Access content directly

Anne SIEGEL

134
Documents

Publications

Image document

Regulus infers signed regulatory relations from few samples' information using discretization and likelihood constraints

Marine Louarn , Guillaume Collet , Eve Barre , Thierry Fest , Olivier Dameron
PLoS Computational Biology, 2024, 20 (1), pp.e1011816. ⟨10.1371/journal.pcbi.1011816⟩
Journal articles hal-04443527v1
Image document

Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85

Ibrahim Fakih , Jeanne Got , Carlos Eduardo Robles-Rodriguez , Anne Siegel , Evelyne Forano
mSystems, 2023, 8 (3), pp.1-23. ⟨10.1128/msystems.01027-22⟩
Journal articles hal-04131368v1
Image document

Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe

Arnaud Belcour , Jeanne Got , Méziane Aite , Ludovic Delage , Jonas Collén
Genome Research, 2023, 33, pp.972 - 987. ⟨10.1101/gr.277056.122⟩
Journal articles hal-04192851v3
Image document

MERRIN: MEtabolic Regulation Rule INference from time series data

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé
Bioinformatics, 2022, 38 (Supplement_2), pp.ii127-ii133. ⟨10.1093/bioinformatics/btac479⟩
Journal articles hal-03701755v2
Image document

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
Briefings in Bioinformatics, 2022, 23 (4), pp.1-11. ⟨10.1093/bib/bbac212⟩
Journal articles hal-03690604v1
Image document

Improving reusability along the data life cycle: a Regulatory Circuits Case Study

Marine Louarn , Fabrice Chatonnet , Xavier Garnier , Thierry Fest , Anne Siegel
Journal of Biomedical Semantics, 2022, 13 (1), pp.1-11. ⟨10.1186/s13326-022-00266-4⟩
Journal articles hal-03602177v1
Image document

Discrete modeling for integration and analysis of large-scale signaling networks

Pierre Vignet , Jean Coquet , Sébastien Aubert , Matéo Boudet , Anne Siegel
PLoS Computational Biology, inPress, ⟨10.1371/journal.pcbi.1010175⟩
Journal articles hal-03693653v1
Image document

Rumen microbial genomics: from cells to genes (and back to cells)

Milka Popova , Ibrahim Fakih , Evelyne Forano , Anne Siegel , Rafael Muñoz-Tamayo
CAB Reviews Perspectives in Agriculture Veterinary Science Nutrition and Natural Resources, 2022, 2022, ⟨10.1079/cabireviews202217025⟩
Journal articles hal-03929845v1
Image document

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⟩
Journal articles hal-03265223v1
Image document

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
Frontiers in Plant Science, 2021, 12, pp.1-10. ⟨10.3389/fpls.2021.648426⟩
Journal articles hal-03222505v1
Image document

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⟩
Journal articles inserm-03355908v1
Image document

Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines

Elham Karimi , Enora Geslain , Arnaud Belcour , Clémence Frioux , Méziane Aite
PeerJ, 2021, 9, pp.1-24. ⟨10.7717/peerj.11344⟩
Journal articles hal-03223662v1
Image document

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
Nucleic Acids Research, 2021, 49 (D1), pp.D667-D676. ⟨10.1093/nar/gkaa958⟩
Journal articles hal-02988562v1

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⟩
Journal articles hal-02964170v1
Image document

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

Dinka Mandakovic , Ángela Cintolesi , Jonathan Maldonado , Sebastián Mendoza , Méziane Aite
Scientific Reports, 2020, 10 (1), pp.1-12. ⟨10.1038/s41598-020-62130-8⟩
Journal articles hal-02524471v1
Image document

Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

Arnaud Belcour , Clémence Frioux , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand
Journal articles hal-02395024v2
Image document

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⟩
Journal articles hal-02569935v1
Image document

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift

Arnaud Belcour , Jean Girard , Méziane Aite , Ludovic Delage , Camille Trottier
iScience, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩
Journal articles hal-01943880v2
Image document

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
Frontiers in Microbiology, 2020, 11, ⟨10.3389/fmicb.2020.01707⟩
Journal articles hal-02929424v1
Image document

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
Frontiers in Marine Science, 2020, 7, pp.1-11. ⟨10.3389/fmars.2020.00085⟩
Journal articles hal-02866101v2
Image document

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
Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩
Journal articles hal-02395080v1
Image document

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⟩
Journal articles hal-01903264v1
Image document

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⟩
Journal articles hal-02018724v1
Image document

MiR-202 controls female fecundity by regulating medaka oogenesis

Stéphanie Gay , Jérôme Bugeon , Amine Bouchareb , Laure Henry , Clara Delahaye
PLoS Genetics, 2018, 14 (9), pp.1-26. ⟨10.1371/journal.pgen.1007593⟩
Journal articles hal-01871468v1
Image document

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⟩
Journal articles hal-01936778v1

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⟩
Journal articles hal-01871600v1
Image document

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
PLoS Computational Biology, 2018, 14, pp.1-23. ⟨10.1371/journal.pcbi.1006538⟩
Journal articles hal-01897020v1
Image document

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
PLoS Computational Biology, 2018, 14 (5), pp.e1006146. ⟨10.1371/journal.pcbi.1006146⟩
Journal articles hal-01807842v1
Image document

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
BMC Genomics, 2017, 18 (1), pp.244. ⟨10.1186/s12864-017-3639-0⟩
Journal articles hal-01494107v1
Image document

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
PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩
Journal articles 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⟩
Journal articles hal-01552190v1
Image document

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⟩
Journal articles hal-01575579v1

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⟩
Journal articles hal-01196326v1

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
INRA Productions Animales, 2016, 29 (3), pp.201-216. ⟨10.20870/productions-animales.2016.29.3.2960⟩
Journal articles hal-01391135v1

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

Philippe Bordron , Mauricio Latorre , Maria-Paz Cortés , Mauricio Gonzales , Sven Thiele
MicrobiologyOpen, 2016, 5 (1), pp.106-117. ⟨10.1002/mbo3.315⟩
Journal articles hal-01246173v1

Deciphering transcriptional regulations coordinating the response to environmental changes

Vicente Acuña , Andrés Aravena , Carito Guziolowski , Damien Eveillard , Anne Siegel
BMC Bioinformatics, 2016, 17 (1), pp.129-42. ⟨10.1186/s12859-016-0885-0⟩
Journal articles hal-01260866v1
Image document

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
Molecular Reproduction and Development, 2016, ⟨10.1002/mrd.22746⟩
Journal articles hal-01390047v1
Image document

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
BMC Genomics, 2016, 17 (1), pp.120. ⟨10.1186/s12864-016-2438-3⟩
Journal articles hal-01286555v1
Image document

Learning Boolean logic models of signaling networks with ASP

Santiago Videla , Carito Guziolowski , Federica Eduati , Sven Thiele , Martin Gebser
Theoretical Computer Science, 2015, 599, pp.79-101. ⟨10.1016/j.tcs.2014.06.022⟩
Journal articles hal-01058610v1

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⟩
Journal articles hal-01196533v1

Designing experiments to discriminate families of logic models

Santiago Videla , Irina Konokotina , Leonidas Alexopoulos , Julio Saez-Rodriguez , Torsten Schaub
Frontiers in Bioengineering and Biotechnology, 2015, pp.9. ⟨10.3389/fbioe.2015.00131⟩
Journal articles hal-01196178v1

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
Plant Journal, 2014, 80 (2), pp.367-381. ⟨10.1111/tpj.12627⟩
Journal articles hal-01057153v1
Image document

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⟩
Journal articles hal-00947219v1
Image document

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⟩
Journal articles hal-00980499v1

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
Frontiers in Genetics, 2014, 5, pp.117. ⟨10.3389/fgene.2014.00117⟩
Journal articles hal-01079758v1

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⟩
Journal articles hal-01079727v1
Image document

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
Frontiers in Genetics, 2014, 5, pp.241. ⟨10.3389/fgene.2014.00241⟩
Journal articles hal-01079739v1

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

Carito Guziolowski , Santiago Videla , Federica Eduati , Sven Thiele , Thomas Cokelaer
Bioinformatics, 2013, 29 (18), pp.2320-2326. ⟨10.1093/bioinformatics/btt393⟩
Journal articles hal-00853704v1

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⟩
Journal articles hal-00626708v1
Image document

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
OMICS, 2011, 15 (12), pp.883-892. ⟨10.1089/omi.2011.0089⟩
Journal articles hal-00661751v1
Image document

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⟩
Journal articles 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⟩
Journal articles inria-00538136v1
Image document

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⟩
Journal articles hal-00400799v2
Image document

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

Tatiana Baumuratova , Didier Surdez , Bernard Delyon , Gautier Stoll , Olivier Delattre
BMC Systems Biology, 2010, 4 (1), pp.146. ⟨10.1186/1752-0509-4-146⟩
Journal articles inserm-00984711v1

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⟩
Journal articles hal-00486418v1

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
Journal articles inria-00429811v1
Image document

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⟩
Journal articles inria-00429804v1

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⟩
Journal articles inria-00330567v1

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⟩
Journal articles inria-00330578v1
Image document

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
Journal articles inria-00178791v1
Image document

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
Journal articles inria-00178914v1
Image document

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⟩
Journal articles inria-00181997v1
Image document

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⟩
Journal articles inria-00178799v1
Image document

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⟩
Journal articles inria-00178842v1
Image document

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
BioSystems, 2006, 84, pp.153-174
Journal articles inria-00178809v1

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
Journal articles inria-00178819v1
Image document

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
Conference papers hal-04420454v1
Image document

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
International Conference on Clinical Metagenomics, Oct 2022, Geneve, Switzerland
Conference papers hal-04155604v1
Image document

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
Conference papers hal-03689107v2

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

Clémence Frioux , Arnaud Belcour , Meziane Aite , Anthony Bretaudeau , Falk Hildebrand
JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France
Conference papers hal-03440232v1

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

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand
MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27
Conference papers hal-03440221v1
Image document

Learning Boolean controls in regulated metabolic networks: a case-study

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé
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⟩
Conference papers hal-03207589v3

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

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand
CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27
Conference papers hal-03440212v1

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
Conference papers hal-03402155v1

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
Conference papers hal-02412419v1

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
Conference papers hal-02412421v1
Image document

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
Conference papers hal-02401750v1
Image document

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
Conference papers hal-01946860v1

Toward the study of metabolic functions in algal holobionts

Claire Lippold , Camille Trottier , Clémence Frioux , Marie Chevallier , Simon M Dittami
4ème Colloque de Génomique Environnementale, Sep 2017, Marseille, France
Conference papers hal-01576484v1
Image document

AskOmics, a web tool to integrate and query biological data using semantic web technologies

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

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

Valentin Wucher , Fabrice Legeai , Lucas Bourneuf , Thomas Derrien , Aurore Gallot
10th Arthropod Genomics Symposium, Jun 2017, Notre Dame, United States
Conference papers hal-01566438v1
Image document

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
Conference papers hal-01557347v1

Toward a better understanding of the plant microbiota

Victoria Potdevin , Marie Chevallier , Ruben Garrido Oter , Anne Siegel , Stéphane Hacquard
4ème colloque de Génomique Environnementale, GDR Génomique Environnementale, Sep 2017, Marseille, France
Conference papers hal-01576743v1

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
49. Journées de la Recherche Porcine, Jan 2017, Paris, France. pp.13-18
Conference papers hal-01602699v1

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
Conference papers hal-01399456v1
Image document

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
Jobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2016, Lyon, France
Conference papers hal-01377844v1
Image document

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⟩
Conference papers hal-01196152v1

Data integration

Florence Gondret , Isabelle Louveau , Magalie Houee , David Causeur , Anne Siegel
Meeting INRA-ISU, Mar 2015, Ames, United States. 11 diapositives
Conference papers hal-01210940v1
Image document

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⟩
Conference papers hal-01164751v1
Image document

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
Conference papers hal-01196598v1

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
Conference papers hal-01095609v1
Image document

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
Conference papers hal-01079768v1
Image document

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
Conference papers hal-01210385v1
Image document

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
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⟩
Conference papers hal-00737112v2
Image document

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
Conference papers 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 Groisillier
Esil 2012: algal post-genomics, Apr 2012, Roscoff, France
Conference papers hal-00760640v1

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

Martin Gebser , Carito Guziolowski , Mihail Ivanchev , Torsten Schaub , Anne Siegel
Principles of Knowledge Representation and Reasoning, 2010, Toronto, Canada
Conference papers inria-00538137v1

From pure discrete spectrum conditions to topological properties of self-affine tiles

Anne Siegel
Aperiodic Order, Sep 2009, Leceister, United Kingdom
Conference papers inria-00429814v1

Rational numbers with purely periodic beta-expansions

Anne Siegel
Fractals and Tilings, Jul 2009, Strobl, Austria
Conference papers inria-00429815v1

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
AIAI 2009 Workshop -- Workshop on Biomedical Informatics and Intelligent Approaches in the Support of Genomic Medicine (BMIINT), Apr 2009, Thessalonik, Greece. pp.72-87
Conference papers inria-00429801v1
Image document

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

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

Topological properties of central tiles and boundary graphs

Anne Siegel
Number Theory and Ergodic Theory, 2008, Kanazawa, Japan
Conference papers inria-00330588v1
Image document

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
Conference papers inria-00331385v1
Image document

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
Conference papers inria-00178854v1

Topological properties of central tiles for substitutions

Anne Siegel , Jorg Thuswaldner
Journées de Numération, Apr 2007, Graz, Austria
Conference papers inria-00180246v1
Image document

Finiteness properties for Pisot $S$-adic tilings

Pierre Arnoux , Valerie Berthe , Anne Siegel
Journées Montoises d'Informatique Théorique, Aug 2006, RENNES, France
Conference papers inria-00180242v1
Image document

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⟩
Book sections hal-03885249v1

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
Book sections hal-01575603v1

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
Book sections hal-02389705v1
Image document

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⟩
Book sections 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
Book sections 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 Milgen
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
Book sections 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⟩
Book sections lirmm-00268671v1

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
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2022, Rennes, France. , pp.181, 2022, Proceedings
Conference poster hal-04155624v1
Image document

Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species

Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand
IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1
Conference poster hal-03438983v1
Image document

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
JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩
Conference poster hal-03151934v1
Image document

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
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
Conference poster 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
Conference poster hal-01210552v1

Topological properties of Rauzy fractals

Anne Siegel , Jorg Thuswaldner
Société Mathématiques de France, 118, pp.144, 2009, Mémoires de la SMF
Books 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
Books inria-00330569v1