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Anne SIEGEL |
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Title |
Research Associate
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| Mail |
This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
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| Address |
Symbiose
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CNRS - Université de Rennes 1 UMR 6074 - INRIA
IRISA
Campus de Beaulieu
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35042 RENNES Cedex - France
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| Tel |
+33 2 99 84 74 48
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| Fax |
+33 2 99 84 71 71
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| Current Position |
Researcher at CNRS
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Research Fields
Dynamical systems at the junction of computer science, biology and mathematics.
Research activities
- French summary of activites pdf
Meetings to be organized
Other activities
- Dissemination : organization of meetings. bioinformatics
seminar (2002-2009). Journée satellite JOBIM (2007-2010). VICANNE
program on systems biology (2004-2007). Workshops and conferences on numeration and tiling
(2003, 04, 05, 06, 07, 09). [More details]
- Supervising. Ph-D students : P. Blavy (defense, 2010; co-advised with S. Lagarrigue) ; C. Guziolowski, (defense, 2010), P. Veber (defense, 2008, co-advised with M. Le Borgne). Post-doc : T. Baumuratova (2008-09, co-advised with O. Radulescu), S. Blachon (2008-09, co-advised with O. Radulescu)
Professional history
I am a former student in mathematics at Ecole Normale Supérieure de Lyon (1994-98), allowing me to succeed at the Agregation de mathematics in 1997. I received my Ph-D thesis in 2000 at the math lab (IML) of Université de la Méditerannée in Marseille. My thesis was focused on combinatorial and number-theoretic 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. I am now 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.
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
non-integer basis (beta-numeration and Dumont-Thomas 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
constraint-based formalism in order to perform confrontations between
large-scale data from molecular biology (transcriptomic, chip-chip,
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.
Main results can be summarized as
- Constraints-based formalism to perform automatic reasoning over large-scale variational data from molecular biology. Validation on E. Coli and S. Cerevisiae networks. Application to EWS-FLI (pediatric Ewing tumor bones) signalling network.
- Construction
of model hierarchies for data interpretation. Applications to the regulations of fatty acid metabolism and the initiation of sea-urchin translation.
- Graph
description of fractal boundaries and topological properties of fractals.
Application to Markov partitions for toral automorphisms and purely
periodic beta-expansions.
- Combinatorial rules to iterately build discrete plane in R3.
Additional links
- Collaborations and co-authors : B. Adamczeswki (numeration systems), S. Akiyama (beta-numeration), P. Arnoux (tilings and discrete geometry), T. Baumuratova (analysis of EWS-FLI1 signalling network), R. Bellé (sea-urchin 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), C. Frougny (numeration systems), C. Guziolowski (study of large-scale networks with constraints-based 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), 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 (EWS-FLI1 signalling network), J. Thuswaldner (topology of fractals), P. Veber (constraints for biological networks).
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