Alain Denise
62
Documents
Publications
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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⟩
Conference papers
hal-03251765v1
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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
Conference papers
hal-02403517v1
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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⟩
Conference papers
hal-02527738v1
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Homology modeling of complex structural RNAsJOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France
Conference papers
hal-01332642v1
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Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic PathwaysSeqBio 2016, Nov 2016, Nantes, France
Conference papers
hal-01745390v1
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Rank aggregation with ties: Experiments and AnalysisThe 41st International Conference on Very Large Data Bases, Aug 2015, Kohala Coast, Hawaï, United States
Conference papers
hal-01152098v1
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Résultats algorithmiques pour le design d’ARN avec contraintes de séquenceSeqBio 2015, Nov 2015, Orsay, France. pp.26-31
Conference papers
hal-01266096v1
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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⟩
Conference papers
hal-01091053v1
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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
Conference papers
hal-00842021v1
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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
Conference papers
hal-00823279v2
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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
Conference papers
hal-00708580v2
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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
Conference papers
hal-00756345v1
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A new approach to suboptimal pairwise sequence alignmentCompBio 2011: IASTED International Conference on Computational Bioscience, 2011, Cambridge, United Kingdom
Conference papers
inria-00594890v1
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Using medians to generate consensus rankings for biological dataSSDBM 2011: Scientific and Statistical Database Management Conference, 2011, Portland, United States
Conference papers
inria-00584690v1
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Uniform Monte-Carlo Model CheckingFASE 2011, 2011, Saarbrücken, Germany
Conference papers
hal-00644834v1
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Uniform and non-uniform random generation of RNA secondary structures with pseudoknotsGASCOM, Sep 2010, Montreal, Canada
Conference papers
inria-00543315v1
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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⟩
Conference papers
hal-01186262v1
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A new dichotomic algorithm for the uniform random generation of words in regular languagesGASCom 2010, 2010, Montreal, Canada
Conference papers
inria-00542683v1
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Benchmarking RNA secondary structure comparison algorithmsJOBIM'08, 2008, Lille, France. pp.67-68
Conference papers
hal-00375710v1
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Motifs Enumeration Algorithms in Biological Networks2006
Conference papers
hal-00126565v1
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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
Conference papers
hal-00080471v1
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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
Conference papers
inria-00099891v1
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CS: a MuPAD Package for Counting and Randomly Generating Combinatorial Structures10-th conference Formal Power Series and Algebraic Combinatorics, 1998, Toronto, pp.195-204
Conference papers
inria-00107518v1
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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
Conference poster
hal-01167840v1
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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
Conference poster
hal-01098231v1
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Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformaticsAlain Denise; Olivier Lespinet; Mireille Régnier. 2015
Books
hal-01264187v1
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Classements consensuels de données biologiques massives[Rapport de recherche] Université Paris-Saclay/Université Paris-Sud; Laboratoire Interdisciplinaire des Sciences du Numérique. 2021
Reports
hal-03230107v1
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Assessing Statistical Significance of Overrepresented Oligonucleotides[Research Report] RR-4132, INRIA. 2001
Reports
inria-00072496v1
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On Generating Functions of Generating Trees[Research Report] RR-3661, INRIA. 1999
Reports
inria-00073011v1
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Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic[Research Report] RR-3242, INRIA. 1997
Reports
inria-00073447v1
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