Estimating Seed Sensitivity on Homogeneous Alignments. - Gregory Kucherov; Laurent Noé; Yann Ponty (BIBE, 2004)

GenRGenS: software for generating random genomic sequences and structures. - Yann Ponty; Michel Termier; Alain Denise (Bioinform., 2006)

Modélisation de séquences génomiques structurées, génération aléatoire et applications. (Models for structured genomic sequences, random generation and applications). - Yann Ponty (2006)

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. - Fabrizio Ferrè; Yann Ponty; W. A. Lorenz; Peter Clote (Nucleic Acids Res., 2007)

Culminating Paths. - Mireille Bousquet-Mélou; Yann Ponty (Discret. Math. Theor. Comput. Sci., 2008)

Asymptotics of RNA Shapes. - W. A. Lorenz; Yann Ponty; Peter Clote (J. Comput. Biol., 2008)

LocalMove: computing on-lattice fits for biopolymers. - Yann Ponty; R. Istrate; E. Porcelli; Peter Clote (Nucleic Acids Res., 2008)

VARNA: Interactive drawing and editing of the RNA secondary structure. - Kévin Darty; Alain Denise; Yann Ponty (Bioinform., 2009)

Multi-dimensional Boltzmann Sampling of context-free Languages - Olivier Bodini; Yann Ponty (CoRR, 2010)

Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models - Danièle Gardy; Yann Ponty (CoRR, 2010)

Non-redundant random generation from weighted context-free languages - Yann Ponty (CoRR, 2010)

Controlled non-uniform random generation of decomposable structures. - Alain Denise; Yann Ponty; Michel Termier (Theor. Comput. Sci., 2010)

A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. - Yann Ponty; Cédric Saule (WABI, 2011)

An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. - Jérôme Waldispühl; Yann Ponty (J. Comput. Biol., 2011)

Biodiversity of Pattern Distributions in Combinatorial Ecosystems. - Cyril Banderier; Olivier Bodini; Yann Ponty; Hanane Tafat Bouzid (ANALCO, 2012)

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. - Saad Sheikh; Rolf Backofen; Yann Ponty (CPM, 2012)

Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots - (Extended Abstract). - Philippe Rinaudo; Yann Ponty; Dominique Barth; Alain Denise (WABI, 2012)

The weighted words collector - Jérémie Du Boisberranger; Danièle Gardy; Yann Ponty (CoRR, 2012)

Rule-weighted and terminal-weighted context-free grammars have identical expressivity - Yann Ponty (CoRR, 2012)

Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. - Philippe Rinaudo; Yann Ponty; Dominique Barth; Alain Denise (CoRR, 2012)

Non-redundant random generation algorithms for weighted context-free languages - W. A. Lorenz; Yann Ponty (CoRR, 2012)

Flexible RNA design under structure and sequence constraints using formal languages. - Yu Zhou 021; Yann Ponty; Stéphane Vialette; Jérôme Waldispühl; Yi Zhang 046; Alain Denise (BCB, 2013)

A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (RECOMB, 2013)

Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. - Evan Senter; Saad Sheikh; Iván Dotú; Yann Ponty; Peter Clote (RECOMB, 2013)

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (Bioinform., 2013)

Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. - Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl (J. Comput. Biol., 2013)

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. - Yang Zhang; Yann Ponty; Mathieu Blanchette; Eric Lécuyer; Jérôme Waldispühl (Nucleic Acids Res., 2013)

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information. - Anne Lopes; Sophie Sacquin-Mora; Viktoriya Dimitrova; Elodie Laine; Yann Ponty; Alessandra Carbone (PLoS Comput. Biol., 2013)

Non-redundant random generation algorithms for weighted context-free grammars. - William Andrew Lorenz; Yann Ponty (Theor. Comput. Sci., 2013)

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. - Jozef Hales; Ján Manuch; Yann Ponty; Ladislav Stacho (CPM, 2015)

Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material. - Ashok Rajaraman; Cédric Chauve; Yann Ponty (ISBRA, 2015)

An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment. - Cédric Chauve; Julien Courtiel; Yann Ponty (CoRR, 2015)

Preface. - Fabrice Jossinet; Yann Ponty; Jérôme Waldispühl (J. Comput. Biol., 2015)

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. - Cédric Chauve; Yann Ponty; João Paulo Pereira Zanetti (BMC Bioinform., 2015)

Counting, Generating and Sampling Tree Alignments. - Cédric Chauve; Julien Courtiel; Yann Ponty (AlCoB, 2016)

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. - Edwin Jacox; Cédric Chauve; Gergely J. Szöllosi; Yann Ponty; Céline Scornavacca (Bioinform., 2016)

incaRNAfbinv: a web server for the fragment-based design of RNA sequences. - Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Nucleic Acids Res., 2016)

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models. - Jozef Hales; Alice Héliou; Ján Manuch; Yann Ponty; Ladislav Stacho (Algorithmica, 2017)

The BRaliBase dent - a tale of benchmark design and interpretation. - Benedikt Löwes; Cédric Chauve; Yann Ponty; Robert Giegerich (Briefings Bioinform., 2017)

Efficient approximations of RNA kinetics landscape using non-redundant sampling. - Juraj Michalik; Hélène Touzet; Yann Ponty (Bioinform., 2017)

Taming reluctant random walks in the positive quadrant. - Jérémie O. Lumbroso; Marni Mishna; Yann Ponty (Electron. Notes Discret. Math., 2017)

Design of RNAs: comparing programs for inverse RNA folding. - Alexander Churkin; Matan Drory Retwitzer; Vladimir Reinharz; Yann Ponty; Jérôme Waldispühl; Danny Barash (Briefings Bioinform., 2018)

Counting, Generating, Analyzing and Sampling Tree Alignments. - Cédric Chauve; Julien Courtiel; Yann Ponty (Int. J. Found. Comput. Sci., 2018)

Meet-U: Educating through research immersion. - Nika Abdollahi; Alexandre Albani; Éric Anthony; Agnes Baud; Mélissa Cardon; Robert Clerc; Dariusz Czernecki; Romain Conte; Laurent David; Agathe Delaune; Samia Djerroud; Pauline Fourgoux; et al. (PLoS Comput. Biol., 2018)

Effective Rotation-Invariant Point CNN with Spherical Harmonics Kernels. - Adrien Poulenard; Marie-Julie Rakotosaona; Yann Ponty; Maks Ovsjanikov (3DV, 2019)

Exponentially Few RNA Structures are Designable. - Hua-Ting Yao; Cédric Chauve; Mireille Régnier; Yann Ponty (BCB, 2019)

Fixed-parameter tractable sampling for RNA design with multiple target structures. - Stefan Hammer; Wei Wang 263; Sebastian Will; Yann Ponty (BMC Bioinform., 2019)

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. - Cédric Chauve; Yann Ponty; Michael Wallner 001 (CoRR, 2019)

Small-World Networks and RNA Secondary Structures. - Defne Surujon; Yann Ponty; Peter Clote (J. Comput. Biol., 2019)

Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond. (Algorithmes ensemblistes et combinatoire analytique en Bioinformatique des ARN). - Yann Ponty (2020)

Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. - Roman Sarrazin-Gendron; Hua-Ting Yao; Vladimir Reinharz; Carlos G. Oliver; Yann Ponty; Jérôme Waldispühl (RECOMB, 2020)

Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. - Yuri Kochnev; Erich Hellemann; Kevin C. Cassidy; Jacob D. Durrant; Yann Ponty (Bioinform., 2020)

HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments. - Weronika Puchala; Michal Burdukiewicz; Michal Kistowski; Katarzyna A. Dabrowska; Aleksandra E. Badaczewska-Dawid; Dominik Cysewski; Michal Dadlez; Yann Ponty (Bioinform., 2020)

incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. - Matan Drory Retwitzer; Vladimir Reinharz; Alexander Churkin; Yann Ponty; Jérôme Waldispühl; Danny Barash (Bioinform., 2020)

DNA Chisel, a versatile sequence optimizer. - Valentin Zulkower; Susan Rosser; Yann Ponty (Bioinform., 2020)

Sequence Graphs Realizations and Ambiguity in Language Models. - Sammy Khalife; Yann Ponty; Laurent Bulteau (COCOON, 2021)

A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics. - Laurent Bulteau; Bertrand Marchand; Yann Ponty (IPEC, 2021)

RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. - Gregor Entzian; Ivo L. Hofacker; Yann Ponty; Ronny Lorenz; Andrea Tanzer (Bioinform., 2021)

Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics. - Bertrand Marchand; Yann Ponty; Laurent Bulteau (Algorithms Mol. Biol., 2022)

IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. - Alexander Churkin; Yann Ponty; Danny Barash (BMC Bioinform., 2022)

Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). - Sven Findeiß; Christoph Flamm; Yann Ponty (Dagstuhl Reports, 2022)

Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. - Théo Boury; Yann Ponty; Vladimir Reinharz (WABI, 2023)

ISMB/ECCB 2023 proceedings. - Yann Ponty; Sushmita Roy (Bioinform., 2023)

Automated design of dynamic programming schemes for RNA folding with pseudoknots. - Bertrand Marchand; Sebastian Will; Sarah J. Berkemer; Yann Ponty; Laurent Bulteau (Algorithms Mol. Biol., 2023)

Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. - Taher Yacoub; Roy González-Alemán; Fabrice Leclerc; Isaure Chauvot de Beauchêne; Yann Ponty (RECOMB, 2024)

RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. - Kimon Boehmer; Sarah J. Berkemer; Sebastian Will; Yann Ponty (WABI, 2024)

RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. - Théo Boury; Laurent Bulteau; Yann Ponty (WABI, 2024)

ISMB 2024 Proceedings. - Tijana Milenkovic; Yann Ponty (Bioinform., 2024)

LinearBPDesign. - Théo Boury; Laurent Bulteau; Yann Ponty (DROPS Artifacts, 2024)

Infrared: a declarative tree decomposition-powered framework for bioinformatics. - Hua-Ting Yao; Bertrand Marchand; Sarah J. Berkemer; Yann Ponty; Sebastian Will (Algorithms Mol. Biol., 2024)

Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. - Théo Boury; Leonhard Sidl; Ivo L. Hofacker; Yann Ponty; Hua-Ting Yao (RECOMB, 2025)