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List of Publications Print
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)(file.ps)


  • 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)(preprint.pdf)

  • O. Radulescu, S. Laguarrigue, A. Siegel, M. Le Borgne, P. Veber
    Topology and linear response of interaction networks in molecular biology,
    Journal of The Royal Society Interface 3(6), 2006, pp. 185 - 196,  (abstract)(preprint.pdf)

  • P. Veber, M. Le Borgne, A. Siegel, S. Lagarrique, O. Radulescu
    Complex Qualitative Models in Biology: a new approach
    Complexus 2, 2004/2005, pp. 140-151   (abstract)(preprint.pdf)
    Revised paper from  ECCS, Paris, November 2005 (slides)

  • A. Siegel,
    Pure discrete spectrum dynamical system and periodic tiling associated with a substitution
    Annales de l'Institut Fourier 2(54), 2004, p. 288-299. (abstract)(preprint.ps)

  • P. Arnoux, V. Berthé and A. Siegel,
    Two-dimensional iterated morphisms and discrete planes
    Theoretical Computer Science 319, 2004, p. 145--176. (abstract) (preprint.ps)


  • A. Siegel,
    Représentation des systèmes dynamiques substitutifs non unimodulaires,
    Ergodic Theory and Dynamical Systems, (2003), 23, 1247-1273. (abstract) (preprint.ps)



  • V. Canterini and A. Siegel,
    Automate des préfixes-suffixes associé à une substitution primitive,
    Journal de théorie des nombres de Bordeaux, 13(2), 2001, pp. 353--369. (abstract) (preprint.ps)

  • V. Canterini and A. Siegel,
    Geometric Representation of primitive substitution of Pisot type,
    Transactions of the AMS, 353(12), 2001, pp. 5121--5144. (abstract) (preprint.ps)

  • A. Siegel,
    Théorème des trois longueurs et suites sturmiennes : mots d'agencement des longueurs,
    Acta Arithmetica 97 (1-3), 2001, pp. 195--210. (abstract) (preprint.pdf)


Conference proceedings



  • S. Lemosquet, O. Abdou-Arbi, A. Siegel, J. Guinard-Flament, J. Van Milgen, J. Bourdon,
    A generic stoichiometric model to analyse the metabolic flexibility of the mammary gland in lactating dairy cows
    Modnut 2009. Proceedings of the 7th international workshop "Modelling nutrient digestion and utilization in farm animals", 2010

  • M. Gebser, C. Guziolowski, M. Ivanchev, T. Schaub, A. Siegel, P. Veber and S. Thiele
    Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming
    KR'2010 - International Conference on the Principles of Knowledge Representation and Reasoning, Toronto, 2010
    (file.pdf)

  • S. Blachon, G. Stoll, C. Guziolowski, A. Zinovyev, E. Barillot, A. Siegel and O. Radulescu 
    Method for relating inter-patient gene copy numbers variations with gene expression via gene influence networks
    BMIINT, Thessalonik, 2009 (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.

  • P. Blavy, F. Gondret,  H. Guillou, S. Lagarrigue,  P. Martin, O. Radulescu, A. Siegel and J. Van Milgen,
    A minimal and dynamic model for fatty acid metabolism in mouse liver,
     JOBIM, Lille,  2008. (file.pdf)

  • A Siegel, M Le Borgne, O Radulescu, C Guziolowski, P Veber
    Qualitative response of interaction networks: application to the validation of biological models
    Contribution to minisymposium
    New research in bioinformatics.
    6th International Congress on Industrial and Applied Mathematics. ICIAM 07, Zurich
    PAAM, Volume 7, Issue 1, p 1121803-1121804, 2007
    (preprint.pdf)

  •  A. Siegel,
    Spectral theory for dynamical systems arising from substitutions,
    EWM, K. Dajani, J. Von Reis (eds.), CWITract, Marseille, 2003.

Book and Conference proceedings Editing



  • Présentation de "Numeration: Mathematics and Computer Science" (CIRM, 2009)
    B. Adamczewski,  A. Siegel,  W. Steiner
    Actes des rencontres du CIRM
    Vol. 1 no. 1 (2009), p. 1-2 (pdf) 

  •  Journées Montoises d'Informatique Théorique (Rennes, 2006)
    Theoretical Informatics and Applications, Vol 42 (3), 2008.
    D. Caucal and A. Siegel, guest editors.



Non peer reviewed journals



  • Torsten Schaub and Anne Siegel
    Testing, Diagnosing, Repairing, and Predicting from Regulatory Networks and Datasets
    ERCIM News (82), 2010. (http)

  • A. Siegel, C. Guziolowski, P. Veber, O. Radulescu, M. Le Borgne 
    Optimiser un plan d'expérience à partir de modèles qualitatifs?
    BioFutur (275), 2007, 27-31(file.pdf)

  • Patrick Durand, Dominique Lavenier, Michel Leborgne, Anne Siegel, Philippe Veber and Jacques Nicolas,
    Applying Complex Models on Genomic Data.
    ERCIM News (60), 2005. (http)

  • A. Siegel,
    Fractals a la carte,
    Tangente, Hors Série 18 Les fractales, 2004, pp. 80-84. (pdf)

  • A. Siegel,
    Répétitions dans les figures géométriques,
    Quadrature, 34, 2002, pp. 40-47. (ps.gz)


Miscellaneous papers



  • O. Radulescu, A. Siegel, S. Laguarrigue, E. Pecou
    A model for regulated fatty acid metabolism in liver; equilibria and their changes
    Arxiv q-bio.CB/0603021, (abstract)(file.pdf)

  • Y. Bastide, S. Lagarrigue, M. Le Borgne, A. Siegel, P. Veber, O. Radulescu and A. Le Bechec,
    Une méthodologie pour l'analyse qualitative des réseaux biologiques: de la base de données à la vérification formelle
    (abstract)(preprint.pdf), Poster session, Jobim 2005.

  • A. Siegel,
    Autour des fractals de Rauzy,
    Journées Femmes et Mathématiques, Paris (03/2002). (ps)


Thesis



  • A. Siegel,
      Analyse de systèmes dynamiques par discrétisation. Exemples d'applications en théorie des nombres et en biologie moléculaire
    Habilitation à diriger les recherches, mention mathématiques et informatique, université de Rennes 1, 2008. [video] [ transparents] [document d'habilitation]

  • A. Siegel,
    Représentations géométrique, combinatoire et arithmétique des systèmes substitutifs de type Pisot,
    Thèse de Doctorat, Université de la Méditérranée, 2000. (abstract) (These.ps.gz)


 
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