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Bibliography

Major publications by the team in recent years
  • 1C. Belleannée, O. Sallou, J. Nicolas.

    Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling, in: PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Stockholm, Sweden, M. Comin, L. Kall, E. Marchiori, A. Ngom, J. Rajapakse (editors), Springer International Publishing, August 2014, vol. 8626, pp. 34-47. [ DOI : 10.1007/978-3-319-09192-1_4 ]

    https://hal.inria.fr/hal-01059506
  • 2J. Bourdon, D. Eveillard, A. Siegel.

    Integrating quantitative knowledge into a qualitative gene regulatory network, in: PLoS Computational Biology, September 2011, vol. 7, no 9. [ DOI : 10.1371/journal.pcbi.1002157 ]

    http://hal.archives-ouvertes.fr/hal-00626708
  • 3L. Bourneuf, J. Nicolas.

    FCA in a Logical Programming Setting for Visualization-oriented Graph Compression, in: International Conference on Formal Concept Analysis 2017, Rennes, France, Lecture Notes in Computer Sciences, June 2017, vol. 10308. [ DOI : 10.1007/978-3-319-59271-8_6 ]

    https://hal.archives-ouvertes.fr/hal-01558302
  • 4A. Bretaudeau, F. Coste, F. Humily, L. Garczarek, G. Le Corguillé, C. Six, M. Ratin, O. Collin, W. M. Schluchter, F. Partensky.

    CyanoLyase: a database of phycobilin lyase sequences, motifs and functions, in: Nucleic Acids Research, November 2012, vol. 41. [ DOI : 10.1093/nar/gks1091 ]

    http://hal.inria.fr/hal-00760946
  • 5F. Coste, G. Kerbellec.

    A Similar Fragments Merging Approach to Learn Automata on Proteins, in: ECML:Machine Learning: ECML 2005, 16th European Conference on Machine Learning, Porto, Portugal, October 3-7, 2005, Proceedings, J. Gama, R. Camacho, P. Brazdil, A. Jorge, L. Torgo (editors), Lecture Notes in Computer Science, Springer, 2005, vol. 3720, pp. 522-529.
  • 6M. Gebser, C. Guziolowski, M. Ivanchev, T. Schaub, A. Siegel, P. Veber, S. Thiele.

    Repair and Prediction (under Inconsistency) in Large Biological Networks with Answer Set Programming, in: Principles of Knowledge Representation and Reasoning, AAAI Press, 2010.
  • 7C. Guziolowski, S. Videla, F. Eduati, S. Thiele, T. Cokelaer, A. Siegel, J. Saez-Rodriguez.

    Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming, in: Bioinformatics, August 2013, vol. 29, no 18, pp. 2320-2326. [ DOI : 10.1093/bioinformatics/btt393 ]

    http://hal.inria.fr/hal-00853704
  • 8S. Prigent, G. Collet, S. M. Dittami, L. Delage, F. Ethis de Corny, O. Dameron, D. Eveillard, S. Thiele, J. Cambefort, C. Boyen, A. Siegel, T. Tonon.

    The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond, in: Plant Journal, September 2014, pp. 367-81. [ DOI : 10.1111/tpj.12627 ]

    https://hal.archives-ouvertes.fr/hal-01057153
  • 9S. Prigent, C. Frioux, S. M. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, J. Got, D. Eveillard, J. Bourdon, F. Plewniak, T. Tonon, A. Siegel.

    Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, in: PLoS Computational Biology, January 2017, vol. 13, no 1, 32 p. [ DOI : 10.1371/journal.pcbi.1005276 ]

    https://hal.inria.fr/hal-01449100
  • 10C. Rousseau, M. Gonnet, M. Le Romancer, J. Nicolas.

    CRISPI: a CRISPR interactive database, in: Bioinformatics, 2009, vol. 25, no 24, pp. 3317-3318.
  • 11S. Videla, J. Saez-Rodriguez, C. Guziolowski, A. Siegel.

    caspo: a toolbox for automated reasoning on the response of logical signaling networks families, in: Bioinformatics, 2017. [ DOI : 10.1093/bioinformatics/btw738 ]

    https://hal.inria.fr/hal-01426880
Publications of the year

Doctoral Dissertations and Habilitation Theses

Articles in International Peer-Reviewed Journals

  • 16M. P. Cortés, S. N. Mendoza, D. Travisany, A. Gaete, A. Siegel, V. Cambiazo, A. Maass.

    Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing, in: Frontiers in Microbiology, December 2017, vol. 8, 15 p. [ DOI : 10.3389/fmicb.2017.02462 ]

    https://hal.inria.fr/hal-01661270
  • 17V. Delannée, S. Langouët, N. Théret, A. Siegel.

    A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes, in: PeerJ, 2017, vol. 5, e3703 p. [ DOI : 10.7717/peerj.3703 ]

    https://hal.inria.fr/hal-01575579
  • 18F. Gondret, A. Vincent, M. Houée-Bigot, A. Siegel, S. Lagarrigue, D. Causeur, H. H. Gilbert, I. Louveau.

    A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs, in: BMC Genomics, 2017, vol. 18, no 1, 244 p. [ DOI : 10.1186/s12864-017-3639-0 ]

    https://hal.archives-ouvertes.fr/hal-01494107
  • 19J. Laniau, C. Frioux, J. Nicolas, C. Baroukh, M. P. Cortés, J. Got, C. Trottier, D. Eveillard, A. Siegel.

    Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks, in: PeerJ, 2017, vol. 5, e3860 p. [ DOI : 10.7717/peerj.3860 ]

    https://hal.archives-ouvertes.fr/hal-01635688
  • 20V. Picard, A. Siegel, J. Bourdon.

    A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks, in: Journal of computational biology : a journal of computational molecular cell biology, August 2017, vol. 24, no 8, pp. 1–12. [ DOI : 10.1089/cmb.2017.0099 ]

    https://hal.archives-ouvertes.fr/hal-01552190
  • 21S. Prigent, C. Frioux, S. M. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, J. Got, D. Eveillard, J. Bourdon, F. Plewniak, T. Tonon, A. Siegel.

    Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, in: PLoS Computational Biology, January 2017, vol. 13, no 1, 32 p. [ DOI : 10.1371/journal.pcbi.1005276 ]

    https://hal.inria.fr/hal-01449100
  • 22S. Videla, J. Saez-Rodriguez, C. Guziolowski, A. Siegel.

    caspo: a toolbox for automated reasoning on the response of logical signaling networks families, in: Bioinformatics, 2017. [ DOI : 10.1093/bioinformatics/btw738 ]

    https://hal.inria.fr/hal-01426880

Invited Conferences

  • 23V. Wucher, F. Legeai, L. Bourneuf, T. Derrien, A. Gallot, S. Hudaverdian, S. Jaubert-Possamai, N. Leterme-Prunier, J. Nicolas, H. Seitz, A. Siegel, S. TANGUY, G. Le Trionnaire, D. Tagu.

    Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid, in: 10th Arthropod Genomics Symposium, Notre Dame, United States, June 2017.

    https://hal.inria.fr/hal-01566438

International Conferences with Proceedings

  • 25J. Coquet, N. Théret, V. Legagneux, O. Dameron.

    Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-β Signaling, in: CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology, Darmstadt, France, Lecture Notes in Computer Sciences, September 2017, 17 p.

    https://hal.archives-ouvertes.fr/hal-01559249

National Conferences with Proceedings

  • 27P. FINET, B. Gibaud, O. Dameron, R. Le Bouquin Jeannes.

    Interoperable infrastructure and implementation of a health data model for remote monitoring of chronic diseases with comorbidities, in: Journées d'Etude sur la TéléSANté, 6ème edition, Bourges, France, Pôle Capteurs, Université d'Orléans, May 2017.

    https://hal.archives-ouvertes.fr/hal-01565009

Conferences without Proceedings

  • 28X. Garnier, A. Bretaudeau, O. Filangi, F. Legeai, A. Siegel, O. Dameron.

    AskOmics, a web tool to integrate and query biological data using semantic web technologies, in: JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Lille, France, July 2017, 1 p.

    https://hal.inria.fr/hal-01577425
  • 29X. Garnier, O. Dameron, O. Filangi, F. Legeai, A. Bretaudeau.

    Integration of Linked Data into Galaxy using Askomics , in: Galaxy Community Conference, Montpellier, France, June 2017.

    https://hal.inria.fr/hal-01576870
  • 30C. Lippold, C. Trottier, C. Frioux, M. Chevallier, S. M. Dittami, A. Siegel.

    Toward the study of metabolic functions in algal holobionts, in: 4ème Colloque de Génomique Environnementale, Marseille, France, September 2017.

    https://hal.inria.fr/hal-01576484
  • 31V. Potdevin, M. Chevallier, R. Garrido Oter, A. Siegel, S. Hacquard, D. Eveillard, P. Vandenkoornhuyse.

    Toward a better understanding of the plant microbiota, in: 4ème colloque de Génomique Environnementale, Marseille, France, GDR Génomique Environnementale, September 2017.

    https://hal.inria.fr/hal-01576743

Scientific Books (or Scientific Book chapters)

  • 32D. Eveillard, A. Siegel, P. Vandenkoornhuyse.

    L'écologie des systèmes, in: Les Big Data à Découvert, M. Bouzeghoub, R. Mosseri (editors), CNRS éditions, 2017.

    https://hal.inria.fr/hal-01575603

Other Publications

  • 33A. Antoine-Lorquin, A. Arnaoty, S. Asgari, M. Batailler, L. Beauclair, C. Belleannée, S. Bire, N. Buisine, V. Coustham, A. Girault, S. Guyetant, T. Lecomte, B. Piégu, B. Pitard, I. Stévant, Y. Bigot.

    First landscape of binding to chromosomes for a domesticated mariner transposase in the human genome: diversity of genomic targets of SETMAR isoforms in two colorectal cell lines, July 2017, working paper or preprint. [ DOI : 10.1101/115030 ]

    https://hal.archives-ouvertes.fr/hal-01558001
  • 34A. Antoine-Lorquin, F. Mahé, M. Dunthorn, C. Belleannée.

    Detection of mutated primers and impact on targeted metagenomics results, July 2017, working paper or preprint.

    https://hal.archives-ouvertes.fr/hal-01564093
  • 35C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.

    De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets, November 2017, working paper or preprint. [ DOI : 10.1101/170035 ]

    https://hal.archives-ouvertes.fr/hal-01643156
  • 36M. Ruffini.

    Better scoring schemes for the recognition of functional proteins by protomata, Rennes 1, June 2017.

    https://hal.inria.fr/hal-01557941
References in notes
  • 37O. Abdou-Arbi, S. Lemosquet, J. Van Milgen, A. Siegel, J. Bourdon.

    Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs, in: BMC Systems Biology, 2014, vol. 8, no 1, 8 p. [ DOI : 10.1186/1752-0509-8-8 ]

    https://hal.inria.fr/hal-00947219
  • 38V. Acuña, A. Aravena, C. Guziolowski, D. Eveillard, A. Siegel, A. Maass.

    Deciphering transcriptional regulations coordinating the response to environmental changes, in: BMC Bioinformatics, January 2016, vol. 17, no 1, pp. 129-42.

    https://hal.archives-ouvertes.fr/hal-01260866
  • 39V. Acuña, A. Aravena, A. Maass, A. Siegel.

    Modeling parsimonious putative regulatory networks: complexity and heuristic approach, in: 15th conference in Verification, Model Checking, and Abstract Interpretation, San Diego, United States, Springer, 2014, vol. 8318, pp. 322-336. [ DOI : 10.1007/978-3-642-54013-4_18 ]

    https://hal.inria.fr/hal-00926477
  • 40G. Andrieux, M. Le Borgne, N. Théret.

    An integrative modeling framework reveals plasticity of TGF-Beta signaling, in: BMC Systems Biology, 2014, vol. 8, no 1, 30 p. [ DOI : 10.1186/1752-0509-8-30 ]

    http://www.hal.inserm.fr/inserm-00978313
  • 41A. Antoine-Lorquin, F. Mahé, M. Dunthorn, C. Belleannée.

    Detection of mutated primers and impact on targeted metagenomics results, in: RCAM'16 ”Recent Computational Advances in Metagenomics”, The Hague, Netherlands, September 2016.

    https://hal.inria.fr/hal-01576304
  • 42A. Antoine-Lorquin, F. Mahé, M. Dunthorn, C. Belleannée.

    Impact de la recherche d'amorces mutées sur les résultats d'analyses métagénomiques, in: Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Rennes, France, Jobim-2016, Société Française de Bioinformatique (SFBI), June 2016.

    https://hal.archives-ouvertes.fr/hal-01343121
  • 43T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant, L. Clementi, J. Ren, W. W. Li, W. S. Noble.

    MEME Suite: tools for motif discovery and searching, in: Nucleic Acids Research, 2009, vol. 37, no suppl_2, W202 p.

    http://dx.doi.org/10.1093/nar/gkp335
  • 44T. L. Bailey, J. Johnson, C. E. Grant, W. S. Noble.

    The MEME Suite, in: Nucleic Acids Research, 2015, vol. 43, no W1, pp. W39-W49.

    http://dx.doi.org/10.1093/nar/gkv416
  • 45F. Balusson, M.-A. Botrel, O. Dameron, Y. Dauxais, E. Drezen, A. Dupuy, T. Guyet, D. Gross-Amblard, A. Happe, N. Le Meur, B. Le Nautout, E. Leray, E. Nowak, C. Rault, E. Oger, E. Polard.

    PEPS: a platform for supporting studies in pharmaco-epidemiology using medico-administrative databases, in: International Congress on e-Health Research, Paris, France, October 2016.

    https://hal.inria.fr/hal-01380939
  • 46C. Baral.

    Knowledge Representation, Reasoning and Declarative Problem Solving, Cambridge University Press, 2010.
  • 47T. Baumuratova, D. Surdez, B. Delyon, G. Stoll, O. Delattre, O. Radulescu, A. Siegel.

    Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network, in: BMC Systems Biology, 2010, vol. 4, no 1, 146 p. [ DOI : 10.1186/1752-0509-4-146 ]

    http://www.hal.inserm.fr/inserm-00984711
  • 48R. Bellazzi.

    Big Data and Biomedical Informatics: A Challenging Opportunity, in: Yearbook of medical informatics, 2014, vol. 9, no 1, In press.
  • 49R. Bellazzi, M. Diomidous, I. N. Sarkar, K. Takabayashi, A. Ziegler, A. T. McCray.

    Data analysis and data mining: current issues in biomedical informatics, in: Methods of information in medicine, 2011, vol. 50, no 6, pp. 536–544.
  • 50C. Belleannée, O. Sallou, J. Nicolas.

    Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling, in: PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Stockholm, Sweden, M. Comin, L. Kall, E. Marchiori, A. Ngom, J. Rajapakse (editors), Springer International Publishing, August 2014, vol. 8626, pp. 34-47. [ DOI : 10.1007/978-3-319-09192-1_4 ]

    https://hal.inria.fr/hal-01059506
  • 51R. Bellé, S. Prigent, A. Siegel, P. Cormier.

    Model of cap-dependent translation initiation in sea urchin: a step towards the eukaryotic translation regulation network, in: Molecular Reproduction and Development, 2010, vol. 77, no 3, pp. 257-64.
  • 52R. Bendaoud, A. Napoli, Y. Toussaint.

    Formal Concept Analysis: A Unified Framework for Building and Refining Ontologies, in: Knowledge Engineering: Practice and Patterns, 16th International Conference, EKAW 2008, Acitrezza, Italy, September 29 - October 2, 2008. Proceedings, A. Gangemi, J. Euzenat (editors), Lecture Notes in Computer Science, Springer, 2008, vol. 5268, pp. 156-171.

    http://dx.doi.org/10.1007/978-3-540-87696-0_16
  • 53C. Bettembourg, O. Dameron, A. Bretaudeau, F. Legeai.

    AskOmics : Intégration et interrogation de réseaux de régulation génomique et post-génomique, in: IN OVIVE (INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement), Rennes, France, June 2015, 7 p.

    https://hal.inria.fr/hal-01184903
  • 54C. Bettembourg, C. Diot, O. Dameron.

    Semantic particularity measure for functional characterization of gene sets using gene ontology, in: PLoS ONE, 2014, vol. 9, no 1, e86525. [ DOI : 10.1371/journal.pone.0086525 ]

    https://hal.inria.fr/hal-00941850
  • 55C. Bettembourg, C. Diot, O. Dameron.

    Optimal threshold determination for interpreting semantic similarity and particularity, in: PLoS ONE, 2015, vol. 10, no 7, e0133579. [ DOI : 10.1371/journal.pone.0133579 ]

    https://hal.archives-ouvertes.fr/hal-01207763
  • 56C. Bettembourg, C. Diot, O. Dameron.

    Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI, in: PLoS ONE, 2015, 30 p. [ DOI : 10.1371/journal.pone.0133579 ]

    https://hal.inria.fr/hal-01184934
  • 57C. Bizer, T. Heath, T. Berners Lee.

    Linked Data–The story so far, in: International Journal on Semantic Web and Information Systems, 2009, vol. 5, no 3, pp. 1–22.
  • 58J. A. Blake, C. J. Bult.

    Beyond the data deluge: Data integration and bio-ontologies, in: Journal of Biomedical Informatics, 2006, vol. 39, no 3, pp. 314–320.
  • 59P. Blavy, F. Gondret, S. Lagarrigue, J. Van Milgen, A. Siegel.

    Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism, in: BMC Systems Biology, 2014, vol. 8, no 1, 32 p. [ DOI : 10.1186/1752-0509-8-32 ]

    https://hal.inria.fr/hal-00980499
  • 60P. Bordron, D. Eveillard, A. Maass, A. Siegel.

    An ASP application in integrative biology: identification of functional gene units, in: LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Corunna, Spain, September 2013.

    http://hal.inria.fr/hal-00853762
  • 61P. Bordron, M. Latorre, M. P. Cortés, M. Gonzales, S. Thiele, A. Siegel, A. Maass, D. Eveillard.

    Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach, in: MicrobiologyOpen, 2015, vol. 5, no 1, pp. 106-117. [ DOI : 10.1002/mbo3.315 ]

    https://hal.inria.fr/hal-01246173
  • 62A. Bretaudeau, F. Coste, F. Humily, L. Garczarek, G. Le Corguillé, C. Six, M. Ratin, O. Collin, W. M. Schluchter, F. Partensky.

    CyanoLyase: a database of phycobilin lyase sequences, motifs and functions, in: Nucleic Acids Research, November 2012, 6 p. [ DOI : 10.1093/nar/gks1091 ]

    https://hal.inria.fr/hal-01094087
  • 63H. Chen, T. Yu, J. Y. Chen.

    Semantic Web meets Integrative Biology: a survey, in: Briefings in bioinformatics, 2012, vol. 14, no 1, pp. 109–125.
  • 64M. Chevallier, M. Aite, J. Got, G. Collet, N. Loira, M. P. Cortés, C. Frioux, J. Laniau, C. Trottier, A. Maass, A. Siegel.

    Handling the heterogeneity of genomic and metabolic networks data within flexible workflows with the PADMet toolbox, in: Jobim 2016 : 17ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Lyon, France, June 2016.

    https://hal.inria.fr/hal-01377844
  • 65G. Collet, D. Eveillard, M. Gebser, S. Prigent, T. Schaub, A. Siegel, S. Thiele.

    Extending the Metabolic Network of Ectocarpus Siliculosus using Answer Set Programming, in: LPNMR - 12th Conference on Logic Programming and Nonmonotonic Reasoning - 2013, Corunna, Spain, September 2013.

    http://hal.inria.fr/hal-00853752
  • 66F. Coste.

    Learning the Language of Biological Sequences, in: Topics in Grammatical Inference, J. Heinz, J. M. Sempere (editors), Springer-Verlag, 2016. [ DOI : 10.1007/978-3-662-48395-4_8 ]

    https://hal.inria.fr/hal-01244770
  • 67F. Coste, G. Garet, A. Groisillier, J. Nicolas, T. Tonon.

    Automated Enzyme classification by Formal Concept Analysis, in: ICFCA - 12th International Conference on Formal Concept Analysis, Cluj-Napoca, Romania, Springer, June 2014.

    https://hal.inria.fr/hal-01063727
  • 68S. Daminelli, V. J. Haupt, M. Reimann, M. Schroeder.

    Drug repositioning through incomplete bi-cliques in an integrated drug-target-disease network, in: Integr. Biol., 2012, vol. 4, pp. 778-788.

    http://dx.doi.org/10.1039/C2IB00154C
  • 69S. M. Dittami, T. Barbeyron, C. Boyen, J. Cambefort, G. Collet, L. Delage, A. Gobet, A. Groisillier, C. Leblanc, G. Michel, D. Scornet, A. Siegel, J. E. Tapia, T. Tonon.

    Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae, in: Frontiers in Genetics, 2014, vol. 5, 241 p. [ DOI : 10.3389/fgene.2014.00241 ]

    https://hal.inria.fr/hal-01079739
  • 70A. Evrard, C. Bettembourg, M. Jubault, O. Dameron, O. Filangi, A. Bretaudeau, F. F. Legeai.

    Integration and query of biological datasets with Semantic Web technologies: AskOmics, June 2016, Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2016), Poster.

    https://hal.inria.fr/hal-01391087
  • 71R. D. Finn, J. Clements, W. Arndt, B. L. Miller, T. J. Wheeler, F. Schreiber, A. Bateman, S. R. Eddy.

    HMMER web server: 2015 update, in: Nucleic Acids Research, 2015, vol. 43, no W1, W30 p.

    http://dx.doi.org/10.1093/nar/gkv397
  • 72C. Galiez, M. Christophe, F. Coste, P. Baldi.

    VIRALpro: a tool to identify viral capsid and tail sequences, in: Bioinformatics, 2016. [ DOI : 10.1093/bioinformatics/btv727 ]

    https://hal.archives-ouvertes.fr/hal-01242251
  • 73M. Gebser, R. Kaminski, B. Kaufmann, T. Schaub.

    Answer Set Solving in Practice, Synthesis Lectures on Artificial Intelligence and Machine Learning, Morgan and Claypool Publishers, 2012.
  • 74F. Gondret, I. Louveau, M. Houee, D. Causeur, A. Siegel.

    Data integration, in: Meeting INRA-ISU, Ames, United States, March 2015, 11 p.

    https://hal.archives-ouvertes.fr/hal-01210940
  • 75F. Gondret, A. Vincent, M. Houee, S. Lagarrigue, A. Siegel, D. Causeur, I. Louveau.

    Integrative responses of pig adipose tissues to high-fat high-fiber diet: towards key regulators of energy flexibility, March 2015, ASAS/ADSA midwest meeting, Poster.

    https://hal.archives-ouvertes.fr/hal-01210925
  • 76F. Gondret, A. Vincent, M. Houée-Bigot, A. Siegel, S. Lagarrigue, I. Louveau, D. Causeur.

    Molecular alterations induced by a high-fat high-fiber diet in porcine adipose tissues: variations according to the anatomical fat location, in: BMC Genomics, December 2016, vol. 17, no 1, 120 p, article number 120. [ DOI : 10.1186/s12864-016-2438-3 ]

    https://hal.archives-ouvertes.fr/hal-01286555
  • 77C. Guziolowski, A. Bourdé, F. Moreews, A. Siegel.

    BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks, in: Bmc Genomics, 2009, vol. 26, no 10, 244 p. [ DOI : 10.1186/1471-2164-10-244 ]

    http://hal.inria.fr/inria-00429804
  • 78C. Guziolowski, S. Videla, F. Eduati, S. Thiele, T. Cokelaer, A. S. Siegel, J. Saez-Rodriguez.

    Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming, in: Bioinformatics, 2013, vol. 29, pp. 2320-2326. [ DOI : 10.1093/bioinformatics/btt393 ]

    https://hal.inria.fr/hal-00853704v1
  • 79F. Herault, A. Vincent, O. Dameron, P. Le Roy, P. Cherel, M. Damon.

    The longissimus and semimembranosus muscles display marked differences in their gene expression profiles in pig, in: PLoS ONE, 2014, vol. 9, no 5, e96491. [ DOI : 10.1371/journal.pone.0096491 ]

    https://hal.inria.fr/hal-00989635
  • 80R. Kaminski, A. Siegel, T. Schaub, S. Videla.

    Minimal Intervention Strategies in Logical Signaling Networks with ASP, in: Theory and Practice of Logic Programming, September 2013, vol. 13, no Special issue 4-5, pp. 675-690. [ DOI : 10.1017/S1471068413000422 ]

    http://hal.inria.fr/hal-00853747
  • 81H. Klarner, A. Streck, H. Siebert.

    PyBoolNet: a python package for the generation, analysis and visualization of boolean networks, in: Bioinformatics, 2017, vol. 33, no 5, pp. 770-772.

    http://dx.doi.org/10.1093/bioinformatics/btw682
  • 82S. Kurtz.

    The Vmatch large scale sequence analysis software, in: Ref Type: Computer Program, 2003, vol. 412.
  • 83S. Laurent, A. Richard, O. Mulner-Lorillon, J. Morales, D. Flament, V. Glippa, J. Bourdon, P. Gosselin, A. Siegel, P. Cormier, R. Bellé.

    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, in: Frontiers in Genetics, 2014, vol. 5, 117 p. [ DOI : 10.3389/fgene.2014.00117 ]

    https://hal.inria.fr/hal-01079758
  • 84F. Legeai, C. Bettembourg, A. Bretaudeau, Y. Chaussin, O. Dameron, D. Tagu.

    BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interaction, in: XXVth International Congress of Entomology 2016, Orlando, Florida, United States, September 2016.

    https://hal.inria.fr/hal-01391080
  • 85F. Legeai, T. Derrien, V. Wucher, D. Audrey, G. Le Trionnaire, D. Tagu.

    Long non-€coding RNA in the pea aphid; identification and comparative expression in sexual and asexual embryos, in: Arthropod Genomics Symposium, Urbana, United States, June 2014.

    https://hal.inria.fr/hal-01091304
  • 86S.-w. Leung, C. Mellish, D. Robertson.

    Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences, in: Bioinformatics, 2001, vol. 17, no 3, pp. 226-236. [ DOI : 10.1093/bioinformatics/17.3.226 ]

    http://bioinformatics.oxfordjournals.org/content/17/3/226.abstract
  • 87A. Lihonosova, A. Kaminskaya.

    Using Formal Concept Analysis for Finding the Closest Relatives among a Group of Organisms, in: Procedia Computer Science, 2014, vol. 31, no Complete, pp. 860-868.

    http://dx.doi.org/10.1016/j.procs.2014.05.337
  • 88K. M. Livingston, M. Bada, W. A. Baumgartner, L. E. Hunter.

    KaBOB: ontology-based semantic integration of biomedical databases, in: BMC bioinformatics, 2015, vol. 16, 126 p.
  • 89M. Martin.

    Cutadapt removes adapter sequences from high-throughput sequencing reads, in: EMBnet.journal, 2011, vol. 17, no 1, 10 p.

    http://dx.doi.org/10.14806/ej.17.1.200
  • 90N. Messai, M.-D. Devignes, A. Napoli, M. Smail-Tabbone.

    Many-Valued Concept Lattices for Conceptual Clustering and Information Retrieval, in: Proceedings of the 2008 Conference on ECAI 2008: 18th European Conference on Artificial Intelligence, Amsterdam, The Netherlands, The Netherlands, IOS Press, 2008, pp. 127–131.

    http://dl.acm.org/citation.cfm?id=1567281.1567313
  • 91P. T. Monteiro, C. Chaouiya.

    , Efficient Verification for Logical Models of Regulatory NetworksM. P. Rocha, N. Luscombe, F. Fdez-Riverola, J. M. C. Rodríguez (editors), Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 259–267.

    https://doi.org/10.1007/978-3-642-28839-5_30
  • 92J. Nicolas, P. Durand, G. Ranchy, S. Tempel, A.-S. Valin.

    Suffix-Tree Analyser (STAN): looking for nucleotidic and peptidic patterns in genomes, in: Bioinformatics (Oxford, England), 2005, vol. 21(24), pp. 4408-4410.

    https://hal.archives-ouvertes.fr/hal-00015234
  • 93M. Obitko, V. Snásel, J. Smid.

    Ontology Design with Formal Concept Analysis, in: Proceedings of the CLA 2004 International Workshop on Concept Lattices and their Applications, Ostrava, Czech Republic, September 23-24, 2004, V. Snásel, R. Belohlávek (editors), CEUR Workshop Proceedings, CEUR-WS.org, 2004, vol. 110.

    http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-110/paper12.pdf
  • 94M. Ostrowski, L. Paulevé, T. Schaub, A. Siegel, C. Guziolowski.

    Boolean Network Identification from Perturbation Time Series Data combining Dynamics Abstraction and Logic Programming, in: BioSystems, 2016. [ DOI : 10.1016/j.biosystems.2016.07.009 ]

    https://hal.archives-ouvertes.fr/hal-01354075
  • 95V. Picard, O. Mulner-Lorillon, J. Bourdon, J. Morales, P. Cormier, A. Siegel, R. Bellé.

    Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization, in: Molecular Reproduction and Development, 2016. [ DOI : 10.1002/mrd.22746 ]

    http://hal.upmc.fr/hal-01390047
  • 96P.-F. Pluchon, T. Fouqueau, C. Creze, S. Laurent, J. Briffotaux, G. Hogrel, A. Palud, G. Henneke, A. Godfroy, W. Hausner, M. Thomm, J. Nicolas, D. Flament.

    An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs, in: PLoS ONE, 2013, vol. 8, no 11, e79707. [ DOI : 10.1371/journal.pone.0079707 ]

    http://hal.inria.fr/hal-00911795
  • 97S. Prigent, G. Collet, S. M. Dittami, L. Delage, F. Ethis de Corny, O. Dameron, D. Eveillard, S. Thiele, J. Cambefort, C. Boyen, A. Siegel, T. Tonon.

    The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond, in: Plant Journal, September 2014, pp. 367-81. [ DOI : 10.1111/tpj.12627 ]

    https://hal.archives-ouvertes.fr/hal-01057153
  • 98Y. Rivault, N. Le Meur, O. Dameron.

    Complications post-opératoires et mode de prise en charge en angioplastie : apport du Programme de Médicalisation des Systèmes d'Information (PMSI), in: Congrès Adelf-Epiter 2016, Rennes, France, Congrès Adelf-Epiter 2016, September 2016.

    https://hal.inria.fr/hal-01389688
  • 99Y. Rivault, N. Le Meur, O. Dameron.

    La gestion de données médico-administratives grâce aux outils du Web sémantique, in: Journées ADELF-EMOIS “ Système d'information hospitalier et Epidémiologie ”, Dijon, France, Revue d'Épidémiologie et de Santé Publique, March 2016, vol. 64, no Supplement 1, S15 p. [ DOI : 10.1016/j.respe.2016.01.051 ]

    https://hal.archives-ouvertes.fr/hal-01297389
  • 100A. Rosier, P. Mabo, L. Temal, P. Van Hille, O. Dameron, L. Deléger, C. Grouin, P. Zweigenbaum, J. Jacques, E. Chazard, L. Laporte, C. Henry, A. Burgun.

    Personalized and automated remote monitoring of atrial fibrillation, in: EP-Europace, 2016, vol. 18, no 3, pp. 347-352. [ DOI : 10.1093/europace/euv234 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01331019
  • 101A. Rosier, P. Mabo, L. Temal, P. Van Hille, O. Dameron, L. Deléger, C. Grouin, P. Zweigenbaum, J. Jacques, E. Chazard, L. Laporte, C. Henry, A. Burgun.

    Remote Monitoring of Cardiac Implantable Devices: Ontology Driven Classification of the Alerts, in: Studies in Health Technology and Informatics, 2016, vol. 221, pp. 59–63. [ DOI : 10.3233/978-1-61499-633-0-59 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01319949
  • 102M. Rouane-Hacene, M. Huchard, A. Napoli, P. Valtchev.

    Using Formal Concept Analysis for Discovering Knowledge Patterns, in: CLA'10: 7th International Conference on Concept Lattices and Their Applications, Sevilla, Spain, M. Kryszkiewicz, S. Obiedkov (editors), CEUR, University of Sevilla, October 2010, no 672, pp. 223-234.

    http://hal-lirmm.ccsd.cnrs.fr/lirmm-00531802
  • 103C. Rousseau, M. Gonnet, M. Le Romancer, N. Nicolas.

    CRISPI: a CRISPR Interactive database, in: Bioinformatics, 2009, vol. 25, pp. 3317-3318. [ DOI : 10.1093/bioinformatics/btp586 ]

    https://hal.inria.fr/inria-00438512
  • 104L. Royer, M. Reimann, B. Andreopoulos, M. Schroeder.

    Unraveling Protein Networks with Power Graph Analysis, in: PLoS Comput Biol, 07 2008, vol. 4, no 7, e1000108.

    http://dx.plos.org/10.1371%2Fjournal.pcbi.1000108
  • 105M. Ruffini.

    Better scoring schemes for the recognition of functional proteins by protomata, Rennes 1, June 2017.

    https://hal.inria.fr/hal-01557941
  • 106T. Schaub, A. Siegel, S. Videla.

    Reasoning on the response of logical signaling networks with Answer Set Programming, in: Logical Modeling of Biological Systems, Wiley Online Librairy, 2014, pp. 49-92. [ DOI : 10.1002/9781119005223.ch2 ]

    https://hal.inria.fr/hal-01079762
  • 107T. Schaub, S. Thiele.

    Metabolic Network Expansion with Answer Set Programming, in: ICLP 2009, LNCS, Springer, 2009, vol. 5649, pp. 312-326.
  • 108S. Schulz, L. Balkanyi, R. Cornet, O. Bodenreider.

    From Concept Representations to Ontologies: A Paradigm Shift in Health Informatics?, in: Healthcare informatics research, 2013, vol. 19, no 4, pp. 235-242.
  • 109D. Searls.

    The language of genes, in: Nature, 2002, vol. 420, pp. 211-217.
  • 110D. Searls.

    String Variable Grammar: A Logic Grammar Formalism for the Biological Language of DNA, in: Journal of Logic Programming, 1995, vol. 24, no 1&2, pp. 73-102.
  • 111C. J. A. Sigrist, E. de Castro, L. Cerutti, B. A. Cuche, N. Hulo, A. Bridge, L. Bougueleret, I. Xenarios.

    New and continuing developments at PROSITE, in: Nucleic Acids Research, 2013, vol. 41, no D1, D344 p.

    http://dx.doi.org/10.1093/nar/gks1067
  • 112Z. D. Stephens, S. Y. Lee, F. Faghri, R. H. Campbell, C. Zhai, M. J. Efron, R. Iyer, M. C. Schatz, S. Sinha, G. E. Robinson.

    Big Data: Astronomical or Genomical?, in: PLoS biology, 2015, vol. 13, no 7, e1002195 p.
  • 113S. Tempel, C. Rousseau, F. Tahi, J. Nicolas.

    ModuleOrganizer: detecting modules in families of transposable elements, in: BMC Bioinformatics, 2010, vol. 11, 474 p. [ DOI : 10.1186/1471-2105-11-474 ]

    http://hal.inria.fr/inria-00536742
  • 114S. Thiele, J. Saez-Rodriguez, L. Cerone, A. Siegel, C. Guziolowski, S. Klamt.

    Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies, in: BMC Bioinformatics, 2015, vol. 16, 345 p. [ DOI : 10.1186/s12859-015-0733-7 ]

    https://hal.inria.fr/hal-01225228
  • 115S. Videla, C. Guziolowski, F. Eduati, S. Thiele, M. Gebser, J. Nicolas, J. Saez-Rodriguez, T. Schaub, A. Siegel.

    Learning Boolean logic models of signaling networks with ASP, in: Journal of Theoretical Computer Science (TCS), September 2015, no 599, pp. 79-101. [ DOI : 10.1016/j.tcs.2014.06.022 ]

    https://hal.inria.fr/hal-01058610
  • 116S. Videla, I. Konokotina, L. Alexopoulos, J. Saez-Rodriguez, T. Schaub, A. Siegel, C. Guziolowski.

    Designing experiments to discriminate families of logic models, in: Frontiers in Bioengineering and Biotechnology, September 2015, 9 p. [ DOI : 10.3389/fbioe.2015.00131 ]

    https://hal.inria.fr/hal-01196178
  • 117R. Wille.

    restructuring lattice theory: an approach based on hierarchies of concepts, in: Proceedings of the 7th International Conference on Formal Concept Analysis, Berlin, Heidelberg, ICFCA '09, Springer-Verlag, 2009, pp. 314–339.

    http://dx.doi.org/10.1007/978-3-642-01815-2_23
  • 118V. Wucher, D. Tagu, J. Nicolas.

    B. Lausen, S. Krolak-Schwerdt, M. Böhmer (editors), Edge Selection in a Noisy Graph by Concept Analysis – Application to a Genomic Network, Data Science, Learning by Latent Structures, and Knowledge Discovery, Springer, 2014, 550 p.

    https://hal.inria.fr/hal-01093337
  • 119V. Wucher.

    Modeling of a gene network between mRNAs and miRNAs to predict gene functions involved in phenotypic plasticity in the pea aphid, Université Rennes 1, November 2014.

    https://tel.archives-ouvertes.fr/tel-01135870
  • 120V. Wucher.

    Modeling of a gene network between mRNAs and miRNAs to predict gene functions involved in phenotypic plasticity in the pea aphid, Universite Rennes 1, November 2014.

    https://hal.archives-ouvertes.fr/tel-01095967
  • 121T. Yan, D. Yoo, T. Z. Berardini, L. A. Mueller, D. C. Weems, S. Weng, J. M. Cherry, S. Y. Rhee.

    PatMatch: a program for finding patterns in peptide and nucleotide sequences, in: Nucleic Acids Research, 2005, vol. 33, no Web-Server-Issue, pp. 262–266.

    https://doi.org/10.1093/nar/gki368