Alain Denise

Julien Allali, Cédric Saule, Cedric Chauve, Yves D'Aubenton-Carafa, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine de Monte, Aïda Ouangraoua, Marie-France Sagot, Michel Termier, Claude Thermes, Hélène Touzet: BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. Adv. Bioinformatics 2012 (2012)

Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, Eric Westhof: Automated prediction of three-way junction topological families in RNA secondary structures. Computational Biology and Chemistry 37: 1-5 (2012)

Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lassaigne, Johan Oudinet, Sylvain Peyronnet: Coverage-biased random exploration of large models and application to testing. STTT 14(1): 73-93 (2012)

Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise: Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots - (Extended Abstract). WABI 2012: 149-164

Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise: Tree decomposition and . CoRR abs/1206.3789 (2012)

Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, Alain Denise: Counting RNA Pseudoknotted Structures. Journal of Computational Biology 18(10): 1339-1351 (2011)

Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, Sylvain Peyronnet: Uniform Monte-Carlo Model Checking. FASE 2011: 127-140

Sarah Cohen Boulakia, Alain Denise, Sylvie Hamel: Using Medians to Generate Consensus Rankings for Biological Data. SSDBM 2011: 73-90

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet: Alignments of RNA Structures. IEEE/ACM Trans. Comput. Biology Bioinform. 7(2): 309-322 (2010)

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. Theor. Comput. Sci. 411(26-28): 2423-2432 (2010)

Alain Denise, Yann Ponty, Michel Termier: Controlled non-uniform random generation of decomposable structures. Theor. Comput. Sci. 411(40-42): 3527-3552 (2010)

Alain Denise, Yann Ponty, Michel Termier: Controlled non uniform random generation of decomposable structures. CoRR abs/1006.0423 (2010)

Kévin Darty, Alain Denise, Yann Ponty: VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25(15): 1974-1975 (2009)

Marie-Claude Gaudel, Alain Denise, Sandrine-Dominique Gouraud, Richard Lassaigne, Johan Oudinet, Sylvain Peyronnet: Coverage-biased Random Exploration of Models. Electr. Notes Theor. Comput. Sci. 220(1): 3-14 (2008)

Romain Rivière, Dominique Barth, Johanne Cohen, Alain Denise: Shuffling biological sequences with motif constraints. J. Discrete Algorithms 6(2): 192-204 (2008)

Yann Ponty, Michel Termier, Alain Denise: GenRGenS: software for generating random genomic sequences and structures. Bioinformatics 22(12): 1534-1535 (2006)

Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lassaigne, Sylvain Peyronnet: Uniform random sampling of traces in very large models. Random Testing 2006: 10-19

Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lassaigne, Sylvain Peyronnet: Uniform Random Sampling of Traces in Very Large Models. CoRR abs/cs/0606086 (2006)

Elodie Nédélec, Thomas Moncion, Elisabeth Gassiat, Bruno Bossard, Guillemette Duchateau-Nguyen, Alain Denise, Michel Termier: A Pairwise Alignment Algorithm Which Favors Clusters of Blocks. Journal of Computational Biology 12(1): 33-47 (2005)

Mireille Régnier, Alain Denise: Rare Events and Conditional Events on Random Strings. Discrete Mathematics & Theoretical Computer Science 6(2): 191-214 (2004)

Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud: A Generic Method for Statistical Testing. ISSRE 2004: 25-34

Cyril Banderier, Philippe Flajolet, Danièle Gardy, Mireille Bousquet-Mélou, Alain Denise, Dominique Gouyou-Beauchamps: Generating functions for generating trees. CoRR math.CO/0411250 (2004)

Michaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset, Michel Termier: Towards a computational model for -1 eukaryotic frameshifting sites. Bioinformatics 19(3): 327-335 (2003)

Sylvie Corteel, Mario Valencia-Pabon, Danièle Gardy, Dominique Barth, Alain Denise: The permutation-path coloring problem on trees. Theor. Comput. Sci. 297(1-3): 119-143 (2003)

Cyril Banderier, Mireille Bousquet-Mélou, Alain Denise, Philippe Flajolet, Danièle Gardy, Dominique Gouyou-Beauchamps: Generating functions for generating trees. Discrete Mathematics 246(1-3): 29-55 (2002)

Sandrine-Dominique Gouraud, Alain Denise, Marie-Claude Gaudel, B. Marr: A New Way of Automating Statistical Testing Methods. ASE 2001: 5-12

Alain Denise, Mireille Régnier, Mathias Vandenbogaert: Assessing the Statistical Significance of Overrepresented Oligonucleotides. WABI 2001: 85-97

Dominique Barth, Sylvie Corteel, Alain Denise, Danièle Gardy, Mario Valencia-Pabon: On the Complexity of Routing Permutations on Trees by Arc-Disjoint Paths. Extended Abstract. LATIN 2000: 308-317

Alain Denise, Paul Zimmermann: Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic. Theor. Comput. Sci. 218(2): 233-248 (1999)

Alain Denise: Génération aléatoire uniforme de mots de langages rationnels. Theor. Comput. Sci. 159(1): 43-63 (1996)

Alain Denise, Rodica Simion: Two combinatorial statistics on Dyck paths. Discrete Mathematics 137(1-3): 155-176 (1995)