Alain Denise

According to our database, Alain Denise authored at least 42 papers between 1995 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

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., November, 2023

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

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

A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures.

Coline Gianfrotta, Vladimir Reinharz, Dominique Barth, Alain Denise

Proceedings of the 19th International Symposium on Experimental Algorithms, 2021

2019

CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts.

Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, Alain Denise

BMC Bioinform., December, 2019

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

Proceedings of the 15th International Conference on eScience, 2019

2017

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

2015

Rank aggregation with ties: Experiments and Analysis.

Bryan Brancotte, Bo Yang, Guillaume Blin, Sarah Cohen Boulakia, Alain Denise, Sylvie Hamel

Proc. VLDB Endow., 2015

2014

Optimisation Problems for Pairwise RNA Sequence and Structure Comparison: A Brief Survey.

Alain Denise, Philippe Rinaudo

Trans. Comput. Collect. Intell., 2014

ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data.

Bryan Brancotte, Bastien Rance, Alain Denise, Sarah Cohen Boulakia

Proceedings of the Data Integration in the Life Sciences - 10th International Conference, 2014

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

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

Flexible RNA design under structure and sequence constraints using formal languages.

Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, Alain Denise

Proceedings of the ACM Conference on Bioinformatics, 2013

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

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

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

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, Marie-France Sagot, Michel Termier, Claude Thermes, Hélène Touzet

Adv. Bioinformatics, 2012

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

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

2011

Counting RNA Pseudoknotted Structures.

Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, Alain Denise

J. Comput. Biol., 2011

Using Medians to Generate Consensus Rankings for Biological Data.

Sarah Cohen Boulakia, Alain Denise, Sylvie Hamel

Proceedings of the Scientific and Statistical Database Management, 2011

Uniform Monte-Carlo Model Checking.

Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, Sylvain Peyronnet

Proceedings of the Fundamental Approaches to Software Engineering, 2011

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

Controlled non-uniform random generation of decomposable structures.

Alain Denise, Yann Ponty, Michel Termier

Theor. Comput. Sci., 2010

Alignments of RNA Structures.

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

2009

VARNA: Interactive drawing and editing of the RNA secondary structure.

Kévin Darty, Alain Denise, Yann Ponty

Bioinform., 2009

2008

Shuffling biological sequences with motif constraints.

Romain Rivière, Dominique Barth, Johanne Cohen, Alain Denise

J. Discrete Algorithms, 2008

Coverage-biased Random Exploration of Models.

Marie-Claude Gaudel, Alain Denise, Sandrine-Dominique Gouraud, Richard Lassaigne, Johan Oudinet, Sylvain Peyronnet

Proceedings of the Fourth Workshop on Model Based Testing, 2008

2006

GenRGenS: software for generating random genomic sequences and structures.

Yann Ponty, Michel Termier, Alain Denise

Bioinform., 2006

Uniform random sampling of traces in very large models.

Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lassaigne, Sylvain Peyronnet

Proceedings of the 1st International Workshop on Random Testing, 2006

2005

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

2004

Rare Events and Conditional Events on Random Strings.

Mireille Régnier, Alain Denise

Discret. Math. Theor. Comput. Sci., 2004

A Generic Method for Statistical Testing.

Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud

Proceedings of the 15th International Symposium on Software Reliability Engineering (ISSRE 2004), 2004

2003

The permutation-path coloring problem on trees.

Sylvie Corteel, Mario Valencia-Pabon, Danièle Gardy, Dominique Barth, Alain Denise

Theor. Comput. Sci., 2003

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

2002

Generating functions for generating trees.

Cyril Banderier, Mireille Bousquet-Mélou, Alain Denise, Philippe Flajolet, Danièle Gardy, Dominique Gouyou-Beauchamps

Discret. Math., 2002

2001

Assessing the Statistical Significance of Overrepresented Oligonucleotides.

Alain Denise, Mireille Régnier, Mathias Vandenbogaert

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

A New Way of Automating Statistical Testing Methods.

Sandrine-Dominique Gouraud, Alain Denise, Marie-Claude Gaudel, B. Marr

Proceedings of the 16th IEEE International Conference on Automated Software Engineering (ASE 2001), 2001

2000

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

Proceedings of the LATIN 2000: Theoretical Informatics, 2000

1999

Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic.

Alain Denise, Paul Zimmermann

Theor. Comput. Sci., 1999

1996

Génération aléatoire uniforme de mots de langages rationnels.

Alain Denise

Theor. Comput. Sci., 1996

Génération aléatoire et uniforme de mots.

Alain Denise

Discret. Math., 1996

1995

Two combinatorial statistics on Dyck paths.

Alain Denise, Rodica Simion

Discret. Math., 1995