Nombre de documents

51

Alain Denise


Article dans une revue26 documents

  • Mélanie Boudard, Julie Bernauer, Dominique Barth, Johanne Cohen, Alain Denise. GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.. PLoS ONE, Public Library of Science, 2015, 10 (8), pp.e0136444. <hal-01201665>
  • Bryan Brancotte, Bo Yang, Guillaume Blin, Sarah Cohen-Boulakia, Alain Denise, et al.. Rank aggregation with ties: Experiments and Analysis. Proceedings of the VLDB Endowment (PVLDB), VLDB Endowment, 2015, pp.2051. <hal-01165336>
  • Alain Denise, Philippe Rinaudo. Optimisation problems for pairwise RNA sequence and structure comparison: a brief survey. Transactions on Computational Collective Intelligence, 2014, 13, pp.70-82. <10.1007/978-3-642-54455-2_3>. <hal-00759573>
  • Cécile Pereira, Alain Denise, Olivier Lespinet. A meta-approach for improving the prediction and the functional annotation of ortholog groups. BMC Genomics, BioMed Central, 2014, <10.1186/1471-2164-15-S6-S16>. <inserm-01229454>
  • Changwei Shao, Bo Yang, Tongbin Wu, Jie Huang, Peng Tang, et al.. Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome. Nature Structural and Molecular Biology, Nature Publishing Group, 2014, 21, pp.997-1005. <10.1038/nsmb.2906>. <hal-01097740>
  • Johan Oudinet, Alain Denise, Marie-Claude Gaudel. A new dichotomic algorithm for the uniform random generation of words in regular languages (journal version). Theoretical Computer Science, Elsevier, 2013, 502, pp.165-176. <hal-00716558>
  • Alexis Lamiable, Franck Quessette, Sandrine Vial, Dominique Barth, Alain Denise. An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure.. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2013, 10 (1), pp.193-199. <10.1109/TCBB.2012.148>. <hal-00832110>
  • Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, et al.. Automated prediction of three-way junction topological families in RNA secondary structures. Computational Biology and Chemistry, Elsevier, 2012, 37, pp.1-5. <10.1016>. <hal-00641738>
  • Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lassaigne, Johan Oudinet, et al.. Coverage-biased random exploration of large models and application to testing. Software Tools for Technology Transfer (STTT), Springer, 2012, 14 (1), pp.73-93. <inria-00560621>
  • Julien Allali, Cédric Saule, Cedric Chauve, Yves D'Aubenton-Carafa, Alain Denise, et al.. BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms. Advances in Bioinformatics, Hindawi Publishing Corporation, 2012, 2012 (893048), 5 p. <10.1155/2012>. <hal-00647725>
  • Cédric Saule, Mireille Regnier, Jean-Marc Steyaert, Alain Denise. Counting RNA pseudoknotted structures. Journal of Computational Biology, Mary Ann Liebert, 2011, 18 (10), pp.1339-1351. <10.1089/cmb.2010.0086>. <inria-00537117>
  • Claire Herrbach, Alain Denise, Serge Dulucq. Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm. Theoretical Computer Science, Elsevier, 2010, 411, pp.2423-2432. <inria-00541269>
  • Alain Denise, Yann Ponty, Michel Termier. Controlled non uniform random generation of decomposable structures. Theoretical Computer Science, Elsevier, 2010, 411 (40-42), pp.3527-3552. <10.1016/j.tcs.2010.05.010>. <hal-00483581>
  • Wei Liu, Yu Zhou, Zexi Hu, Tao Sun, Alain Denise, et al.. Regulation of splicing enhancer activities by RNA secondary structures. FEBS Letters, Wiley, 2010, 584 (21), pp.4401-7. <10.1016/j.febslet.2010.09.039>. <hal-00534366>
  • Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet. Alignments of RNA structures.. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2010, 7 (2), pp.309-322. <10.1109/TCBB.2008.28>. <hal-00506348>
  • Kévin Darty, Alain Denise, Yann Ponty. VARNA: Interactive drawing and editing of the RNA secondary structure.. Bioinformatics, Oxford University Press (OUP), 2009, 25 (15), pp.1974-5. <10.1093/bioinformatics/btp250>. <hal-00432548>
  • M. Djelloul, Alain Denise. A method for automated discovering of RNA tertiary motifs. Proc. JOBIM, 2008, pp.47-52. <hal-00297159>
  • Mahassine Djelloul, Alain Denise. Automated motif extraction and classification in RNA tertiary structures.. RNA, Cold Spring Harbor Laboratory Press, 2008, 14 (12), pp.2489-97. <10.1261/rna.1061108>. <hal-00353402>
  • R. Rivière, D. Barth, J. Cohen, Alain Denise. Shuffling biological sequences with motif constraints. Journal of Discrete Algorithms, Elsevier, 2008, 6 (2), pp.192-204. <hal-00297151>
  • Dominique Barth, Johanne Cohen, Alain Denise, Romain Rivière. Shuffling biological sequences with motif constraints.. Journal of Discrete Algorithms, Elsevier, 2007, <10.1016/j.jda.2007.06.001>. <inria-00187827>
  • Olivier Namy, Yu Zhou, Sarath Gundllapalli, Carla R Polycarpo, Alain Denise, et al.. Adding pyrrolysine to the Escherichia coli genetic code.. FEBS Letters, Wiley, 2007, 581 (27), pp.5282-8. <10.1016/j.febslet.2007.10.022>. <hal-00195226>
  • Yann Ponty, Michel Termier, Alain Denise. GenRGenS: Software for Generating Random Genomic Sequences and Structures. Bioinformatics, Oxford University Press (OUP), 2006, 22 (12), pp.1534--1535. <10.1093/bioinformatics/btl113>. <inria-00548871>
  • Mireille Régnier, Alain Denise. Rare Events and Conditional Events on Random Strings. Discrete Mathematics and Theoretical Computer Science, DMTCS, 2004, 6 (2), pp.191-214. <hal-00959004>
  • Cyril Banderier, Philippe Flajolet, Danièle Gardy, Mireille Bousquet-Mélou, Alain Denise, et al.. Generating functions for generating trees. Discrete Mathematics, Elsevier, 2002, 246 (1-3), pp.29-55. <hal-00003258>
  • Alain Denise, Paul Zimmermann. Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic. Theoretical Computer Science, Elsevier, 1999, 218 (2), pp.233-248. <inria-00098797>
  • Alain Denise, Isabelle Dutour, Paul Zimmermann. CS: a MuPAD package for counting and randomly generating combinatorial structures. MathPAD, Paderborn University, 1998, 8, pp.23-30. <hal-00306639>

Communication dans un congrès19 documents

  • Wei Wang​, Matthieu Barba​, Philippe Rinaudo​, Alain Denise, Yann Ponty. Homology ­modeling of complex structural RNAs. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France. 2016. <hal-01332642>
  • Bryan Brancotte, Bo Yang, Guillaume Blin, Sarah Cohen-Boulakia, Alain Denise, et al.. Rank aggregation with ties: Experiments and Analysis. The 41st International Conference on Very Large Data Bases, Aug 2015, Kohala Coast, Hawaï, United States. 8 (11). <hal-01152098>
  • Vincent Le Gallic, Alain Denise, Yann Ponty. Résultats algorithmiques pour le design d’ARN avec contraintes de séquence. SeqBio 2015, Nov 2015, Orsay, France. Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics, pp.26-31, 2015. <hal-01266096>
  • Bryan Brancotte, Bastien Rance, Alain Denise, Sarah Cohen-Boulakia. ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data. 10th International Conference, Data Integration in the Life Sciences, Jul 2014, Lisbon, Portugal. pp.128 - 142, 2014, <10.1007/978-3-319-08590-6_13>. <hal-01091053>
  • Cécile Pereira, Jérôme Azé, Alain Denise, Christine Drevet, Christine Froidevaux, et al.. Comparative analysis of phylogenetic profiles for the enzymatic characterization of fungal group. JOBIM 2013, 2013, Toulouse, France. à paraître, 2013. <hal-00842021>
  • Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, et al.. Flexible RNA design under structure and sequence constraints using formal languages. ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States. 2013. <hal-00823279v2>
  • Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise. Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. Ben Raphael and Jijun Tang. WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, Sep 2012, Ljubljana, Slovenia. 2012, tba. <hal-00708580v2>
  • Fabrice Jossinet, Alexis Lamiable, Philippe Rinaudo, Liza Al-Shikhley, Franck Quessette, et al.. Graph Algorithms and Software Framework for Interactive RNA Structure Modelling. Journees Ouvertes de Biologie Informatique et Mathematiques - JOBIM'12, Jul 2012, Rennes, France. pp.475-476, 2012. <hal-00756345>
  • Peter Clote, Lou Feng, Alain Denise. A new approach to suboptimal pairwise sequence alignment. CompBio 2011: IASTED International Conference on Computational Bioscience, 2011, Cambridge, United Kingdom. 2011. <inria-00594890>
  • Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, Sylvain Peyronnet. Uniform Monte-Carlo Model Checking. FASE 2011, 2011, Saarbrücken, Germany. 2011. <hal-00644834>
  • Sarah Cohen-Boulakia, Alain Denise, Sylvie Hamel. Using medians to generate consensus rankings for biological data. SSDBM 2011: Scientific and Statistical Database Management Conference, 2011, Portland, United States. 2011. <inria-00584690>
  • Cédric Saule, Mireille Regnier, Jean-Marc Steyaert, Alain Denise. Counting RNA pseudoknotted structures (extended abstract). Billey, Sara and Reiner, Victor. 22nd International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC 2010), 2010, San Francisco, United States. Discrete Mathematics and Theoretical Computer Science, AN, pp.1037-1048, 2010, DMTCS Proceedings. <hal-01186262>
  • Cédric Saule, Claire Wallon, Alain Denise. Uniform and non-uniform random generation of RNA secondary structures with pseudoknots. GASCOM, Sep 2010, Montreal, Canada. 2010. <inria-00543315>
  • Johan Oudinet, Alain Denise, Marie-Claude Gaudel. A new dichotomic algorithm for the uniform random generation of words in regular languages. GASCom 2010, 2010, Montreal, Canada. 2010. <inria-00542683>
  • Julien Allali, Yves D'Aubenton-Carafa, Cedric Chauve, Alain Denise, Christine Drevet, et al.. Benchmarking RNA secondary structure comparison algorithms. JOBIM'08, 2008, Lille, France. pp.67-68, 2008. <hal-00375710>
  • Dominique Barth, Alain Denise, Romain Rivière. Motifs Enumeration Algorithms in Biological Networks. 2006, aaa, 2006. <hal-00126565>
  • Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lasseigne, Sylvain Peyronnet. Uniform Random Sampling of Traces in Very Large Models. Johannes Mayer, Robert Merkel. First International Workshop on Random Testing, 2006, Portland, Maine, United States. ACM, pp.10-19, 2006. <hal-00080471>
  • Dominique Barth, Johanne Cohen, Alain Denise, Romain Rivière. Shuffling biological sequencess with motifs constraints. Algorithms and Computational Methods for Biochemical and Evolutionary Networks - CompBioNets'2004, Dec 2004, Recife, Brazil. 18 p, 2004. <inria-00099891>
  • Alain Denise, Isabelle Dutour, Paul Zimmermann. CS: a MuPAD Package for Counting and Randomly Generating Combinatorial Structures. The Fields Institute. 10-th conference Formal Power Series and Algebraic Combinatorics, 1998, Toronto, pp.195-204, 1998. <inria-00107518>

Poster2 documents

  • Bryan Brancotte, Bastien Rance, Alain Denise, Sarah Cohen-Boulakia. Interrogation de bases de données biologiques publiques par reformulation de requêtes et classement des résultats avec ConQuR-Bio. JOBIM (Journées Ouvertes Biologie Informatique Mathématiques), Jul 2015, Clermont-Ferrand, France. <hal-01167840>
  • Cécile Pereira, Alain Denise, Olivier Lespinet. A new method for improving the prediction and the functional annotation of ortholog groups. Proc. ECCB'14, the 13th European Conference on Computational Biology, 2014, Strasbourg, France. Proc. ECCB'14, the 13th European Conference on Computational Biology, 2014. <hal-01098231>

Direction d'ouvrage, Proceedings1 document

  • Alain Denise, Olivier Lespinet, Mireille Régnier. Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics: COMATEGE working group workshop. Alain Denise; Olivier Lespinet; Mireille Régnier. Nov 2015, Orsay, France. 2015. <hal-01264187>

Rapport3 documents

  • Alain Denise, Mireille Regnier, Mathias Vandenbogaert. Assessing Statistical Significance of Overrepresented Oligonucleotides. [Research Report] RR-4132, INRIA. 2001. <inria-00072496>
  • Cyril Banderier, Mireille Bousquet-Mélou, Alain Denise, Philippe Flajolet, Danièle Gardy, et al.. On Generating Functions of Generating Trees. [Research Report] RR-3661, INRIA. 1999. <inria-00073011>
  • Alain Denise, Paul Zimmermann. Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic. [Research Report] RR-3242, INRIA. 1997. <inria-00073447>