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Journal articles22 documents

  • Grégoire Siekaniec, Emeline Roux, Téo Lemane, Eric Guédon, Jacques Nicolas. Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer. Microbial Genomics, Society for General Microbiology, 2021, 7 (11), pp.1-14. ⟨10.1099/mgen.0.000654⟩. ⟨hal-03444296⟩
  • Clara Delahaye, Jacques Nicolas. Sequencing DNA with nanopores: Troubles and biases. PLoS ONE, Public Library of Science, 2021, pp.1-29. ⟨10.1371/journal.pone.0257521⟩. ⟨hal-03362956⟩
  • Arnaud Belcour, Jean Girard, Méziane Aite, Ludovic Delage, Camille Trottier, et al.. Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift. iScience, Elsevier, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩. ⟨hal-01943880v2⟩
  • Méline Wery, Olivier Dameron, Jacques Nicolas, Elisabeth Rémy, Anne Siegel. Formalizing and enriching phenotype signatures using Boolean networks. Journal of Theoretical Biology, Elsevier, 2019, 467, pp.66-79. ⟨10.1016/j.jtbi.2019.01.015⟩. ⟨hal-02018724⟩
  • Camille Marchet, Lolita Lecompte, Corinne da Silva, Corinne Cruaud, Jean-Marc Aury, et al.. De Novo Clustering of Long Reads by Gene from Transcriptomics Data. Nucleic Acids Research, Oxford University Press, In press, pp.1-12. ⟨10.1093/nar/gky834⟩. ⟨hal-01643156v2⟩
  • Julie Laniau, Clémence Frioux, Jacques Nicolas, Caroline Baroukh, Maria-Paz Cortés, et al.. Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks. PeerJ, PeerJ, 2017, 5, pp.e3860. ⟨10.7717/peerj.3860⟩. ⟨hal-01635688⟩
  • Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Martin Gebser, et al.. Learning Boolean logic models of signaling networks with ASP. Theoretical Computer Science, 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.1-15. ⟨10.1371/journal.pone.0079707⟩. ⟨hal-00911795⟩
  • 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⟩
  • Klau Gunnar, Jacques Nicolas. Introduction Special Theme Computational Biology. ERCIM News, ERCIM, 2010, Special Theme Computational Biology. ⟨inria-00537580⟩
  • Jacques Nicolas. Décoder le vivant. Interstices, INRIA, 2010. ⟨hal-01350190⟩
  • 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⟩
  • 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⟩
  • Jacques Nicolas. Décoder le vivant. DocSciences, Édition du CRDP de l'académie de Versailles, 2009, Le numérique et les sciences du vivant, pp.26-33. ⟨inria-00438517⟩
  • 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⟩
  • 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, pp.477. ⟨10.1186/1471-2105-7-477⟩. ⟨hal-00129773⟩
  • 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 University Press (OUP), 2006, 22(16), pp.1948-1954. ⟨hal-00090517⟩
  • 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 University Press (OUP), 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⟩

Conference papers22 documents

  • Lucas Bourneuf, Jacques Nicolas. Concept Lattices as a Search Space for Graph Compression. ICFCA 2019 - 15th International Conference on Formal Concept Analysis, Jun 2019, Francfort, Germany. pp.274-289, ⟨10.1007/978-3-030-21462-3_18⟩. ⟨hal-02399578⟩
  • François Coste, Jacques Nicolas. Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction. ICGI 2018 - 14th International Conference on Grammatical Inference, Sep 2018, Wrocław, Poland. pp.155 - 168. ⟨hal-01872266⟩
  • Lucas Bourneuf, Jacques Nicolas. FCA in a Logical Programming Setting for Visualization-oriented Graph Compression. International Conference on Formal Concept Analysis 2017, Jun 2017, Rennes, France. ⟨10.1007/978-3-319-59271-8_6⟩. ⟨hal-01558302⟩
  • 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. pp.8. ⟨hal-01327368⟩
  • Laurent Miclet, Jacques Nicolas. From formal concepts to analogical complexes. CLA 2015, LIMOS, CNRS et Université Blaise Pascal, Oct 2015, Clermont-Ferrand, France. pp.12. ⟨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⟩
  • 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. ⟨hal-01063727⟩
  • Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling. PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Lukas KALL, Aug 2014, Stockholm, Sweden. pp.34-47, ⟨10.1007/978-3-319-09192-1_4⟩. ⟨hal-01059506⟩
  • François Coste, Gaelle Garet, Jacques Nicolas. A bottom-up efficient algorithm learning substitutable languages from positive examples. ICGI (International Conference on Grammatical Inference), Sep 2014, Kyoto, Japan. pp.49--63. ⟨hal-01080249⟩
  • 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), Nicos Angelopoulos (Imperial College, UK) Simon de Givry (MIAT-INRA, France), Sep 2014, Lyon, France. ⟨hal-01063030⟩
  • 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⟩
  • 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. ⟨hal-00924413⟩
  • François Coste, Gaelle Garet, Jacques Nicolas. Local Substitutability for Sequence Generalization. ICGI 2012, University of Maryland, Sep 2012, Washington, United States. pp.97-111. ⟨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. ⟨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), École Nationale Supérieure des Mines de Saint-Étienne, Mar 2011, Saint-Étienne, France. pp.791-792. ⟨inria-00611457⟩
  • Lazaros Mavridis, Vishwesh Venkatraman, David Ritchie, Naoto Morikawa, Rumen Andonov, et al.. SHREC'10 Track: Protein Models. Eurographics Workshop on 3D Object Retrieval - 3DOR 2010, May 2010, Norrköping, Sweden. ⟨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. ⟨inria-00537927⟩
  • Pierre Peterlongo, Jacques Nicolas, Dominique Lavenier, Raoul Vorc'H, Joël Querellou. c-GAMMA: Comparative Genome Analysis of Molecular Markers. Pattern Recognition in Bioinformatics, Sep 2009, Sheffield, United Kingdom. pp.255-269, ⟨10.1007/978-3-642-04031-3_23⟩. ⟨inria-00425373⟩
  • 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⟩
  • 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. ⟨inria-00435823⟩
  • 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. ⟨hal-00015261⟩

Poster communications4 documents

  • Grégoire Siekaniec, Rania Ouazahrou, Gaëlle Boudry, Eric Guédon, Emeline Roux, et al.. Identification of bacterial strains using ORI (Oxford nanopore Reads Identification). Microbes 2021 - Société Française de Microbiologie, Sep 2021, Nantes, France. ⟨hal-03374572⟩
  • Grégoire Siekaniec, Emeline Roux, Eric Guédon, Jacques Nicolas. Bacterial strains identification using Oxford Nanopore sequencing. JOBIM2020, Jun 2020, Montpellier, France. ⟨hal-03121440⟩
  • 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⟩

Book sections6 documents

  • Jacques Nicolas. Artificial Intelligence and Bioinformatics. Marquis, P., Papini, O., Prade, H. A Guided Tour of Artificial Intelligence Research, III, Springer, pp.575, 2020, Interfaces and Applications of Artificial Intelligence, 978-3-030-06169-2. ⟨hal-01850570v2⟩
  • Jacques Nicolas. IA et bioinformatique. Sébastien Konieczny; Henri Prade. L’intelligence artificielle: De quoi s’agit-il vraiment ?, Cépaduès, pp.101, 2020, 9782364938502. ⟨hal-03127545⟩
  • 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, 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⟩
  • 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. Data Science, Learning by Latent Structures, and Knowledge Discovery, Springer, pp.550, 2014, Data Science, Learning by Latent Structures, and Knowledge Discovery, 978-3-662-44982-0. ⟨10.1007/978-3-662-44983-7_31⟩. ⟨hal-01093337⟩
  • 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⟩

Other publications1 document

  • Patrick Durand, Frédéric Mahé, Anne-Sophie Valin, Jacques Nicolas. Pyramid diagram: visualizing the organization of repetitive sequences in genomes.. 2005. ⟨hal-00129758⟩

Reports6 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⟩

Habilitation à diriger des recherches1 document

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