Anne Siegel

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Anne Siegel, Research director, computer science, CNRS

Contact
IRISA - CNRS
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.

  • Bio-informatics :  systems biology;  constraint-programming; hierarchies of models
  • Theoretical computer science & mathematics: symbolic dynamics; self-induced systems; number systems, tilings and discrete geometry.

Publications

Responsibilities

  • Leader of the Dyliss team (IRISA & Inria Rennes)
  • Coordinator of the Biotempo project, funded by ANR Blanc SIMI2 (2011-2014; IRISA, LINA, Iircyyn, I3S,  Inria-Contraintes, UMR Mer&Santé, Irset);
  • Coordinator of an associated team Inria-Chile (2011-2017): web-site
CV to be updated [pdf]

 

Recent papers

 
  • Sylvain Prigent, Guillaume Collet, Simon M. Dittami, Ludovic Delage, Floriane Ethis de Corny,Olivier Dameron,Damien Eveillard, Sven Thiele,Jeanne Cambefort,Catherine Boyen,Anne Siegel, Thierry Tonon,The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond, the Plant Journal, 2014
  • Santiago Videla; Carito Guziolowski; Federica Eduati; Sven Thiele; Martin Gebser; Jacques Nicolas; Julio Saez-Rodriguez; Torsten Schaub; Anne Siegel, Learning Boolean logic models of signaling networks with ASP, Theoretical Computer Science, 2014.
  • Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap Van Milgen and Anne Siegel. Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism  BMC Systems biology. 2014.
  • Oumarou Abdou-Arbi, Sophie Lemosquet, Jaap Van Milgen, Anne Siegel and Jérémie Bourdon. Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. BMC Systems biology. 2014.
  • Valérie Berthé, Timo Jolivet and Anne Siegel. Connectedness of fractals associated with Arnoux-Rauzy substitution. Special issue of the RAIRO-Theoretical Informatics and Applications dedicated to the "Journées Montoises d'Informatique Théorique 2012". 2014.
  • Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel and Julio Saez-Rodriguez. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics., 2013.

 

Research activities

Participation

to

research programs

  • Macro-alguae metabolism. ANR IDEALG. Investissement avenir bioressources et biotechnologies, 2011-2021
  • CIRIC-omics research line of the Inria center in Chile. Equipe Associée Inria-Chile (2011-2016): web-site
  • Inria Project Lab AlgaeInSilico. 2014-2017.
  • Cyanobacteria diversity. ANR Samosa. 2014-2017.
  • Pea-aphid micro-RNA. ANR Mirnadapt. ANR Blanc SVE6 2011
  • Fatty acid regulation. ANR Fatinteger. ANR Blanc SVE7 2011.
  • Biotempo project, funded by ANR Blanc SIMI2 2010
  • PHC procope (2011-13)
  • Inria-Conycit IntegrativeBioChile (2011-2012);
  • PEPS-CNRS Quantoursin (2010-2011; IRISA, LINA, UMR Mer&Santé Roscoff);
  • ANR Sitcon (2006-09),
  • ANR DyCoNum (2006-09),
  • PHC Amadeus (2006-08), PHC SAKURA (2007-09), 
  • ARC Moca (2006-07),
  • ACI MathResoGen (2003-06)

Supervising

  • V. Delannée (phD, Région bretagne & ANSES, started 2014)
  • J. Laniau (phD, Inria, started 2013)
  • V. Picard (phD, Rennes 1/ENS, started 2012)
  • G. Collet (Post-doc/engineer, ANR Idealg, 2012-2014)
  • C. Bettembourg (Post-doc, ADT Mirnadapt, 2014-2015)
  • M. Chevallier (Engineer, ADT inria, 2014-2016)
  • S. Prigent (phD, MNRT, 2011-2014)
  • S. Videla (phD, ANR Biotempo, 2011-2014)
  • O. Quenez (engineer, ANR Fatinteger, 2013)
  • A. Aravena, (co-supervised chilean phD, 2010-2013. Assistant professor in Turkey)
  • O. Abdou-Arbi (phD, MnRT, 2010-2013. Assistant professor in Niger)
  • S. Thiele (post-doc, Inria, 2012-2013)
  • P. Blavy (phD, defense: 2010; co-supervised with S. Lagarrigue)
  • C. Guziolowski, (phD, defense: 2010. Assistant professor in Nantes.)
  • P. Veber (defense: 2008, co-supervised with M. Le Bogne. Research Engineer in Lyon.)
  • Post-doc : T. Baumuratova (2008-09, co-supervised with O. Radulescu)
  • Post-doc: S. Blachon (2008-09, co-supervised with O. Radulescu)

Dissemination

Teaching

Meeting organization

 

Short Bio

Short Bio

I am a former student in mathematics at Ecole Normale Supérieure de Lyon (1994-98). I succeeded 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. 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 spin-off 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 non-modeled 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 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.

Collaborations and co-authors (to be updated...)

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), D. Eveillard (systems biology), 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), 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 (EWS-FLI1 signalling network), J. Thuswaldner (topology of fractals), T. Tonon (algae metabolism), P. Veber (constraints for biological networks).
Dissemination