Yann Ponty

ORCID

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 38

Top Venues

University of Paris-Sud, Orsay, France (PHD)

Education History

University of Paris-Sud, Orsay, France

PHD

Publications

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)
Sammy Khalife, Yann Ponty, Laurent Bulteau
Sequence graphs realizations and ambiguity in language models. CoRR (2024)
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)
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) (2024)
Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty
RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. WABI (2024)
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) (2023)
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)
Yann Ponty, Sushmita Roy
ISMB/ECCB 2023 proceedings. Bioinform. 39 (Supplement-1) (2023)
Sven Findeiß, Christoph Flamm, Yann Ponty
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). Dagstuhl Reports 12 (9) (2022)
Alexander Churkin, Yann Ponty, Danny Barash
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. BMC Bioinform. (8) (2022)
Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, Yann Ponty
Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. WABI (2022)
Bertrand Marchand, Yann Ponty, Laurent Bulteau
Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics. Algorithms Mol. Biol. 17 (1) (2022)
Sammy Khalife, Yann Ponty, Laurent Bulteau
Sequence Graphs Realizations and Ambiguity in Language Models. COCOON (2021)
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) (2021)
Laurent Bulteau, Bertrand Marchand, Yann Ponty
A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics. IPEC (2021)
Bertrand Marchand, Yann Ponty, Laurent Bulteau
Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. WABI (2021)
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)
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) (2020)
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) (2020)
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) (2020)
Valentin Zulkower, Susan Rosser, Yann Ponty
DNA Chisel, a versatile sequence optimizer. Bioinform. 36 (16) (2020)
Stefan Hammer, Wei Wang, Sebastian Will, Yann Ponty
Fixed-parameter tractable sampling for RNA design with multiple target structures. BMC Bioinform. 20 (1) (2019)
Defne Surujon, Yann Ponty, Peter Clote
Small-World Networks and RNA Secondary Structures. J. Comput. Biol. 26 (1) (2019)
Hua-Ting Yao, Cédric Chauve, Mireille Régnier, Yann Ponty
Exponentially Few RNA Structures are Designable. BCB (2019)
Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov
Effective Rotation-invariant Point CNN with Spherical Harmonics kernels. CoRR (2019)
Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov
Effective Rotation-Invariant Point CNN with Spherical Harmonics Kernels. 3DV (2019)
Cédric Chauve, Yann Ponty, Michael Wallner
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. CoRR (2019)
Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will
Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB (2018)
Cédric Chauve, Julien Courtiel, Yann Ponty
Counting, Generating, Analyzing and Sampling Tree Alignments. Int. J. Found. Comput. Sci. 29 (5) (2018)
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) (2018)
Nika Abdollahi, Alexandre Albani, Eric 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)
Jérémie O. Lumbroso, Marni Mishna, Yann Ponty
Taming reluctant random walks in the positive quadrant. Electron. Notes Discret. Math. 59 (2017)
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) (2017)
Juraj Michalik, Hélène Touzet, Yann Ponty
Efficient approximations of RNA kinetics landscape using non-redundant sampling. Bioinform. 33 (14) (2017)
Benedikt Löwes, Cédric Chauve, Yann Ponty, Robert Giegerich
The BRaliBase dent - a tale of benchmark design and interpretation. Briefings Bioinform. 18 (2) (2017)
Cédric Chauve, Julien Courtiel, Yann Ponty
Counting, Generating and Sampling Tree Alignments. AlCoB (2016)
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) (2016)
Edwin Jacox, Cédric Chauve, Gergely J. Szöllosi, Yann Ponty, Céline Scornavacca
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinform. 32 (13) (2016)
Ashok Rajaraman, Cédric Chauve, Yann Ponty
Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material. ISBRA (2015)
Jozef Hales, Ján Manuch, Yann Ponty, Ladislav Stacho
Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CPM (2015)
Cédric Chauve, Julien Courtiel, Yann Ponty
An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment. CoRR (2015)
Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl
Preface. J. Comput. Biol. 22 (3) (2015)
Jozef Hales, Ján Manuch, Yann Ponty, Ladislav Stacho
Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CoRR (2015)
Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinform. 16 (S19) (2015)
Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti
Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach. BSB (2014)
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)
William Andrew Lorenz, Yann Ponty
Non-redundant random generation algorithms for weighted context-free grammars. Theor. Comput. Sci. 502 (2013)
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)
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)
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) (2013)
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) (2013)
Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. RECOMB (2013)
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) (2013)
W. A. Lorenz, Yann Ponty
Non-redundant random generation algorithms for weighted context-free languages CoRR (2012)
Jérémie Du Boisberranger, Danièle Gardy, Yann Ponty
The weighted words collector CoRR (2012)
Yann Ponty
Rule-weighted and terminal-weighted context-free grammars have identical expressivity CoRR (2012)
Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise
Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. CoRR (2012)
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)
Saad Sheikh, Rolf Backofen, Yann Ponty
Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. CPM (2012)
Cyril Banderier, Olivier Bodini, Yann Ponty, Hanane Tafat Bouzid
Biodiversity of Pattern Distributions in Combinatorial Ecosystems. ANALCO (2012)
Yann Ponty, Cédric Saule
A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. WABI (2011)
Jérôme Waldispühl, Yann Ponty
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. J. Comput. Biol. 18 (11) (2011)
Jérôme Waldispühl, Yann Ponty
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. RECOMB (2011)
Alain Denise, Yann Ponty, Michel Termier
Controlled non-uniform random generation of decomposable structures. Theor. Comput. Sci. 411 (40-42) (2010)
Olivier Bodini, Yann Ponty
Multi-dimensional Boltzmann Sampling of context-free Languages CoRR (2010)
Alain Denise, Yann Ponty, Michel Termier
Controlled non uniform random generation of decomposable structures CoRR (2010)
Danièle Gardy, Yann Ponty
Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models CoRR (2010)
Yann Ponty
Non-redundant random generation from weighted context-free languages CoRR (2010)
Kévin Darty, Alain Denise, Yann Ponty
VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinform. 25 (15) (2009)
Mireille Bousquet-Mélou, Yann Ponty
Culminating Paths. Discret. Math. Theor. Comput. Sci. 10 (2) (2008)
Yann Ponty, R. Istrate, E. Porcelli, Peter Clote
LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
W. A. Lorenz, Yann Ponty, Peter Clote
Asymptotics of RNA Shapes. J. Comput. Biol. 15 (1) (2008)
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) (2007)
Gregory Kucherov, Laurent Noé, Yann Ponty
Estimating seed sensitivity on homogeneous alignments CoRR (2006)
Yann Ponty, Michel Termier, Alain Denise
GenRGenS: software for generating random genomic sequences and structures. Bioinform. 22 (12) (2006)
Gregory Kucherov, Laurent Noé, Yann Ponty
Estimating Seed Sensitivity on Homogeneous Alignments. BIBE (2004)

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Publication Activity (10 Years)

Top Topics

Top Venues

Yann Ponty