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Alain Denise

Professeur, Université Paris-Saclay
64
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Publications

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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⟩
Journal articles hal-04227695v1
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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⟩
Journal articles hal-03864666v1
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Efficient, robust and effective rank aggregation for massive biological datasets

Pierre Andrieu , Bryan Brancotte , Laurent Bulteau , Sarah Cohen-Boulakia , Alain Denise
Future Generation Computer Systems, 2021, 124, pp.406-421. ⟨10.1016/j.future.2021.06.013⟩
Journal articles hal-03388443v1
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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⟩
Journal articles hal-03381570v1

CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts

Alexandra Zaharia , Bernard Labedan , Christine Froidevaux , Alain Denise
BMC Bioinformatics, 2019, 20 (1), ⟨10.1186/s12859-018-2542-2⟩
Journal articles hal-01979512v1

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⟩
Journal articles hal-02431369v1
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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, ⟨10.1093/nar/gky197⟩
Journal articles 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⟩
Journal articles hal-01589347v1
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Rank aggregation with ties: Experiments and Analysis

Bryan Brancotte , Bo Yang , Guillaume Blin , Sarah Cohen-Boulakia , Alain Denise
Proceedings of the VLDB Endowment (PVLDB), 2015, Proceedings of the VLDB Endowment (PVLDB), 8 (11), pp.1202-1213. ⟨10.14778/2809974.2809982⟩
Journal articles 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⟩
Journal articles hal-01201665v1
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A meta-approach for improving the prediction and the functional annotation of ortholog groups

Cécile Pereira , Alain Denise , Olivier Lespinet
Journal articles inserm-01229454v1

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⟩
Journal articles hal-00759573v1

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 Tang
Nature Structural and Molecular Biology, 2014, 21, pp.997-1005. ⟨10.1038/nsmb.2906⟩
Journal articles hal-01097740v1

A meta-approach for improving the prediction and the functional annotation of ortholog groups

Cécile Pereira , Alain Denise , Olivier Lespinet
BMC Genomics, 2014, 15 (S6), pp.S16. ⟨10.1186/1471-2164-15-S6-S16⟩
Journal articles hal-04011150v1
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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
Journal articles 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⟩
Journal articles hal-00832110v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Journal articles hal-00647725v1

Automated prediction of three-way junction topological families in RNA secondary structures

Alexis Lamiable , Dominique Barth , Alain Denise , Franck Quessette , Sandrine Vial
Computational Biology and Chemistry, 2012, 37, pp.1-5
Journal articles hal-00641738v1

Coverage-biased random exploration of large models and application to testing

Alain Denise , Marie-Claude Gaudel , Sandrine-Dominique Gouraud , Richard Lassaigne , Johan Oudinet
International Journal on Software Tools for Technology Transfer, 2012, 14 (1), pp.73-93
Journal articles inria-00560621v1
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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⟩
Journal articles inria-00537117v1
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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⟩
Journal articles hal-00483581v2

Regulation of splicing enhancer activities by RNA secondary structures

Wei Liu , Yu Zhou , Zexi Hu , Tao Sun , Alain Denise
FEBS Letters, 2010, 584 (21), pp.4401-7. ⟨10.1016/j.febslet.2010.09.039⟩
Journal articles hal-00534366v1
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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
Journal articles inria-00541269v1
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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⟩
Journal articles hal-00506348v1
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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⟩
Journal articles hal-00432548v1

Automated motif extraction and classification in RNA tertiary structures.

Mahassine Djelloul , Alain Denise
RNA, 2008, 14 (12), pp.2489-97. ⟨10.1261/rna.1061108⟩
Journal articles hal-00353402v1

Shuffling biological sequences with motif constraints

R. Rivière , D. Barth , J. Cohen , Alain Denise
Journal of Discrete Algorithms, 2008, 6 (2), pp.192-204
Journal articles hal-00297151v1

A method for automated discovering of RNA tertiary motifs

M. Djelloul , Alain Denise
Proc. JOBIM, 2008, pp.47-52
Journal articles hal-00297159v1

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⟩
Journal articles inria-00187827v1

Adding pyrrolysine to the Escherichia coli genetic code.

Olivier Namy , Yu Zhou , Sarath Gundllapalli , Carla R Polycarpo , Alain Denise
FEBS Letters, 2007, 581 (27), pp.5282-8. ⟨10.1016/j.febslet.2007.10.022⟩
Journal articles hal-00195226v1
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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⟩
Journal articles inria-00548871v1
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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⟩
Journal articles hal-00959004v1
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Generating functions for generating trees

Cyril Banderier , Philippe Flajolet , Danièle Gardy , Mireille Bousquet-Mélou , Alain Denise
Discrete Mathematics, 2002, 246 (1-3), pp.29-55
Journal articles 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⟩
Journal articles 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
Journal articles hal-00306639v1
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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⟩
Conference papers 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, Institut Pasteur (Paris), France. pp.15
Conference papers hal-04469623v1
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Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data

Pierre Andrieu , Bryan Brancotte , Laurent Bulteau , Sarah Cohen-Boulakia , Alain Denise
2019 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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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
Conference papers hal-02403517v1
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Heterogeneous Graph Mining for Biological Pattern Discovery in Metabolic Pathways

Alexandra Zaharia , Bernard Labedan , Christine Froidevaux , Alain Denise
SeqBio 2016, Nov 2016, Nantes, France
Conference papers hal-01745390v1
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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
Conference papers hal-01332642v1

Rank aggregation with ties: Experiments and Analysis

Bryan Brancotte , Bo Yang , Guillaume Blin , Sarah Cohen-Boulakia , Alain Denise
The 41st International Conference on Very Large Data Bases, Aug 2015, Kohala Coast, Hawaï, United States
Conference papers 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
Conference papers hal-01266096v1
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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⟩
Conference papers hal-01091053v1

Comparative analysis of phylogenetic profiles for the enzymatic characterization of fungal group

Cécile Pereira , Jérôme Azé , Alain Denise , Christine Drevet , Christine Froidevaux
JOBIM 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 languages

Yu Zhou , Yann Ponty , Stéphane Vialette , Jérôme Waldispühl , Yi Zhang
ACM-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 pseudoknots

Philippe Rinaudo , Yann Ponty , Dominique Barth , Alain Denise
WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, University of Ljubljana, Sep 2012, Ljubljana, Slovenia
Conference papers hal-00708580v2

Graph Algorithms and Software Framework for Interactive RNA Structure Modelling

Fabrice Jossinet , Alexis Lamiable , Philippe Rinaudo , Liza Al-Shikhley , Franck Quessette
Journees Ouvertes de Biologie Informatique et Mathematiques - JOBIM'12, Jul 2012, Rennes, France. pp.475-476
Conference papers hal-00756345v1

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
Conference papers inria-00584690v1

Uniform Monte-Carlo Model Checking

Johan Oudinet , Alain Denise , Marie-Claude Gaudel , Richard Lassaigne , Sylvain Peyronnet
FASE 2011, 2011, Saarbrücken, Germany
Conference papers 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
Conference papers 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
Conference papers inria-00542683v1
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Uniform and non-uniform random generation of RNA secondary structures with pseudoknots

Cédric Saule , Claire Wallon , Alain Denise
GASCOM, Sep 2010, Montreal, Canada
Conference papers inria-00543315v1
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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⟩
Conference papers hal-01186262v1

Benchmarking RNA secondary structure comparison algorithms

Julien Allali , Yves d'Aubenton-Carafa , Cedric Chauve , Alain Denise , Christine Drevet
JOBIM'08, 2008, Lille, France. pp.67-68
Conference papers hal-00375710v1
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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
Conference papers hal-00080471v1

Motifs Enumeration Algorithms in Biological Networks

Dominique Barth , Alain Denise , Romain Rivière
2006
Conference papers hal-00126565v1
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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
Conference papers inria-00099891v1
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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, 1998, Toronto, pp.195-204
Conference papers inria-00107518v1

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
Conference poster hal-04469625v1

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
Conference poster hal-04469616v1

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
Conference poster 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
Conference poster hal-01098231v1