Anne Siegel - RankMe

57 papers A* 2B 4C 1Journal 40Unranked 9

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression. PLoS Comput. Biol. Matthieu Bouguéon, Vincent Legagneux, Octave Hazard, Jérémy Bomo, Anne Siegel, Jérôme Feret, Nathalie Théret
2024	A*	`conf`	CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems. AAAI Kerian Thuillier, Anne Siegel, Loïc Paulevé
2024	—	`conf`	Modelling Behavior of Microbiota Metabolic Network Subject to Diets. CARI Oumarou Abdou-Arbi, Jérémie Bourdon, Anne Siegel
2024	J	`jnl`	Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints. PLoS Comput. Biol. Marine Louarn, Guillaume Collet, Ève Barré, Thierry Fest, Olivier Dameron, Anne Siegel, Fabrice Chatonnet
2024	J	`jnl`	SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects. PLoS Comput. Biol. Baptiste Ruiz, Arnaud Belcour, Samuel Blanquart, Sylvie Buffet-Bataillon, Isabelle Le Huërou-Luron, Anne Siegel, Yann Le Cunff
2022	J	`jnl`	Addressing Briefings Bioinform. 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
2022	J	`jnl`	Discrete modeling for integration and analysis of large-scale signaling networks. PLoS Comput. Biol. Pierre Vignet, Jean Coquet, Sébastien Auber, Matéo Boudet, Anne Siegel, Nathalie Théret
2022	J	`jnl`	Improving reusability along the data life cycle: a regulatory circuits case study. J. Biomed. Semant. Marine Louarn, Fabrice Chatonnet, Xavier Garnier, Thierry Fest, Anne Siegel, Catherine Faron, Olivier Dameron
2022	J	`jnl`	MERRIN: MEtabolic regulation rule INference from time series data. Bioinform. Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, Anne Siegel
2021	J	`jnl`	Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA. BMC Bioinform. Maël Conan, Nathalie Théret, Sophie Langouet, Anne Siegel
2021	J	`jnl`	Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Res. 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
2021	—	`conf`	Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study. CMSB Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loïc Paulevé, Anne Siegel
2021	J	`jnl`	PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX. Bioinform. François Moreews, Hugo Simon, Anne Siegel, Florence Gondret, Emmanuelle Becker
2019	J	`jnl`	Hybrid metabolic network completion. Theory Pract. Log. Program. Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko
2019	—	`conf`	Increasing Life Science Resources Re-Usability using Semantic Web Technologies. eScience Marine Louarn, Fabrice Chatonnet, Xavier Garnier, Thierry Fest, Anne Siegel, Olivier Dameron
2018	J	`jnl`	Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PLoS Comput. Biol. Misbah Razzaq, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, Carito Guziolowski
2018	J	`jnl`	Hybrid Metabolic Network Completion. CoRR Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko
2018	J	`jnl`	Scalable and exhaustive screening of metabolic functions carried out by microbial consortia. Bioinform. Clémence Frioux, Enora Fremy, Camille Trottier, Anne Siegel
2018	J	`jnl`	Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PLoS Comput. Biol. Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián Nelson Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V. Markov, Alejandro Maass, Anne Siegel
2017	J	`jnl`	A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks. J. Comput. Biol. Vincent Picard, Anne Siegel, Jérémie Bourdon
2017	B	`conf`	Hybrid Metabolic Network Completion. LPNMR Clémence Frioux, Torsten Schaub, Sebastian Schellhorn, Anne Siegel, Philipp Wanko
2017	J	`jnl`	Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks. PLoS Comput. Biol. 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
2017	J	`jnl`	caspo: a toolbox for automated reasoning on the response of logical signaling networks families. Bioinform. Santiago Videla, Julio Saez-Rodriguez, Carito Guziolowski, Anne Siegel
2016	J	`jnl`	Boolean network identification from perturbation time series data combining dynamics abstraction and logic programming. Biosyst. Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski
2016	J	`jnl`	Deciphering transcriptional regulations coordinating the response to environmental changes. BMC Bioinform. Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel, Alejandro Maass
2015	—	`conf`	Boolean Network Identification from Multiplex Time Series Data. CMSB Max Ostrowski, Loïc Paulevé, Torsten Schaub, Anne Siegel, Carito Guziolowski
2015	C	`conf`	Decidability Problems for Self-induced Systems Generated by a Substitution. MCU Timo Jolivet, Anne Siegel
2015	J	`jnl`	Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. BMC Bioinform. Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziolowski, Steffen Klamt
2015	J	`jnl`	Learning Boolean logic models of signaling networks with ASP. Theor. Comput. Sci. Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, Jacques Nicolas, Julio Saez-Rodriguez, Torsten Schaub, Anne Siegel
2014	J	`jnl`	A combinatorial approach to products of Pisot substitutions. CoRR Valérie Berthé, Jérémie Bourdon, Timo Jolivet, Anne Siegel
2014	J	`jnl`	Connectedness of fractals associated with Arnoux-Rauzy substitutions. RAIRO Theor. Informatics Appl. Valérie Berthé, Timo Jolivet, Anne Siegel
2014	J	`jnl`	Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
2014	J	`jnl`	Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. BMC Syst. Biol. Oumarou Abdou-Arbi, Sophie Lemosquet, Jaap Van Milgen, Anne Siegel, Jérémie Bourdon
2014	B	`conf`	Modeling Parsimonious Putative Regulatory Networks: Complexity and Heuristic Approach. VMCAI Vicente Acuña, Andrés Aravena, Alejandro Maass, Anne Siegel
2014	—	`conf`	Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications. SASB Vincent Picard, Anne Siegel, Jérémie Bourdon
2014	J	`jnl`	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. Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap Van Milgen, Anne Siegel
2013	B	`conf`	An ASP Application in Integrative Biology: Identification of Functional Gene Units. LPNMR Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel, Sven Thiele
2013	J	`jnl`	Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinform. Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez
2013	B	`conf`	Extending the Metabolic Network of LPNMR Guillaume Collet, Damien Eveillard, Martin Gebser, Sylvain Prigent, Torsten Schaub, Anne Siegel, Sven Thiele
2013	—	`conf`	Generating Discrete Planes with Substitutions. WORDS Valérie Berthé, Jérémie Bourdon, Timo Jolivet, Anne Siegel
2013	J	`jnl`	Minimal intervention strategies in logical signaling networks with ASP. Theory Pract. Log. Program. Roland Kaminski, Torsten Schaub, Anne Siegel, Santiago Videla
2012	—	`conf`	Revisiting the Training of Logic Models of Protein Signaling Networks with ASP. CMSB Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel
2012	J	`jnl`	Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming CoRR Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, Anne Siegel
2011	J	`jnl`	Connectedness of fractals associated with Arnoux-Rauzy substitutions CoRR Valérie Berthé, Timo Jolivet, Anne Siegel
2011	J	`jnl`	Designing Logical Rules to Model the Response of Biomolecular Networks with Complex Interactions: An Application to Cancer Modeling. IEEE ACM Trans. Comput. Biol. Bioinform. Carito Guziolowski, Sylvain Blachon, Tatiana Baumuratova, Gautier Stoll, Ovidiu Radulescu, Anne Siegel
2011	J	`jnl`	Genetically Regulated Metabolic Networks: Gale-Nikaido Modules and Differential Inequalities. Trans. Comp. Sys. Biology Ovidiu Radulescu, Anne Siegel, Elisabeth Pécou, Clément Chatelain, Sandrine Lagarrigue
2011	J	`jnl`	Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network. PLoS Comput. Biol. Jérémie Bourdon, Damien Eveillard, Anne Siegel
2011	J	`jnl`	Substitutive Arnoux-Rauzy sequences have pure discrete spectrum CoRR Valérie Berthé, Timo Jolivet, Anne Siegel
2010	J	`jnl`	Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network. BMC Syst. Biol. Tatiana Baumuratova, Didier Surdez, Bernard Delyon, Gautier Stoll, Olivier Delattre, Ovidiu Radulescu, Anne Siegel
2010	A*	`conf`	Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming. KR Martin Gebser, Carito Guziolowski, Mihail Ivanchev, Torsten Schaub, Anne Siegel, Sven Thiele, Philippe Veber
2010	J	`jnl`	Testing, Diagnosing, Repairing, and Predicting from Regulatory Networks and Datasets. ERCIM News Torsten Schaub, Anne Siegel
2009	—	`conf`	Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks. AIAI (Workshops) Sylvain Blachon, Gautier Stoll, Carito Guziolowski, Andrei Yu. Zinovyev, Emmanuel Barillot, Anne Siegel, Ovidiu Radulescu
2008	—	`book`	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	—	`conf`	Curating a Large-Scale Regulatory Network by Evaluating Its Consistency with Expression Datasets. CIBB Carito Guziolowski, Jeremy Gruel, Ovidiu Radulescu, Anne Siegel
2008	J	`jnl`	Inferring the role of transcription factors in regulatory networks. BMC Bioinform. Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu, Anne Siegel
2008	J	`jnl`	Preface. RAIRO Theor. Informatics Appl. Didier Caucal, Anne Siegel
2004	J	`jnl`	Two-dimensional iterated morphisms and discrete planes. Theor. Comput. Sci. Pierre Arnoux, Valérie Berthé, Anne Siegel