Anne SIEGEL

Publications

Article dans une revue (83)

Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria Catherine A. Pfister,Johanna Berlinghof,Maximiliana Bogan,Ulisse Cardini,Angelique Gobetet al. MSphere, 2025, 10 (6), pp.e00996--24. ⟨10.1128/msphere.00996-24⟩ Article dans une revue hal-05195842v1
Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria Catherine Pfister,Johanna Berlinghof,Maximiliana Bogan,Ulisse Cardini,Angélique Gobetet al. MSphere, 2025, 10 (6), ⟨10.1128/msphere.00996-24⟩ Article dans une revue hal-05557791v1
Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes Constanza M Andreani-Gerard,Natalia E Jiménez,Ricardo Palma,Coralie Muller,Pauline Hamon-Giraudet al. Environmental Microbiome, 2025, 20 (142), pp.1-19. ⟨10.1186/s40793-025-00749-8⟩ Article dans une revue hal-05368332v1
Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints Marine Louarn,Guillaume Collet,Eve Barre,Thierry Fest,Olivier Dameronet al. PLoS Computational Biology, 2024, 20 (1), pp.e1011816. ⟨10.1371/journal.pcbi.1011816⟩ Article dans une revue hal-04443527v1
Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems France Denoeud,Olivier Godfroy,Corinne Cruaud,Svenja Heesch,Zofia Nehret al. Cell, 2024, 187 (24), pp.6943-6965. ⟨10.1016/j.cell.2024.10.049⟩ Article dans une revue hal-04794231v1
SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects Baptiste Ruiz,Arnaud Belcour,Samuel Blanquart,Sylvie Buffet-Bataillon,Isabelle Luron Le Huërou-Luronet al. PLoS Computational Biology, 2024, 20 (11), pp.e1012577. ⟨10.1371/journal.pcbi.1012577⟩ Article dans une revue hal-04816962v1
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,Jeremy Bomo,Anne Siegelet al. PLoS Computational Biology, 2024, 20 (7), pp.e1011858. ⟨10.1371/journal.pcbi.1011858⟩ Article dans une revue hal-04689199v1
Empirical evidence for metabolic drift in plant and algal lipid biosynthesis pathways Maëlle Zonnequin,Arnaud Belcour,Ludovic Delage,Anne Siegel,Samuel Blanquartet al. Frontiers in Plant Science, 2024, 15, pp.1339132. ⟨10.3389/fpls.2024.1339132⟩ Article dans une revue (article de synthèse) hal-04473577v1
Insights into the potential for mutualistic and harmful host‐microbe interactions affecting brown alga freshwater acclimation Hetty Kleinjan,Clémence Frioux,Gianmaria Califano,Méziane Aite,Enora Fremyet al. Molecular Ecology, In press, 32 (3), pp.703-723. ⟨10.1111/mec.16766⟩ Article dans une revue hal-03868898v1
Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium &lt;i&gt;Fibrobacter succinogenes&lt;/i&gt; S85 Ibrahim Fakih,Jeanne Got,Carlos Eduardo Robles-Rodriguez,Anne Siegel,Evelyne Foranoet al. mSystems, 2023, 8 (3), pp.1-23. ⟨10.1128/msystems.01027-22⟩ Article dans une revue hal-04131368v1
Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe Arnaud Belcour,Jeanne Got,Méziane Aite,Ludovic Delage,Jonas Collénet al. Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩ Article dans une revue hal-04192851v3
Rumen microbial genomics: from cells to genes (and back to cells) Milka Popova,Ibrahim Fakih,Evelyne Forano,Anne Siegel,Rafael Muñoz-Tamayoet al. CAB Reviews Perspectives in Agriculture Veterinary Science Nutrition and Natural Resources, 2022, 2022, ⟨10.1079/cabireviews202217025⟩ Article dans une revue (article de synthèse) hal-03929845v1
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology Anna Niarakis,Dagmar Waltemath,James Glazier,Falk Schreiber,Sarah Keatinget al. Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩ Article dans une revue hal-03690604v1
Discrete modeling for integration and analysis of large-scale signaling networks Pierre Vignet,Jean Coquet,Sébastien Aubert,Matéo Boudet,Anne Siegelet al. PLoS Computational Biology, 2022, 18 (6), pp.e1010175. ⟨10.1371/journal.pcbi.1010175⟩ Article dans une revue hal-03693653v1
Improving reusability along the data life cycle: a Regulatory Circuits Case Study Marine Louarn,Fabrice Chatonnet,Xavier Garnier,Thierry Fest,Anne Siegelet al. Journal of Biomedical Semantics, 2022, 13 (1), pp.1-11. ⟨10.1186/s13326-022-00266-4⟩ Article dans une revue hal-03602177v1
MERRIN: MEtabolic Regulation Rule INference from time series data Kerian Thuillier,Caroline Baroukh,Alexander Bockmayr,Ludovic Cottret,Loïc Paulevéet al. Bioinformatics, 2022, 38 (Supplement_2), pp.ii127-ii133. ⟨10.1093/bioinformatics/btac479⟩ Article dans une revue hal-03701755v2
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 Farrant,Mark Hoebekeet al. Nucleic Acids Research, 2021, 49 (D1), pp.D667-D676. ⟨10.1093/nar/gkaa958⟩ Article dans une revue hal-02988562v1
Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA Mael Conan,Nathalie Theret,Sophie Langouet,Anne Siegel BMC Bioinformatics, 2021, 22 (1), pp.1-26. ⟨10.1186/s12859-021-04363-6⟩ Article dans une revue inserm-03355908v1
Semi-Quantitative Targeted Gas Chromatography-Mass Spectrometry Profiling Supports a Late Side-Chain Reductase Cycloartenol-to-Cholesterol Biosynthesis Pathway in Brown Algae Jean Girard,Goulven Lanneau,Ludovic Delage,Cédric Leroux,Arnaud Belcouret al. Frontiers in Plant Science, 2021, 12, pp.1-10. ⟨10.3389/fpls.2021.648426⟩ Article dans une revue hal-03222505v1
PAX2GRAPHML: a Python library for large-scale regulation network analysis using BIOPAX François Moreews,Hugo Simon,Anne Siegel,Florence Gondret,Emmanuelle Becker Bioinformatics, 2021, 37 (24), pp.4889-4891. ⟨10.1093/bioinformatics/btab441⟩ Article dans une revue hal-03265223v1
Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines Elham Karimi,Enora Geslain,Arnaud Belcour,Clémence Frioux,Méziane Aiteet al. PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩ Article dans une revue hal-03223662v1
Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803 Ulysse Guyet,Ngoc Thanh Nguyen,Hugo Doré,Julie Haguait,Justine Pitteraet al. Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01707⟩ Article dans une revue hal-02929424v1
Metabolic Complementarity Between a Brown Alga and Associated Cultivable Bacteria Provide Indications of Beneficial Interactions Bertille Burgunter-Delamare,Hetty Kleinjan,Clémence Frioux,Enora Fremy,Margot Wagneret al. Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩ Article dans une revue hal-02866101v2
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species Arnaud Belcour,Clémence Frioux,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. eLife, 2020, 9, ⟨10.7554/eLife.61968⟩ Article dans une revue hal-02395024v2
The genome of Ectocarpus subulatus – A highly stress-tolerant brown alga Simon M. Dittami,Erwan Corre,Loraine Brillet-Guéguen,Agnieszka Lipinska,Noé Pontoizeauet al. Marine Genomics, 2020, 52, pp.100740. ⟨10.1016/j.margen.2020.100740⟩ Article dans une revue hal-02866117v1
Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions Clémence Frioux,Simon Dittami,Anne Siegel Biochemical Society Transactions, 2020, 48 (3), pp.901-913. ⟨10.1042/BST20190667⟩ Article dans une revue hal-02569935v1
Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift Arnaud Belcour,Jean Girard,Méziane Aite,Ludovic Delage,Camille Trottieret al. iScience, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩ Article dans une revue hal-01943880v2
Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment Dinka Mandakovic,Ángela Cintolesi,Jonathan Maldonado,Sebastián Mendoza,Méziane Aiteet al. Scientific Reports, 2020, 10 (1), pp.1-12. ⟨10.1038/s41598-020-62130-8⟩ Article dans une revue hal-02524471v1
Innovative Approach to Predict DNA Adduct Formation of Environnemental Contaminants Maël Conan,Sophie Langouët,Anne Siegel,Nathalie Theret Environmental and Molecular Mutagenesis, 2020, 61 (S1), pp.58. ⟨10.1002/em.22405⟩ Article dans une revue hal-02964170v1
Formalizing and enriching phenotype signatures using Boolean networks Méline Wery,Olivier Dameron,Jacques Nicolas,Elisabeth Rémy,Anne Siegel Journal of Theoretical Biology, 2019, 467, pp.66-79. ⟨10.1016/j.jtbi.2019.01.015⟩ Article dans une revue hal-02018724v1
In silico prediction of Heterocyclic Aromatic Amines metabolism susceptible to form DNA adducts in humans Victorien Delannée,Sophie Langouët,Anne Siegel,Nathalie Théret Toxicology Letters, 2019, 300, pp.18-30. ⟨10.1016/j.toxlet.2018.10.011⟩ Article dans une revue hal-01903264v1
Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus Delphine Nègre,Méziane Aite,Arnaud Belcour,Clémence Frioux,Loraine Brillet-Guéguenet al. Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩ Article dans une revue hal-02395080v1
Hybrid Metabolic Network Completion Clémence Frioux,Torsten Schaub,Sebastian Schellhorn,Anne Siegel,Philipp Wanko Theory and Practice of Logic Programming, 2018, pp.1-23. ⟨10.1017/S1471068418000455⟩ Article dans une revue hal-01936778v1
Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data Misbah Razzaq,Loïc Paulevé,Anne Siegel,Julio Saez-Rodriguez,Jérémie Bourdonet al. PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩ Article dans une revue hal-01897020v1
MiR-202 controls female fecundity by regulating medaka oogenesis Stéphanie Gay,Jérôme Bugeon,Amine Bouchareb,Laure Henry,Clara Delahayeet al. PLoS Genetics, 2018, 14 (9), pp.1-26. ⟨10.1371/journal.pgen.1007593⟩ Article dans une revue hal-01871468v1
Traceability, reproducibility and wiki-exploration for &quot;à-la-carte&quot; reconstructions of genome-scale metabolic models Méziane Aite,Marie Chevallier,Clémence Frioux,Camille Trottier,Jeanne Gotet al. PLoS Computational Biology, 2018, 14 (5), pp.e1006146. ⟨10.1371/journal.pcbi.1006146⟩ Article dans une revue hal-01807842v1
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia Clémence Frioux,Enora Fremy,Camille Trottier,Anne Siegel Bioinformatics, 2018, 34 (17), pp.i934-i943. ⟨10.1093/bioinformatics/bty588⟩ Article dans une revue hal-01871600v1
Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks Julie Laniau,Clémence Frioux,Jacques Nicolas,Caroline Baroukh,Maria-Paz Cortéset al. PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩ Article dans une revue hal-01635688v1
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks Vincent Picard,Anne Siegel,Jérémie Bourdon Journal of Computational Biology, 2017, 24 (8), pp.1--12. ⟨10.1089/cmb.2017.0099⟩ Article dans une revue hal-01552190v1
Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing Maria-Paz Cortés,Sebastián N. Mendoza,Dante Travisany,Alexis Gaete,Anne Siegelet al. Frontiers in Microbiology, 2017, 8, pp.15. ⟨10.3389/fmicb.2017.02462⟩ Article dans une revue hal-01661270v1
A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs Florence Gondret,Annie Vincent,Magalie Houée-Bigot,Anne Siegel,Sandrine Lagarrigueet al. BMC Genomics, 2017, 18 (1), pp.244. ⟨10.1186/s12864-017-3639-0⟩ Article dans une revue hal-01494107v1
A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes Victorien Delannée,Sophie Langouët,Nathalie Théret,Anne Siegel PeerJ, 2017, 5, pp.e3703. ⟨10.7717/peerj.3703⟩ Article dans une revue hal-01575579v1
caspo: a toolbox for automated reasoning on the response of logical signaling networks families Santiago Videla,Julio Saez-Rodriguez,Carito Guziolowski,Anne Siegel Bioinformatics, 2017, ⟨10.1093/bioinformatics/btw738⟩ Article dans une revue hal-01426880v1
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks Sylvain Prigent,Clémence Frioux,Simon M Dittami,Sven Thiele,Abdelhalim Larhlimiet al. PLoS Computational Biology, 2017, 13 (1), pp.32. ⟨10.1371/journal.pcbi.1005276⟩ Article dans une revue hal-01449100v1
Deciphering transcriptional regulations coordinating the response to environmental changes Vicente Acuña,Andrés Aravena,Carito Guziolowski,Damien Eveillard,Anne Siegelet al. BMC Bioinformatics, 2016, 17 (1), pp.129-42. ⟨10.1186/s12859-016-0885-0⟩ Article dans une revue hal-01260866v1
Modélisation de la flexibilité métabolique : vers une meilleure compréhension des capacités adaptatives de l’animal Masoomeh Taghipoor,Sophie Lemosquet,Jaap J. van Milgen,Anne Siegel,Daniel Sauvantet al. INRA Productions Animales, 2016, 29 (3), pp.201-216. ⟨10.20870/productions-animales.2016.29.3.2960⟩ Article dans une revue (article de synthèse) hal-01391135v1
Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach Philippe Bordron,Mauricio Latorre,Maria-Paz Cortés,Mauricio Gonzales,Sven Thieleet al. MicrobiologyOpen, 2016, 5 (1), pp.106-117. ⟨10.1002/mbo3.315⟩ Article dans une revue hal-01246173v1
Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization Vincent Picard,Odile Mulner-Lorillon,Jérémie Bourdon,Julia Morales,Patrick Cormieret al. Molecular Reproduction and Development, 2016, ⟨10.1002/mrd.22746⟩ Article dans une revue hal-01390047v1
Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location Florence Gondret,Annie Vincent,Magalie Houée-Bigot,Anne Siegel,Sandrine Lagarrigueet al. BMC Genomics, 2016, 17 (1), pp.120. ⟨10.1186/s12864-016-2438-3⟩ Article dans une revue hal-01286555v1
Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming Max Ostrowski,Loïc Paulevé,Torsten Schaub,Anne Siegel,Carito Guziolowski BioSystems, 2016, ⟨10.1016/j.biosystems.2016.07.009⟩ Article dans une revue hal-01354075v1
A combinatorial approach to products of Pisot substitutions Valérie Berthé,Jérémie Bourdon,Timo Jolivet,Anne Siegel Ergodic Theory and Dynamical Systems, 2016, 36 (6), pp.1757-1794. ⟨10.1017/etds.2014.141⟩ Article dans une revue hal-01196326v1
Multivariate Normal Approximation for the Stochastic Simulation Algorithm: Limit Theorem and Applications Vincent Picard,Anne Siegel,Jérémie Bourdon Electronic Notes in Theoretical Computer Science, 2015, 316C, pp.67-82. ⟨10.1016/j.entcs.2015.06.011⟩ Article dans une revue hal-01196533v1
Designing experiments to discriminate families of logic models Santiago Videla,Irina Konokotina,Leonidas Alexopoulos,Julio Saez-Rodriguez,Torsten Schaubet al. Frontiers in Bioengineering and Biotechnology, 2015, pp.9. ⟨10.3389/fbioe.2015.00131⟩ Article dans une revue hal-01196178v1
Learning Boolean logic models of signaling networks with ASP Santiago Videla,Carito Guziolowski,Federica Eduati,Sven Thiele,Martin Gebseret al. Theoretical Computer Science, 2015, 599, pp.79-101. ⟨10.1016/j.tcs.2014.06.022⟩ Article dans une revue hal-01058610v1
Modelization of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive Sébastien Laurent,Adrien Richard,Odile Mulner-Lorillon,Julia Morales,Didier Flamentet al. Frontiers in Genetics, 2014, 5, pp.117. ⟨10.3389/fgene.2014.00117⟩ Article dans une revue hal-01079758v1
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 J. van Milgen,Anne Siegel BMC Systems Biology, 2014, 8 (1), pp.32. ⟨10.1186/1752-0509-8-32⟩ Article dans une revue hal-00980499v1
Genome and metabolic network of &quot;Candidatus Phaeomarinobacter ectocarpi&quot; Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae Simon M Dittami,Tristan Barbeyron,Catherine Boyen,Jeanne Cambefort,Guillaume Colletet al. Frontiers in Genetics, 2014, 5, pp.241. ⟨10.3389/fgene.2014.00241⟩ Article dans une revue hal-01079739v1
Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs Oumarou Abdou-Arbi,Sophie Lemosquet,Jaap J. van Milgen,Anne Siegel,Jérémie Bourdon BMC Systems Biology, 2014, 8 (1), pp.8. ⟨10.1186/1752-0509-8-8⟩ Article dans une revue hal-00947219v1
Connectedness of fractals associated with Arnoux–Rauzy substitutions Valérie Berthé,Timo Jolivet,Anne Siegel RAIRO - Theoretical Informatics and Applications (RAIRO: ITA), 2014, 48 (3), pp.249-266. ⟨10.1051/ita/2014008⟩ Article dans une revue hal-01079727v1
The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond. Sylvain Prigent,Guillaume Collet,Simon M Dittami,Ludovic Delage,Floriane Ethis de Cornyet al. The Plant Journal, 2014, 80 (2), pp.367-381. ⟨10.1111/tpj.12627⟩ Article dans une revue hal-01057153v1
Minimal Intervention Strategies in Logical Signaling Networks with ASP Roland Kaminski,Anne Siegel,Torsten Schaub,Santiago Videla Theory and Practice of Logic Programming, 2013, 29th International Conference on Logic Programming, 13 (Special issue 4-5.), pp.675-690. ⟨10.1017/S1471068413000422⟩ Article dans une revue hal-00853747v1
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming Carito Guziolowski,Santiago Videla,Federica Eduati,Sven Thiele,Thomas Cokelaeret al. Bioinformatics, 2013, 29 (18), pp.2320-2326. ⟨10.1093/bioinformatics/btt393⟩ Article dans une revue hal-00853704v1
Substitutive Arnoux-rauzy sequences have pure discrete spectrum Valérie Berthé,Timo Jolivet,Anne Siegel Uniform Distribution Theory, 2012, 7 (1), pp.173-197 Article dans une revue hal-00750209v1
Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment. Thierry Tonon,Damien Eveillard,Sylvain Prigent,Jérémie Bourdon,Philippe Potinet al. OMICS, 2011, 15 (12), pp.883-892. ⟨10.1089/omi.2011.0089⟩ Article dans une revue hal-00661751v1
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 Radulescuet al. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, 8 (5), pp.1223-1234. ⟨10.1109/TCBB.2010.71⟩ Article dans une revue inria-00538134v1
Fractal tiles associated with shift radix systems Valerie Berthe,Anne Siegel,Wolfgang Steiner,Paul Surer,Jörg Thuswaldner Advances in Mathematics, 2011, 226 (1), pp.139-175. ⟨10.1016/j.aim.2010.06.010⟩ Article dans une revue hal-00407999v2
Genetically regulated metabolic networks: Gale-Nikaido modules and differential inequalities Ovidiu Radulescu,Anne Siegel,Elisabeth Pecou,Clément Chatelain,Sandrine Lagarrigue Transactions on Computational Systems Biology, 2011, Transactions on Computational Systems Biology XIII, 6575 (Lecture Notes in Computer Science 6575), pp.110-130. ⟨10.1007/978-3-642-19748-2_6⟩ Article dans une revue istex inria-00538136v1
Integrating quantitative knowledge into a qualitative gene regulatory network. Jérémie Bourdon,Damien Eveillard,Anne Siegel PLoS Computational Biology, 2011, 7 (9), pp.e1002157. ⟨10.1371/journal.pcbi.1002157⟩ Article dans une revue hal-00626708v1
Model of cap-dependent translation initiation in sea urchin: a step towards the eukaryotic translation regulation network. Robert Bellé,Sylvain Prigent,Anne Siegel,Patrick Cormier Molecular Reproduction and Development, 2010, 77 (3), pp.257-64. ⟨10.1002/mrd.21142⟩ Article dans une revue istex hal-00486418v1
Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network. Tatiana Baumuratova,Didier Surdez,Bernard Delyon,Gautier Stoll,Olivier Delattreet al. BMC Systems Biology, 2010, 4 (1), pp.146. ⟨10.1186/1752-0509-4-146⟩ Article dans une revue inserm-00984711v1
Rational numbers with purely periodic $\beta$-expansion Boris Adamczewski,Christiane Frougny,Anne Siegel,Wolfgang Steiner Bulletin of the London Mathematical Society, 2010, 42 (3), pp.538-552. ⟨10.1112/blms/bdq019⟩ Article dans une revue hal-00400799v2
Présentation de &quot;Numeration: Mathematics and Computer Science&quot; (CIRM, 2009) Anne Siegel,Boris Adamczewski,Wolfgang Steiner Actes des rencontres du CIRM, 2009, 1 (1), pp.1-2 Article dans une revue inria-00429811v1
BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks Carito Guziolowski,Annabel Bourdé,François Moreews,Anne Siegel BMC Genomics, 2009, 26 (10), pp.244. ⟨10.1186/1471-2164-10-244⟩ Article dans une revue inria-00429804v1
Inferring the role of transcription factors in regulatory networks Philippe Veber,Carito Guziolowski,Michel Le Borgne,Ovidiu Radulescu,Anne Siegel BMC Bioinformatics, 2008, 9, ⟨10.1186/1471-2105-9-228⟩ Article dans une revue inria-00330578v1
Boundary of central tiles associated with Pisot beta-numeration and purely periodic expansions Shigeki Akiyama,Guy Barat,Valerie Berthe,Anne Siegel Monatshefte für Mathematik, 2008, 155 (3-4), pp.377-419. ⟨10.1007/s00605-008-0009-7⟩ Article dans une revue inria-00330567v1
Purely Periodic beta-Expansions in the Pisot Non-unit Case Valerie Berthe,Anne Siegel Journal of Number Theory, 2007, 127 (2), pp.153-172. ⟨10.1016/j.jnt.2007.07.005⟩ Article dans une revue inria-00181997v1
Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study Carito Guziolowski,Philippe Veber,Michel Le Borgne,Ovidiu Radulescu,Anne Siegel Journal of Biological Physics and Chemistry, 2007, 7, pp.37-43 Article dans une revue inria-00178914v1
Optimiser un plan d'expérience à partir de modèles qualitatifs? Anne Siegel,Carito Guziolowski,Philippe Veber,Ovidiu Radulescu,Michel Le Borgne Biofutur, 2007, 275, pp.27-31 Article dans une revue inria-00178791v1
Topology and static response of interaction networks in molecular biology Ovidiu Radulescu,Sandrine Lagarrigue,Anne Siegel,Philippe Veber,Michel Le Borgne Journal of the Royal Society Interface, 2006, 3 (6), pp.185 - 196. ⟨10.1098/rsif.2005.0092⟩ Article dans une revue inria-00178842v1
Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks Anne Siegel,Ovidiu Radulescu,Michel Le Borgne,Philippe Veber,Julien Ouyet al. BioSystems, 2006, 84, pp.153-174 Article dans une revue inria-00178809v1
Fractal representation of the attractive lamination of an automorphism of the free group Pierre Arnoux,Valerie Berthe,Arnaud Hilion,Anne Siegel Annales de l'Institut Fourier, 2006, 56 (7), pp.2161-2212. ⟨10.5802/aif.2237⟩ Article dans une revue inria-00178799v1
Complex Qualitative Models in Biology: a new approach Philippe Veber,Michel Le Borgne,Anne Siegel,Sandrine Lagarrigue,Ovidiu Radulescu Complexus, 2005, 2, pp.140-151 Article dans une revue inria-00178819v1
Tilings Associated with Beta-numeration and Substitutions Valerie Berthe,Anne Siegel Integers : Electronic Journal of Combinatorial Number Theory, 2005, Proceedings of the 2004 Number Theoretic Algorithms and Related Topics Workshop, 5 (3), pp.A2 Article dans une revue lirmm-00105299v1

Communication dans un congrès (55)

Evidencing strain-dependency of metabolic pathways within 1,494 lactic bacteria genomes with the in silico screening Prolipipe pipeline Noé Robert,Jeanne Got,Pauline Hamon-Giraud,Hélène Falentin,Anne Siegel JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Romain Bourqui; Clémence Frioux; Simon Labarthe, Jul 2025, Bordeaux, France Communication dans un congrès hal-05045657v4
Metagenomic taxonomic assignment using Nanopore reads, reconstruction of metabolic networks and prediction of metabolite production Lune Angevin,Pierre Peterlongo,Riccardo Vicedomini,Anne Siegel,Jeanne Gotet al. 2025 - Journées Nutrition et Ecosystèmes Microbiens, May 2025, Rennes, France Communication dans un congrès hal-05384891v1
Methods for a species-specific genome-scale metabolic model designed for eukaryotes and applied to the Ascophyllum nodosum macroalga Pauline Hamon-Giraud,Benoît Bergk Pinto,Jeanne Got,Coralie Rousseau,Erwan Correet al. JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.109-117 Communication dans un congrès hal-05374724v1
CEGAR-Based Approach for Solving Combinatorial Optimization Modulo Quantified Linear Arithmetics Problems Kerian Thuillier,Anne Siegel,Loïc Paulevé AAAI 2024 - The 38th Annual AAAI Conference on Artificial Intelligence, Feb 2024, Vancouver, Canada. pp.1-8 Communication dans un congrès hal-04420454v1
Contributions des entrées sur les sorties pour les réseaux métaboliques sur génomes entiers: performances et utilisation pour des études en nutrition humaine Oumarou Abdou Arbi,Anne Siegel,Jérémie Bourdon CARI 2022 - Colloque Africain sur la Recherche en Informatique et en Mathématiques Appliquées, Oct 2022, Yaoundé, Cameroun. pp.1-12 Communication dans un congrès hal-03689107v2
Highlighting discriminating functional annotations in patients' gut microbiota through Machine Learning classification applied to functional descriptions of the microbiome Baptiste Ruiz,Arnaud Belcour,Samuel Blanquart,Isabelle Luron Le Huërou-Luron,Sylvie Buffet-Bataillonet al. International Conference on Clinical Metagenomics, Oct 2022, Geneve, Switzerland Communication dans un congrès hal-04155604v1
Genome-scale network reconstruction of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85 Fakih Ibrahim,Jeanne Got,Anne Siegel,Evelyne Forano,Rafael Munoz Tamayo 2021 - 12th International Symposium on Gut Microbiology, INRAE ; Rowett Institute UK, Oct 2021, En ligne, France. pp.1 P; Communication dans un congrès hal-03402155v1
Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux,Arnaud Belcour,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27 Communication dans un congrès hal-03440212v1
Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux,Arnaud Belcour,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27 Communication dans un congrès hal-03440221v1
Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux,Arnaud Belcour,Meziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France Communication dans un congrès hal-03440232v1
Learning Boolean controls in regulated metabolic networks: a case-study Kerian Thuillier,Caroline Baroukh,Alexander Bockmayr,Ludovic Cottret,Loïc Paulevéet al. CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, 2021, Bordeaux, France. pp.159-180, ⟨10.1007/978-3-030-85633-5_10⟩ Communication dans un congrès hal-03207589v3
Increasing life science resources re-usability using Semantic Web technologies Marine Louarn,Fabrice Chatonnet,Xavier Garnier,Thierry Fest,Anne Siegelet al. eScience 2019 - 15th International eScience Conference, Sep 2019, San Diego, United States. pp.1-9 Communication dans un congrès hal-02274982v1
AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resources Xavier Garnier,Anthony Bretaudeau,Fabrice Legeai,Anne Siegel,Olivier Dameron JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1 Communication dans un congrès hal-02401750v1
Learning boolean regulations based on prior-knowledge data: a logical-based viewpoint Anne Siegel SASB 2019 - 10th International Workshop on Static Analysis for Systems Biology, Oct 2019, Porto, Portugal Communication dans un congrès hal-02412421v1
Using automated reasoning to explore unconventional organisms: a first step to explore host-microbial interactions Anne Siegel MPA 2019 - Conference on Metabolic Pathway Analysis, Aug 2019, Riga, Latvia Communication dans un congrès hal-02412419v1
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia Clémence Frioux,Enora Fremy,Camille Trottier,Anne Siegel ECCB - 2018 - 17th European Conference on Computational Biology, Sep 2018, Athènes, Greece. pp.i934-i943, ⟨10.1093/bioinformatics/bty588⟩ Communication dans un congrès hal-01946860v1
Identification des fonctions biologiques, spécifiques d’un tissu ou partagées entre tissus, associées aux différences d’efficacité alimentaire chez le porc en croissance Florence Gondret,Annie Vincent,Magalie Houee,Anne Siegel,Sandrine Lagarrigueet al. 49. Journées de la Recherche Porcine, Jan 2017, Paris, France. pp.13-18 Communication dans un congrès hal-01602699v1
Toward a better understanding of the plant microbiota Victoria Potdevin,Marie Chevallier,Ruben Garrido Oter,Anne Siegel,Stéphane Hacquardet al. 4ème colloque de Génomique Environnementale, GDR Génomique Environnementale, Sep 2017, Marseille, France Communication dans un congrès hal-01576743v1
Hybrid Metabolic Network Completion Clémence Frioux,Torsten Schaub,Sebastian Schellhorn,Anne Siegel,Philipp Wanko 14th International Conference on Logic Programming and Nonmonotonic Reasoning - LPNMR 2017, Jul 2017, Espoo, Finland. pp.308-321 Communication dans un congrès hal-01557347v1
Toward the study of metabolic functions in algal holobionts Claire Lippold,Camille Trottier,Clémence Frioux,Marie Chevallier,Simon M Dittamiet al. 4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France Communication dans un congrès hal-01576484v1
AskOmics, a web tool to integrate and query biological data using semantic web technologies Xavier Garnier,Anthony Bretaudeau,Olivier Filangi,Fabrice Legeai,Anne Siegelet al. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. pp.1 Communication dans un congrès hal-01577425v1
Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid Valentin Wucher,Fabrice Legeai,Lucas Bourneuf,Thomas Derrien,Aurore Gallotet al. 10th Arthropod Genomics Symposium, Jun 2017, Notre Dame, United States Communication dans un congrès hal-01566438v1
A system biology loop for the identification of boolean networks to model signaling networks. Anne Siegel European Conference on Mathematical and Theoretical Biology, 2016, Nottingham, France Communication dans un congrès hal-01399456v1
Handling the heterogeneity of genomic and metabolic networks data within flexible workflows with the PADMet toolbox Marie Chevallier,Méziane Aite,Jeanne Got,Guillaume Collet,Nicolas Loiraet al. Jobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2016, Lyon, France Communication dans un congrès hal-01377844v1
Decidability Problems for Self-induced Systems Generated by a Substitution Timo Jolivet,Anne Siegel MCU 2015 : Machines, Computation and Universality, 2015, Famagusta, Cyprus. ⟨10.1007/978-3-319-23111-2⟩ Communication dans un congrès hal-01196152v1
Data integration Florence Gondret,Isabelle Louveau,Magalie Houee,David Causeur,Anne Siegel Meeting INRA-ISU, Mar 2015, Ames, United States. 11 diapositives Communication dans un congrès hal-01210940v1
Boolean Network Identification from Multiplex Time Series Data Max Ostrowski,Loïc Paulevé,Torsten Schaub,Anne Siegel,Carito Guziolowski CMSB 2015 - 13th conference on Computational Methods for Systems Biology, Sep 2015, Nantes, France. pp.170-181, ⟨10.1007/978-3-319-23401-4_15⟩ Communication dans un congrès hal-01164751v1
A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks Vincent Picard,Anne Siegel,Jérémie Bourdon IJCAI workshop BAI: Bioinformatics and Artificial Intelligence, 2015, Buenos Aeres, Argentina Communication dans un congrès hal-01196598v1
Modeling parsimonious putative regulatory networks: complexity and heuristic approach Vicente Acuña,Andrés Aravena,Alejandro Maass,Anne Siegel 15th conference in Verification, Model Checking, and Abstract Interpretation, 2014, San Diego, United States. pp.322-336, ⟨10.1007/978-3-642-54013-4_18⟩ Communication dans un congrès hal-00926477v1
Multivariate Normal Approximation for the Stochastic Simulation Algorithm: limit theorem and applications Vincent Picard,Anne Siegel,Jérémie Bourdon SASB - 5th International Workshop on Static Analysis and Systems Biology, 2014, Munchen, Germany Communication dans un congrès hal-01079768v1
Using ASP to integrate large-scale heterogeneous information about the response of a biological system Anne Siegel 5th Workshop on Logic and Systems Biology (associated with CSL/LICS 2014), Jul 2014, VIenna, Austria Communication dans un congrès hal-01095609v1
Improving robustness in the study of logical model of signalling networks with answer set programming Anne Siegel,Carito Guziolowski,Santiago Videla,Torsten Schaub ECCB 2014 - Workshop on Logical Modelling and Analysis of Cellular Networks, Sep 2014, Strasbourg, France Communication dans un congrès hal-01095607v1
Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming Guillaume Collet,Damien Eveillard,Martin Gebser,Sylvain Prigent,Torsten Schaubet al. LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain Communication dans un congrès hal-00853752v1
Extending the Metabolic Network of &lt;em&gt;Ectocarpus Siliculosus&lt;/em&gt; Using Answer Set Programming Guillaume Collet,Damien Eveillard,Martin Gebser,Sylvain Prigent,Torsten Schaubet al. LPNMR, 2013, ⟨10.1007/978-3-642-40564-8_25⟩ Communication dans un congrès istex hal-02745669v1
An ASP application in integrative biology: identification of functional gene units Philippe Bordron,Damien Eveillard,Alejandro Maass,Anne Siegel,Sven Thiele LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Sep 2013, Corunna, Spain Communication dans un congrès hal-00853762v1
Extracting robust information from knowledge and observations on a biological system: a formal system framework Anne Siegel PRIB - Eighth IAPR International Conference on Pattern Recognition in Bioinformatics - 2013, Jun 2013, Nice, France Communication dans un congrès hal-00853839v1
Generating discrete planes with substitutions Valerie Berthe,Jérémie Bourdon,Timo Jolivet,Anne Siegel WORDS - 9th International Conference on Words - 2013, Sep 2013, Turku, Finland Communication dans un congrès hal-00853758v1
Using large scale knowledge database about reactions and regulations to find key regulators of sets of genes Pierre Blavy,Florence Gondret,Sandrine Lagarrigue,Jaap J. van Milgen,Anne Siegel JOBIM 2012, Inria, 2012, Rennes, France. pp.123-132 Communication dans un congrès hal-00750512v1
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 Grabeet al. CMSB - 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⟩ Communication dans un congrès hal-00737112v2
Using Mutual Information and Answer Set Programming to refine PWM based transcription regulation network Andres Aravena,Carito Guziolowski,Anne Siegel,Alejandro Maass Jobim 2012, Jul 2012, Rennes, France. pp.171 Communication dans un congrès hal-00740722v1
Systems biology approaches at cellular level in the model organism Ectocarpus siliculosus to better understand brown algal physiology Thierry Tonon,Patricia Bonin,Sylvain Prigent,Z. Shao,Agnès Groisillieret al. Esil 2012: algal post-genomics, Apr 2012, Roscoff, France Communication dans un congrès hal-00760640v1
Exploitation à large échelle de bases de données de connaissance sur les réactions et régulations pour trouver des régulateurs clés de groupe de gènes Pierre Blavy,Florence Gondret,Sandrine Lagarrigue,Jaap J. van Milgen,Anne Siegel Journées ouvertes en biologie, informatique et mathématiques, Jul 2012, Rennes, France. pp.161-170 Communication dans un congrès hal-01210385v1
A new method for modeling reactions and regulations to analyze high-throughout data Pierre Blavy,Florence Gondret,Sven Thiele,Carito Guziolowski,Sandrine Lagarrigueet al. 4. International Symposium on Animal Functional Genomics, Sorcha De Gras; Sorcha De Gras, Oct 2011, Dublin, Ireland Communication dans un congrès hal-02748096v1
Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming Martin Gebser,Carito Guziolowski,Mihail Ivanchev,Torsten Schaub,Anne Siegelet al. Principles of Knowledge Representation and Reasoning, 2010, Toronto, Canada Communication dans un congrès inria-00538137v1
CURATING A LARGE-SCALE REGULATORY NETWORK BY EVALUATING ITS CONSISTENCY WITH EXPRESSION DATASETS Carito Guziolowski,Jérémy Gruel,Ovidiu Radulescu,Anne Siegel CIBB 2008: COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS, Oct 2008, Salerno, Italy. pp.144-155 Communication dans un congrès inria-00331385v1
Method for Relating Inter-patient Gene Copy Numbers Variations with Gene Expression via Gene Influence Networks Sylvain Blachon,Gautier Stoll,Carito Guziolowski,Andrei Zinovyev,Emmanuel Barillotet al. AIAI 2009 Workshop -- Workshop on Biomedical Informatics and Intelligent Approaches in the Support of Genomic Medicine (BMIINT), Apr 2009, Thessalonik, Greece. pp.72-87 Communication dans un congrès inria-00429801v1
Rational numbers with purely periodic beta-expansions Anne Siegel Fractals and Tilings, Jul 2009, Strobl, Austria Communication dans un congrès inria-00429815v1
La calculette métabolique&quot;: une approche de modélisation biochimique pour explorer les contraintes au sein du métabolisme des mammifères Oumarou Abdou-Arbi,Jérémie Bourdon,Anne Siegel,Jaap J. van Milgen,Sophie Lemosquet 3. Journées d’Animation Scientifique du Département de Physiologie Animale et Systèmes d’Elevage, Oct 2009, Tours, France Communication dans un congrès hal-02758027v1
From pure discrete spectrum conditions to topological properties of self-affine tiles Anne Siegel Aperiodic Order, Sep 2009, Leceister, United Kingdom Communication dans un congrès inria-00429814v1
A minimal and dynamic model for fatty acid metabolism in mouse liver Pierre Blavy,Florence Gondret,Hervé Guillou,Sandrine Lagarrigue,Pascal G.P. Martinet al. Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2008, Lille (FR), France Communication dans un congrès hal-00729742v1
Topological properties of central tiles and boundary graphs Anne Siegel Number Theory and Ergodic Theory, 2008, Kanazawa, Japan Communication dans un congrès inria-00330588v1
Qualitative response of interaction networks: application to the validation of biological models Anne Siegel,Carito Guziolowski,Philippe Veber,Ovidiu Radulescu,Michel Le Borgne 6th International Congress on Industrial and Applied Mathematics. ICIAM 07, Jul 2007, Zurich, Switzerland Communication dans un congrès inria-00178854v1
Topological properties of central tiles for substitutions Anne Siegel,Jorg Thuswaldner Journées de Numération, Apr 2007, Graz, Austria Communication dans un congrès inria-00180246v1
Modélisation multi-organes et multi-espèces du métabolisme des lipides Pierre Blavy,Anne Siegel,Ovidiu Radulescu,Florence Gondret,Jaap J. van Milgenet al. 2. Journées d'Animation Scientifique du Département PHASE, Oct 2007, Tours, France Communication dans un congrès hal-02756643v1
Finiteness properties for Pisot $S$-adic tilings Pierre Arnoux,Valerie Berthe,Anne Siegel Journées Montoises d'Informatique Théorique, Aug 2006, RENNES, France Communication dans un congrès inria-00180242v1

Pré-publication, Document de travail (7)

Estimating consensus proteomes and metabolic functions from taxonomic affiliations Arnaud Belcour,Pauline Hamon-Giraud,Alice Mataigne,Baptiste Ruiz,Yann Le Cunffet al. 2025 Pré-publication, Document de travail hal-03697249v2
Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes Constanza M Andreani-Gerard,Natalia E Jiménez,Ricardo Palma,Coralie Muller,Pauline Hamon-Giraudet al. 2024 Pré-publication, Document de travail hal-04854948v1
Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium&lt;i&gt;Fibrobacter succinogenes&lt;/i&gt;S85 Ibrahim Fakih,Jeanne Got,Carlos Eduardo Robles-Rodriguez,Anne Siegel,Evelyne Foranoet al. 2022 Pré-publication, Document de travail hal-03871397v1
Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus Hetty Kleinjan,Gianmaria Caliafano,Méziane Aite,Enora Fremy,Clémence Friouxet al. 2021 Pré-publication, Document de travail hal-03429533v1
The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga Simon M. Dittami,Erwan Corre,Loraine Brillet-Guéguen,Agnieszka Lipinska,Méziane Aiteet al. 2019 Pré-publication, Document de travail hal-02333021v1
Combinatorial optimization methods to complete and analyse a metabolic network Julie Laniau,Anne Siegel,Damien Eveillard 2015 Pré-publication, Document de travail hal-01244179v1
Purely periodic beta-expansions in the Pisot non-unit case Valerie Berthe,Anne Siegel 2004 Pré-publication, Document de travail hal-00002208v1

Poster de conférence (7)

Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in Microcystis-associated microbial communities, in the context of freshwater cyanobacterial blooms Juliette Audemard,Sébastien Halary,Gabriel Markov,Jeanne Got,Anne Siegelet al. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. pp.1-1, 2024 Poster de conférence hal-04654522v1
Machine Learning classification performance on mechanistic representations of the gut microbiota built from abundance profiles Baptiste Ruiz,Arnaud Belcour,Samuel Blanquart,Isabelle Luron Le Huërou-Luron,Sylvie Buffet-Bataillonet al. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2022, Rennes, France. , pp.181, 2022, Proceedings Poster de conférence hal-04155624v1
Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species Clémence Frioux,Arnaud Belcour,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1 Poster de conférence hal-03438983v1
Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species Arnaud Belcour,Clémence Frioux,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩ Poster de conférence hal-03151934v1
Identification of causal signature using omics data integration and network reasoning-based analysis Méline Wery,Emmanuelle Becker,Franck Auge,Charles Bettembourg,Olivier Dameronet al. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1 Poster de conférence hal-02193860v1
Integrative responses of pig adipose tissues to high-fat high-fiber diet: towards key regulators of energy flexibility Florence Gondret,Annie Vincent,Magalie Houee,Sandrine Lagarrigue,Anne Siegelet al. ASAS/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 Poster de conférence hal-01210925v1
Exploring the metabolic flexibility of the mammary gland of dairy cows through flux-balance analysis Sophie Lemosquet,O. Abdou Arbi,Jaap J. van Milgen,Anne Siegel,J. Bourdon Meeting of the Animal Science Modelling Group, Jul 2013, Indianapolis, United States. , Canadian Journal of Animal Science, 93 (4), 2013, Canadian Journal of Animal Science Poster de conférence hal-01210552v1

Chapitre d'ouvrage (7)

Problèmes d'optimisation combinatoire pour l'étude du métabolisme Clémence Frioux,Anne Siegel Approches symboliques de la modélisation et de l’analyse des systèmes biologiques, ISTE éditions, 2022, Encyclopédie Sciences, 9781789480290. ⟨10.51926/ISTE.9029.ch2⟩ Chapitre d'ouvrage hal-03885249v1
L’écologie des systèmes Damien Eveillard,Anne Siegel,Philippe Vandenkoornhuyse CNRS éditions. Les big data à découvert, Mokrane Bouzeghoub et Rémy Mosseri, 2017, 978-2-271-11464-8 Chapitre d'ouvrage hal-02389705v1
L'écologie des systèmes Damien Eveillard,Anne Siegel,Philippe Vandenkoornhuyse Mokrane Bouzeghoub et Rémy Mosseri. Les Big Data à Découvert, CNRS éditions, 2017, 978-2-271-11464-8 Chapitre d'ouvrage hal-01575603v1
Reasoning on the response of logical signaling networks with Answer Set Programming Torsten Schaub,Anne Siegel,Santiago Videla Logical Modeling of Biological Systems, Wiley Online Librairy, pp.49-92, 2014, ⟨10.1002/9781119005223.ch2⟩ Chapitre d'ouvrage hal-01079762v1
Substitutions, Rauzy fractals and tilings Valerie Berthe,Anne Siegel,Jorg Thuswaldner Cambridge University Press. Combinatorics, Automata and Number Theory, 135, Cambridge University Press, 2010, Encyclopedia of Mathematics and its Applications, 9780521515979 Chapitre d'ouvrage inria-00538135v1
A generic stoichiometric model to analyse the metabolic flexibility of the mammary gland in lactating dairy cows Sophie Lemosquet,Oumarou Abdou-Arbi,Anne Siegel,Jocelyne Guinard-Flament,Jaap J. van Milgenet al. D. 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 Chapitre d'ouvrage inria-00538138v1
Basic notions on substitutions Valerie Berthe,Anne Siegel Substitutions 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⟩ Chapitre d'ouvrage istex lirmm-00268671v1

Ouvrages (3)

Les décodeuses du numérique Léa Castor,Célia Esnoult,Laure Thiébault,Ali Charara,Olivier Serreet al. CNRS Editions, 2021, 2271139481 Ouvrages hal-03661197v1
Topological properties of Rauzy fractals Anne Siegel,Jorg Thuswaldner Société Mathématiques de France, 118, pp.144, 2009, Mémoires de la SMF Ouvrages inria-00539742v1
Special Issue: Journées Montoises d'informatique théorique (Rennes, 2006) Didier Caucal,Anne Siegel Caucal, Didier and Siegel, Anne. RAIRO - Theoretical Informatics and Applications, EDP Sciences, RAIRO - Theoretical Informatics and Applications 42(3), pp.240, 2008 Ouvrages inria-00330569v1

Rapport (7)

Atelier MoDaL (Multi-Scale Data Links) Aurélien Cornet,Christian Barillot,Olivier Dameron,Alban Gaignard,Camille Maumetet al. [Rapport de recherche] IRISA, Inria Rennes. 2020 Rapport (rapport de recherche) inserm-02507799v4
État des lieux MoDaL (Multi-Scale Data Links) Aurélien Cornet,Christian Barillot,Olivier Dameron,Alban Gaignard,Camille Maumetet al. [Rapport de recherche] IRISA, Inria Rennes. 2020 Rapport (rapport de recherche) hal-02557351v1
Modeling local repeats on genomic sequences Jacques Nicolas,Christine Rousseau,Anne Siegel,Pierre Peterlongo,François Costeet al. [Research Report] RR-6802, INRIA. 2008, pp.43 Rapport (rapport de recherche) inria-00353690v1
Boundary of central tiles associated with Pisot beta-numeration and purely periodic expansions Shigeki Akiyama,Guy Barat,Valerie Berthe,Anne Siegel [Research Report] 2007 Rapport (rapport de recherche) inria-00180239v1
Checking Consistency Between Expression Data and Large Scale Regulatory Networks: A Case Study Carito Guziolowski,Philippe Veber,Michel Le Borgne,Ovidiu Radulescu,Anne Siegel [Research Report] RR-6190, INRIA. 2007, pp.14 Rapport (rapport de recherche) inria-00145537v2
Inferring the role of transcription factors in regulatory networks Philippe Veber,Carito Guziolowski,Michel Le Borgne,Ovidiu Radulescu,Anne Siegel [Research Report] 2007 Rapport (rapport de recherche) inria-00185038v1
Purely Periodic beta-Expansions in the Pisot Non-unit Case Valerie Berthe,Anne Siegel [Research Report] RR-4619, INRIA. 2002 Rapport (rapport de recherche) inria-00071966v1

HDR (1)

Analyse de systèmes dynamiques par discrétisation. Exemples d'applications en théorie des nombres et en biologie moléculaire Anne Siegel Mathématiques [math]. Université Rennes 1, 2008 HDR tel-00358996v1