Anne Siegel

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Anne Siegel, Research director, computer science, CNRS

Contact
IRISA - CNRS
Univ Rennes, Inria, CNRS, IRISA
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

Short Bio. Anne Siegel is a research director at CNRS, located at IRISA, the computer science laboratory of Rennes. She is the leader of the Dyliss group (IRISA and Inria Rennes) which develops formal methods for the integration of heterogenous data in biology. She started her carreer in mathematics and theoretical computer science by studying symbolic dynamical systems to investigate self-similar structures in number theory and tilings. Then she explored the field of systems biology, that is, the modeling and study of dynamical systems in molecular biology.

Her main research now focuses on constraint-based methods to interpret large-scale observations of a molecular system in a dynamical system framework, with applications to marine biology and extremophile microbiology.

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

  • Bio-informatics : constraint programming and discrete dynamical systems to predict response of biological systems by the integration of large scale heterogeneous datasets.
  • 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)
  • Nominated member of the Inria evaluation commitee [2015-2019].
  • Creator and co-animator of the french working group BIOSS 
  • Member of the inria commitee on gender equality.
  • Member of the laboratory council.
  • Co-leader of the WP4 of the IDEALG investissement-avenir project (2012-2020).
  • Coordinator of an associated team Inria-Chile (2011-2017).
CV Research Director (DR1). to be updated [pdf]

 

Recent papers

 
  • Clémence Frioux, Enora Fremy, Camille Trottier, Anne Siegel, Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. To appear in ECCB2018 / bioinformatics (september 2018).
  • Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko Marcello Balduccini; Tomi Janhunen. Hybrid Metabolic Network Completion. 14th International Conference on Logic Programming and Nonmonotonic Reasoning - LPNMR 2017. Springer, Lecture Notes in Artificial Intelligence, 10377, pp.308-321, 2017, Logic Programming and Nonmonotonic Reasoning. Best student paper award. (2017)
  • Sylvain Prigent, Clémence Frioux, Simon M. Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, Plos Computational Biology, 2017 (electronic access)

  • Santiago Videla, Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel, caspo: a toolbox for automated reasoning on the response of logical signaling networks families, Bioinformatics, 2017 (electronic access)

  • Philippe Bordon, Mauricio Latorre, Maria-Paz Cortes, Mauricio Gonzalez, Sven Thiele, Anne Siegel, Alejandro Maass, Damien Eveillard, Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach. Microbiology open, 2015. (electronic access).

  • Santiago Videla, Irina Konokotina, Leonidas G. Alexopoulos, Julio Saez-Rodriguez, Torsten Schaub, Anne Siegel and Carito Guziolowski, Designing experiments to discriminate families of logical models. Frontiers Bioeng. Biotech., 2015.

  • 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

 

 

Research activities

Participation

to

research programs

Contracts funded by institutions.
  • TGF-SysBio. Cancer and micro-environment. Plan CANCER. INSERM. 2015-2018.
  • Macro-alguae metabolism. ANR IDEALG. Investissement avenir bioressources et biotechnologies, 2011-2021

Internal supports.

  • CIRIC-omics research line of the Inria center in Chile. Equipe Associée Inria-Chile (2011-2016): web-site
  • Inria Project Lab AlgaeInSilico. 2014-2017.

Former projects.

  • Mecagenotox: modeling the toxicity of HAA. ANSES. 2013-2016.
  • 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

  • P. Vignet (engineer then phD, Irset/Health dpt of univ, started 2018)
  • M. Louarn (phD, Inserm/Inria, started 2017)
  • M. Wery (phD, Ciffre Sanofi, started 2017)
  • M. Conan (phD, Irset/Health dpt of univ, stated 2017)
  • A. Belcour (engineer, CNRS/Idealg, 2018-2019)
  • C. Frioux (phD, Inria, started 2015)
  • M. Aite (Engineer, ADT Inria and then CNRS/IDEALG, 2015-2019).
  • M. Chevallier (Engineer, ADT and then animation of Ecosyst network, 2014-2017)
  • V. Delannée (phD, Région bretagne & ANSES, 2014-2017, NIH, Washington)
  • J. Laniau (phD, Inria, started 2013-2017)
  • C. Bettembourg (Post-doc, ADT Mirnadapt, 2014-2015, Sanofi R&D)
  • V. Picard (phD, Rennes 1/ENS, 2012-2015, teacher in class preparatoires)
  • G. Collet (Post-doc/engineer, ANR Idealg, 2012-2015, Rennes university hospital)
  • S. Prigent (phD, MNRT, 2011-2014, researcher at INRA Bordeaux)
  • S. Videla (phD, ANR Biotempo, 2011-2014)
  • O. Quenez (engineer, ANR Fatinteger, 2013, Rouen university hospital)
  • 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

 

Longer (old) 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. After a 4 monthes service as an assistant professor position (McF) at the laboratory of mathematics in Rennes (IRMAR), the CNRS offered me a position of research scientist (CR2) at the computer science laboratory of Rennes (IRISA). I joined the bioinformatics group. Since then, I have been conducting researches in both symbolic dynamics (focusing on applications in numeration and discrete geometry) and systems biology. 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 2010. Since 2012, I have been the leader of the Dyliss 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. I have been an elected member (2009-2012) then a nominated member (2015-2019) of the Inria Evaluation committee, as well as a nominated member (2012-2014) of the CNRS comittee for evaluation in mathematics. I also regularly join or preside some project or laboratory evaluation panels (ERANet in plant sciences, Cancer Plan in Systems Biology, HCERES, ANR). In 2014, I was a founder then a co-animator of a national working group about computational/symbolic systems biology (bioss) at the cross-over of the two national networks (GDR) in Informatics-Mathematics (GDR IM) and Bioinformatics (GDM BIM).

 

Dissemination