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Alain Denise

Enseignant Chercheur - Responsable d’équipe

Équipe : Bioinformatique moléculaire

Tél : 01 69 15 46 54
Email : alain.denise(AT)igmors.u-psud.fr

Bât. 400, pièce n°101

My main research interest is Bioinformatics and Computational Biology, notably

  • In silico genome analysis.
  • Algorithmics and combinatorics of genomic sequences and structures.

I work in two labs at University Paris-Sud 11 and CNRS : IGM (Molecular Bioinformatics group) and LRI (Bioinformatics group). I teach bioinformatics and computer science, notably in the Master of Bioinformatics and Biostatistics.
More infos :

My homepage at LRI : http://www.lri.fr/ denise


Publications in Bioinformatics and Biology :

Since 2007 (founding of the Molecular Bioinformatics group at IGM).

* Lamiable A, Barth D, Denise A, Quessette F, Vial S, Westhof E, (2012), Automated prediction of three-way junction topological families in RNA secondary structures, Computational Biology and Chemistry, 37.

* Saule C, Régnier M, Steyaert JM, and Denise A, (2011), Counting RNA pseudoknotted structures, Journal of Computational Biology, 19(10):1339-51

* Liu W, Zhou Y, Hu Z, Sun T, Denise A, Fu X, and Zhang Y, (2010), Regulation of splicing enhancer activities by RNA secondary structures, FEBS Letters, 584(21):4401-7

* Denise A, Ponty Y, and Termier M, (2010), Controlled non uniform random generation of decomposable structures, Theoretical Computer Science 411:3527-3552

* Herrbach C, Denise A and Dulucq S, (2010), Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm. Theoretical Computer Science, 411:2423-2432

* Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet, (2010), Alignment of RNA structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics 7(2) : 309-322.

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

* Mahassine Djelloul and Alain Denise.(2008) Automated motif extraction and classification in RNA tertiary structures. RNA 14, 2489-2497.

* Romain Rivière, Dominique Barth, Johanne Cohen and Alain Denise.(2008) Shuffling biological sequences with motif constraints. Journal of Discrete Algorithms 6 (2), 192-204.

* 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.

Before 2007

* Yann Ponty, Michel Termier and Alain Denise. GenRGenS : Software for generating random genomic sequences and structures. Bioinformatics 22 (2006) 1534-1535 (Software : GenRGenS).

* 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.

* 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.
* 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.

* 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.

* Sylvie Corteel, Alain Denise and Dominique Gouyou-Beauchamps. Bijections for directed animals on infinite families of lattices. Annals of Combinatorics 4 (2000) 269-284.

* Alain Denise and Paul Zimmermann, Uniform random generation of decomposable structures using floating-point arithmetic. Theoretical Computer Science 218 (1999) 233-248.

* Alain Denise, Marcio Vasconcellos and Dominic J.A. Welsh, The random planar graph. Congressus Numerantium 113 (1996) 61-79.

* 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.

* Alain Denise and Rodica Simion, Two combinatorial statistics on Dyck paths. Discrete Mathematics 137 (1995) 155-176.