| VARNA: Interactive drawing and editing of the RNA secondary structure K Darty, A Denise, Y Ponty Bioinformatics 25 (15), 1974, 2009 | 924 | 2009 |
| GenRGenS: software for generating random genomic sequences and structures Y Ponty, M Termier, A Denise Bioinformatics 22 (12), 1534-1535, 2006 | 79 | 2006 |
| DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities F Ferrè, Y Ponty, WA Lorenz, P Clote Nucleic acids research 35 (suppl_2), W659-W668, 2007 | 78 | 2007 |
| ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony E Jacox, C Chauve, GJ Szöllősi, Y Ponty, C Scornavacca Bioinformatics 32 (13), 2056-2058, 2016 | 55 | 2016 |
| Multi-dimensional Boltzmann Sampling of Languages Y Ponty, O Bodini Discrete Mathematics & Theoretical Computer Science, 2010 | 46* | 2010 |
| Asymptotics of RNA shapes WA Lorenz, Y Ponty, P Clote Journal of Computational Biology 15 (1), 31-63, 2008 | 45 | 2008 |
| Estimating seed sensitivity on homogeneous alignments G Kucherov, L Noé, Y Ponty Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering, 387-394, 2004 | 45 | 2004 |
| A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution V Reinharz, Y Ponty, J Waldispühl Bioinformatics 29 (13), i308-i315, 2013 | 41 | 2013 |
| Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information A Lopes, S Sacquin-Mora, V Dimitrova, E Laine, Y Ponty, A Carbone PLoS Computational Biology, 2013 | 38 | 2013 |
| Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy Y Ponty Journal of Mathematical Biology 56 (1-2), 107-127, 2008 | 35 | 2008 |
| A global sampling approach to designing and reengineering RNA secondary structures A Levin, M Lis, Y Ponty, CW O’Donnell, S Devadas, B Berger, ... Nucleic acids research 40 (20), 10041-10052, 2012 | 34 | 2012 |
| DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies W Duchemin, Y Anselmetti, M Patterson, Y Ponty, S Bérard, C Chauve, ... Genome Biology and Evolution 9 (5), 1312-1319, 2017 | 28 | 2017 |
| Design of RNAs: comparing programs for inverse RNA folding A Churkin, MD Retwitzer, V Reinharz, Y Ponty, J Waldispühl, D Barash Briefings in bioinformatics 19 (2), 350-358, 2018 | 26 | 2018 |
| Controlled non-uniform random generation of decomposable structures A Denise, Y Ponty, M Termier Theoretical Computer Science 411 (40-42), 3527-3552, 2010 | 26 | 2010 |
| A combinatorial framework for designing (pseudoknotted) RNA algorithms Y Ponty, C Saule International Workshop on Algorithms in Bioinformatics, 250-269, 2011 | 24 | 2011 |
| Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches E Senter, S Sheikh, I Dotu, Y Ponty, P Clote PLOS ONE 7 (12), e50506, 2012 | 23 | 2012 |
| Expected distance between terminal nucleotides of RNA secondary structures P Clote, Y Ponty, JM Steyaert Journal of mathematical biology 65 (3), 581-599, 2012 | 23 | 2012 |
| Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame J Deforges, S De Breyne, M Ameur, N Ulryck, N Chamond, A Saaidi, ... Nucleic acids research 45 (12), 7382-7400, 2017 | 21 | 2017 |
| An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure J Waldispühl, Y Ponty Journal of Computational Biology 18 (11), 1465-1479, 2011 | 19 | 2011 |
| Culminating paths M Bousquet-Mélou, Y Ponty Discrete Mathematics & Theoretical Computer Science (DMTCS) 10 (2), 125-152, 2008 | 19 | 2008 |
Alain DeniseUniversité Paris-SaclayVerified email at lri.fr
