Two combinatorial statistics on Dyck paths. - Alain Denise; Rodica Simion (Discret. Math., 1995)

Génération aléatoire et uniforme de mots. - Alain Denise (Discret. Math., 1996)

Génération aléatoire uniforme de mots de langages rationnels. - Alain Denise (Theor. Comput. Sci., 1996)

Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic. - Alain Denise; Paul Zimmermann (Theor. Comput. Sci., 1999)

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

A New Way of Automating Statistical Testing Methods. - Sandrine-Dominique Gouraud; Alain Denise; Marie-Claude Gaudel; B. Marr (ASE, 2001)

Assessing the Statistical Significance of Overrepresented Oligonucleotides. - Alain Denise; Mireille Régnier; Mathias Vandenbogaert (WABI, 2001)

Generating functions for generating trees. - Cyril Banderier; Mireille Bousquet-Mélou; Alain Denise; Philippe Flajolet; Danièle Gardy; Dominique Gouyou-Beauchamps (Discret. Math., 2002)

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

The permutation-path coloring problem on trees. - Sylvie Corteel; Mario Valencia-Pabon; Danièle Gardy; Dominique Barth; Alain Denise (Theor. Comput. Sci., 2003)

A Generic Method for Statistical Testing. - Alain Denise; Marie-Claude Gaudel; Sandrine-Dominique Gouraud (ISSRE, 2004)

Rare Events and Conditional Events on Random Strings. - Mireille Régnier; Alain Denise (Discret. Math. Theor. Comput. Sci., 2004)

A Pairwise Alignment Algorithm Which Favors Clusters of Blocks. - Elodie Nédélec; Thomas Moncion; Elisabeth Gassiat; Bruno Bossard; Guillemette Duchateau-Nguyen; Alain Denise; Michel Termier (J. Comput. Biol., 2005)

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

GenRGenS: software for generating random genomic sequences and structures. - Yann Ponty; Michel Termier; Alain Denise (Bioinform., 2006)

Coverage-biased Random Exploration of Models. - Marie-Claude Gaudel; Alain Denise; Sandrine-Dominique Gouraud; Richard Lassaigne; Johan Oudinet; Sylvain Peyronnet (MBT@ETAPS, 2008)

Shuffling biological sequences with motif constraints. - Romain Rivière; Dominique Barth; Johanne Cohen; Alain Denise (J. Discrete Algorithms, 2008)

VARNA: Interactive drawing and editing of the RNA secondary structure. - Kévin Darty; Alain Denise; Yann Ponty (Bioinform., 2009)

Alignments of RNA Structures. - Guillaume Blin; Alain Denise; Serge Dulucq; Claire Herrbach; Hélène Touzet (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Controlled non-uniform random generation of decomposable structures. - Alain Denise; Yann Ponty; Michel Termier (Theor. Comput. Sci., 2010)

Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm. - Claire Herrbach; Alain Denise; Serge Dulucq (Theor. Comput. Sci., 2010)

Uniform Monte-Carlo Model Checking. - Johan Oudinet; Alain Denise; Marie-Claude Gaudel; Richard Lassaigne; Sylvain Peyronnet (FASE, 2011)

Using Medians to Generate Consensus Rankings for Biological Data. - Sarah Cohen Boulakia; Alain Denise; Sylvie Hamel (SSDBM, 2011)

Counting RNA Pseudoknotted Structures. - Cédric Saule; Mireille Régnier; Jean-Marc Steyaert; Alain Denise (J. Comput. Biol., 2011)

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

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. - Julien Allali; Cédric Saule; Cédric Chauve; Yves D'Aubenton-Carafa; Alain Denise; Christine Drevet; Pascal Ferraro; Daniel Gautheret; Claire Herrbach; Fabrice Leclerc; Antoine de Monte; Aïda Ouangraoua; et al. (Adv. Bioinformatics, 2012)

Automated prediction of three-way junction topological families in RNA secondary structures. - Alexis Lamiable; Dominique Barth; Alain Denise; Franck Quessette; Sandrine Vial; Eric Westhof (Comput. Biol. Chem., 2012)

Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. - Philippe Rinaudo; Yann Ponty; Dominique Barth; Alain Denise (CoRR, 2012)

Coverage-biased random exploration of large models and application to testing. - Alain Denise; Marie-Claude Gaudel; Sandrine-Dominique Gouraud; Richard Lassaigne; Johan Oudinet; Sylvain Peyronnet (Int. J. Softw. Tools Technol. Transf., 2012)

Flexible RNA design under structure and sequence constraints using formal languages. - Yu Zhou 021; Yann Ponty; Stéphane Vialette; Jérôme Waldispühl; Yi Zhang 046; Alain Denise (BCB, 2013)

An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure. - Alexis Lamiable; Franck Quessette; Sandrine Vial; Dominique Barth; Alain Denise (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

A new dichotomic algorithm for the uniform random generation of words in regular languages. - Johan Oudinet; Alain Denise; Marie-Claude Gaudel (Theor. Comput. Sci., 2013)

ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data. - Bryan Brancotte; Bastien Rance; Alain Denise; Sarah Cohen Boulakia (DILS, 2014)

Optimisation Problems for Pairwise RNA Sequence and Structure Comparison: A Brief Survey. - Alain Denise; Philippe Rinaudo (Trans. Comput. Collect. Intell., 2014)

Rank aggregation with ties: Experiments and Analysis. - Bryan Brancotte; Bo Yang 030; Guillaume Blin; Sarah Cohen Boulakia; Alain Denise; Sylvie Hamel (Proc. VLDB Endow., 2015)

GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization. - Mélanie Boudard; Dominique Barth; Julie Bernauer; Alain Denise; Johanne Cohen (Bioinform., 2017)

Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data. - Pierre Andrieu; Bryan Brancotte; Laurent Bulteau; Sarah Cohen-Boulakia; Alain Denise; Adeline Pierrot; Stéphane Vialette (eScience, 2019)

CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts. - Alexandra Zaharia; Bernard Labedan; Christine Froidevaux; Alain Denise (BMC Bioinform., 2019)

A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures. - Coline Gianfrotta; Vladimir Reinharz; Dominique Barth; Alain Denise (SEA, 2021)

Efficient, robust and effective rank aggregation for massive biological datasets. - Pierre Andrieu; Bryan Brancotte; Laurent Bulteau; Sarah Cohen-Boulakia; Alain Denise; Adeline Pierrot; Stéphane Vialette (Future Gener. Comput. Syst., 2021)

Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs. - Antoine Soulé; Vladimir Reinharz; Roman Sarrazin-Gendron; Alain Denise; Jérôme Waldispühl (PLoS Comput. Biol., 2021)

A unifying rank aggregation framework to suitably and efficiently aggregate any kind of rankings. - Pierre Andrieu; Sarah Cohen-Boulakia; Miguel Couceiro; Alain Denise; Adeline Pierrot (Int. J. Approx. Reason., 2023)