default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDYann Ponty
Person information
- affiliation: École Polytechnique, Palaiseau, France
- affiliation (former): University of Paris-Sud, Laboratory for Computer Science (LRI), France
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
showing all ?? records
Books and Theses
- 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- 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
Journal Articles
- 2024
- [j36]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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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) - 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
- [j1]Yann Ponty, Michel Termier, Alain Denise:
GenRGenS: software for generating random genomic sequences and structures. Bioinform. 22(12): 1534-1535 (2006)
Conference and Workshop Papers
- 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 - 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
- [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 - 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
- [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 - 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 - 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 - 2016
- [c13]Cédric Chauve, Julien Courtiel, Yann Ponty:
Counting, Generating and Sampling Tree Alignments. AlCoB 2016: 53-64 - 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 - 2014
- [c10]Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti:
Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach. BSB 2014: 49-56 - 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 - 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 - 2004
- [c1]Gregory Kucherov, Laurent Noé, Yann Ponty:
Estimating Seed Sensitivity on Homogeneous Alignments. BIBE 2004: 387-394
Editorship
- 2014
- [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]
Informal and Other Publications
- 2024
- [i15]Sammy Khalife, Yann Ponty, Laurent Bulteau:
Sequence graphs realizations and ambiguity in language models. CoRR abs/2402.08830 (2024) - 2022
- [i14]Sven Findeiß, Christoph Flamm, Yann Ponty:
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). Dagstuhl Reports 12(9): 121-149 (2022) - 2019
- [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) - 2015
- [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) - 2012
- [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) - 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) - 2006
- [i1]Gregory Kucherov, Laurent Noé, Yann Ponty:
Estimating seed sensitivity on homogeneous alignments. CoRR abs/cs/0603106 (2006)
Coauthor Index
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from 
.
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-10-07 22:19 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
