Anne SIEGEL

140
Documents

Publications

Publications

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Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria]{Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline

Noé Robert , Jeanne Got , Pauline Hamon-Giraud , Hélène Falentin , Anne Siegel
2025
Pré-publication, Document de travail hal-05045657 v1
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Estimating consensus proteomes and metabolic functions from taxonomic affiliations

Arnaud Belcour , Pauline Hamon-Giraud , Alice Mataigne , Baptiste Ruiz , Yann Le Cunff et al.
2025
Pré-publication, Document de travail hal-03697249 v2
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Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes

Constanza M Andreani-Gerard , Natalia E Jiménez , Ricardo Palma , Coralie Muller , Pauline Hamon-Giraud et al.
2024
Pré-publication, Document de travail hal-04854948 v1
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Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium<i>Fibrobacter succinogenes</i>S85

Ibrahim Fakih , Jeanne Got , Carlos Eduardo Robles-Rodriguez , Anne Siegel , Evelyne Forano et al.
2022
Pré-publication, Document de travail hal-03871397 v1
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Changing microbial activities during low salinity acclimation in the brown alga Ectocarpus subulatus

Hetty Kleinjan , Gianmaria Caliafano , Méziane Aite , Enora Fremy , Clémence Frioux et al.
2021
Pré-publication, Document de travail hal-03429533 v1
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The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga

Simon M. Dittami , Erwan Corre , Loraine Brillet-Guéguen , Agnieszka Lipinska , Méziane Aite et al.
2019
Pré-publication, Document de travail hal-02333021 v1
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Combinatorial optimization methods to complete and analyse a metabolic network

Julie Laniau , Anne Siegel , Damien Eveillard
2015
Pré-publication, Document de travail hal-01244179 v1
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Purely periodic beta-expansions in the Pisot non-unit case

Valerie Berthe , Anne Siegel
2004
Pré-publication, Document de travail hal-00002208 v1
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Regulus infers signed regulatory relations from few samples&#039; information using discretization and likelihood constraints

Marine Louarn , Guillaume Collet , Eve Barre , Thierry Fest , Olivier Dameron et al.
PLoS Computational Biology, 2024, 20 (1), pp.e1011816. ⟨10.1371/journal.pcbi.1011816⟩
Article dans une revue hal-04443527 v1
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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-Luron et al.
PLoS Computational Biology, 2024, 20 (11), pp.e1012577. ⟨10.1371/journal.pcbi.1012577⟩
Article dans une revue hal-04816962 v1
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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 Siegel et al.
PLoS Computational Biology, 2024, 20 (7), pp.e1011858. ⟨10.1371/journal.pcbi.1011858⟩
Article dans une revue hal-04689199 v1
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Empirical evidence for metabolic drift in plant and algal lipid biosynthesis pathways

Maëlle Zonnequin , Arnaud Belcour , Ludovic Delage , Anne Siegel , Samuel Blanquart et al.
Frontiers in Plant Science, 2024, 15, pp.1339132. ⟨10.3389/fpls.2024.1339132⟩
Article dans une revue (article de synthèse) hal-04473577 v1
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Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium <i>Fibrobacter succinogenes</i> S85

Ibrahim Fakih , Jeanne Got , Carlos Eduardo Robles-Rodriguez , Anne Siegel , Evelyne Forano et al.
mSystems, 2023, 8 (3), pp.1-23. ⟨10.1128/msystems.01027-22⟩
Article dans une revue hal-04131368 v1
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Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Arnaud Belcour , Jeanne Got , Méziane Aite , Ludovic Delage , Jonas Collén et al.
Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩
Article dans une revue hal-04192851 v3
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Rumen microbial genomics: from cells to genes (and back to cells)

Milka Popova , Ibrahim Fakih , Evelyne Forano , Anne Siegel , Rafael Muñoz-Tamayo et 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-03929845 v1
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Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Anna Niarakis , Dagmar Waltemath , James Glazier , Falk Schreiber , Sarah Keating et al.
Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩
Article dans une revue hal-03690604 v1
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Discrete modeling for integration and analysis of large-scale signaling networks

Pierre Vignet , Jean Coquet , Sébastien Aubert , Matéo Boudet , Anne Siegel et al.
PLoS Computational Biology, 2022, 18 (6), pp.e1010175. ⟨10.1371/journal.pcbi.1010175⟩
Article dans une revue hal-03693653 v1
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Improving reusability along the data life cycle: a Regulatory Circuits Case Study

Marine Louarn , Fabrice Chatonnet , Xavier Garnier , Thierry Fest , Anne Siegel et al.
Journal of Biomedical Semantics, 2022, 13 (1), pp.1-11. ⟨10.1186/s13326-022-00266-4⟩
Article dans une revue hal-03602177 v1
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MERRIN: MEtabolic Regulation Rule INference from time series data

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et al.
Bioinformatics, 2022, 38 (Supplement_2), pp.ii127-ii133. ⟨10.1093/bioinformatics/btac479⟩
Article dans une revue hal-03701755 v2
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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 Hoebeke et al.
Nucleic Acids Research, 2021, 49 (D1), pp.D667-D676. ⟨10.1093/nar/gkaa958⟩
Article dans une revue hal-02988562 v1
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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-03355908 v1
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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-03265223 v1
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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 Belcour et al.
Frontiers in Plant Science, 2021, 12, pp.1-10. ⟨10.3389/fpls.2021.648426⟩
Article dans une revue hal-03222505 v1
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Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

Elham Karimi , Enora Geslain , Arnaud Belcour , Clémence Frioux , Méziane Aite et al.
PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩
Article dans une revue hal-03223662 v1
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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 Pittera et al.
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01707⟩
Article dans une revue hal-02929424 v1
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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 Wagner et al.
Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩
Article dans une revue hal-02866101 v2
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Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

Arnaud Belcour , Clémence Frioux , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
Article dans une revue hal-02395024 v2
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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-02569935 v1
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Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

Arnaud Belcour , Jean Girard , Méziane Aite , Ludovic Delage , Camille Trottier et al.
iScience, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩
Article dans une revue hal-01943880 v2

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-02964170 v1
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Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

Dinka Mandakovic , Ángela Cintolesi , Jonathan Maldonado , Sebastián Mendoza , Méziane Aite et al.
Scientific Reports, 2020, 10 (1), pp.1-12. ⟨10.1038/s41598-020-62130-8⟩
Article dans une revue hal-02524471 v1
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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-02018724 v1
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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-01903264 v1
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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-Guéguen et al.
Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩
Article dans une revue hal-02395080 v1
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Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data

Misbah Razzaq , Loïc Paulevé , Anne Siegel , Julio Saez-Rodriguez , Jérémie Bourdon et al.
PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩
Article dans une revue hal-01897020 v1
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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-01936778 v1
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MiR-202 controls female fecundity by regulating medaka oogenesis

Stéphanie Gay , Jérôme Bugeon , Amine Bouchareb , Laure Henry , Clara Delahaye et al.
PLoS Genetics, 2018, 14 (9), pp.1-26. ⟨10.1371/journal.pgen.1007593⟩
Article dans une revue hal-01871468 v1
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Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models

Méziane Aite , Marie Chevallier , Clémence Frioux , Camille Trottier , Jeanne Got et al.
PLoS Computational Biology, 2018, 14 (5), pp.e1006146. ⟨10.1371/journal.pcbi.1006146⟩
Article dans une revue hal-01807842 v1
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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-01871600 v1
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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-01575579 v1
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Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks

Julie Laniau , Clémence Frioux , Jacques Nicolas , Caroline Baroukh , Maria-Paz Cortés et al.
PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩
Article dans une revue hal-01635688 v1
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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 Lagarrigue et al.
BMC Genomics, 2017, 18 (1), pp.244. ⟨10.1186/s12864-017-3639-0⟩
Article dans une revue hal-01494107 v1

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-01552190 v1
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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 Lagarrigue et al.
BMC Genomics, 2016, 17 (1), pp.120. ⟨10.1186/s12864-016-2438-3⟩
Article dans une revue hal-01286555 v1
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Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization

Vincent Picard , Odile Mulner-Lorillon , Jérémie Bourdon , Julia Morales , Patrick Cormier et al.
Molecular Reproduction and Development, 2016, ⟨10.1002/mrd.22746⟩
Article dans une revue hal-01390047 v1

Deciphering transcriptional regulations coordinating the response to environmental changes

Vicente Acuña , Andrés Aravena , Carito Guziolowski , Damien Eveillard , Anne Siegel et al.
BMC Bioinformatics, 2016, 17 (1), pp.129-42. ⟨10.1186/s12859-016-0885-0⟩
Article dans une revue hal-01260866 v1

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 Sauvant et 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-01391135 v1

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

Philippe Bordron , Mauricio Latorre , Maria-Paz Cortés , Mauricio Gonzales , Sven Thiele et al.
MicrobiologyOpen, 2016, 5 (1), pp.106-117. ⟨10.1002/mbo3.315⟩
Article dans une revue hal-01246173 v1
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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-01196326 v1

Designing experiments to discriminate families of logic models

Santiago Videla , Irina Konokotina , Leonidas Alexopoulos , Julio Saez-Rodriguez , Torsten Schaub et al.
Frontiers in Bioengineering and Biotechnology, 2015, pp.9. ⟨10.3389/fbioe.2015.00131⟩
Article dans une revue hal-01196178 v1

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-01196533 v1
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Learning Boolean logic models of signaling networks with ASP

Santiago Videla , Carito Guziolowski , Federica Eduati , Sven Thiele , Martin Gebser et al.
Theoretical Computer Science, 2015, 599, pp.79-101. ⟨10.1016/j.tcs.2014.06.022⟩
Article dans une revue hal-01058610 v1
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Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

Simon M Dittami , Tristan Barbeyron , Catherine Boyen , Jeanne Cambefort , Guillaume Collet et al.
Frontiers in Genetics, 2014, 5, pp.241. ⟨10.3389/fgene.2014.00241⟩
Article dans une revue hal-01079739 v1
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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-00980499 v1

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 Flament et al.
Frontiers in Genetics, 2014, 5, pp.117. ⟨10.3389/fgene.2014.00117⟩
Article dans une revue hal-01079758 v1
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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-00947219 v1
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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-01079727 v1

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 Corny et al.
The Plant Journal, 2014, 80 (2), pp.367-381. ⟨10.1111/tpj.12627⟩
Article dans une revue hal-01057153 v1

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

Carito Guziolowski , Santiago Videla , Federica Eduati , Sven Thiele , Thomas Cokelaer et al.
Bioinformatics, 2013, 29 (18), pp.2320-2326. ⟨10.1093/bioinformatics/btt393⟩
Article dans une revue hal-00853704 v1
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Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.

Thierry Tonon , Damien Eveillard , Sylvain Prigent , Jérémie Bourdon , Philippe Potin et al.
OMICS, 2011, 15 (12), pp.883-892. ⟨10.1089/omi.2011.0089⟩
Article dans une revue hal-00661751 v1

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-00538136 v1
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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-00407999 v2

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-00626708 v1

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-00486418 v1
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Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.

Tatiana Baumuratova , Didier Surdez , Bernard Delyon , Gautier Stoll , Olivier Delattre et al.
BMC Systems Biology, 2010, 4 (1), pp.146. ⟨10.1186/1752-0509-4-146⟩
Article dans une revue inserm-00984711 v1
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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-00400799 v2

Présentation de "Numeration: Mathematics and Computer Science" (CIRM, 2009)

Anne Siegel , Boris Adamczewski , Wolfgang Steiner
Actes des rencontres du CIRM, 2009, 1 (1), pp.1-2
Article dans une revue inria-00429811 v1
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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-00429804 v1

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-00330567 v1

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-00330578 v1
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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-00181997 v1
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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-00178914 v1
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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-00178791 v1
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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 Ouy et al.
BioSystems, 2006, 84, pp.153-174
Article dans une revue inria-00178809 v1
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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-00178842 v1
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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-00178799 v1

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-00178819 v1
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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-04420454 v1
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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 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-03689107 v2
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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-Bataillon et al.
International Conference on Clinical Metagenomics, Oct 2022, Geneve, Switzerland
Communication dans un congrès hal-04155604 v1

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27
Communication dans un congrès hal-03440221 v1

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Clémence Frioux , Arnaud Belcour , Meziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France
Communication dans un congrès hal-03440232 v1

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
Communication dans un congrès hal-03402155 v1

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27
Communication dans un congrès hal-03440212 v1
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Learning Boolean controls in regulated metabolic networks: a case-study

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et al.
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.159-180, ⟨10.1007/978-3-030-85633-5_10⟩
Communication dans un congrès hal-03207589 v3

Genome-scale network recostruction of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85

Ibrahim Fakih , J. Got , Anne Siegel , Evelyne Forano , Rafael Muñoz-Tamayo
12th International Symposium on Gut Microbiology, Oct 2021, Virtual conference, France
Communication dans un congrès hal-04843685 v1
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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-02401750 v1

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-02412421 v1

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-02412419 v1
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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-01946860 v1

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 Lagarrigue et al.
49. Journées de la Recherche Porcine, Jan 2017, Paris, France. pp.13-18
Communication dans un congrès hal-01602699 v1

Toward a better understanding of the plant microbiota

Victoria Potdevin , Marie Chevallier , Ruben Garrido Oter , Anne Siegel , Stéphane Hacquard et al.
4ème colloque de Génomique Environnementale, GDR Génomique Environnementale, Sep 2017, Marseille, France
Communication dans un congrès hal-01576743 v1
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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-01557347 v1
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AskOmics, a web tool to integrate and query biological data using semantic web technologies

Xavier Garnier , Anthony Bretaudeau , Olivier Filangi , Fabrice Legeai , Anne Siegel et al.
JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. pp.1
Communication dans un congrès hal-01577425 v1

Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid

Valentin Wucher , Fabrice Legeai , Lucas Bourneuf , Thomas Derrien , Aurore Gallot et al.
10th Arthropod Genomics Symposium, Jun 2017, Notre Dame, United States
Communication dans un congrès hal-01566438 v1

Toward the study of metabolic functions in algal holobionts

Claire Lippold , Camille Trottier , Clémence Frioux , Marie Chevallier , Simon M Dittami et al.
4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France
Communication dans un congrès hal-01576484 v1

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-01399456 v1
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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 Loira et al.
Jobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2016, Lyon, France
Communication dans un congrès hal-01377844 v1
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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-01196598 v1
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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-01196152 v1

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-01210940 v1
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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-01164751 v1
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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-01079768 v1

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-01095609 v1

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 Groisillier et al.
Esil 2012: algal post-genomics, Apr 2012, Roscoff, France
Communication dans un congrès hal-00760640 v1
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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-00740722 v1
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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 Grabe et 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-00737112 v2
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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 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-01210385 v1

Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming

Martin Gebser , Carito Guziolowski , Mihail Ivanchev , Torsten Schaub , Anne Siegel et al.
Principles of Knowledge Representation and Reasoning, 2010, Toronto, Canada
Communication dans un congrès inria-00538137 v1
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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-00331385 v1

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 Barillot et 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-00429801 v1

Rational numbers with purely periodic beta-expansions

Anne Siegel
Fractals and Tilings, Jul 2009, Strobl, Austria
Communication dans un congrès inria-00429815 v1

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-00429814 v1
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A minimal and dynamic model for fatty acid metabolism in mouse liver

Pierre Blavy , Florence Gondret , Hervé Guillou , Sandrine Lagarrigue , Pascal G.P. Martin et al.
Journées Ouvertes de Biologie, Informatique et Mathématique (JOBIM), Jun 2008, Lille (FR), France
Communication dans un congrès hal-00729742 v1

Topological properties of central tiles and boundary graphs

Anne Siegel
Number Theory and Ergodic Theory, 2008, Kanazawa, Japan
Communication dans un congrès inria-00330588 v1
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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-00178854 v1

Topological properties of central tiles for substitutions

Anne Siegel , Jorg Thuswaldner
Journées de Numération, Apr 2007, Graz, Austria
Communication dans un congrès inria-00180246 v1
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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-00180242 v1
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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-03885249 v1

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-02389705 v1

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-01575603 v1
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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-01079762 v1

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-00538135 v1

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 Milgen et 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-00538138 v1

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-00268671 v1

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-Bataillon et al.
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2022, Rennes, France. , pp.181, 2022, Proceedings
Poster de conférence hal-04155624 v1
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Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand et al.
IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1
Poster de conférence hal-03438983 v1
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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 Hildebrand et al.
JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩
Poster de conférence hal-03151934 v1
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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 Siegel et 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-01210925 v1

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-01210552 v1
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Atelier MoDaL (Multi-Scale Data Links)

Aurélien Cornet , Christian Barillot , Olivier Dameron , Alban Gaignard , Camille Maumet et al.
[Rapport de recherche] IRISA, Inria Rennes. 2020
Rapport (rapport de recherche) inserm-02507799 v4
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État des lieux MoDaL (Multi-Scale Data Links)

Aurélien Cornet , Christian Barillot , Olivier Dameron , Alban Gaignard , Camille Maumet et al.
[Rapport de recherche] IRISA, Inria Rennes. 2020
Rapport (rapport de recherche) hal-02557351 v1
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Modeling local repeats on genomic sequences

Jacques Nicolas , Christine Rousseau , Anne Siegel , Pierre Peterlongo , François Coste et al.
[Research Report] RR-6802, INRIA. 2008, pp.43
Rapport (rapport de recherche) inria-00353690 v1
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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-00145537 v2
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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-00180239 v1
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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-00185038 v1
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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-00071966 v1

Topological properties of Rauzy fractals

Anne Siegel , Jorg Thuswaldner
Société Mathématiques de France, 118, pp.144, 2009, Mémoires de la SMF
Ouvrages inria-00539742 v1

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-00330569 v1