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inria-00073447v1  Rapport
Alain Denise, Paul Zimmermann. Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic
[Research Report] RR-3242, INRIA. 1997
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hal-00823279v2  Communication dans un congrès
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-00644834v1  Communication dans un congrès
Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, Sylvain Peyronnet. Uniform Monte-Carlo Model Checking
FASE 2011, 2011, Saarbrücken, Germany. 2011
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hal-01264187v1  Direction d'ouvrage, Proceedings
Alain Denise, Olivier Lespinet, Mireille Régnier. Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics
Alain Denise; Olivier Lespinet; Mireille Régnier. Nov 2015, Orsay, France. 2015
hal-01152098v1  Communication dans un congrès
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-00375710v1  Communication dans un congrès
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-00759573v1  Article dans une revue
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>
inria-00560621v1  Article dans une revue
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
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inria-00099891v1  Communication dans un congrès
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
hal-01098231v1  Poster
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
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hal-00483581v1  Article dans une revue
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>
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inria-00541269v1  Article dans une revue
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-00098797v1  Article dans une revue
Alain Denise, Paul Zimmermann. Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic
Theoretical Computer Science, Elsevier, 1999, 218 (2), pp.233-248
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hal-00716558v1  Article dans une revue
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
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inria-00073011v1  Rapport
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
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inria-00072496v1  Rapport
Alain Denise, Mireille Regnier, Mathias Vandenbogaert. Assessing Statistical Significance of Overrepresented Oligonucleotides
[Research Report] RR-4132, INRIA. 2001
inria-00594890v1  Communication dans un congrès
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
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inria-00543315v1  Communication dans un congrès
Cédric Saule, Claire Wallon, Alain Denise. Uniform and non-uniform random generation of RNA secondary structures with pseudoknots
GASCOM, Sep 2010, Montreal, Canada. 2010
hal-01266096v1  Communication dans un congrès
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
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hal-00080471v1  Communication dans un congrès
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
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hal-01332642v1  Communication dans un congrès
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
inria-00584690v1  Communication dans un congrès
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
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hal-01091053v1  Communication dans un congrès
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-00756345v1  Communication dans un congrès
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
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hal-00708580v2  Communication dans un congrès
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
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inria-00107518v1  Communication dans un congrès
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
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