Alain Denise
- BioInformatique - LISN (BioInfo)
- Institut de Biologie Intégrative de la Cellule (I2BC)
- Bioinformatique (LRI) (BioInfo - LRI)
- Bioinformatique (LRI) (BioInfo - LRI)
Publications
Publications
Searching for variable structural motifs in RNA graphs using simple descriptorsJOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Université de Bordeaux, Jul 2025, Bordeaux, France |
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A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures19th Symposium on Experimental Algorithms, Jun 2021, Nice (virtuel), France. ⟨10.4230/LIPIcs.SEA.2021.19⟩ |
A Graph-based Similarity Approach to Classify Recurrent Complex Motifs from their Context in RNA StructuresJOBIM 2021, Jul 2021, Paris, France. pp.15 |
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Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data2019 15th International Conference on eScience (eScience), Sep 2019, San Diego, France. pp.136-145, ⟨10.1109/eScience.2019.00022⟩ |
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Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity testsSEQBIM 2019 - Séquences en Bioinformatique, Informatique et Mathématiques, Dec 2019, Marne-la-Vallée, France |
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Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic PathwaysSeqBio 2016, Nov 2016, Nantes, France |
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Homology modeling of complex structural RNAsJOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France |
Rank aggregation with ties: Experiments and AnalysisThe 41st International Conference on Very Large Data Bases, Aug 2015, Kohala Coast, Hawaï, United States |
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Résultats algorithmiques pour le design d’ARN avec contraintes de séquenceSeqBio 2015, Nov 2015, Orsay, France. pp.26-31 |
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ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data10th International Conference, Data Integration in the Life Sciences, Jul 2014, Lisbon, Portugal. pp.128 - 142, ⟨10.1007/978-3-319-08590-6_13⟩ |
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Flexible RNA design under structure and sequence constraints using formal languagesACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States |
Comparative analysis of phylogenetic profiles for the enzymatic characterization of fungal groupJOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. à paraître |
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Graph Algorithms and Software Framework for Interactive RNA Structure ModellingJournees Ouvertes de Biologie Informatique et Mathematiques - JOBIM'12, Jul 2012, Rennes, France. pp.475-476 |
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Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknotsWABI - 12th Workshop on Algorithms in Bioinformatics - 2012, University of Ljubljana, Sep 2012, Ljubljana, Slovenia |
Using medians to generate consensus rankings for biological dataSSDBM 2011: Scientific and Statistical Database Management Conference, 2011, Portland, United States |
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Uniform Monte-Carlo Model CheckingFASE 2011, 2011, Saarbrücken, Germany |
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A new approach to suboptimal pairwise sequence alignmentCompBio 2011: IASTED International Conference on Computational Bioscience, 2011, Cambridge, United Kingdom |
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A new dichotomic algorithm for the uniform random generation of words in regular languagesGASCom 2010, 2010, Montreal, Canada |
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Counting RNA pseudoknotted structures (extended abstract)22nd International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC 2010), 2010, San Francisco, United States. pp.1037-1048, ⟨10.46298/dmtcs.2834⟩ |
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Uniform and non-uniform random generation of RNA secondary structures with pseudoknotsGASCOM, Sep 2010, Montreal, Canada |
Benchmarking RNA secondary structure comparison algorithmsJOBIM'08, 2008, Lille, France. pp.67-68 |
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Uniform Random Sampling of Traces in Very Large ModelsFirst International Workshop on Random Testing, 2006, Portland, Maine, United States. pp.10-19 |
Motifs Enumeration Algorithms in Biological Networks2006 |
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Shuffling biological sequencess with motifs constraintsAlgorithms and Computational Methods for Biochemical and Evolutionary Networks - CompBioNets'2004, Dec 2004, Recife, Brazil. 18 p |
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CS: a MuPAD Package for Counting and Randomly Generating Combinatorial Structures10-th conference Formal Power Series and Algebraic Combinatorics, Jun 1998, Toronto, Canada. pp.195-204 |
A graph-based approach to classify A-minor motifs in RNA structures according to their structural contextISMB: Intelligent Systems for Molecular Biology, Jul 2020, Virtual conference (Covid), Canada. ⟨10.7490/f1000research.1118288.1⟩ |
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A graph-based approach to classify A-minor motifs in RNA structures according to their structural contextJOBIM 2020, Jun 2020, Montpellier, France. JOBIM 2020 Poster Proceedings, pp.34, 2020 |
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Interrogation de bases de données biologiques publiques par reformulation de requêtes et classement des résultats avec ConQuR-BioJOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , pp.35 slides, 2015 |
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A new method for improving the prediction and the functional annotation of ortholog groupsProc. ECCB'14, the 13th European Conference on Computational Biology, 2014, Strasbourg, France. Proc. ECCB'14, the 13th European Conference on Computational Biology, 2014 |
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Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformaticsAlain Denise; Olivier Lespinet; Mireille Régnier. 2015 |
Modélisation des systèmes biologiques, bioinformatiqueRapport de conjoncture 2010 du Comité national de la recherche scientifique, CNRS Editions, chapitre 43, 845-858, 2011, 978-2-271-07263-4 |