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ORCIDYann Ponty
Person information
- affiliation: École Polytechnique, Palaiseau, France
- affiliation (former): University of Paris-Sud, Laboratory for Computer Science (LRI), France
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2020 – today
- 2024
[j37]Hua-Ting Yao, Bertrand Marchand
, Sarah J. Berkemer, Yann Ponty, Sebastian Will:
Infrared: a declarative tree decomposition-powered framework for bioinformatics. Algorithms Mol. Biol. 19(1): 13 (2024)- [j36]Tijana Milenkovic, Yann Ponty:
ISMB 2024 Proceedings. Bioinform. 40(Supplement_1): i1-i2 (2024) - [c25]Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty:
Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. RECOMB 2024: 147-163 - [c24]Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty:
RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. WABI 2024: 18:1-18:23 - [c23]Théo Boury, Laurent Bulteau, Yann Ponty:
RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. WABI 2024: 19:1-19:23 - [d1]Théo Boury, Laurent Bulteau, Yann Ponty:
LinearBPDesign. DROPS Artifacts, 2024
- [i15]Sammy Khalife, Yann Ponty, Laurent Bulteau:
Sequence graphs realizations and ambiguity in language models. CoRR abs/2402.08830 (2024) - 2023
- [j35]Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Yann Ponty, Laurent Bulteau:
Automated design of dynamic programming schemes for RNA folding with pseudoknots. Algorithms Mol. Biol. 18(1): 18 (2023) - [j34]Yann Ponty, Sushmita Roy:
ISMB/ECCB 2023 proceedings. Bioinform. 39(Supplement-1): 1-2 (2023) - [c22]Théo Boury, Yann Ponty, Vladimir Reinharz:
Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. WABI 2023: 20:1-20:22 - 2022
- [j33]Bertrand Marchand, Yann Ponty, Laurent Bulteau:
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics. Algorithms Mol. Biol. 17(1): 8 (2022) - [j32]Alexander Churkin, Yann Ponty, Danny Barash:
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. BMC Bioinform. 23-S(8): 424 (2022) - [c21]Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, Yann Ponty:
Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. WABI 2022: 7:1-7:24 - [i14]Sven Findeiß, Christoph Flamm, Yann Ponty:
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). Dagstuhl Reports 12(9): 121-149 (2022) - 2021
- [j31]Gregor Entzian, Ivo L. Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer:
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. Bioinform. 37(15): 2126-2133 (2021) - [c20]Sammy Khalife, Yann Ponty, Laurent Bulteau:
Sequence Graphs Realizations and Ambiguity in Language Models. COCOON 2021: 153-163 - [c19]Laurent Bulteau, Bertrand Marchand, Yann Ponty:
A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics. IPEC 2021: 11:1-11:15 - [c18]Bertrand Marchand, Yann Ponty, Laurent Bulteau:
Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. WABI 2021: 7:1-7:23 - 2020
- [b2]Yann Ponty:
Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond. (Algorithmes ensemblistes et combinatoire analytique en Bioinformatique des ARN). University of Paris-Saclay, France, 2020 - [j30]Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash:
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. Bioinform. 36(9): 2920-2922 (2020) - [j29]Valentin Zulkower, Susan Rosser, Yann Ponty:
DNA Chisel, a versatile sequence optimizer. Bioinform. 36(16): 4508-4509 (2020) - [j28]Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, Jacob D. Durrant, Yann Ponty:
Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. Bioinform. 36(16): 4513-4515 (2020) - [j27]Weronika Puchala, Michal Burdukiewicz, Michal Kistowski, Katarzyna A. Dabrowska, Aleksandra E. Badaczewska-Dawid, Dominik Cysewski, Michal Dadlez, Yann Ponty:
HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments. Bioinform. 36(16): 4516-4518 (2020) - [c17]Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jérôme Waldispühl:
Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. RECOMB 2020: 186-201
2010 – 2019
- 2019
- [j26]Stefan Hammer, Wei Wang, Sebastian Will, Yann Ponty:
Fixed-parameter tractable sampling for RNA design with multiple target structures. BMC Bioinform. 20(1): 209:1-209:13 (2019) - [j25]Defne Surujon, Yann Ponty, Peter Clote:
Small-World Networks and RNA Secondary Structures. J. Comput. Biol. 26(1): 16-26 (2019) - [c16]Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov:
Effective Rotation-Invariant Point CNN with Spherical Harmonics Kernels. 3DV 2019: 47-56 - [c15]Hua-Ting Yao, Cédric Chauve, Mireille Régnier, Yann Ponty:
Exponentially Few RNA Structures are Designable. BCB 2019: 289-298 - [i13]Cédric Chauve, Yann Ponty, Michael Wallner:
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. CoRR abs/1905.04971 (2019) - [i12]Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov:
Effective Rotation-invariant Point CNN with Spherical Harmonics kernels. CoRR abs/1906.11555 (2019) - 2018
- [j24]Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash:
Design of RNAs: comparing programs for inverse RNA folding. Briefings Bioinform. 19(2): 350-358 (2018) - [j23]Cédric Chauve, Julien Courtiel, Yann Ponty:
Counting, Generating, Analyzing and Sampling Tree Alignments. Int. J. Found. Comput. Sci. 29(5): 741-767 (2018) - [j22]Nika Abdollahi, Alexandre Albani, Éric Anthony, Agnes Baud, Mélissa Cardon, Robert Clerc, Dariusz Czernecki, Romain Conte, Laurent David, Agathe Delaune, Samia Djerroud, Pauline Fourgoux, Nadège Guiglielmoni, Jeanne Laurentie, Nathalie Lehmann, Camille Lochard, Rémi Montagne, Vasiliki Myrodia, Vaitea Opuu, Elise Parey, Lélia Polit, Sylvain Privé, Chloé Quignot, Maria Ruiz-Cuevas, Mariam Sissoko, Nicolas Sompairac, Audrey Vallerix, Violaine Verrecchia, Marc Delarue, Raphaël Guérois, Yann Ponty, Sophie Sacquin-Mora, Alessandra Carbone, Christine Froidevaux, Stéphane Le Crom, Olivier Lespinet, Martin Weigt, Samer Abboud, Juliana S. Bernardes, Guillaume Bouvier, Chloé Dequeker, Arnaud Ferré, Patrick Fuchs, Gaëlle Lelandais, Pierre Poulain, Hugues Richard, Hugo Schweke, Elodie Laine, Anne Lopes:
Meet-U: Educating through research immersion. PLoS Comput. Biol. 14(3) (2018) - [c14]Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will:
Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB 2018: 256-258 - 2017
- [j21]Jozef Hales, Alice Héliou, Ján Manuch, Yann Ponty, Ladislav Stacho:
Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models. Algorithmica 79(3): 835-856 (2017) - [j20]Benedikt Löwes, Cédric Chauve, Yann Ponty, Robert Giegerich:
The BRaliBase dent - a tale of benchmark design and interpretation. Briefings Bioinform. 18(2): 306-311 (2017) - [j19]Juraj Michalik, Hélène Touzet, Yann Ponty:
Efficient approximations of RNA kinetics landscape using non-redundant sampling. Bioinform. 33(14): i283-i292 (2017) - [j18]Jérémie O. Lumbroso, Marni Mishna, Yann Ponty:
Taming reluctant random walks in the positive quadrant. Electron. Notes Discret. Math. 59: 99-114 (2017) - 2016
- [j17]Edwin Jacox, Cédric Chauve, Gergely J. Szöllosi, Yann Ponty, Céline Scornavacca:
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinform. 32(13): 2056-2058 (2016) - [j16]Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash:
incaRNAfbinv: a web server for the fragment-based design of RNA sequences. Nucleic Acids Res. 44(Webserver-Issue): W308-W314 (2016) - [c13]Cédric Chauve, Julien Courtiel, Yann Ponty:
Counting, Generating and Sampling Tree Alignments. AlCoB 2016: 53-64 - 2015
- [j15]Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti:
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinform. 16(S19): S6 (2015) - [j14]Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl:
Preface. J. Comput. Biol. 22(3): 189 (2015) - [c12]Jozef Hales, Ján Manuch, Yann Ponty, Ladislav Stacho:
Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CPM 2015: 231-246 - [c11]Ashok Rajaraman, Cédric Chauve, Yann Ponty:
Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material. ISBRA 2015: 260-271 - [i11]Jozef Hales, Ján Manuch, Yann Ponty, Ladislav Stacho:
Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CoRR abs/1502.03201 (2015) - [i10]Cédric Chauve, Julien Courtiel, Yann Ponty:
An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment. CoRR abs/1505.05983 (2015) - 2014
- [c10]Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti:
Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach. BSB 2014: 49-56 - [e1]Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl:
Proceedings of the 1st Workshop on Computational Methods for Structural RNAs (CMSR 2014), Strasbourg, France, September 7, 2014. McGill University 2014 [contents] - 2013
- [j13]Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. Bioinform. 29(13): 308-315 (2013) - [j12]Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. J. Comput. Biol. 20(11): 905-919 (2013) - [j11]Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl:
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res. 41(Webserver-Issue): 480-485 (2013) - [j10]Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone:
Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information. PLoS Comput. Biol. 9(12) (2013) - [j9]William Andrew Lorenz, Yann Ponty:
Non-redundant random generation algorithms for weighted context-free grammars. Theor. Comput. Sci. 502: 177-194 (2013) - [c9]Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, Alain Denise:
Flexible RNA design under structure and sequence constraints using formal languages. BCB 2013: 229 - [c8]Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl:
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. RECOMB 2013: 199-211 - [c7]Evan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote:
Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. RECOMB 2013: 264-265 - 2012
- [c6]Cyril Banderier, Olivier Bodini, Yann Ponty, Hanane Tafat Bouzid:
Biodiversity of Pattern Distributions in Combinatorial Ecosystems. ANALCO 2012: 107-115 - [c5]Saad Sheikh, Rolf Backofen, Yann Ponty:
Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. CPM 2012: 321-333 - [c4]Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise:
Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots - (Extended Abstract). WABI 2012: 149-164 - [i9]Jérémie Du Boisberranger, Danièle Gardy, Yann Ponty:
The weighted words collector. CoRR abs/1202.0920 (2012) - [i8]Yann Ponty:
Rule-weighted and terminal-weighted context-free grammars have identical expressivity. CoRR abs/1205.0627 (2012) - [i7]Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise:
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. CoRR abs/1206.3789 (2012) - [i6]W. A. Lorenz, Yann Ponty:
Non-redundant random generation algorithms for weighted context-free languages. CoRR abs/1211.0303 (2012) - 2011
- [j8]Jérôme Waldispühl, Yann Ponty:
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. J. Comput. Biol. 18(11): 1465-1479 (2011) - [c3]Jérôme Waldispühl, Yann Ponty:
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. RECOMB 2011: 501-515 - [c2]Yann Ponty, Cédric Saule:
A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. WABI 2011: 250-269 - 2010
- [j7]Alain Denise, Yann Ponty, Michel Termier:
Controlled non-uniform random generation of decomposable structures. Theor. Comput. Sci. 411(40-42): 3527-3552 (2010) - [i5]Olivier Bodini, Yann Ponty:
Multi-dimensional Boltzmann Sampling of context-free Languages. CoRR abs/1002.0046 (2010) - [i4]Alain Denise, Yann Ponty, Michel Termier:
Controlled non uniform random generation of decomposable structures. CoRR abs/1006.0423 (2010) - [i3]Danièle Gardy, Yann Ponty:
Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models. CoRR abs/1012.1129 (2010) - [i2]Yann Ponty:
Non-redundant random generation from weighted context-free languages. CoRR abs/1012.4560 (2010)
2000 – 2009
- 2009
- [j6]Kévin Darty, Alain Denise, Yann Ponty:
VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinform. 25(15): 1974-1975 (2009) - 2008
- [j5]Mireille Bousquet-Mélou, Yann Ponty:
Culminating Paths. Discret. Math. Theor. Comput. Sci. 10(2) (2008) - [j4]W. A. Lorenz, Yann Ponty, Peter Clote:
Asymptotics of RNA Shapes. J. Comput. Biol. 15(1): 31-63 (2008) - [j3]Yann Ponty, R. Istrate, E. Porcelli, Peter Clote:
LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res. 36(Web-Server-Issue): 216-222 (2008) - 2007
- [j2]Fabrizio Ferrè, Yann Ponty, W. A. Lorenz, Peter Clote:
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res. 35(Web-Server-Issue): 659-668 (2007) - 2006
- [b1]Yann Ponty:
Modélisation de séquences génomiques structurées, génération aléatoire et applications. (Models for structured genomic sequences, random generation and applications). University of Paris-Sud, Orsay, France, 2006 - [j1]Yann Ponty, Michel Termier, Alain Denise:
GenRGenS: software for generating random genomic sequences and structures. Bioinform. 22(12): 1534-1535 (2006) - [i1]Gregory Kucherov, Laurent Noé, Yann Ponty:
Estimating seed sensitivity on homogeneous alignments. CoRR abs/cs/0603106 (2006) - 2004
- [c1]Gregory Kucherov, Laurent Noé, Yann Ponty:
Estimating Seed Sensitivity on Homogeneous Alignments. BIBE 2004: 387-394
Coauthor Index
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