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2020 – today
- 2024
[j33]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)- [j32]Matthieu Bouguéon, Vincent Legagneux, Octave Hazard, Jérémy Bomo, Anne Siegel, Jérôme Feret, Nathalie Théret:
A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. PLoS Comput. Biol. 20(7): 1011858 (2024) - [j31]Baptiste Ruiz, Arnaud Belcour, Samuel Blanquart, Sylvie Buffet-Bataillon, Isabelle Le Huërou-Luron, Anne Siegel, Yann Le Cunff:
SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects. PLoS Comput. Biol. 20(11): 1012577 (2024) - [c15]Kerian Thuillier, Anne Siegel, Loïc Paulevé:
CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems. AAAI 2024: 8146-8153 - 2022
- [j30]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, Laurence Calzone:
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. Briefings Bioinform. 23(4) (2022) - [j29]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): 11 (2022) - [j28]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) - 2021
- [j27]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): 4889-4891 (2021) - [j26]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. 22-S(3): 450 (2021) - [j25]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, 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): D667-D676 (2021) - [c14]Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, Anne Siegel:
Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study. CMSB 2021: 159-180
2010 – 2019
- 2019
- [j24]Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko:
Hybrid metabolic network completion. Theory Pract. Log. Program. 19(1): 83-108 (2019) - [c13]Marine Louarn, Fabrice Chatonnet, Xavier Garnier, Thierry Fest, Anne Siegel, Olivier Dameron:
Increasing Life Science Resources Re-Usability using Semantic Web Technologies. eScience 2019: 217-225 - 2018
- [j23]Clémence Frioux, Enora Fremy, Camille Trottier, Anne Siegel:
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. Bioinform. 34(17): i934-i943 (2018) - [j22]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) - [j21]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) - [i6]Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko:
Hybrid Metabolic Network Completion. CoRR abs/1808.04149 (2018) - 2017
- [j20]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): 947-950 (2017) - [j19]Vincent Picard, Anne Siegel, Jérémie Bourdon:
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. J. Comput. Biol. 24(8): 734-745 (2017) - [j18]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) - [c12]Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko:
Hybrid Metabolic Network Completion. LPNMR 2017: 308-321 - 2016
- [j17]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: 139-153 (2016) - [j16]Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, Alejandro Maass:
Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinform. 17: 35 (2016) - 2015
- [j15]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: 345:1-345:13 (2015) - [j14]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: 79-101 (2015) - [c11]Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski:
Boolean Network Identification from Multiplex Time Series Data. CMSB 2015: 170-181 - [c10]Timo Jolivet, Anne Siegel:
Decidability Problems for Self-induced Systems Generated by a Substitution. MCU 2015: 3-16 - 2014
- [j13]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): 1942 (2014) - [j12]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: 8 (2014) - [j11]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: 32 (2014) - [j10]Valérie Berthé, Timo Jolivet, Anne Siegel:
Connectedness of fractals associated with Arnoux-Rauzy substitutions. RAIRO Theor. Informatics Appl. 48(3): 249-266 (2014) - [c9]Vicente Acuña, Andrés Aravena, Alejandro Maass, Anne Siegel:
Modeling Parsimonious Putative Regulatory Networks: Complexity and Heuristic Approach. VMCAI 2014: 322-336 - [c8]Vincent Picard, Anne Siegel, Jérémie Bourdon:
Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications. SASB 2014: 67-82 - [i5]Valérie Berthé, Jérémie Bourdon, Timo Jolivet, Anne Siegel:
A combinatorial approach to products of Pisot substitutions. CoRR abs/1401.0704 (2014) - 2013
- [j9]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): 2320-2326 (2013) - [j8]Roland Kaminski, Torsten Schaub, Anne Siegel, Santiago Videla:
Minimal intervention strategies in logical signaling networks with ASP. Theory Pract. Log. Program. 13(4-5): 675-690 (2013) - [c7]Valérie Berthé, Jérémie Bourdon, Timo Jolivet, Anne Siegel:
Generating Discrete Planes with Substitutions. WORDS 2013: 58-70 - [c6]Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel, Sven Thiele:
An ASP Application in Integrative Biology: Identification of Functional Gene Units. LPNMR 2013: 206-218 - [c5]Guillaume Collet, Damien Eveillard, Martin Gebser, Sylvain Prigent, Torsten Schaub, Anne Siegel, Sven Thiele:
Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming. LPNMR 2013: 245-256 - 2012
- [c4]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: 342-361 - [i4]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 abs/1210.0690 (2012) - 2011
- [j7]Jérémie Bourdon, Damien Eveillard, Anne Siegel:
Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network. PLoS Comput. Biol. 7(9) (2011) - [j6]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): 1223-1234 (2011) - [j5]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: 110-130 (2011) - [i3]Valérie Berthé, Timo Jolivet, Anne Siegel:
Connectedness of fractals associated with Arnoux-Rauzy substitutions. CoRR abs/1101.1784 (2011) - [i2]Valérie Berthé, Timo Jolivet, Anne Siegel:
Substitutive Arnoux-Rauzy sequences have pure discrete spectrum. CoRR abs/1108.5574 (2011) - 2010
- [j4]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: 146 (2010) - [c3]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 - [i1]Torsten Schaub, Anne Siegel:
Testing, Diagnosing, Repairing, and Predicting from Regulatory Networks and Datasets. ERCIM News 2010(82): 30 (2010)
2000 – 2009
- 2009
- [c2]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: 72-87 - 2008
- [b1]Anne Siegel:
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). University of Rennes 1, France, 2008 - [j3]Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel:
Inferring the role of transcription factors in regulatory networks. BMC Bioinform. 9 (2008) - [j2]Didier Caucal, Anne Siegel:
Preface. RAIRO Theor. Informatics Appl. 42(3): 415 (2008) - [c1]Carito Guziolowski, Jeremy Gruel, Ovidiu Radulescu, Anne Siegel:
Curating a Large-Scale Regulatory Network by Evaluating Its Consistency with Expression Datasets. CIBB 2008: 144-155 - 2004
- [j1]Pierre Arnoux, Valérie Berthé, Anne Siegel:
Two-dimensional iterated morphisms and discrete planes. Theor. Comput. Sci. 319(1-3): 145-176 (2004)
Coauthor Index
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