Publications by authors named "Alain Denise"

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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 Biol· January 2022

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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 Comput Biol· May 2021

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CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts.
Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, Alain Denise

BMC Bioinformatics· January 2019

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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 Res· May 2018

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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· August 2017

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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· May 2016

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A meta-approach for improving the prediction and the functional annotation of ortholog groups.
Cécile Pereira, Alain Denise, Olivier Lespinet

BMC Genomics· December 2015

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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, Alain Denise

Nat Struct Mol Biol· November 2014

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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 Trans Comput Biol Bioinform· January 2014

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BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.
Julien Allali, Cédric Saule, Cédric Chauve, Yves d'Aubenton-Carafa, Alain Denise

Adv Bioinformatics· August 2012

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Automated prediction of three-way junction topological families in RNA secondary structures.
Alexis Lamiable, Dominique Barth, Alain Denise, Franck Quessette, Sandrine Vial

Comput Biol Chem· April 2012

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Counting RNA pseudoknotted structures.
Cédric Saule, Mireille Régnier, Jean-Marc Steyaert, Alain Denise

J Comput Biol· October 2011

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Regulation of splicing enhancer activities by RNA secondary structures.
Wei Liu, Yu Zhou, Zexi Hu, Tao Sun, Alain Denise

FEBS Lett· November 2010

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Alignments of RNA structures.
Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Hélène Touzet

IEEE/ACM Trans Comput Biol Bioinform· August 2010

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VARNA: Interactive drawing and editing of the RNA secondary structure.
Kévin Darty, Alain Denise, Yann Ponty

Bioinformatics· August 2009

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Automated motif extraction and classification in RNA tertiary structures.
Mahassine Djelloul, Alain Denise

RNA· December 2008

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Adding pyrrolysine to the Escherichia coli genetic code.
Olivier Namy, Yu Zhou, Sarath Gundllapalli, Carla R Polycarpo, Alain Denise

FEBS Lett· November 2007

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GenRGenS: software for generating random genomic sequences and structures.
Yann Ponty, Michel Termier, Alain Denise

Bioinformatics· June 2006

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A pairwise alignment algorithm which favors clusters of blocks.
Elodie Nédélec, Thomas Moncion, Elisabeth Gassiat, Bruno Bossard, Guillemette Duchateau-Nguyen, Alain Denise

J Comput Biol· June 2005

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Towards a computational model for -1 eukaryotic frameshifting sites.
Michaël Bekaert, Laure Bidou, Alain Denise, Guillemette Duchateau-Nguyen, Jean-Paul Forest

Bioinformatics· February 2003

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