Alain Denise

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 7

Top Topics

Closed Patterns

Regret Minimization

Rank Aggregation

Top Venues

Proc. VLDB Endow.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Pierre Andrieu, Sarah Cohen-Boulakia, Miguel Couceiro, Alain Denise, Adeline Pierrot
A unifying rank aggregation framework to suitably and efficiently aggregate any kind of rankings. Int. J. Approx. Reason. 162 (2023)
Pierre Andrieu, Bryan Brancotte, Laurent Bulteau, Sarah Cohen-Boulakia, Alain Denise, Adeline Pierrot, Stéphane Vialette
Efficient, robust and effective rank aggregation for massive biological datasets. Future Gener. Comput. Syst. 124 (2021)
Coline Gianfrotta, Vladimir Reinharz, Dominique Barth, Alain Denise
A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures. SEA (2021)
Antoine Soulé, Vladimir Reinharz, Roman Sarrazin-Gendron, Alain Denise, Jérôme Waldispühl
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs. PLoS Comput. Biol. 17 (5) (2021)
Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, Alain Denise
CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts. BMC Bioinform. 20 (1) (2019)
Pierre Andrieu, Bryan Brancotte, Laurent Bulteau, Sarah Cohen-Boulakia, Alain Denise, Adeline Pierrot, Stéphane Vialette
Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data. eScience (2019)
Mélanie Boudard, Dominique Barth, Julie Bernauer, Alain Denise, Johanne Cohen
GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization. Bioinform. 33 (16) (2017)
Bryan Brancotte, Bo Yang, Guillaume Blin, Sarah Cohen Boulakia, Alain Denise, Sylvie Hamel
Rank aggregation with ties: Experiments and Analysis. Proc. VLDB Endow. 8 (11) (2015)
Bryan Brancotte, Bastien Rance, Alain Denise, Sarah Cohen Boulakia
ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data. DILS (2014)
Alain Denise, Philippe Rinaudo
Optimisation Problems for Pairwise RNA Sequence and Structure Comparison: A Brief Survey. Trans. Comput. Collect. Intell. 13 (2014)
Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, Alain Denise
Flexible RNA design under structure and sequence constraints using formal languages. BCB (2013)
Johan Oudinet, Alain Denise, Marie-Claude Gaudel
A new dichotomic algorithm for the uniform random generation of words in regular languages. Theor. Comput. Sci. 502 (2013)
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 Trans. Comput. Biol. Bioinform. 10 (1) (2013)
Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, Eric Westhof
Automated prediction of three-way junction topological families in RNA secondary structures. Comput. Biol. Chem. 37 (2012)
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
BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. Adv. Bioinformatics 2012 (2012)
Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. CoRR (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)
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. Int. J. Softw. Tools Technol. Transf. 14 (1) (2012)
Sarah Cohen Boulakia, Alain Denise, Sylvie Hamel
Using Medians to Generate Consensus Rankings for Biological Data. SSDBM (2011)
Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, Alain Denise
Counting RNA Pseudoknotted Structures. J. Comput. Biol. 18 (10) (2011)
Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, Sylvain Peyronnet
Uniform Monte-Carlo Model Checking. FASE (2011)
Alain Denise, Yann Ponty, Michel Termier
Controlled non-uniform random generation of decomposable structures. Theor. Comput. Sci. 411 (40-42) (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) (2010)
Alain Denise, Yann Ponty, Michel Termier
Controlled non uniform random generation of decomposable structures CoRR (2010)
Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet
Alignments of RNA Structures. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (2) (2010)
Kévin Darty, Alain Denise, Yann Ponty
VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinform. 25 (15) (2009)
Marie-Claude Gaudel, Alain Denise, Sandrine-Dominique Gouraud, Richard Lassaigne, Johan Oudinet, Sylvain Peyronnet
Coverage-biased Random Exploration of Models. Electron. Notes Theor. Comput. Sci. 220 (1) (2008)
Romain Rivière, Dominique Barth, Johanne Cohen, Alain Denise
Shuffling biological sequences with motif constraints. J. Discrete Algorithms 6 (2) (2008)
Yann Ponty, Michel Termier, Alain Denise
GenRGenS: software for generating random genomic sequences and structures. Bioinform. 22 (12) (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)
Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard Lassaigne, Sylvain Peyronnet
Uniform Random Sampling of Traces in Very Large Models CoRR (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. J. Comput. Biol. 12 (1) (2005)
Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud
A Generic Method for Statistical Testing. ISSRE (2004)
Mireille Régnier, Alain Denise
Rare Events and Conditional Events on Random Strings. Discret. Math. Theor. Comput. Sci. 6 (2) (2004)
Cyril Banderier, Philippe Flajolet, Danièle Gardy, Mireille Bousquet-Mélou, Alain Denise, Dominique Gouyou-Beauchamps
Generating functions for generating trees CoRR (2004)
Sylvie Corteel, Mario Valencia-Pabon, Danièle Gardy, Dominique Barth, Alain Denise
The permutation-path coloring problem on trees. Theor. Comput. Sci. 297 (1-3) (2003)
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. Bioinform. 19 (3) (2003)
Cyril Banderier, Mireille Bousquet-Mélou, Alain Denise, Philippe Flajolet, Danièle Gardy, Dominique Gouyou-Beauchamps
Generating functions for generating trees. Discret. Math. 246 (1-3) (2002)
Alain Denise, Mireille Régnier, Mathias Vandenbogaert
Assessing the Statistical Significance of Overrepresented Oligonucleotides. WABI (2001)
Sandrine-Dominique Gouraud, Alain Denise, Marie-Claude Gaudel, B. Marr
A New Way of Automating Statistical Testing Methods. ASE (2001)
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)
Alain Denise, Paul Zimmermann
Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic. Theor. Comput. Sci. 218 (2) (1999)
Alain Denise
Génération aléatoire uniforme de mots de langages rationnels. Theor. Comput. Sci. 159 (1) (1996)
Alain Denise, Rodica Simion
Two combinatorial statistics on Dyck paths. Discret. Math. 137 (1-3) (1995)