 
Dissemination 
