User:Alain DENISE

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Current position : Professor, Université Paris-Sud, Orsay (France). Research units : IGM (Institut de Génétique et Microbiologie), UMR CNRS 8621 LRI (Laboratoire de Recherche en Informatique), UMR CNRS 8623 INRIA Saclay, Equipe-projet AMIB

Diploma Habilitation à Diriger les Recherches en Informatique, Université Paris-Sud 11, 2001 Thèse d’Informatique, Université Bordeaux 1, 1994

Professional experiences 1995-2002 : Assistant Professor (Maître de Conférences) in Computer Science Université Paris-Sud. 2000-2002: CNRS fellow (délégation) at IGM (Institut de Génétique et Microbiologie), UMR CNRS 8621, Orsay

Main responsabilities Vice-head of the Computer Science Departmnet of Université Paris-Sud, in charge of Teaching. Member of the Comité National de la Recherche Scientifique, section 7 and CID 43 from 2008 to 2012. Headof the du Master of Bioinformatics and Biostatistics of U'université Paris-Sud 11 from 2004 to 2012.

Resarch activities Min research interests : Bioinformatics – algorithms for genomic sequences and structures – in silico sequence and structure analysis Head of the ANR project “Blanc” 2009-2012 AMIS-ARN (Graph Algorithms and Automatic Softwares for Interactive RNA Structure Modelling).

Publications Selective international journals: 25 Selective international conferences (with proceedings): 22

Some recent publications (recent in 2012):

Philippe Rinaudo, Yann Ponty, Dominique Barth, and Alain Denise. Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots (extended abstract). To appear in Proc. WABI 2012: 12th Workshop on Algorithms in Bioinformatics, 2012.

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. Computational Biology and Chemistry, 37, 2012.

Julien Allali, Cedric Saule, Cedric Chauve, Yves D'Aubenton-Carafa, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine De Monte, Aida Ouangraoua, Marie-France Sagot, Michel Termier, Claude Thermes, and Helene Touzet. BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms. Advances in Bioinformatics vol. 2012, Article ID 893048, 5 pages, 2012. doi:10.1155/2012/893048.

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.

Saule C, Régnier M, Steyaert J-M, and Denise A (2011). Counting RNA pseudoknotted structures. Journal of Computational Biology 19(10) pages 1339-1351, 2011 (free acces).

Liu W, Zhou Y, Hu Z, Sun T, Denise A, Fu X-D, and Zhang Y. Regulation of splicing enhancer activities by RNA secondary structures. FEBS Letters 584(21) (2010), pages 4401-4407.

Alain Denise, Yann Ponty and Michel Termier. Controlled non uniform random generation of decomposable structures. Theoretical Computer Science 411 (2010) 3527-3552.

Blin G, Denise A, Dulucq S, Herrbach C, and Touzet H, (2010), Alignment of RNA structures, IEEE:ACM Transactions on Computational Biology and Bioinformatics 7(2): 309-322 (2010)

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.

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 (2010) 2423-2432.

Darty K, Denise A, and Ponty Y (2009). VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 25(15) 1974-1975.

Djelloul M, and Denise A (2008). Automated motif extraction and classification in RNA tertiary structures. RNA 14:2489-2497.

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