• 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)

• V. Berthé and A. Siegel,
  Tilings associated with beta-numeration and substitutions,
  INTEGERS (Electronic Journal of Combinatorial Number Theory), 5(3), pp. A2, 2005 (abstract)(file.pdf)

• 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. Berthé and A. Siegel,
  Basic notions on substitutions,
  in N. Pytheas-Fogg, Substitutions in Dynamics, Arithmetics and Combinatorics,
  Lectures Notes in Mathematics 1794, Springer-Verlag, 2002, Chapter 1, pp. 1--34. (preprint.ps)

• A. Siegel,
  Spectral theory and geometric representation of substitutions,
  in N. Pytheas-Fogg, Substitutions in Dynamics, Arithmetics and Combinatorics,
  Lectures Notes in Mathematics 1794, Springer-Verlag, 2002. Chapter 7, pp. 199--252. (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

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• 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