Two-dimensional iterated morphisms and discrete planes. - Pierre Arnoux; Valérie Berthé; Anne Siegel (Theor. Comput. Sci., 2004)

Analyse de systèmes dynamiques par discrétisation. Exemples d'applications en théorie des nombres et en biologie moléculaire. (Analyzing dynamical system with discrete approaches. Application in number theory and molecular biology). - Anne Siegel (2008)

Curating a Large-Scale Regulatory Network by Evaluating Its Consistency with Expression Datasets. - Carito Guziolowski; Jeremy Gruel; Ovidiu Radulescu; Anne Siegel (CIBB, 2008)

Inferring the role of transcription factors in regulatory networks. - Philippe Veber; Carito Guziolowski; Michel Le Borgne; Ovidiu Radulescu; Anne Siegel (BMC Bioinform., 2008)

Preface. - Didier Caucal; Anne Siegel (RAIRO Theor. Informatics Appl., 2008)

Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. - Sylvain Blachon; Gautier Stoll; Carito Guziolowski; Andrei Yu. Zinovyev; Emmanuel Barillot; Anne Siegel; Ovidiu Radulescu (AIAI (Workshops), 2009)

Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming. - Martin Gebser; Carito Guziolowski; Mihail Ivanchev; Torsten Schaub; Anne Siegel; Sven Thiele; Philippe Veber (KR, 2010)

Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network. - Tatiana Baumuratova; Didier Surdez; Bernard Delyon; Gautier Stoll; Olivier Delattre; Ovidiu Radulescu; Anne Siegel (BMC Syst. Biol., 2010)

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

Substitutive Arnoux-Rauzy sequences have pure discrete spectrum - Valérie Berthé; Timo Jolivet; Anne Siegel (CoRR, 2011)

Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network. - Jérémie Bourdon; Damien Eveillard; Anne Siegel (PLoS Comput. Biol., 2011)

Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. - Carito Guziolowski; Sylvain Blachon; Tatiana Baumuratova; Gautier Stoll; Ovidiu Radulescu; Anne Siegel (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Genetically Regulated Metabolic Networks: Gale-Nikaido Modules and Differential Inequalities. - Ovidiu Radulescu; Anne Siegel; Elisabeth Pécou; Clément Chatelain 001; Sandrine Lagarrigue (Trans. Comp. Sys. Biology, 2011)

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP. - Santiago Videla; Carito Guziolowski; Federica Eduati; Sven Thiele; Niels Grabe; Julio Saez-Rodriguez; Anne Siegel (CMSB, 2012)

Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming - Santiago Videla; Carito Guziolowski; Federica Eduati; Sven Thiele; Niels Grabe; Julio Saez-Rodriguez; Anne Siegel (CoRR, 2012)

Generating Discrete Planes with Substitutions. - Valérie Berthé; Jérémie Bourdon; Timo Jolivet; Anne Siegel (WORDS, 2013)

An ASP Application in Integrative Biology: Identification of Functional Gene Units. - Philippe Bordron; Damien Eveillard; Alejandro Maass; Anne Siegel; Sven Thiele (LPNMR, 2013)

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming. - Guillaume Collet; Damien Eveillard; Martin Gebser; Sylvain Prigent 001; Torsten Schaub; Anne Siegel; Sven Thiele (LPNMR, 2013)

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

Minimal intervention strategies in logical signaling networks with ASP. - Roland Kaminski; Torsten Schaub; Anne Siegel; Santiago Videla (Theory Pract. Log. Program., 2013)

Modeling Parsimonious Putative Regulatory Networks: Complexity and Heuristic Approach. - Vicente Acuña; Andrés Aravena; Alejandro Maass; Anne Siegel (VMCAI, 2014)

Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. - Oumarou Abdou-Arbi; Sophie Lemosquet; Jaap Van Milgen; Anne Siegel; Jérémie Bourdon (BMC Syst. Biol., 2014)

Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism. - Pierre Blavy; Florence Gondret; Sandrine Lagarrigue; Jaap Van Milgen; Anne Siegel (BMC Syst. Biol., 2014)

A combinatorial approach to products of Pisot substitutions. - Valérie Berthé; Jérémie Bourdon; Timo Jolivet; Anne Siegel (CoRR, 2014)

Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications. - Vincent Picard; Anne Siegel; Jérémie Bourdon (SASB, 2014)

Connectedness of fractals associated with Arnoux-Rauzy substitutions. - Valérie Berthé; Timo Jolivet; Anne Siegel (RAIRO Theor. Informatics Appl., 2014)

Boolean Network Identification from Multiplex Time Series Data. - Max Ostrowski; Loïc Paulevé; Torsten Schaub; Anne Siegel; Carito Guziolowski (CMSB, 2015)

Decidability Problems for Self-induced Systems Generated by a Substitution. - Timo Jolivet; Anne Siegel (MCU, 2015)

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. - Sven Thiele; Luca Cerone; Julio Saez-Rodriguez; Anne Siegel; Carito Guziolowski; Steffen Klamt (BMC Bioinform., 2015)

Learning Boolean logic models of signaling networks with ASP. - Santiago Videla; Carito Guziolowski; Federica Eduati; Sven Thiele; Martin Gebser; Jacques Nicolas; Julio Saez-Rodriguez; Torsten Schaub; Anne Siegel (Theor. Comput. Sci., 2015)

Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming. - Max Ostrowski; Loïc Paulevé; Torsten Schaub; Anne Siegel; Carito Guziolowski (Biosyst., 2016)

Deciphering transcriptional regulations coordinating the response to environmental changes. - Vicente Acuña; Andrés Aravena; Carito Guziolowski; Damien Eveillard; Anne Siegel; Alejandro Maass (BMC Bioinform., 2016)

caspo: a toolbox for automated reasoning on the response of logical signaling networks families. - Santiago Videla; Julio Saez-Rodriguez; Carito Guziolowski; Anne Siegel (Bioinform., 2017)

A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. - Vincent Picard; Anne Siegel; Jérémie Bourdon (J. Comput. Biol., 2017)

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. - Sylvain Prigent 001; Clémence Frioux; Simon M. Dittami; Sven Thiele; Abdelhalim Larhlimi; Guillaume Collet; Fabien Gutknecht; Jeanne Got; Damien Eveillard; Jérémie Bourdon; Frédéric Plewniak; Thierry Tonon; et al. (PLoS Comput. Biol., 2017)

Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. - Clémence Frioux; Enora Fremy; Camille Trottier; Anne Siegel (Bioinform., 2018)

Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. - Méziane Aite; Marie Chevallier; Clémence Frioux; Camille Trottier; Jeanne Got; María Paz Cortés; Sebastián N. Mendoza; Grégory Carrier; Olivier Dameron; Nicolas Guillaudeux; Mauricio Latorre; Nicolás Loira; et al. (PLoS Comput. Biol., 2018)

Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. - Misbah Razzaq; Loïc Paulevé; Anne Siegel; Julio Saez-Rodriguez; Jérémie Bourdon; Carito Guziolowski (PLoS Comput. Biol., 2018)

Increasing Life Science Resources Re-Usability using Semantic Web Technologies. - Marine Louarn; Fabrice Chatonnet; Xavier Garnier; Thierry Fest; Anne Siegel; Olivier Dameron (eScience, 2019)

Hybrid metabolic network completion. - Clémence Frioux; Torsten Schaub; Sebastian Schellhorn; Anne Siegel; Philipp Wanko (Theory Pract. Log. Program., 2019)

Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study. - Kerian Thuillier; Caroline Baroukh; Alexander Bockmayr; Ludovic Cottret; Loïc Paulevé; Anne Siegel (CMSB, 2021)

PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX. - François Moreews; Hugo Simon; Anne Siegel; Florence Gondret; Emmanuelle Becker (Bioinform., 2021)

Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA. - Maël Conan; Nathalie Théret; Sophie Langouet; Anne Siegel (BMC Bioinform., 2021)

Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. - Laurence Garczarek; Ulysse Guyet; Hugo Doré; Gregory K. Farrant; Mark Hoebeke; Loraine Brillet-Guéguen; Antoine Bisch; Mathilde Ferrieux; Jukka Siltanen; Erwan Le Corre; Gildas Le Corguillé; Morgane Ratin; et al. (Nucleic Acids Res., 2021)

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. - Anna Niarakis; Dagmar Waltemath; James A. Glazier; Falk Schreiber; Sarah M. Keating; David P. Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomás Helikar; Sylvain Soliman; et al. (Briefings Bioinform., 2022)

MERRIN: MEtabolic regulation rule INference from time series data. - Kerian Thuillier; Caroline Baroukh; Alexander Bockmayr; Ludovic Cottret; Loïc Paulevé; Anne Siegel (Bioinform., 2022)

Improving reusability along the data life cycle: a regulatory circuits case study. - Marine Louarn; Fabrice Chatonnet; Xavier Garnier; Thierry Fest; Anne Siegel; Catherine Faron; Olivier Dameron (J. Biomed. Semant., 2022)

Discrete modeling for integration and analysis of large-scale signaling networks. - Pierre Vignet; Jean Coquet; Sébastien Auber; Matéo Boudet; Anne Siegel; Nathalie Théret (PLoS Comput. Biol., 2022)

CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems. - Kerian Thuillier; Anne Siegel; Loïc Paulevé (AAAI, 2024)

Modelling Behavior of Microbiota Metabolic Network Subject to Diets. - Oumarou Abdou-Arbi; Jérémie Bourdon; Anne Siegel (CARI, 2024)

A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. - Matthieu Bouguéon; Vincent Legagneux; Octave Hazard; Jérémy Bomo; Anne Siegel; Jérôme Feret; Nathalie Théret (PLoS Comput. Biol., 2024)

SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects. - Baptiste Ruiz; Arnaud Belcour; Samuel Blanquart; Sylvie Buffet-Bataillon; Isabelle Le Huërou-Luron; Anne Siegel; Yann Le Cunff (PLoS Comput. Biol., 2024)

Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. - Marine Louarn; Guillaume Collet; Ève Barré; Thierry Fest; Olivier Dameron; Anne Siegel; Fabrice Chatonnet (PLoS Comput. Biol., 2024)