Anne SIEGEL
Publications
Publications
Metagenomic taxonomic assignment using Nanopore reads, reconstruction of metabolic networks and prediction of metabolite production2025 - Journées Nutrition et Ecosystèmes Microbiens, May 2025, Rennes, France |
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Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with the in silico screening Prolipipe pipelineJOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Romain Bourqui; Clémence Frioux; Simon Labarthe, Jul 2025, Bordeaux, France |
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Methods for a species-specific genome-scale metabolic model designed for eukaryotes and applied to the Ascophyllum nodosum macroalgaJOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.109-117 |
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CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics ProblemsAAAI 2024 - The 38th Annual AAAI Conference on Artificial Intelligence, Feb 2024, Vancouver, Canada. pp.1-8 |
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Contributions des entrées sur les sorties pour les réseaux métaboliques sur génomes entiers: performances et utilisation pour des études en nutrition humaineCARI 2022 - Colloque Africain sur la Recherche en Informatique et en Mathématiques Appliquées, Oct 2022, Yaoundé, Cameroun. pp.1-12 |
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Highlighting discriminating functional annotations in patients' gut microbiota through Machine Learning classification applied to functional descriptions of the microbiomeInternational Conference on Clinical Metagenomics, Oct 2022, Geneve, Switzerland |
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Genome-scale network reconstruction of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S852021 - 12th International Symposium on Gut Microbiology, INRAE ; Rowett Institute UK, Oct 2021, En ligne, France. pp.1 P; |
Metabolic complementarity applied to the screening of microbiota and the identification of key speciesCMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27 |
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Metabolic complementarity applied to the screening of microbiota and the identification of key speciesMPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27 |
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Metabolic complementarity applied to the screening of microbiota and the identification of key speciesJOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France |
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Learning Boolean controls in regulated metabolic networks: a case-studyCMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, 2021, Bordeaux, France. pp.159-180, ⟨10.1007/978-3-030-85633-5_10⟩ |
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Increasing life science resources re-usability using Semantic Web technologieseScience 2019 - 15th International eScience Conference, Sep 2019, San Diego, United States. pp.1-9 |
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AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resourcesJOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1 |
Learning boolean regulations based on prior-knowledge data: a logical-based viewpointSASB 2019 - 10th International Workshop on Static Analysis for Systems Biology, Oct 2019, Porto, Portugal |
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Using automated reasoning to explore unconventional organisms: a first step to explore host-microbial interactionsMPA 2019 - Conference on Metabolic Pathway Analysis, Aug 2019, Riga, Latvia |
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Scalable and exhaustive screening of metabolic functions carried out by microbial consortiaECCB - 2018 - 17th European Conference on Computational Biology, Sep 2018, Athènes, Greece. pp.i934-i943, ⟨10.1093/bioinformatics/bty588⟩ |
Identification des fonctions biologiques, spécifiques d’un tissu ou partagées entre tissus, associées aux différences d’efficacité alimentaire chez le porc en croissance49. Journées de la Recherche Porcine, Jan 2017, Paris, France. pp.13-18 |
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Toward a better understanding of the plant microbiota4ème colloque de Génomique Environnementale, GDR Génomique Environnementale, Sep 2017, Marseille, France |
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Hybrid Metabolic Network Completion14th International Conference on Logic Programming and Nonmonotonic Reasoning - LPNMR 2017, Jul 2017, Espoo, Finland. pp.308-321 |
Toward the study of metabolic functions in algal holobionts4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France |
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AskOmics, a web tool to integrate and query biological data using semantic web technologiesJOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. pp.1 |
Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid10th Arthropod Genomics Symposium, Jun 2017, Notre Dame, United States |
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A system biology loop for the identification of boolean networks to model signaling networks.European Conference on Mathematical and Theoretical Biology, 2016, Nottingham, France |
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Handling the heterogeneity of genomic and metabolic networks data within flexible workflows with the PADMet toolboxJobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2016, Lyon, France |
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A Logic for Checking the Probabilistic Steady-State Properties of Reaction NetworksIJCAI workshop BAI: Bioinformatics and Artificial Intelligence, 2015, Buenos Aeres, Argentina |
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Decidability Problems for Self-induced Systems Generated by a SubstitutionMCU 2015 : Machines, Computation and Universality, 2015, Famagusta, Cyprus. ⟨10.1007/978-3-319-23111-2⟩ |
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Boolean Network Identification from Multiplex Time Series DataCMSB 2015 - 13th conference on Computational Methods for Systems Biology, Sep 2015, Nantes, France. pp.170-181, ⟨10.1007/978-3-319-23401-4_15⟩ |
Data integrationMeeting INRA-ISU, Mar 2015, Ames, United States. 11 diapositives |
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Modeling parsimonious putative regulatory networks: complexity and heuristic approach15th conference in Verification, Model Checking, and Abstract Interpretation, 2014, San Diego, United States. pp.322-336, ⟨10.1007/978-3-642-54013-4_18⟩ |
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Multivariate Normal Approximation for the Stochastic Simulation Algorithm: limit theorem and applicationsSASB - 5th International Workshop on Static Analysis and Systems Biology, 2014, Munchen, Germany |
Using ASP to integrate large-scale heterogeneous information about the response of a biological system5th Workshop on Logic and Systems Biology (associated with CSL/LICS 2014), Jul 2014, VIenna, Austria |
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Improving robustness in the study of logical model of signalling networks with answer set programmingECCB 2014 - Workshop on Logical Modelling and Analysis of Cellular Networks, Sep 2014, Strasbourg, France |
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Extending the Metabolic Network of <em>Ectocarpus Siliculosus</em> Using Answer Set ProgrammingLPNMR, 2013, ⟨10.1007/978-3-642-40564-8_25⟩ |
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An ASP application in integrative biology: identification of functional gene unitsLPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain |
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Extracting robust information from knowledge and observations on a biological system: a formal system frameworkPRIB - Eighth IAPR International Conference on Pattern Recognition in Bioinformatics - 2013, Jun 2013, Nice, France |
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Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set ProgrammingLPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain |
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Generating discrete planes with substitutionsWORDS - 9th International Conference on Words - 2013, Sep 2013, Turku, Finland |
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Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation networkJobim 2012, Jul 2012, Rennes, France. pp.171 |
Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiologyEsil 2012: algal post-genomics, Apr 2012, Roscoff, France |
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Using large scale knowledge database about reactions and regulations to find key regulators of sets of genesJOBIM 2012, Inria, 2012, Rennes, France. pp.123-132 |
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Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set ProgrammingCMSB - 10th Computational Methods in Systems Biology 2012, D. Gilbert and M. Heiner, Oct 2012, London, United Kingdom. pp.342-361, ⟨10.1007/978-3-642-33636-2_20⟩ |
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Exploitation à large échelle de bases de données de connaissance sur les réactions et régulations pour trouver des régulateurs clés de groupe de gènesJournées ouvertes en biologie, informatique et mathématiques, Jul 2012, Rennes, France. pp.161-170 |
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A new method for modeling reactions and regulations to analyze high-throughout data4. International Symposium on Animal Functional Genomics, Sorcha De Gras; Sorcha De Gras, Oct 2011, Dublin, Ireland |
Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set ProgrammingPrinciples of Knowledge Representation and Reasoning, 2010, Toronto, Canada |
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CURATING A LARGE-SCALE REGULATORY NETWORK BY EVALUATING ITS CONSISTENCY WITH EXPRESSION DATASETSCIBB 2008: COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS, Oct 2008, Salerno, Italy. pp.144-155 |
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence NetworksAIAI 2009 Workshop -- Workshop on Biomedical Informatics and Intelligent Approaches in the Support of Genomic Medicine (BMIINT), Apr 2009, Thessalonik, Greece. pp.72-87 |
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Rational numbers with purely periodic beta-expansionsFractals and Tilings, Jul 2009, Strobl, Austria |
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La calculette métabolique": une approche de modélisation biochimique pour explorer les contraintes au sein du métabolisme des mammifères3. Journées d’Animation Scientifique du Département de Physiologie Animale et Systèmes d’Elevage, Oct 2009, Tours, France |
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From pure discrete spectrum conditions to topological properties of self-affine tilesAperiodic Order, Sep 2009, Leceister, United Kingdom |
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A minimal and dynamic model for fatty acid metabolism in mouse liverJournées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2008, Lille (FR), France |
Topological properties of central tiles and boundary graphsNumber Theory and Ergodic Theory, 2008, Kanazawa, Japan |
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Modélisation multi-organes et multi-espèces du métabolisme des lipides2. Journées d'Animation Scientifique du Département PHASE, Oct 2007, Tours, France |
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Topological properties of central tiles for substitutionsJournées de Numération, Apr 2007, Graz, Austria |
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Qualitative response of interaction networks: application to the validation of biological models6th International Congress on Industrial and Applied Mathematics. ICIAM 07, Jul 2007, Zurich, Switzerland |
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Finiteness properties for Pisot $S$-adic tilingsJournées Montoises d'Informatique Théorique, Aug 2006, RENNES, France |
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Estimating consensus proteomes and metabolic functions from taxonomic affiliations2025 |
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Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes2024 |
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Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium<i>Fibrobacter succinogenes</i>S852022 |
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Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus2021 |
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The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga2019 |
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Combinatorial optimization methods to complete and analyse a metabolic network2015 |
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Purely periodic beta-expansions in the Pisot non-unit case2004 |
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Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in Microcystis-associated microbial communities, in the context of freshwater cyanobacterial bloomsJOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. pp.1-1, 2024 |
Machine Learning classification performance on mechanistic representations of the gut microbiota built from abundance profilesJournées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2022, Rennes, France. , pp.181, 2022, Proceedings |
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Assessment of metabolic complementarity in large-scale microbiotas for the identification of key speciesIHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1 |
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Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone speciesJOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩ |
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Identification of causal signature using omics data integration and network reasoning-based analysisJOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1 |
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Integrative responses of pig adipose tissues to high-fat high-fiber diet: towards key regulators of energy flexibilityASAS/ADSA midwest meeting, Mar 2015, Des Moines, United States. Journal of Animal Science, 93 (Suppl. 2), 2015, Abstract book of the ASAS/ADSA midwest meeting |
Exploring the metabolic flexibility of the mammary gland of dairy cows through flux-balance analysisMeeting of the Animal Science Modelling Group, Jul 2013, Indianapolis, United States. , Canadian Journal of Animal Science, 93 (4), 2013, Canadian Journal of Animal Science |
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Problèmes d'optimisation combinatoire pour l'étude du métabolismeApproches symboliques de la modélisation et de l’analyse des systèmes biologiques, ISTE éditions, 2022, Encyclopédie Sciences, 9781789480290. ⟨10.51926/ISTE.9029.ch2⟩ |
L’écologie des systèmesCNRS éditions. Les big data à découvert, Mokrane Bouzeghoub et Rémy Mosseri, 2017, 978-2-271-11464-8 |
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L'écologie des systèmesMokrane Bouzeghoub et Rémy Mosseri. Les Big Data à Découvert, CNRS éditions, 2017, 978-2-271-11464-8 |
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Reasoning on the response of logical signaling networks with Answer Set ProgrammingLogical Modeling of Biological Systems, Wiley Online Librairy, pp.49-92, 2014, ⟨10.1002/9781119005223.ch2⟩ |
Substitutions, Rauzy fractals and tilingsCambridge University Press. Combinatorics, Automata and Number Theory, 135, Cambridge University Press, 2010, Encyclopedia of Mathematics and its Applications, 9780521515979 |
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A generic stoichiometric model to analyse the metabolic flexibility of the mammary gland in lactating dairy cowsD. Sauvant, J. Van Milgen, P. Faverdin and N. Friggens. Modelling nutrient digestion and utilization in farm animals, Wageningen Academic Publishers, 2010, 978-90-8686-156-9 |
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Basic notions on substitutionsSubstitutions in Dynamics, Arithmetics and Combinatorics, 1794, Springer Verlag, pp.1-32, 2002, Lecture Note Mathematical Series, 978-3-540-44141-0. ⟨10.1007/3-540-45714-3_1⟩ |
Les décodeuses du numériqueCNRS Editions, 2021, 2271139481 |
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Topological properties of Rauzy fractalsSociété Mathématiques de France, 118, pp.144, 2009, Mémoires de la SMF |
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Special Issue: Journées Montoises d'informatique théorique (Rennes, 2006)Caucal, Didier and Siegel, Anne. RAIRO - Theoretical Informatics and Applications, EDP Sciences, RAIRO - Theoretical Informatics and Applications 42(3), pp.240, 2008 |
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Analyse de systèmes dynamiques par discrétisation. Exemples d'applications en théorie des nombres et en biologie moléculaireMathématiques [math]. Université Rennes 1, 2008 |