Anne Siegel

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 21

Top Topics

Metabolic Networks

Stochastic Simulation

Top Venues

PLoS Comput. Biol.

Publications

Kerian Thuillier, Anne Siegel, Loïc Paulevé
CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems. AAAI (2024)
Marine Louarn, Guillaume Collet, Ève Barré, Thierry Fest, Olivier Dameron, Anne Siegel, Fabrice Chatonnet
Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. PLoS Comput. Biol. 20 (1) (2024)
Pierre Vignet, Jean Coquet, Sébastien Auber, Matéo Boudet, Anne Siegel, Nathalie Théret
Discrete modeling for integration and analysis of large-scale signaling networks. PLoS Comput. Biol. 18 (6) (2022)
Marine Louarn, Fabrice Chatonnet, Xavier Garnier, Thierry Fest, Anne Siegel, Catherine Faron, Olivier Dameron
Improving reusability along the data life cycle: a regulatory circuits case study. J. Biomed. Semant. 13 (1) (2022)
Anna Niarakis, Dagmar Waltemath, James Glazier, Falk Schreiber, Sarah M. Keating, David P. Nickerson, Claudine Chaouiya, Anne Siegel, Vincent Noël, Henning Hermjakob, Tomás Helikar, Sylvain Soliman, Laurence Calzone
. Briefings Bioinform. 23 (4) (2022)
Laurence Garczarek, Ulysse Guyet, Hugo Doré, Gregory K. Farrant, Mark Hoebeke, Loraine Brillet-Guéguen, Antoine Bisch, Mathilde Ferrieux, Jukka Siltanen, Erwan Corre, Gildas Le Corguillé, Morgane Ratin, Frances D. Pitt, Martin Ostrowski, Maël Conan, Anne Siegel, Karine Labadie, Jean-Marc Aury, Patrick Wincker, David J. Scanlan, Frédéric Partensky
Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Res. 49 (Database-Issue) (2021)
Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, Anne Siegel
Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study. CMSB (2021)
François Moreews, Hugo Simon, Anne Siegel, Florence Gondret, Emmanuelle Becker
PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX. Bioinform. 37 (24) (2021)
Maël Conan, Nathalie Théret, Sophie Langouet, Anne Siegel
Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA. BMC Bioinform. (3) (2021)
Marine Louarn, Fabrice Chatonnet, Xavier Garnier, Thierry Fest, Anne Siegel, Olivier Dameron
Increasing Life Science Resources Re-Usability using Semantic Web Technologies. eScience (2019)
Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko
Hybrid metabolic network completion. Theory Pract. Log. Program. 19 (1) (2019)
Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko
Hybrid Metabolic Network Completion. CoRR (2018)
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, Gabriel V. Markov, Alejandro Maass, Anne Siegel
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PLoS Comput. Biol. 14 (5) (2018)
Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, Carito Guziolowski
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PLoS Comput. Biol. 14 (10) (2018)
Clémence Frioux, Enora Fremy, Camille Trottier, Anne Siegel
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. Bioinform. 34 (17) (2018)
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 Comput. Biol. 13 (1) (2017)
Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko
Hybrid Metabolic Network Completion. LPNMR (2017)
Vincent Picard, Anne Siegel, Jérémie Bourdon
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. J. Comput. Biol. 24 (8) (2017)
Santiago Videla, Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel
caspo: a toolbox for automated reasoning on the response of logical signaling networks families. Bioinform. 33 (6) (2017)
Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, Alejandro Maass
Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinform. 17 (2016)
Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski
Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming. Biosyst. 149 (2016)
Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski
Boolean Network Identification from Multiplex Time Series Data. CMSB (2015)
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 Bioinform. 16 (2015)
Timo Jolivet, Anne Siegel
Decidability Problems for Self-induced Systems Generated by a Substitution. MCU (2015)
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. Theor. Comput. Sci. 599 (2015)
Vincent Picard, Anne Siegel, Jérémie Bourdon
Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications. Electron. Notes Theor. Comput. Sci. 316 (2015)
Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap Van Milgen, 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 Syst. Biol. 8 (2014)
Valérie Berthé, Jérémie Bourdon, Timo Jolivet, Anne Siegel
A combinatorial approach to products of Pisot substitutions. CoRR (2014)
Oumarou Abdou-Arbi, Sophie Lemosquet, Jaap Van Milgen, Anne Siegel, Jérémie Bourdon
Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. BMC Syst. Biol. 8 (2014)
Vicente Acuña, Andrés Aravena, Alejandro Maass, Anne Siegel
Modeling Parsimonious Putative Regulatory Networks: Complexity and Heuristic Approach. VMCAI (2014)
Valérie Berthé, Timo Jolivet, Anne Siegel
Connectedness of fractals associated with Arnoux-Rauzy substitutions. RAIRO Theor. Informatics Appl. 48 (3) (2014)
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. 30 (13) (2014)
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. 29 (18) (2013)
Roland Kaminski, Torsten Schaub, Anne Siegel, Santiago Videla
Minimal intervention strategies in logical signaling networks with ASP. Theory Pract. Log. Program. 13 (4-5) (2013)
Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel, Sven Thiele
An ASP Application in Integrative Biology: Identification of Functional Gene Units. LPNMR (2013)
Valérie Berthé, Jérémie Bourdon, Timo Jolivet, Anne Siegel
Generating Discrete Planes with Substitutions. WORDS (2013)
Guillaume Collet, Damien Eveillard, Martin Gebser, Sylvain Prigent, Torsten Schaub, Anne Siegel, Sven Thiele
Using Answer Set Programming. LPNMR (2013)
Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel
Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming CoRR (2012)
Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel
Revisiting the Training of Logic Models of Protein Signaling Networks with ASP. CMSB (2012)
Valérie Berthé, Timo Jolivet, Anne Siegel
Substitutive Arnoux-Rauzy sequences have pure discrete spectrum CoRR (2011)
Ovidiu Radulescu, Anne Siegel, Elisabeth Pécou, Clément Chatelain, Sandrine Lagarrigue
Genetically Regulated Metabolic Networks: Gale-Nikaido Modules and Differential Inequalities. Trans. Comp. Sys. Biology 13 (2011)
Valérie Berthé, Timo Jolivet, Anne Siegel
Connectedness of fractals associated with Arnoux-Rauzy substitutions CoRR (2011)
Carito Guziolowski, Sylvain Blachon, Tatiana Baumuratova, Gautier Stoll, Ovidiu Radulescu, Anne Siegel
Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (5) (2011)
Jérémie Bourdon, Damien Eveillard, Anne Siegel
Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network. PLoS Comput. Biol. 7 (9) (2011)
Martin Gebser, Carito Guziolowski, Mihail Ivanchev, Torsten Schaub, Anne Siegel, Sven Thiele, Philippe Veber
Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming. KR (2010)
Torsten Schaub, Anne Siegel
Testing, Diagnosing, Repairing, and Predicting from Regulatory Networks and Datasets. ERCIM News 2010 (82) (2010)
Tatiana Baumuratova, Didier Surdez, Bernard Delyon, Gautier Stoll, Olivier Delattre, Ovidiu Radulescu, Anne Siegel
Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network. BMC Syst. Biol. 4 (2010)
Sylvain Blachon, Gautier Stoll, Carito Guziolowski, Andrei Yu. Zinovyev, Emmanuel Barillot, Anne Siegel, Ovidiu Radulescu
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. AIAI Workshops (2009)
Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel
Inferring the role of transcription factors in regulatory networks. BMC Bioinform. 9 (2008)
Carito Guziolowski, Jeremy Gruel, Ovidiu Radulescu, Anne Siegel
Curating a Large-Scale Regulatory Network by Evaluating Its Consistency with Expression Datasets. CIBB (2008)
Didier Caucal, Anne Siegel
Preface. RAIRO Theor. Informatics Appl. 42 (3) (2008)
Pierre Arnoux, Valérie Berthé, Anne Siegel
Two-dimensional iterated morphisms and discrete planes. Theor. Comput. Sci. 319 (1-3) (2004)