A. Denise

发表

Random generation of words of context-free languages according to the frequencies of letters

A. Denise, Olivier Roques, M. Termier, 2000 .

CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts

B. Labedan, A. Denise, C. Froidevaux, 2019, BMC Bioinformatics.

Algorithmique des séquences pour la bioinformatique String algorithms for bioinformatics Editeurs

M. Régnier, A. Denise, O. Lespinet, 2020 .

Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics

M. Régnier, A. Denise, O. Lespinet, 2015 .

Uniform random generation of words of rational languages

Alain Denise, A. Denise, 1996 .

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies

D. Barth, Johanne Cohen, A. Denise, 2015, PloS one.

Random and uniform word generation

A. Denise, 1996 .

The permutation-path coloring problem on trees

Dominique Barth, Danièle Gardy, Mario Valencia-Pabon, 2003, Theor. Comput. Sci..

Bijections for Directed Animals on Infinite Families of Lattices

A. Denise, S. Corteel, D. Gouyou-Beauchamps, 2000 .

Adding pyrrolysine to the Escherichia coli genetic code

D. Söll, O. Namy, J. Rousset, 2007, FEBS letters.

Threshold Phenomena in an "easy" Class of Random Lattices and Eecient Reduction Algorithms Random Assignment Problem and Asymptotic Essential Uniqueness in Optimization over Random Data the Kernel Method the Height and Width of Simple Trees

D. Aldous, M. Yor, P. Flajolet, 2022 .

On the predictibility of A-minor motifs from their local contexts

A. Denise, Vladimir Reinharz, O. Lespinet, 2022, RNA biology.

Uniform Random Generation of Decomposable Structures Using Floating-Point Arithmetic

Alain Denise, Paul Zimmermann, P. Zimmermann, 1999, Theor. Comput. Sci..

Generating functions for generating trees

Mireille Bousquet-Mélou, Danièle Gardy, Cyril Banderier, 2002, Discret. Math..

GARN2: coarse‐grained prediction of 3D structure of large RNA molecules by regret minimization

Johanne Cohen, Dominique Barth, Alain Denise, 2017, Bioinform..

Regulation of splicing enhancer activities by RNA secondary structures

Alain Denise, Xiang-Dong Fu, Yi Zhang, 2010, FEBS letters.

VARNA: Interactive drawing and editing of the RNA secondary structure

Yann Ponty, Alain Denise, Kévin Darty, 2009, Bioinform..

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

Alain Denise, Jérôme Waldispühl, Vladimir Reinharz, 2018, Nucleic acids research.

Automated motif extraction and classification in RNA tertiary structures.

Alain Denise, A. Denise, Mahassine Djelloul, 2008, RNA.

Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity tests

Alain Denise, Maher Mallem, Yann Ponty, 2019 .

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

Alain Denise, Olivier Lespinet, Cecile Pereira, 2014, BMC Genomics.

Mechanisms for U2AF to define 3′ splice sites and regulate alternative splicing in the human genome

Yi Zhang, Alain Denise, Jie Zhou, 2014, Nature Structural &Molecular Biology.

Towards a computational model for −1 eukaryotic frameshifting sites

Michel Termier, Christine Froidevaux, Alain Denise, 2003, Bioinform..

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Daniel Gautheret, Michel Termier, Julien Allali, 2012, Adv. Bioinformatics.

On Generating Functions of Generating Trees on Generating Functions of Generating Trees on Generating Functions of Generating Trees

Philippe Flajolet, Alain Denise, Cyril Banderier, 1999 .

GenRGenS: software for generating random genomic sequences and structures

Yann Ponty, Michel Termier, Alain Denise, 2006, Bioinform..

Optimisation Problems for Pairwise RNA Sequence and Structure Comparison: A Brief Survey

Alain Denise, Philippe Rinaudo, A. Denise, 2013, Trans. Comput. Collect. Intell..

Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm

Alain Denise, Claire Herrbach, Serge Dulucq, 2010, Theor. Comput. Sci..

Alignments of RNA Structures

Alain Denise, Hélène Touzet, Guillaume Blin, 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Automated motif discovering in RNA molecules

A. Denise, M. Djelloul, 2008 .

Alignment of RNA secondary structures using a full set of operations

Alain Denise, Hélène Touzet, Claire Herrbach, 2006 .

An Algorithmic Game-Theory Approach for Coarse-Grain Prediction of RNA 3D Structure

Dominique Barth, Alain Denise, Franck Quessette, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Controlled non uniform random generation of decomposable structures pdf

Yann Ponty, Michel Termier, Alain Denise, 2010, Theor. Comput. Sci..

Using Medians to Generate Consensus Rankings for Biological Data

Alain Denise, Sarah Cohen Boulakia, Sylvie Hamel, 2011, SSDBM.

Flexible RNA design under structure and sequence constraints using formal languages

Yu Zhou, Yi Zhang, Yann Ponty, 2013, BCB.

Uniform Monte-Carlo Model Checking

Alain Denise, Richard Lassaigne, Sylvain Peyronnet, 2011, FASE.

A Graph-Based Similarity Approach to Classify Recurrent Complex Motifs from Their Context in RNA Structures

Dominique Barth, Alain Denise, Vladimir Reinharz, 2021, SEA.

A new approach to suboptimal pairwise sequence alignment

Peter Clote, Alain Denise, Lou Feng, 2011 .

Dissemination - Animation of the scientific community

Jean-Marc Steyaert, Christine Froidevaux, Sarah Cohen-Boulakia, 2011 .

Random and uniform word generation

A. Denise, 1996 .

Motifs Enumeration Algorithms in Biological Networks

Dominique Barth, Alain Denise, Romain Rivière, 2006 .

Efficient, robust and effective rank aggregation for massive biological datasets

Alain Denise, Laurent Bulteau, Bryan Brancotte, 2021, Future Gener. Comput. Syst..

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

Dominique Barth, Alain Denise, Franck Quessette, 2012, Comput. Biol. Chem..

A method for automated discovering of RNA tertiary motifs

A. Denise, M. Djelloul, 2008 .

Rank aggregation with ties: Experiments and Analysis

Alain Denise, Sarah Cohen Boulakia, Bryan Brancotte, 2015, Proc. VLDB Endow..

Rare Events and Conditional Events on Random Strings

Mireille Régnier, Alain Denise, M. Régnier, 2004, Discret. Math. Theor. Comput. Sci..

ConQuR-Bio: Consensus Ranking with Query Reformulation for Biological Data

Alain Denise, Sarah Cohen Boulakia, Bryan Brancotte, 2014, DILS.

Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs

Jérôme Waldispühl, Vladimir Reinharz, Alain Denise, 2020, bioRxiv.

Shuffling biological sequences with motif constraints

Johanne Cohen, Dominique Barth, Alain Denise, 2008, J. Discrete Algorithms.

Shuffling biological sequencess with motifs constraints

Johanne Cohen, Dominique Barth, Alain Denise, 2004 .

Assessing the Statistical Significance of Overrepresented Oligonucleotides

M. Régnier, Mathias Vandenbogaert, A. Denise, 2001, WABI.

Rare Events and Conditional Events on Random Strings

M. Régnier, A. Denise, 2004, Discret. Math. Theor. Comput. Sci..

Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies

Paolo Marcatili, Anna Tramontano, Rosalba Lepore, 2014, Bioinform..

A new dichotomic algorithm for the uniform random generation of words in regular languages

Alain Denise, Marie-Claude Gaudel, Johan Oudinet, 2013, Theor. Comput. Sci..

A new way of automating statistical testing methods

Alain Denise, Marie-Claude Gaudel, Sandrine-Dominique Gouraud, 2001, Proceedings 16th Annual International Conference on Automated Software Engineering (ASE 2001).

Generating Random Genomic Sequences and Structures with GenRGenS ?

Yann Ponty, Michel Termier, Alain Denise, 2006 .

Proceedings of the SeqBio 2015 workshop: String algorithms for bioinformatics

T. Lecroq, G. Fertin, R. Chikhi, 2021 .

Structural Bioinformatics

A. Denise, Yann Ponty, Kévin Darty, 2022 .

Scientific Foundations - Annotation and Combinatorics

Jean-Marc Steyaert, Jiuqiang Chen, Christine Froidevaux, 2011 .

Assessing the Statistical Significance of Overrepresented Oligonucleotides

Mireille Régnier, Alain Denise, Mathias Vandenbogaert, 2001, WABI.

Reliability-Aware and Graph-Based Approach for Rank Aggregation of Biological Data

Bryan Brancotte, Sarah Cohen-Boulakia, Alain Denise, 2019, 2019 15th International Conference on eScience (eScience).

Benchmarking RNA secondary structure comparison algorithms

Cedric Chauve, Daniel Gautheret, Michel Termier, 2008 .