Anne Siegel

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Anne Siegel, Research director (DR1), 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

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 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

  • 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

 

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. 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