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ORCIDAlain Denise
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- affiliation: University of Paris-Sud, Laboratory for Computer Science (LRI), France
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2020 – today
- 2023
[j28]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: 109035 (2023)- 2021
- [j27]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: 406-421 (2021) - [j26]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) - [c13]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: 19:1-19:18
2010 – 2019
- 2019
- [j25]Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, Alain Denise:
CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts. BMC Bioinform. 20(1): 19 (2019) - [c12]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: 136-145 - 2017
- [j24]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): 2479-2486 (2017) - 2015
- [j23]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): 1202-1213 (2015) - 2014
- [j22]Alain Denise, Philippe Rinaudo:
Optimisation Problems for Pairwise RNA Sequence and Structure Comparison: A Brief Survey. Trans. Comput. Collect. Intell. 13: 70-82 (2014) - [c11]Bryan Brancotte, Bastien Rance, Alain Denise, Sarah Cohen Boulakia:
ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data. DILS 2014: 128-142 - 2013
- [j21]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): 193-199 (2013) - [j20]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: 165-176 (2013) - [c10]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: 229 - 2012
- [j19]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: 893048:1-893048:5 (2012) - [j18]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: 1-5 (2012) - [j17]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): 73-93 (2012) - [c9]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 - [i4]Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise:
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. CoRR abs/1206.3789 (2012) - 2011
- [j16]Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, Alain Denise:
Counting RNA Pseudoknotted Structures. J. Comput. Biol. 18(10): 1339-1351 (2011) - [c8]Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, Sylvain Peyronnet:
Uniform Monte-Carlo Model Checking. FASE 2011: 127-140 - [c7]Sarah Cohen Boulakia, Alain Denise, Sylvie Hamel:
Using Medians to Generate Consensus Rankings for Biological Data. SSDBM 2011: 73-90 - 2010
- [j15]Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet:
Alignments of RNA Structures. IEEE ACM Trans. Comput. Biol. Bioinform. 7(2): 309-322 (2010) - [j14]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) - [j13]Alain Denise, Yann Ponty, Michel Termier:
Controlled non-uniform random generation of decomposable structures. Theor. Comput. Sci. 411(40-42): 3527-3552 (2010) - [i3]Alain Denise, Yann Ponty, Michel Termier:
Controlled non uniform random generation of decomposable structures. CoRR abs/1006.0423 (2010)
2000 – 2009
- 2009
- [j12]Kévin Darty, Alain Denise, Yann Ponty:
VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinform. 25(15): 1974-1975 (2009) - 2008
- [j11]Romain Rivière, Dominique Barth, Johanne Cohen, Alain Denise:
Shuffling biological sequences with motif constraints. J. Discrete Algorithms 6(2): 192-204 (2008) - [c6]Marie-Claude Gaudel, Alain Denise, Sandrine-Dominique Gouraud, Richard Lassaigne, Johan Oudinet, Sylvain Peyronnet:
Coverage-biased Random Exploration of Models. MBT@ETAPS 2008: 3-14 - 2006
- [j10]Yann Ponty, Michel Termier, Alain Denise:
GenRGenS: software for generating random genomic sequences and structures. Bioinform. 22(12): 1534-1535 (2006) - [c5]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 - [i2]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) - 2005
- [j9]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): 33-47 (2005) - 2004
- [j8]Mireille Régnier, Alain Denise:
Rare Events and Conditional Events on Random Strings. Discret. Math. Theor. Comput. Sci. 6(2): 191-214 (2004) - [c4]Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud:
A Generic Method for Statistical Testing. ISSRE 2004: 25-34 - [i1]Cyril Banderier, Philippe Flajolet, Danièle Gardy, Mireille Bousquet-Mélou, Alain Denise, Dominique Gouyou-Beauchamps:
Generating functions for generating trees. CoRR math.CO/0411250 (2004) - 2003
- [j7]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): 327-335 (2003) - [j6]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) - 2002
- [j5]Cyril Banderier, Mireille Bousquet-Mélou, Alain Denise, Philippe Flajolet, Danièle Gardy, Dominique Gouyou-Beauchamps:
Generating functions for generating trees. Discret. Math. 246(1-3): 29-55 (2002) - 2001
- [c3]Sandrine-Dominique Gouraud, Alain Denise, Marie-Claude Gaudel, B. Marr:
A New Way of Automating Statistical Testing Methods. ASE 2001: 5-12 - [c2]Alain Denise, Mireille Régnier, Mathias Vandenbogaert:
Assessing the Statistical Significance of Overrepresented Oligonucleotides. WABI 2001: 85-97 - 2000
- [c1]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
1990 – 1999
- 1999
- [j4]Alain Denise, Paul Zimmermann:
Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic. Theor. Comput. Sci. 218(2): 233-248 (1999) - 1996
- [j3]Alain Denise:
Génération aléatoire et uniforme de mots. Discret. Math. 153(1-3): 69-84 (1996) - [j2]Alain Denise:
Génération aléatoire uniforme de mots de langages rationnels. Theor. Comput. Sci. 159(1): 43-63 (1996) - 1995
- [j1]Alain Denise, Rodica Simion:
Two combinatorial statistics on Dyck paths. Discret. Math. 137(1-3): 155-176 (1995)
Coauthor Index
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