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Article dans une revue16 documents

  • Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, et al.. Learning Boolean logic models of signaling networks with ASP. Journal of Theoretical Computer Science (TCS), Elsevier, 2015, pp.79-101. <10.1016/j.tcs.2014.06.022>. <hal-01058610>
  • Jacques Nicolas, Catherine Belleannée, François Coste. Le langage des molécules du vivant. Bibliothèque Tangente, Editions Pôle Paris, 2014, pp.8. <hal-01100051>
  • Pierre-François Pluchon, Thomas Fouqueau, Christophe Crezé, Sébastien Laurent, Julien Briffotaux, et al.. An Extended Network of Genomic Maintenance in the Archaeon Pyrococcus abyssi Highlights Unexpected Associations between Eucaryotic Homologs. PLoS ONE, Public Library of Science, 2013, 8 (11), pp.e79707. <10.1371/journal.pone.0079707>. <hal-00911795>
  • Jacques Nicolas. Décoder le vivant. Interstices, INRIA, 2010, <>. <hal-01350190>
  • Klau Gunnar, Jacques Nicolas. Introduction Special Theme Computational Biology. ERCIM News, ERCIM, 2010, Special Theme Computational Biology, <>. <inria-00537580>
  • Fabrice Legeai, Guillaume Rizk, Thomas Walsh, Owain Edwards, Karl Gordon, et al.. Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum.. BMC Genomics, BioMed Central, 2010, 11 (1), pp.281. <10.1186/1471-2164-11-281>. <inserm-00482283>
  • Sebastien Tempel, Christine Rousseau, Fariza Tahi, Jacques Nicolas. ModuleOrganizer: detecting modules in families of transposable elements.. BMC Bioinformatics, BioMed Central, 2010, 11, pp.474. <10.1186/1471-2105-11-474>. <inria-00536742>
  • Jacques Nicolas. Décoder le vivant. Doc Sciences, Édition du CRDP de l'académie de Versailles, 2009, Le numérique et les sciences du vivant, pp.26-33. <inria-00438517>
  • Yves Bigot, Sylvaine Renault, Jacques Nicolas, Corinne Moundras, Marie-Véronique Demattei, et al.. Symbiotic Virus at the Evolutionary Intersection of Three Types of Large DNA Viruses; Iridoviruses, Ascoviruses, and Ichnoviruses. PLoS ONE, Public Library of Science, 2009, 4 (7), pp.e6397. <10.1371/journal.pone.0006397>. <inria-00448730>
  • Christine Rousseau, Mathieu Gonnet, Marc Le Romancer, Jacques Nicolas. CRISPI: a CRISPR Interactive database. Bioinformatics, Oxford University Press (OUP), 2009, 25 (24), pp.3317-3318. <>. <10.1093/bioinformatics/btp586>. <inria-00438512>
  • Sébastien Tempel, Jacques Nicolas, Abdelhak El Amrani, Ivan Couée. Model-based Identification of Helitrons Results in a New Classification of Their Families in Arabidopsis thaliana. Gene, Elsevier, 2007, 403 (1-2), <10.1016/j.gene.2007.06.030>. <inria-00180376>
  • Sébastien Tempel, Mathieu Giraud, Dominique Lavenier, Israël-César Lerman, Anne-Sophie Valin, et al.. Domain organization within repeated DNA sequences: application to the study of a family of transposable elements.. Bioinformatics (Oxford, England), 2006, 22(16), pp.1948-1954. <hal-00090517>
  • Patrick Durand, Frédéric Mahé, Anne-Sophie Valin, Jacques Nicolas. Browsing repeats in genomes : Pygram and an application to non-coding region analysis.. BMC Bioinformatics, BioMed Central, 2006, 7, 477 (17p.). <hal-00129773>
  • Jacques Nicolas, Patrick Durand, Grégory Ranchy, Sébastien Tempel, Anne-Sophie Valin. Suffix-Tree Analyser (STAN): looking for nucleotidic and peptidic patterns in genomes. Bioinformatics (Oxford, England), 2005, 21(24), pp.4408-4410. <hal-00015234>
  • Pascale Quignon, Mathieu Giraud, Maud Rimbault, Patricia Lavigne, Sandrine Tacher, et al.. The dog and rat olfactory receptor repertoires. Genome Biology, BioMed Central, 2005, 6 (10), pp.R83. <10.1186/gb-2005-6-10-r83>. <hal-00107100>
  • Olivier Gascuel, Bernadette Bouchon-Meunier, Gilles Caraux, Patrick Gallinari, Alain Guénoche, et al.. Twelve numerical, symbolic and hybrid supervised classification methods. International Journal of Pattern Recognition and Artificial Intelligence, World Scientific Publishing, 1998, 12 (5), pp.517-572. <10.1142/S0218001498000336>. <hal-01184805>

Communication dans un congrès20 documents

  • Thomas Guyet, Yves Moinard, Jacques Nicolas, René Quiniou. Packing graphs with ASP for landscape simulation. IJCAI 2016 - 25th International joint conference on artificial intelligence , Jul 2016, New-york, United States. AAAI, Proceedings of the international joint conference on artificial intelligence (IJCAI), pp.8. <hal-01327368>
  • Bonnet Nicolas, Beauvais Anicet, Arnaud Nicolas, Chardon Dominique, Dupont-Nivet Guillaume. WEATHERING AND DENUDATION OF THE WESTERN CONTINENTAL MARGIN OF PENINSULAR INDIA: THE 40 Ar/ 39 Ar DATING OF LATERITIC K-RICH MANGANESE OXIDES. SOURCE TO SINK: A long term perspective of sediment budgets and sources characterization, Nov 2016, Rennes, France. 2016. <insu-01421005>
  • Laurent Miclet, Jacques Nicolas. From formal concepts to analogical complexes. CLA 2015, Oct 2015, Clermont-Ferrand, France. The 12th International Conference on Concept Lattices and their Applications, pp.12, 2015, <>. <hal-01198943>
  • Aymeric Antoine-Lorquin, Sandrine Lagarrigue, Frédéric Lecerf, Jacques Nicolas, Catherine Belleannée. Comparaison des cibles d’une matrice de score et d’une expression régulière. Application à la recherche de sites de fixation du facteur de transcription LXR. JOBIM 2015- 16e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2015, Clermont-Ferrand, France. <>. <hal-01197050>
  • Valentin Wucher, Jacques Nicolas, Fabrice Legeai, Hervé Seitz, Denis Tagu. Integration of miRNAs data into a gene network of the pea aphid. . 7th International Symposium on Molecular Insect Science., 2014, Amsterdam, Netherlands. <hal-01566284>
  • François Coste, Gaëlle Garet, Agnès Groisillier, Jacques Nicolas, Thierry Tonon. Automated Enzyme classification by Formal Concept Analysis. ICFCA - 12th International Conference on Formal Concept Analysis, Jun 2014, Cluj-Napoca, Romania. Springer, 2014. <hal-01063727>
  • Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling. Comin, Matteo; Kall, Lukas; Marchiori, Elena; Ngom, Alioune; Rajapakse, Jagath. PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Aug 2014, Stockholm, Sweden. Springer International Publishing, 8626, pp.34-47, 2014, <10.1007/978-3-319-09192-1_4>. <hal-01059506>
  • Hugo Bazille, Jacques Nicolas. Computational Protein Design: trying an Answer Set Programming approach to solve the problem. 10th Workshop on Constraint-Based Methods for Bioinformatics (WCB'14), Sep 2014, Lyon, France. 2014. <hal-01063030>
  • François Coste, Gaelle Garet, Jacques Nicolas. A bottom-up efficient algorithm learning substitutable languages from positive examples. Alexander Clark; Makoto Kanazawa; Ryo Yoshinaka. ICGI (International Conference on Grammatical Inference), Sep 2014, Kyoto, Japan. JMLR Workshop and Conference Proceedings, 34, pp.49-63, 2014, The 12th International Conference on Grammatical Inference. <hal-01080249>
  • Valentin Wucher, Denis Tagu, Jacques Nicolas. Edge Selection in a Noisy Graph by Concept Analysis: Application to a Genomic Network. ECDA - European Conference on Data Analysis - 2013, Jul 2013, Luxembourg, Luxembourg. 2013. <hal-00924413>
  • François Coste, Gaelle Garet, Jacques Nicolas. Local Substitutability for Sequence Generalization. Jeffrey Heinz and Colin de la Higuera and Tim Oates. ICGI 2012, Sep 2012, Washington, United States. MIT Press, 21, pp.97-111, 2012, JMLR Workshop and Conference Proceedings; Proceedings of the Eleventh International Conference on Grammatical Inference. <>. <hal-00730553>
  • Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Recherche d'instances de motifs expressifs avec Logol. Application à la modélisation d'événements de frameshift -1. JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.5-14, 2012, <>. <hal-00726791>
  • Mathilde Le Boudic-Jamin, Noël Malod-Dognin, Alexandre Cornu, Jacques Nicolas, Rumen Andonov. Identification rapide de familles protéiques par dominance. 12th Annual Congress of the French National Society of Operations Research and Decision Science (ROADEF), Mar 2011, Saint-Étienne, France. 2, pp.791-792, 2011. <inria-00611457>
  • Lazaros Mavridis, Vishwesh Venkatraman, David Ritchie, H. Morikawa, Rumen Andonov, et al.. SHREC'10 Track: Protein Models. Eurographics Workshop on 3D Object Retrieval - 3DOR 2010, May 2010, Norrköping, Sweden. 2010. <inria-00536680>
  • Fabrice Legeai, Guillaume Rizk, T. Walsh, Owain Edwards, Jacques Nicolas, et al.. Prediction and analyzes of non coding RNA sequences in the pea aphid genome. Arthropods Genomics, Jun 2010, Kansas City, United States. 2010. <inria-00537927>
  • Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'H, Joël Querellou. c-GAMMA: Comparative Genome Analysis of Molecular Markers. LNCS. Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. SpringerLink, 5780/2009, pp.255-269, 2009, Pattern Recognition in Bioinformatics. <10.1007/978-3-642-04031-3_23>. <inria-00425373>
  • Fabrice Legeai, Jean-Pierre Gauthier, François Cousserans, Emmanuelle D'Alençon, Olivier Collin, et al.. From AphidBase and Lepido-DB to an Information System for Insect Plant pest genomics studies.. 1st Workshop on Information System for Insect Pest, Nov 2009, Rennes, France. 2009. <inria-00435823>
  • Frédéric Bourgeon, Jacques Nicolas, Nathalie Melaine, Charles Pineau. Identification and characterization of novel anti-infectious peptides from the male genital tract.. 34th Federation of European Biochemical Societies (FEBS) Congress, Jul 2009, Prague, Czech Republic. <hal-00667141>
  • Philippe Veber, Sébastien Tempel, Rumen Andonov, Dominique Lavenier, Jacques Nicolas. Détection de domaines dans des séquences génomiques : un problème de couverture optimale. FRANCORO V/ROADEF 2007, Feb 2007, Grenoble, France. <hal-00186471>
  • Sébastien Tempel, Mathieu Giraud, Israël-César Lerman, Ivan Couée, Abdelhak El Amrani, et al.. Organisation modulaire des séquences d'ADN répétées: application à l'étude des hélitrons non-autonomes dans le génome d'Arabidopsis thaliana. XIIIe colloque Eléments Transposables, 2005, Orsay, France. 2005, 4-6/07/2005. <hal-00015261>

Poster2 documents

  • Jean Coquet, Geoffroy Andrieux, Jacques Nicolas, Olivier Dameron, Nathalie Théret. Topological and semantic Web based method for analyzing TGF-β signaling pathways. JOBIM 2015, Dec 2015, Clermont-Ferrand, France. JOBIM : Journées Ouvertes en Biologie, Informatique & Mathématiques, 2015. <hal-01242893>
  • Douglas Gonçalves, Jacques Nicolas, Antonio Mucherino. Searching for Optimal Orders for Discretized Distance Geometry. Proceedings of Many Faces of Distances (MDF14), Oct 2014, Campinas, São Paulo, Brazil. 2014. <hal-01093072>

Ouvrage (y compris édition critique et traduction)1 document

  • Valentin Wucher, Denis Tagu, Jacques Nicolas. Edge Selection in a Noisy Graph by Concept Analysis – Application to a Genomic Network. Lausen, Berthold; Krolak-Schwerdt, Sabine; Böhmer, Matthias. Springer, pp.550, 2014, Data Science, Learning by Latent Structures, and Knowledge Discovery, 978-3-662-44982-0. <hal-01093337>

Chapitre d'ouvrage3 documents

  • Jacques Nicolas, Pierre Peterlongo, Sébastien Tempel. Finding and Characterizing Repeats in Plant Genomes. David Edwards. Plant Bioinformatics: Methods and Protocols, Humana Press - Springer Science+Business Media, pp.365, 2015, Methods in Molecular Biology, 978-1-4939-3166-8. <10.1007/978-1-4939-3167-5_17>. <hal-01228488>
  • Douglas S. Gonçalves, Jacques Nicolas, Antonio Mucherino, Carlile Lavor. Finding Optimal Discretization Orders for Molecular Distance Geometry by Answer Set Programming. S. Fidanova. Studies in Computational Intelligence, 610, Springer, pp.1-15, 2015, Recent Advances in Computational Optimization. <hal-01196714>
  • Jacques Nicolas. To detect and analyze sequence repeats whatever be their origin. Yves Bigot. Mobile genetic elements : protocols and genomic applications, 859, Springer, pp.69-90, 2012, Springer Protocols, 978-1-61779-602-9. <10.1007/978-1-61779-603-6>. <hal-00730207>

Autre publication1 document

  • Patrick Durand, Frédéric Mahé, Anne-Sophie Valin, Jacques Nicolas. Pyramid diagram: visualizing the organization of repetitive sequences in genomes.. FR2116. Rapport de recherche n°5798 Projet Symbiose. 2005. <hal-00129758>

Rapport6 documents

  • Christophe Vroland, Catherine Belleannée, Jacques Nicolas. Recherche et annotation des structures de CRISPR dans l'ensemble des génomes procaryotes. [Rapport de recherche] PI-1986, 2011, pp.24. <hal-00643408>
  • Jacques Nicolas, Christine Rousseau, Anne Siegel, Pierre Peterlongo, François Coste, et al.. Modeling local repeats on genomic sequences. [Research Report] RR-6802, INRIA. 2008, pp.43. <inria-00353690>
  • Catherine Belleannée, Jacques Nicolas. Logol : Modelling evolving sequence families through a dedicated constrained string language. [Research Report] RR-6350, INRIA. 2007, pp.19. <inria-00186568v3>
  • Maximilian Häußler, Jacques Nicolas. Motif Discovery on Promotor Sequences. [Research Report] RR-5714, INRIA. 2005, pp.136. <inria-00070303>
  • Jacques Nicolas. Grammatical Inference as Unification. [Research Report] RR-3632, INRIA. 1999. <inria-00073042>
  • Christine Sinoquet, Jacques Nicolas. Analyse syntaxique non déterministe utilisant un modèle de n-grams. [Rapport de recherche] RR-3262, INRIA. 1997. <inria-00073427>

HDR1 document

  • Jacques Nicolas. Syntaxe, raisonnement et génomes. Sciences du Vivant [q-bio]. Université Rennes 1, 2008. <tel-00355156>