Publications d'Alain Denise
in DBLP
in PubMed
in HAL
in LRI Bioinfo group
in Google Scholar
2011
- Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial, and Eric Westhof.
Automated prediction of three-way junction topological families in RNA secondary structures.
To appear in Computational Biology and Chemistry, 2011.
- Peter Clote, Feng Lou and Alain Denise.
A new approach to suboptimal pairwise sequence alignment.
To appear in Proc. CompBio 2011: The Second IASTED International Conference
on Computational Bioscience.
- Sarah Cohen-Boulakia, Alain Denise, and Sylvie Hamel.
Using medians to generate consensus rankings for biological data.
Proc. SSDBM 2011: Scientific and Statistical Database Management Conference.
Lecture Notes in Computer Science 6809, pages 73-90.
- Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, and Alain Denise.
Counting RNA pseudoknotted structures.
Journal of
Computational Biology 19(10) pages 1339-1351, 2011 (free acces).
- Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard
Lassaigne, Johan Oudinet, and Sylvain Peyronnet.
Coverage-biased random exploration of large models and application to testing.
Software Tools for Technology Transfer, 2011.
- Johan Oudinet, Alain Denise, Marie-Claude Gaudel, Richard Lassaigne, and
Sylvain Peyronnet. Uniform Monte-Carlo Model checking. To appear in Proc. FASE,
Conference on Fundamental Approaches to Software Engineering, Saarbrücken, March
2011. Lecture Notes in Computer Science 6603, pages 127-140.
2010
- Wei Liu, Yu Zhou, Zexi Hu, Tao Sun, Alain Denise, Xiang-Dong Fu, and Yi Zhang.
Regulation of splicing enhancer activities by RNA secondary structures.
FEBS Letters 584(21) (2010), pages 4401-4407.
- Johan Oudinet, Alain Denise, and Marie-Claude Gaudel.
A new dichotomic algorithm for the uniform random generation
of words in regular languages. Proc. GASCom 2010. Preprint
(pdf).
- Cédric Saule, Claire Wallon, and Alain Denise.
Uniform and non-uniform random generation of RNA secondary
structures with pseudoknots. Proc. GASCom 2010. Preprint
(pdf).
- Alain Denise, Yann Ponty and Michel Termier.
Controlled non uniform random generation of decomposable structures.
Theoretical Computer Science 411 (2010) 3527-3552. Preprint
(pdf).
- Claire Herrbach, Alain Denise and Serge Dulucq.
Average complexity of the Jiang-Wang-Zhang pairwise tree alignment
algorithm and of a RNA secondary structure alignment algorithm.
Theoretical Computer Science 411 (2010) 2423-2432. Preprint
(pdf).
- Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, and Alain Denise.
Counting RNA pseudoknotted structures (extended abstract). Proc.
of FPSAC'10 (poster session).
Preprint (pdf).
- Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach
and Hélène Touzet. Alignments of RNA structures.
IEEE/ACM Transactions on Computational Biology and
Bioinformatics 7(2): 309-322 (2010). Preprint
(pdf).
2009
2008
- Mahassine Djelloul and Alain Denise. Automated motif extraction
and classification in RNA tertiary structures.
RNA 14, 2489-2497, 2008.
- Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, Richard
Lassaigne, Johan Oudinet, and Sylvain Peyronnet.
Coverage-biased random exploration of large models and application to
testing.
Technical Report 1494, 25 pages, LRI, Université Paris-Sud XI, June 2008.
[ bib |
pdf ]
- Mahassine Djelloul and Alain Denise. A method for automated
discovering of RNA tertiary motifs. Proc.
JOBIM 2008 47-52.
- Marie-Claude Gaudel, Alain Denise, Sandrine-Dominique Gouraud, Richard
Lassaigne, Johan Oudinet, and Sylvain Peyronnet.
Coverage-biased random exploration of large models.
In ETAPS Workshop on Model Based Testing, Electronic Notes in
Theoretical Computer Science, March 2008, 11 pages.
[ bib ]
- Romain Rivière, Dominique Barth, Johanne Cohen and
Alain Denise. Shuffling biological sequences with motif
constraints. Journal of Discrete Algorithms 6 (2), 192-204,
2008. Preprint
(postscript).
2007
- Claire Herrbach, Alain Denise, and Serge Dulucq. Average
complexity of the Jiang-Wang-Zhang pairwise tree alignment
algorithm and of a RNA secondary structure alignment
algorithm. Proceedings of MACIS 2007. Preprint (pdf).
- Olivier Namy, Yu Zhou, Sarath Gundllapalli, Carla R
Polycarpo, Alain Denise, Jean-Pierre Rousset, Dieter Söll and
Alexandre Ambrogelly. Adding Pyrrolysine to the Escherichia coli
genetic code. FEBS
Letters, 581 (27), 5282-5288, 2007.
2006
-
Romain Rivière, Dominique Barth, and Alain
Denise. Algorithmes d'énumération de motifs dans les réseaux biologiques.
Proc. RIAMS 2006, Lyon, November 2006.
-
Claire Herrbach, Alain Denise, Serge Dulucq and Hélène
Touzet. Alignment of RNA secondary structures using a full set of
operations. LRI
Research Report 1451 (2006), 22 pages, Université Paris-Sud
11.
-
Yann Ponty, Michel Termier and Alain Denise. GenRGenS: Software for
generating random genomic sequences and structures. Bioinformatics
22 (2006) 1534-1535. (Software: GenRGenS).
-
Yann Ponty and Alain Denise. GenRGenS Version 2.0 User Manual.
LRI Research Report 1447 (2006), 42 pages, Université Paris-Sud 11.
- Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud,
Richard Lassaigne, and Sylvain Peyronnet. Uniform random sampling of
traces in very large models. Proceedings
of the First International Workshop on Random Testing (RT 2006),
July 2006, pages 10-19. The ACM Digital Library. Preprint: LRI
Research Report 1445 (2006), 10 pages, Université Paris-Sud
11.
2005
2004
- Romain Rivière, Dominique Barth, Johanne Cohen, and Alain
Denise. Shuffling biological sequences with motifs constraints. In Proc
1st Algorithms and Computational Methods for Biochemical and Evolutionary
Networks (CompBioNets 2004). KCL publications, King's College, London,
2004.
- Alain Denise, Marie-Claude Gaudel, and Sandrine-Dominique Gouraud.
A generic method for statistical testing. In Proc. of 15th IEEE International
Symposium on Software Reliability Engineering (ISSRE 2004), 2004. Preprint: LRI
Research Report 1386 (2004), 10 pages, Université Paris-Sud 11.
- Mireille Régnier and Alain Denise. Rare events and conditional
events on random strings. Discrete
Mathematics an Theoretical Computer Science vol. 6 n° 2 (2004), pp. 191-214.
2003
- Michaël Bekaert, Jean-Paul Forest, Laure Bidou, Alain Denise,
Guillemette Duchateau-Nguyen, Céline Fabret, Christine Froidevaux,
Isabelle Hatin, Jean-Pierre Rousset and Michel Termier. Searching the Saccharomyces
cerevisiae genome for -1 frameshifting sites. Proceedings of ECCB 2003
(European Conference on Computational Biology), September 2003, Paris, pp
4-6. (pdf).
- Sylvie Corteel, Danièle Gardy, Mario Valencia-Pabon, Dominique
Barth and Alain Denise. The permutation-path coloring problem on trees.
Theoretical Computer Science 297 (2003) 119-143. (Preliminary version :
ps)
- Michaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen,
Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset
and Michel Termier. Towards a computational model for eukaryotic -1 frameshifting
sites. Bioinformatics
19 (2003) 327-335.
2002
- Cyril Banderier, Mireille Bousquet-Mélou, Alain Denise, Philippe
Flajolet, Danièle Gardy and Dominique Gouyou-Beauchamps. Generating
functions for generating trees. Discrete Mathematics 246 (2002) 29-55.
(Preliminary version : ps)
2001
- Alain Denise. Structures aléatoires, modèles et analyse
des génomes. Habilitation à Diriger des Recherches, December
2001. (ps).
- Sandrine-Dominique Gouraud, Alain Denise, Marie-Claude Gaudel
and Bruno Marre. A new way for automating statistical testing methods.
In Proceedings of IEEE ASE'01 (Automated Software Engineering), San Diego,
November 2001. (Preliminary version : ps)
- Alain Denise, Mireille Régnier and Mathias Vandenbogaert.
Assessing statistical significance of overrepresented oligonucleotides.
In Proceedings of WABI'01 (Workshop on Algorithms in Bioinformatics), Aarhus,
August 2001. Lecture Notes in Computer Science 2149, pages 85-97. (Preliminary
version : ps)
- Alain Denise, Michaël Bekaert, Laure Bidou, Guillemette Duchateau-Nguyen,
Jean-Paul Forest, Christine Froidevaux, Isabelle Hatin, Jean-Pierre Rousset
and Michel Termier, Vers une modélisation des gènes à
décalage de cadre en -1 dans les génomes eucaryotes. In
Actes de JOBIM'01, Toulouse, May-June 2001, pages 229-237.
2000
- Sylvie Corteel, Alain Denise
and Dominique Gouyou-Beauchamps. Bijections for directed animals on infinite
families of lattices. Annals of Combinatorics 4 (2000) 269-284. (Preliminary
version : ps)
- Alain Denise, Olivier Roques and Michel Termier, Random generation
of words of context-free languages according to the frequencies of letters.
In "Mathematics and Computer Science: Algorithms, Trees, Combinatorics and
Probabilities". Trends in Mathematics, Birkhaüser (2000) 113-125. (Proceedings
of Colloquium on Mathematics and Computer Science, Versailles, September
2000.) (Preliminary version : ps)
- Dominique Barth, Sylvie Corteel, Alain Denise, Danièle Gardy
and Mario Valencia-Pabon, On the complexity of routing permutations on
trees by arc-disjoint paths. In Proceedings of LATIN'2000. Lecture
Notes in Computer Science 1776, 308-317.
1999
- Cyril Banderier, Mireille Bousquet-Mélou, Alain Denise, Philippe
Flajolet, Danièle Gardy and Dominique Gouyou-Beauchamps, On generating
series of generating trees. Proceedings of FPSAC'99, 40-52, June 1999,
Barcelone. (Preliminary version: INRIA Report 3661, April 1999.)
- Alain Denise and Paul
Zimmermann, Uniform random generation of decomposable structures using
floating-point arithmetic. Theoretical Computer Science 218 (1999) 233-248.
(Preliminary version: INRIA
Report 3242, September 1997.)
1998
1997
1996
- Alain Denise, Marcio Vasconcellos and Dominic J.A. Welsh, The random
planar graph. Congressus Numerantium 113 (1996) 61-79. (Preliminary version:
ps)
- Alain Denise, Génération aléatoire uniforme
de mots de langages rationnels.Theoretical Computer Science 159 (1996)
43-63.
- Alain Denise, Génération aléatoire et uniforme
de mots. Discrete Mathematics 153 (1996) 69-84. (Preliminary version:
ps)
1995
- Alain Denise and Rodica
Simion, Two combinatorial statistics on Dyck paths. Discrete Mathematics
137 (1995) 155-176. (Preliminary version: ps)
1994
- Alain Denise, Enumération et génération aléatoire
de chemins. Proceedings of FPSAC'94, 91-97.
- Alain Denise, Méthodes de génération aléatoire
d'objets combinatoires de grande taille et problèmes d'énumération.
Thèse, Université Bordeaux I, Janvier 1994. (Résumé.)
1993
- Alain Denise, Génération aléatoire et uniforme
de mots. Proceedings of FPSAC'93, 153-164.
1992
- Alain Denise and Jean-Guy Penaud, Génération aléatoire
d'animaux dirigés, Actes des Journées Pavages et Polyominos
(1992) 61-69.
- Alain Denise and Nadine Rouillon, Génération de structures
arborescentes. Actes des Journées GROPLAN (1992) 83-90.
Dernière mise à jour le 16 novembre 2011. / Last update
on November 16, 2011.