Publications d'Alain Denise

• 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.

• 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).

• Kevin Darty, Alain Denise and Yann Ponty. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25(15):1974-1975, 2009.

• 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).

• 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.

• 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.

• Elodie Nédélec, Thomas Moncion, Elisabeth Gassiat, Bruno Bossard, Guillemette Duchateau-Nguyen, Alain Denise and Michel Termier. A pairwise alignment algorithm which favours clusters of blocks. Journal of Computational Biology, vol. 12, n° 1 (2005) , pp 33-47.

• 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.
  
  

• 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.

• 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) 

• 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.

• 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.

• 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.)

• Alain Denise, Isabelle Dutour and Paul Zimmermann, CS: a MuPAD package for Counting and Randomly Generating Combinatorial Structures.Proceedings of FPSAC'98, 195-204. (Also in MathPAD 8 (1) 1998.) (ps, package.)

Alain Denise, Christoph Dürr and Fouad Ibn-Majdoub-Hassani, Enumération et génération aléatoire de polyominos en réseau hexagonal. Proceedings of FPSAC'97, 222-234. (ps, program by Christoph Dürr.)

• 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)

• Alain Denise and Rodica Simion, Two combinatorial statistics on Dyck paths. Discrete Mathematics 137 (1995) 155-176. (Preliminary version: ps)

• 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.)

• Alain Denise, Génération aléatoire et uniforme de mots. Proceedings of FPSAC'93, 153-164.

• 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.