Alain Denise Professeur, Université Paris-Saclay

Publications

Article dans une revue (36)

A unifying rank aggregation framework to suitably and efficiently aggregate any kind of rankings Pierre Andrieu,Sarah Cohen-Boulakia,Miguel Couceiro,Alain Denise,Adeline Pierrot International Journal of Approximate Reasoning, 2023, 162, pp.109035. ⟨10.1016/j.ijar.2023.109035⟩ Article dans une revue hal-04227695v1
On the predictibility of A-minor motifs from their local contexts Coline Gianfrotta,Vladimir Reinharz,Olivier Lespinet,Dominique Barth,Alain Denise RNA Biology, 2022, 19 (1), pp.1208-1227. ⟨10.1080/15476286.2022.2144611⟩ Article dans une revue hal-03864666v1
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs Antoine Soulé,Vladimir Reinharz,Roman Sarrazin-Gendron,Alain Denise,Jérôme Waldispühl PLoS Computational Biology, 2021, 17 (5), pp.e1008990. ⟨10.1371/journal.pcbi.1008990⟩ Article dans une revue hal-03381570v1
Efficient, robust and effective rank aggregation for massive biological datasets Pierre Andrieu,Bryan Brancotte,Laurent Bulteau,Sarah Cohen-Boulakia,Alain Deniseet al. Future Generation Computer Systems, 2021, 124, pp.406-421. ⟨10.1016/j.future.2021.06.013⟩ Article dans une revue hal-03388443v1
Bounds on Autocorrelation Coefficients of Rudin-Shapiro Polynomials Jean-Paul Allouche,S. Choi,Alain Denise,T. Erdélyi,B. Saffari Analysis Mathematica, 2019, 45 (4), pp.705-726. ⟨10.1007/s10476-019-0003-4⟩ Article dans une revue hal-02431369v1
CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts Alexandra Zaharia,Bernard Labedan,Christine Froidevaux,Alain Denise BMC Bioinformatics, 2019, 20 (1), pp.19. ⟨10.1186/s12859-018-2542-2⟩ Article dans une revue hal-01979512v1
Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families Vladimir Reinharz,Antoine Soulé,Eric Westhof,Jérôme Waldispühl,Alain Denise Nucleic Acids Research, 2018, 46 (8), pp.3841-3851. ⟨10.1093/nar/gky197⟩ Article dans une revue hal-01745345v1
GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization. Mélanie Boudard,Dominique Barth,Julie Bernauer,Alain Denise,Johanne Cohen Bioinformatics, 2017, 16, pp.2479-2486. ⟨10.1093/bioinformatics/btx175⟩ Article dans une revue hal-01589347v1
Rank aggregation with ties: Experiments and Analysis Bryan Brancotte,Bo Yang,Guillaume Blin,Sarah Cohen-Boulakia,Alain Deniseet al. Proceedings of the VLDB Endowment (PVLDB), 2015, Proceedings of the VLDB Endowment (PVLDB), 8 (11), pp.1202-1213. ⟨10.14778/2809974.2809982⟩ Article dans une revue hal-01165336v1
GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies. Mélanie Boudard,Julie Bernauer,Dominique Barth,Johanne Cohen,Alain Denise PLoS ONE, 2015, 10 (8), pp.e0136444. ⟨10.1371/journal.pone.0136444⟩ Article dans une revue hal-01201665v1
Optimisation problems for pairwise RNA sequence and structure comparison: a brief survey Alain Denise,Philippe Rinaudo Transactions on Computational Collective Intelligence, 2014, 13, pp.70-82. ⟨10.1007/978-3-642-54455-2_3⟩ Article dans une revue hal-00759573v1
A meta-approach for improving the prediction and the functional annotation of ortholog groups Cécile Pereira,Alain Denise,Olivier Lespinet BMC Genomics, 2014, ⟨10.1186/1471-2164-15-S6-S16⟩ Article dans une revue inserm-01229454v1
Mechanisms for U2AF to define 3' splice sites and regulate alternative splicing in the human genome Changwei Shao,Bo Yang,Tongbin Wu,Jie Huang,Peng Tanget al. Nature Structural and Molecular Biology, 2014, 21, pp.997-1005. ⟨10.1038/nsmb.2906⟩ Article dans une revue hal-01097740v1
A new dichotomic algorithm for the uniform random generation of words in regular languages (journal version) Johan Oudinet,Alain Denise,Marie-Claude Gaudel Theoretical Computer Science, 2013, 502, pp.165-176. ⟨10.1016/j.tcs.2012.07.025⟩ Article dans une revue hal-00716558v1
An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure. Alexis Lamiable,Franck Quessette,Sandrine Vial,Dominique Barth,Alain Denise IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, 10 (1), pp.193-199. ⟨10.1109/TCBB.2012.148⟩ Article dans une revue hal-00832110v1
BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms Julien Allali,Cédric Saule,Cedric Chauve,Yves d'Aubenton-Carafa,Alain Deniseet al. Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩ Article dans une revue hal-00647725v1
Automated prediction of three-way junction topological families in RNA secondary structures Alexis Lamiable,Dominique Barth,Alain Denise,Franck Quessette,Sandrine Vialet al. Computational Biology and Chemistry, 2012, 37, pp.1-5. ⟨10.1016/j.compbiolchem.2011.11.001⟩ Article dans une revue istex hal-00641738v1
Coverage-biased random exploration of large models and application to testing Alain Denise,Marie-Claude Gaudel,Sandrine-Dominique Gouraud,Richard Lassaigne,Johan Oudinetet al. International Journal on Software Tools for Technology Transfer, 2012, 14 (1), pp.73-93. ⟨10.1007/s10009-011-0190-1⟩ Article dans une revue istex inria-00560621v1
Counting RNA pseudoknotted structures Cédric Saule,Mireille Regnier,Jean-Marc Steyaert,Alain Denise Journal of Computational Biology, 2011, 18 (10), pp.1339-1351. ⟨10.1089/cmb.2010.0086⟩ Article dans une revue inria-00537117v1
Controlled non uniform random generation of decomposable structures Alain Denise,Yann Ponty,Michel Termier Theoretical Computer Science, 2010, 411 (40-42), pp.3527-3552. ⟨10.1016/j.tcs.2010.05.010⟩ Article dans une revue hal-00483581v2
Regulation of splicing enhancer activities by RNA secondary structures Wei Liu,Yu Zhou,Zexi Hu,Tao Sun,Alain Deniseet al. FEBS Letters, 2010, 584 (21), pp.4401-7. ⟨10.1016/j.febslet.2010.09.039⟩ Article dans une revue hal-00534366v1
Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm Claire Herrbach,Alain Denise,Serge Dulucq Theoretical Computer Science, 2010, 411, pp.2423-2432 Article dans une revue inria-00541269v1
Alignments of RNA structures. Guillaume Blin,Alain Denise,Serge Dulucq,Claire Herrbach,Helene Touzet IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, 7 (2), pp.309-322. ⟨10.1109/TCBB.2008.28⟩ Article dans une revue hal-00506348v1
VARNA: Interactive drawing and editing of the RNA secondary structure. Kévin Darty,Alain Denise,Yann Ponty Bioinformatics, 2009, 25 (15), pp.1974-5. ⟨10.1093/bioinformatics/btp250⟩ Article dans une revue hal-00432548v1
Benchmarking RNA secondary structure comparison algorithms J. Allali,Y. d'Aubenton-Carafa,C. Chauve,A. Denise,C. Drevetet al. Proc. JOBIM, 2008, pp.67-68 Article dans une revue hal-00297167v1
Classification automatique en famille des jonctions triples de l'ARN D. Barth,A. Denise,A. Lamiable,F. Quessette,S. Vial Proc. JOBIM, 2008, pp.65-66 Article dans une revue hal-00297171v1
Shuffling biological sequences with motif constraints R. Rivière,D. Barth,J. Cohen,A. Denise Journal of Discrete Algorithms, 2008, 6 (2), pp.192-204. ⟨10.1016/j.jda.2007.06.001⟩ Article dans une revue istex hal-00665609v1
Shuffling biological sequences with motif constraints R. Rivière,D. Barth,J. Cohen,Alain Denise Journal of Discrete Algorithms, 2008, 6 (2), pp.192-204. ⟨10.1016/j.jda.2007.06.001⟩ Article dans une revue istex hal-00297151v1
Automated motif extraction and classification in RNA tertiary structures. Mahassine Djelloul,Alain Denise RNA, 2008, 14 (12), pp.2489-97. ⟨10.1261/rna.1061108⟩ Article dans une revue hal-00353402v1
Shuffling biological sequences with motif constraints. Dominique Barth,Johanne Cohen,Alain Denise,Romain Rivière Journal of Discrete Algorithms, 2007, ⟨10.1016/j.jda.2007.06.001⟩ Article dans une revue istex inria-00187827v1
Adding pyrrolysine to the Escherichia coli genetic code Olivier Namy,Yu Zhou,Sarath Gundllapalli,Carla R Polycarpo,Alain Deniseet al. FEBS Letters, 2007, 581 (27), pp.5282-8. ⟨10.1016/j.febslet.2007.10.022⟩ Article dans une revue hal-00195226v1
GenRGenS: Software for Generating Random Genomic Sequences and Structures Yann Ponty,Michel Termier,Alain Denise Bioinformatics, 2006, 22 (12), pp.1534--1535. ⟨10.1093/bioinformatics/btl113⟩ Article dans une revue inria-00548871v1
Rare Events and Conditional Events on Random Strings Mireille Régnier,Alain Denise Discrete Mathematics and Theoretical Computer Science, 2004, Vol. 6 no. 2 (2), pp.191-214. ⟨10.46298/dmtcs.310⟩ Article dans une revue hal-00959004v1
Generating functions for generating trees Cyril Banderier,Philippe Flajolet,Danièle Gardy,Mireille Bousquet-Mélou,Alain Deniseet al. Discrete Mathematics, 2002, 246 (1-3), pp.29-55 Article dans une revue hal-00003258v1
Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic Alain Denise,Paul Zimmermann Theoretical Computer Science, 1999, 218 (2), pp.233-248. ⟨10.1016/S0304-3975(98)00323-5⟩ Article dans une revue inria-00098797v1
CS: a MuPAD package for counting and randomly generating combinatorial structures Alain Denise,Isabelle Dutour,Paul Zimmermann MathPAD, 1998, 8, pp.23-30 Article dans une revue hal-00306639v1

Communication dans un congrès (26)

Searching for variable structural motifs in RNA graphs using simple descriptors Camille de Amorim,Alain Denise JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Université de Bordeaux, Jul 2025, Bordeaux, France Communication dans un congrès hal-05301347v1
A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures Coline Gianfrotta,Vladimir Reinharz,Dominique Barth,Alain Denise 19th Symposium on Experimental Algorithms, Jun 2021, Nice (virtuel), France. ⟨10.4230/LIPIcs.SEA.2021.19⟩ Communication dans un congrès hal-03251765v1
A Graph-based Similarity Approach to Classify Recurrent Complex Motifs from their Context in RNA Structures Coline Gianfrotta,Vladimir Reinharz,Dominique Barth,Alain Denise JOBIM 2021, Jul 2021, Paris, France. pp.15 Communication dans un congrès hal-04469623v1
Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data Pierre Andrieu,Bryan Brancotte,Laurent Bulteau,Sarah Cohen-Boulakia,Alain Deniseet al. 2019 15th International Conference on eScience (eScience), Sep 2019, San Diego, France. pp.136-145, ⟨10.1109/eScience.2019.00022⟩ Communication dans un congrès hal-02527738v1
Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity tests Maher Mallem,Alain Denise,Yann Ponty SEQBIM 2019 - Séquences en Bioinformatique, Informatique et Mathématiques, Dec 2019, Marne-la-Vallée, France Communication dans un congrès hal-02403517v1
Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic Pathways Alexandra Zaharia,Bernard Labedan,Christine Froidevaux,Alain Denise SeqBio 2016, Nov 2016, Nantes, France Communication dans un congrès hal-01745390v1
Homology ­modeling of complex structural RNAs Wei Wang​,Matthieu Barba​,Philippe Rinaudo​,Alain Denise,Yann Ponty JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France Communication dans un congrès hal-01332642v1
Rank aggregation with ties: Experiments and Analysis Bryan Brancotte,Bo Yang,Guillaume Blin,Sarah Cohen-Boulakia,Alain Deniseet al. The 41st International Conference on Very Large Data Bases, Aug 2015, Kohala Coast, Hawaï, United States Communication dans un congrès hal-01152098v1
Résultats algorithmiques pour le design d’ARN avec contraintes de séquence Vincent Le Gallic,Alain Denise,Yann Ponty SeqBio 2015, Nov 2015, Orsay, France. pp.26-31 Communication dans un congrès hal-01266096v1
ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data Bryan Brancotte,Bastien Rance,Alain Denise,Sarah Cohen-Boulakia 10th International Conference, Data Integration in the Life Sciences, Jul 2014, Lisbon, Portugal. pp.128 - 142, ⟨10.1007/978-3-319-08590-6_13⟩ Communication dans un congrès hal-01091053v1
Flexible RNA design under structure and sequence constraints using formal languages Yu Zhou,Yann Ponty,Stéphane Vialette,Jérôme Waldispühl,Yi Zhanget al. ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States Communication dans un congrès hal-00823279v2
Comparative analysis of phylogenetic profiles for the enzymatic characterization of fungal group Cécile Pereira,Jérôme Azé,Alain Denise,Christine Drevet,Christine Froidevauxet al. JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. à paraître Communication dans un congrès hal-00842021v1
Graph Algorithms and Software Framework for Interactive RNA Structure Modelling Fabrice Jossinet,Alexis Lamiable,Philippe Rinaudo,Liza Al-Shikhley,Franck Quessetteet al. Journees Ouvertes de Biologie Informatique et Mathematiques - JOBIM'12, Jul 2012, Rennes, France. pp.475-476 Communication dans un congrès hal-00756345v1
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots Philippe Rinaudo,Yann Ponty,Dominique Barth,Alain Denise WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, University of Ljubljana, Sep 2012, Ljubljana, Slovenia Communication dans un congrès hal-00708580v2
Using medians to generate consensus rankings for biological data Sarah Cohen-Boulakia,Alain Denise,Sylvie Hamel SSDBM 2011: Scientific and Statistical Database Management Conference, 2011, Portland, United States Communication dans un congrès inria-00584690v1
Uniform Monte-Carlo Model Checking Johan Oudinet,Alain Denise,Marie-Claude Gaudel,Richard Lassaigne,Sylvain Peyronnet FASE 2011, 2011, Saarbrücken, Germany Communication dans un congrès hal-00644834v1
A new approach to suboptimal pairwise sequence alignment Peter Clote,Lou Feng,Alain Denise CompBio 2011: IASTED International Conference on Computational Bioscience, 2011, Cambridge, United Kingdom Communication dans un congrès inria-00594890v1
A new dichotomic algorithm for the uniform random generation of words in regular languages Johan Oudinet,Alain Denise,Marie-Claude Gaudel GASCom 2010, 2010, Montreal, Canada Communication dans un congrès inria-00542683v1
Counting RNA pseudoknotted structures (extended abstract) Cédric Saule,Mireille Regnier,Jean-Marc Steyaert,Alain Denise 22nd International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC 2010), 2010, San Francisco, United States. pp.1037-1048, ⟨10.46298/dmtcs.2834⟩ Communication dans un congrès hal-01186262v1
Uniform and non-uniform random generation of RNA secondary structures with pseudoknots Cédric Saule,Claire Wallon,Alain Denise GASCOM, Sep 2010, Montreal, Canada Communication dans un congrès inria-00543315v1
Benchmarking RNA secondary structure comparison algorithms Julien Allali,Yves d'Aubenton-Carafa,Cedric Chauve,Alain Denise,Christine Drevetet al. JOBIM'08, 2008, Lille, France. pp.67-68 Communication dans un congrès hal-00375710v1
A method for automated discovering of RNA tertiary motifs M. Djelloul,Alain Denise JOBIM 2008, Jun 2008, Lille, France. pp.47-52 Communication dans un congrès hal-00297159v1
Uniform Random Sampling of Traces in Very Large Models Alain Denise,Marie-Claude Gaudel,Sandrine-Dominique Gouraud,Richard Lasseigne,Sylvain Peyronnet First International Workshop on Random Testing, 2006, Portland, Maine, United States. pp.10-19 Communication dans un congrès hal-00080471v1
Motifs Enumeration Algorithms in Biological Networks Dominique Barth,Alain Denise,Romain Rivière 2006 Communication dans un congrès hal-00126565v1
Shuffling biological sequencess with motifs constraints Dominique Barth,Johanne Cohen,Alain Denise,Romain Rivière Algorithms and Computational Methods for Biochemical and Evolutionary Networks - CompBioNets'2004, Dec 2004, Recife, Brazil. 18 p Communication dans un congrès inria-00099891v1
CS: a MuPAD Package for Counting and Randomly Generating Combinatorial Structures Alain Denise,Isabelle Dutour,Paul Zimmermann 10-th conference Formal Power Series and Algebraic Combinatorics, Jun 1998, Toronto, Canada. pp.195-204 Communication dans un congrès inria-00107518v1

Poster de conférence (4)

A graph-based approach to classify A-minor motifs in RNA structures according to their structural context Coline Gianfrotta,Vladimir Reinharz,Olivier Lespinet,Dominique Barth,Alain Denise ISMB: Intelligent Systems for Molecular Biology, Jul 2020, Virtual conference (Covid), Canada. ⟨10.7490/f1000research.1118288.1⟩ Poster de conférence hal-04469616v1
A graph-based approach to classify A-minor motifs in RNA structures according to their structural context Coline Gianfrotta,Vladimir Reinharz,Olivier Lespinet,Dominique Barth,Alain Denise JOBIM 2020, Jun 2020, Montpellier, France. JOBIM 2020 Poster Proceedings, pp.34, 2020 Poster de conférence hal-04469625v1
Interrogation de bases de données biologiques publiques par reformulation de requêtes et classement des résultats avec ConQuR-Bio Bryan Brancotte,Bastien Rance,Alain Denise,Sarah Cohen-Boulakia JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , pp.35 slides, 2015 Poster de conférence hal-01167840v1
A new method for improving the prediction and the functional annotation of ortholog groups Cécile Pereira,Alain Denise,Olivier Lespinet Proc. ECCB'14, the 13th European Conference on Computational Biology, 2014, Strasbourg, France. Proc. ECCB'14, the 13th European Conference on Computational Biology, 2014 Poster de conférence hal-01098231v1

Ouvrages (1)

Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics Alain Denise,Olivier Lespinet,Mireille Régnier Alain Denise; Olivier Lespinet; Mireille Régnier. 2015 Ouvrages hal-01264187v1

Chapitre d'ouvrage (1)

Modélisation des systèmes biologiques, bioinformatique Olivier Gascuel,P. Benas,C. Brun,D. Burnouf,Alexandre de Brevernet al. Rapport de conjoncture 2010 du Comité national de la recherche scientifique, CNRS Editions, chapitre 43, 845-858, 2011, 978-2-271-07263-4 Chapitre d'ouvrage hal-00799641v1