Publications - Anne Siegel

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Publications are classified according to applications domains of dynamical systems which are quite independant (at least for the moment) : (bio-info) is related to bioinformatics and systems biology, (math-info) is related to theoretical computer science, symbolic dynamics and numeration systems

Peer Reviewed journals and book chapters


(bio-info) Laniau J, Frioux C, Nicolas J, Baroukh C, Cortes M, Got J, Trottier C, Eveillard D, Siegel A. Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks. PeerJ 5:e3860 (2017)  (electronic access).

(bio-info) Vincent Picard, Anne Siegel, Jérémie Bourdon A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks Journal of computational biology : a journal of computational molecular cell biology, Mary Ann Liebert 2017, 24 (8), pp.1--12.  (electronic access).

(bio-math) A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytesVictorien Delannée, Sophie Langouët, Nathalie Théret, Anne Siegel PeerJ, 2017 (electronic access). 

(bio-info) 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)

(bio-info) 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).

(bio-info) Loic Paulevé, Max Ostrowski, Torsten Schaub, Anne Siegel, Carito Guziolowski, Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming, Biosystems, 2016 (electronic access).

(bio-info) Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel and Alejandro Maass. Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinformatics 17:35 2016. (electronic access).

(bio-math) Picard V, Mulner-Lorillon O, Bourdon J, Morales J, Cormier P, Siegel A, Bellé R. Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization. Mol Reprod Dev. 2016 doi: 10.1002/mrd.22746.

(biology) Florence Gondret, Annie Vincent, Magalie Houée-Bigot, Anne Siegel, Sandrine Lagarrigue, Isabelle Louveau and David Causeur,  Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat locationBMC Genomics 17:120 2016. (electronic access).

(math-info)  Valérie Berthé, Jérémie Bourdon, Anne Siegel, Timo Jolivet, A combinatorial approach to produts of Pisot substitutions. Ergodic Theory and dynamical systems. 2016. (preprint on arxiv)(doi)

(bio-info) 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, 2016. (electronic access).

(bio-info) 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. (electronic access).

(bio-info) Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziolowski, Steffen Klamt, Extended Notions of Sign Consistency to Relate Experimental Data to Signaling and Regulatory Network Topologies, BMC bioinformatics 16:345. 2015. (electronic access)

(math)  Shigeki Akiyama, Marcy Barge, Valérie Berthé, Jeong-Yup Lee , Anne Siegel, On the Pisot substitution conjecture. Mathematics of Aperiodic order. J. Kellendonk, D. Lenz, J. Savinien (ed.).  Progress in Mathematics Volume 309. Birkhaeuser.  p.33-72 (electronic access)

(bio-info)  Torsten Schaub, Anne Siegel, Santiago Videla, Reasoning on the Response of Logical Signaling Networks with ASP, in Logical Modeling of Biological Systems, ed. by Luis Fariñas del Cerro, Katsumi Inoue, John Wiley and Sons, 2014  (electronic access) (pdf)

(biology) 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  (electronic access)

(biology)  Simon M Dittami, Tristan Barbeyron, Catherine Boyen, Jeanne Cambefort, Guillaume Collet, Ludovic Delage, Angélique Gobet, Agnès Groisillier, Catherine Leblanc, Gurvan Michel, Delphine Scornet, Anne Siegel, Javier E Tapia and Thierry Tonon Genome and metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae, Frontiers in Genetics, section Systems Biology, 2014. (electronic access)

(bio-info) 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. (electronic access)

(biology) Sébastien Laurent, Adrien Richard, Odile Mulner-Lorillon, Julia Morales, Didier Flament, Virginie Glippa, Jérémie Bourdon, Pauline Gosselin, Anne Siegel, Patrick Cormier, Robert Bellé Modelisation of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive,  Frontiers in Genetics, section Systems Biology, may 2014 (electronic access).

(bio-info) Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap Van Milgen and Anne Siegel. Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism   BMC Systems biology. 2014, 8:32 (electronic access).

(bio-info) Oumarou Abdou-Arbi, Sophie Lemosquet, Jaap Van Milgen, Anne Siegel and Jérémie Bourdon. Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. BMC Systems biology. 2014, 8:8 (electronic access).

(math-info) Valérie Berthé, Timo Jolivet and Anne Siegel. Connectedness of fractals associated with Arnoux-Rauzy substitution. Special issue of the RAIRO-Theoretical Informatics and Applications dedicated to the "Journées Montoises d'Informatique Théorique 2012"., 2014.  (electronic access)

(bio-info) Roland Kaminski, Torsten Schaub, Anne Siegel and Santiago Videla, Minimal Intervention Strategies in Logical Signaling Networks with Answer Set Programming Theory and Practice of Logic Programming 13 (Special Issue 4-5. 29th International Conference on Logic Programming)  2013, pp 675-690  (electronic access)

(bio-info) Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel and Julio Saez-Rodriguez. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics. 2013. (electronic access)

(math-info) V. Berthé, T. Jolivet, A. Siegel, Substitutive Arnoux-rauzy sequences have pure discrete spectrum Uniform Distribution Theory 7(1), 2012 (electronic access)

(biology)  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)

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

(bio-info) 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)

(bio-info) 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)

(math-info)  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)

(bio-info) 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)

(math-info)  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)

(math-info)  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

(biology) 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)

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

(biology) 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)

(bio-info) 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)

(bio-info) 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)

(math-info)  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)

(bio-info) 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)

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

(bio-info) 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)

(math-info) 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, (file.pdf)

(bio-info) 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  (preprint.pdf)

(bio-info) 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, (preprint.pdf)

(bio-info) 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  (preprint.pdf) Revised paper from  ECCS, Paris, November 2005 (slides)

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

(math-info)  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. (preprint.ps)

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

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

(math-info)  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)

(math-info)  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)

(math-info)  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. (preprint.ps)

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

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

Conference proceedings


(bio-info) 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

(bio-info) Vincent Picard, Jérémie Bourdon, Anne Siegel, A logic for Checking the Probabilistic Steady-State Properties of Reaction Networks, IJCAI-BAI 2015 : advances in bioinformatics and artificial intelligence: bridging the gap, Argentina.

(info) Timo Jolivet and Anne Siegel. Decidability problems for self-induced systems generated by a substitution.  MCU'2015. Machine, Computation and Universality. LNCS 9288, 2015. North Cyprus.

(bio-info) Loic Paulevé, Max Ostrowski, Anne Siegel, Carito Guziolowski, Boolean Network Identification from Multiplex Time Series Data, LNBI 9308. CMSB'2015 : Computational Methods in Systems Biology, 2015. Nantes, France.

(bio-info) Vincent Picard, Anne Siegel, Jérémie Bourdon.   Multivariate Normal Approximation for the Stochastic Simulation Algorithm: limit theorem and applications  SASB - 5th International Workshop on Static Analysis and Systems Biology. Electronic Notes in Theoretical Computer Science.

(bio-info) Vicente Acuna, Andres Aravena, Alejandro Maass, Anne Siegel.  Modeling Parsimonious Putative Regulatory Networks: Complexity and Heuristic ApproachVMCAI - Verification, Model Checking, and Abstract Interpretation  2014. (access on line)

(bio-info) Guillaume Collet, Martin Gebser, Sylvain Prigent, Torsten Schaub, Anne Siegel and Sven Thiele, Extending the Metabolic Network of Ectocarpus~Siliculosus using Answer Set Programming, LPNMR 2013. (preprint)

(bio-info) Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel and Sven Thiele, An ASP application in integrative biology: identification of functional gene units, Conference LPNMR 2013. (preprint)

(bio-info) Roland Kaminski, Torsten Schaub, Anne Siegel and Santiago Videla, Minimal Intervention Strategies in Logical Signaling Networks with Answer Set Programming, Conference ICLP 2013.

(math-info) V. Berthé, J. Bourdon, T. Jolivet, A. Siegel. Generating discrete planes with substitutions. Conference WORDS 2013.

(bio-info) Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez and Anne Siegel.  Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming.  CMSB 2012. London. Best paper award  (pdf)

(bio-info)  Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap van Milgen and Anne Siegel. Using large scale knowledge databases about reactions and regulations to find key regulators of sets of genes Preliminary results.  JOBIM Conference. 2012

(bio-info)  Andres Aravena, Carito Guziolowski, Anne Siegel and Alejandro Maass. Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network . Preliminary results. JOBIM Conference. 2012

(biology) 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

(bio-info) 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)

(bio-info) 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)

(bio-info) 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.

(bio-info) 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)

(bio-info) 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)

(math-info)  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


(math-info)  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)

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

(math-info)  N. Pytheas-Fogg. Substitutions in Dynamics, Arithmetics and Combinatorics,   Lectures Notes in Mathematics 1794, Springer-Verlag, 2002.  Edited by V. Berthe, S. Ferenczi, C. Mauduit and A. Siegel. (abstract) ps

Non peer reviewed journals


 

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

(bio-info) 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)

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

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

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

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)