Symbiose Project Team - INRIA/Irisa © 2007 - 2008

List of Publications
Written by Anne SIEGEL   

List of publications (A. Siegel)

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Colors / Domains

  • black colored publications are related to bioinformatics and systems biology

  • grey colored publications deal with theoretical computer science, symbolic dynamics and numeration systems

Peer Reviewed journals and book chapters

  • V. Berthé, T. Jolivet, A. Siegel,
    Substitutive Arnoux-rauzy sequences have pure discrete spectrum
      Uniform Distribution Theory, 2012, to appear
      (Arxiv file.pdf)


  • T. Tonon, D. Eveillard, S. Prigent, J. Bourdon, P. Potin, C. Boyen, and A. Siegel. Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. OMICS: A Journal of Integrative Biology 15(12), 2011, (electronic access)


  • J. Bourdon, D. Eveillard, A. Siegel. Integrating quantitative knowledge into a qualitative gen regulatory network. PLoS Comput Biol 7(9), 2011, e1002157 (electronic access)

  • O. Radulescu, A. Siegel, E. Pécou, C. Chatelain and S. Lagarrigue
    Genetically regulated metabolic networks: Gale-Nikaido modules and differential inequalities
    Transactions on Computational Systems biology, 2011,
    (electronic access)
  • C. Guziolowski, S. Blachon, T. Baumuratova, G. Stoll, O. Radulescu, A. Siegel,
    Designing logical rules to model the response of biomolecular networks with complex interactions : an application to cancer modeling.
    Transactions on Computational Biology and bioinformatics 8 (5), 2011, pp. 1223-1234
    (electronic access)
  • V. Berthé, A. Siegel, W. Steiner, P. Surer, J. Thuswaldner
    Fractal tiles associated with shift radix systems
    Advances in mathematics 226 (1), 2011, p. 139-175
      (file.pdf) (electronic access)

  • T. Baumuratova, D. Surdez, B. Delyon, G. Stoll, O. Delattre, O. Radulescu, A. Siegel,
    Localizing potentially active post-transcriptional regulations in the Ewing’s sarcoma gene regulatory network
    BMC Systems Biology 4 (1), 2010, p. 144. (electronic access)

  • B. Adamczewski, C. Frougny, A. Siegel, W. Steiner
    Rational numbers with purely periodic beta-expansion
    Bulletin of the London Mathematical Society, 42 (3), 2010, 538-552 (file.pdf)

  • V. Berthé, A. Siegel, J. Thuswaldner
    Substitutions, Rauzy fractals and tilings (chapter 5) (file.pdf)
    In Combinatorics, Automata and Number Theory (electronic access)
    © Cambridge University Press, 2010

  • R. Bellé, S. Prigent, A. Siegel and P. Cormier,
    Model of cap-dependent translation initiation in sea urchin. A step towards the eukaryotic translation regulation network
    Molecular Reproduction and Development 77(3), 2010, 257-264
    (electronic access)

  • A. Siegel and J. Thuswaldner,
    Topological properties of Rauzy fractals
     Mémoires de la SMF 118 (2009), 144 pages  (preliminary version.pdf)

  • P. Blavy, F. Gondret, H. Guillou, S. Lagarrigue, P.G.P. Martin ,J. van Milgen, O. Radulescu and A. Siegel.
    A minimal model for hepatic fatty acid balance during fasting: Application to PPAR alpha-deficient mice ,
    Journal of Theoretical Biology, 261 (2009), pp. 266-278
    (electronic access)

  • C. Guziolowski, A. Bourdé, F. Moreews and A. Siegel,
    BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks,
    BMC genomics, 2009, 10:244 (electronic access)

  • C. Guziolowski, J. Gruel, O. Radulescu and A. Siegel, 
    Curating a large-scale regulatory network by evaluating its consistency with expression datasets,
    CIBB 2008: Computational Intelligence Methods for Bioinformatics and Biostatistics - Selected revised papers
    Lecture Notes in Computer Sciences LNCS, Springer-Verlag, volume  5488, p.144-155, 2009. (electronic version)

  • S. Akiyama, G. Barat, V. Berthé and A. Siegel,
    Boundary of central tiles associated with Pisot beta-numeration and purely periodic expansions,
    Monashefte für Mathematik, 2008  (file.pdf)   (electronic access)

  • P Veber, C Guziolowski, M Le Borgne, O Radulescu, and A Siegel,
     Inferring the role of transcription factors in regulatory networks, 
    BMC BioInformatics 9, 2008:228 (file.pdf)

  • V. Berthé and A. Siegel,
     Purely Periodic beta-Expansions in the Pisot Non-unit Case
    Journal of Number Theory 153 (2) 2007, 153-172. (abstract)(

  • C Guziolowski, P Veber, M Le Borgne, O Radulescu, and A Siegel
    Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study
    Journal of Biological Physics and Chemistry (7) 2007, 37-43 (preprint.pdf)
    Revised paper from Réseaux d'interaction : analyse, modélisation et simulation. RIAMS'06, Lyon, France. (slides)

  • P. Arnoux, V. Berthé, A. Hilion and A. Siegel  
    Fractal representation of the attractive lamination of an automorphism of the free group,
    Annales de l'Institut Fourier 56(7), 2006, 2161-2212, (abstract)(file.pdf)

  • A. Siegel, O. Radulescu, M. Le Borgne, P. Veber, J. Ouy, S. Laguarrigue
    Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks
    BioSystems 84, 2006, 153-174  (abstract)