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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
  • 2C. 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
  • 3P. 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
  • 4J. 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, Lecture Notes in Computer Sciences, September 2017, 17 p.

    https://hal.archives-ouvertes.fr/hal-01559249
  • 5F. 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
  • 6F. Coste, J. Nicolas.

    Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wrocław, Poland, September 2018, vol. 93, pp. 155 - 168.

    https://hal.inria.fr/hal-01872266
  • 7C. Frioux, E. Fremy, C. Trottier, A. Siegel.

    Scalable and exhaustive screening of metabolic functions carried out by microbial consortia, in: Bioinformatics, September 2018, vol. 34, no 17, pp. i934 - i943. [ DOI : 10.1093/bioinformatics/bty588 ]

    https://hal.inria.fr/hal-01871600
  • 8C. Frioux, T. Schaub, S. Schellhorn, A. Siegel, P. Wanko.

    Hybrid Metitebolic Network Completion, in: Theory and Practice of Logic Programming, November 2018, pp. 1-23.

    https://hal.inria.fr/hal-01936778
  • 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
  • 10S. 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

  • 11C. Frioux.

    Investigating host-microbiota cooperation with gap-filling optimization problems, Université de Rennes 1, November 2018.

    https://hal.inria.fr/tel-01945853

Articles in International Peer-Reviewed Journals

  • 12M. Aite, M. Chevallier, C. Frioux, C. Trottier, J. Got, M. P. Cortés, S. N. Mendoza, G. Carrier, O. Dameron, N. Guillaudeux, M. Latorre, N. Loira, G. V. Markov, A. Maass, A. Siegel.

    Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models, in: PLoS Computational Biology, 2018, vol. 14, no 5, e1006146 p. [ DOI : 10.1371/journal.pcbi.1006146 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01807842
  • 13V. Delannée, S. Langouët, A. Siegel, N. Théret.

    In silico prediction of Heterocyclic Aromatic Amines metabolism susceptible to form DNA adducts in humans, in: Toxicology Letters, January 2019, vol. 300, pp. 18-30. [ DOI : 10.1016/j.toxlet.2018.10.011 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01903264
  • 14C. Frioux, E. Fremy, C. Trottier, A. Siegel.

    Scalable and exhaustive screening of metabolic functions carried out by microbial consortia, in: Bioinformatics, September 2018, vol. 34, no 17, pp. i934 - i943. [ DOI : 10.1093/bioinformatics/bty588 ]

    https://hal.inria.fr/hal-01871600
  • 15C. Frioux, T. Schaub, S. Schellhorn, A. Siegel, P. Wanko.

    Hybrid Metabolic Network Completion, in: Theory and Practice of Logic Programming, November 2018, pp. 1-23. [ DOI : 10.1017/S1471068418000455 ]

    https://hal.inria.fr/hal-01936778
  • 16S. Gay, J. Bugeon, A. BOUCHAREB, L. Henry, C. DELAHAYE, F. Legeai, J. Montfort, A. Le Cam, A. Siegel, J. Bobe, V. Thermes.

    MiR-202 controls female fecundity by regulating medaka oogenesis, in: PLoS Genetics, September 2018, vol. 14, no 9, pp. 1-26. [ DOI : 10.1371/journal.pgen.1007593 ]

    https://hal.archives-ouvertes.fr/hal-01871468
  • 17M. Razzaq, L. Paulevé, A. Siegel, J. Saez-Rodriguez, J. Bourdon, C. Guziolowski.

    Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data, in: PLoS Computational Biology, 2018, vol. 14, pp. 1-23. [ DOI : 10.1371/journal.pcbi.1006538 ]

    https://hal.archives-ouvertes.fr/hal-01897020

International Conferences with Proceedings

  • 18P. Boutillier, F. Camporesi, J. Coquet, J. Feret, K. Q. , N. Théret, P. Vignet.

    KaSa A Static Analyzer for Kappa, in: CMSB 2018 - 16th International Conference on Computational Methods in Systems Biology, Brno, Czech Republic, M. Češka, D. Šafránek (editors), LNCS, Springer Verlag, September 2018, vol. 11095, pp. 285-291. [ DOI : 10.1007/978-3-319-99429-1_17 ]

    https://hal-univ-rennes1.archives-ouvertes.fr/hal-01888951
  • 19F. Coste, J. Nicolas.

    Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wrocław, Poland, September 2018, vol. 93, pp. 155 - 168.

    https://hal.inria.fr/hal-01872266
  • 20V. J. Henry, I. Moszer, O. Dameron, M.-C. Potier, M. Hofmann-Apitius, O. Colliot.

    Converting Alzheimer's disease map into a heavyweight ontology: a formal network to integrate data, in: DILS 2018 - 13th International Conference on Data Integration in the Life Sciences, Hannover, Germany, DILS 2018 - 13th International Conference on Data Integration in the Life Sciences, November 2018, pp. 1-9.

    https://hal.archives-ouvertes.fr/hal-01917742
  • 21M. Pyzik, F. Coste, W. Dyrka.

    How to measure the topological quality of protein parse trees?, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wroclaw, Poland, September 2018, vol. 93, pp. 118 - 138.

    https://hal.inria.fr/hal-01938608
  • 22T. Ribeiro, M. Folschette, M. Magnin, O. Roux, K. Inoue.

    Learning Dynamics with Synchronous, Asynchronous and General Semantics, in: 28th International Conference on Inductive Logic Programming, Ferrara, Italy, Inductive Logic Programming, Springer, Cham, September 2018, vol. LNCS, volume 11105. [ DOI : 10.1007/978-3-319-99960-9_8 ]

    https://hal.archives-ouvertes.fr/hal-01826564

Conferences without Proceedings

  • 23L. Bourneuf.

    An Answer Set Programming Environment for High-Level Specification and Visualization of FCA, in: FCA4AI'18 - 6th Workshop «What can FCA do for Artificial Intelligence?», Stockholm, Sweden, July 2018, pp. 1-12.

    https://hal.archives-ouvertes.fr/hal-01945938
  • 24W. Dyrka, F. Coste, H. Talibart.

    Where the context-free grammar meets the contact map: a probabilistic model of protein sequences aware of contacts between amino acids, in: ISMB 2018 - 3DSIG: Structural Bioinformatics and Computational Biophysics, Chicago, United States, July 2018.

    https://hal.inria.fr/hal-01939021
  • 25V. HENRY, I. Moszer, O. Dameron, M.-C. Potier, M. Hofmann-Apitius, O. Colliot.

    Integrating ontological representation and reasoning into a disease map: application to Alzheimer's disease, in: DMCM 2018 - 3rd Disease Maps Community Meeting, Paris, France, June 2018, pp. 1-2.

    https://hal.archives-ouvertes.fr/hal-01873474
  • 26Y. Rivault, O. Dameron, N. Le Meur.

    Ontologies biomédicales et Web Sémantique pour la réutilisation des bases de données médico-administratives en pharmaco-épidémiologie, in: JFO 2018 - 7ème Journées Francophones sur les Ontologies, Hammamet, Tunisia, November 2018, pp. 1-6.

    https://hal.archives-ouvertes.fr/hal-01912046
  • 27Y. Rivault, O. Dameron, N. Le Meur.

    queryMed : enrichissement des données de recherche en pharmaco-épidémiologie, in: Septièmes rencontres R, Rennes, France, July 2018, pp. 1-2.

    https://hal.archives-ouvertes.fr/hal-01834137

Scientific Popularization

  • 28C. Frioux, E. Fremy, C. Trottier, A. Siegel.

    Scalable and exhaustive screening of metabolic functions carried out by microbial consortia, in: European Conference on Computational Biology, Athènes, Greece, September 2018.

    https://hal.inria.fr/hal-01946860

Other Publications

  • 29A. Belcour, J. Girard, M. Aite, L. Delage, C. Trottier, C. Marteau, C. J.-J. Leroux, S. M. Dittami, P. Sauleau, E. Corre, J. Nicolas, C. Boyen, C. Leblanc, J. Collén, A. Siegel, G. V. Markov.

    Inferring biochemical reactions and metabolite structures to cope with metabolic pathway drift, December 2018, working paper or preprint.

    https://hal.inria.fr/hal-01943880
  • 30N. Guillaudeux.

    Prédiction de transcriptome : analyse comparative multi-gènes, orthologues, Univ Rennes ; Inria ; CNRS ; Irisa, June 2018, 42 p.

    https://hal.inria.fr/hal-01948461
  • 31C. Marchet, L. Lecompte, C. Da Silva, C. Cruaud, J.-M. Aury, J. Nicolas, P. Peterlongo.

    CARNAC-LR: De novo Clustering of Gene Expressed Variants in Transcriptomic Long Reads Data Sets, April 2018, pp. 1-2, RECOMB-seq 2018 - Eighth RECOMB Satellite Workshop on Massively Parallel Sequencing, Poster.

    https://hal.archives-ouvertes.fr/hal-01929963
  • 32J. Yon, N. Bareille, B. Bed'Hom, X. Berthelot, S. Combes, O. Dameron, G. Foucras, A. Journaux, F. Launay, P.-Y. Le Bail, N. Le Floc'h, M. Martignon, C. Nédellec, M.-H. Pinard - Van Der Laan, E. Quillet, M.-C. Meunier-Salaün.

    Ontologie ATOL : amélioration de l'outil par l'intégration des caractères de santé, April 2018, Journées d'Animation Scientifique du département Phase (JAS Phase 2018), Poster.

    https://hal.archives-ouvertes.fr/hal-01768063
References in notes
  • 33G. 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
  • 34T. Berners Lee, W. Hall, J. A. Hendler, K. O'Hara, N. Shadbolt, D. J. Weitzner.

    A Framework for Web Science, in: Foundations and Trends in Web Science, 2007, vol. 1, no 1, pp. 1–130.
  • 35S. Blanquart, J.-S. Varré, P. Guertin, A. Perrin, A. Bergeron, K. M. Swenson.

    Assisted transcriptome reconstruction and splicing orthology, in: BMC Genomics, Nov 2016, vol. 17, no 10, 786 p.

    https://doi.org/10.1186/s12864-016-3103-6
  • 36P. 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
  • 37L. 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
  • 38A. 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
  • 39M. 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
  • 40F. Coste, G. Garet, J. Nicolas.

    A bottom-up efficient algorithm learning substitutable languages from positive examples, in: ICGI (International Conference on Grammatical Inference), Kyoto, Japan, A. Clark, M. Kanazawa, R. Yoshinaka (editors), Proceedings of Machine Learning Research, September 2014, vol. 34, pp. 49–63.

    https://hal.inria.fr/hal-01080249
  • 41K. Faust, J. Raes.

    Microbial interactions: from networks to models, in: Nat. Rev. Microbiol., Jul 2012, vol. 10, no 8, pp. 538–550.
  • 42M. Y. Galperin, D. J. Rigden, X. M. Fernández-Suárez.

    The 2015 nucleic acids research database issue and molecular biology database collection, in: Nucleic acids research, 2015, vol. 43, no D1, pp. D1–D5.
  • 43M. 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.
  • 44S. 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
  • 45M. H. Saier, V. S. Reddy, B. V. Tsu, M. S. Ahmed, C. Li, G. Moreno-Hagelsieb.

    The Transporter Classification Database (TCDB): recent advances, in: Nucleic Acids Res., Jan 2016, vol. 44, no D1, pp. D372–379.
  • 46D. B. Searls.

    String variable grammar: A logic grammar formalism for the biological language of DNA, in: The Journal of Logic Programming, 1995, vol. 24, no 1, pp. 73 - 102, Computational Linguistics and Logic Programming. [ DOI : 10.1016/0743-1066(95)00034-H ]

    http://www.sciencedirect.com/science/article/pii/074310669500034H
  • 47Z. 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.
  • 48R. Verborgh, M. Vander Sande, O. Hartig, J. Van Herwegen, L. De Vocht, B. De Meester, G. Haesendonck, P. Colpaert.

    Triple Pattern Fragments: a Low-cost Knowledge Graph Interface for the Web, in: Journal of Web Semantics, March 2016, vol. 37–38, pp. 184–206. [ DOI : doi:10.1016/j.websem.2016.03.003 ]

    http://linkeddatafragments.org/publications/jws2016.pdf