| 2026 | WABI | RNA Inverse Folding Under Stacked Base Pair Maximization. | Tho Boury, Laurent Bulteau, Yann Ponty |
| 2026 | WABI | FPT Learning of Sparse, Robust and Interpretable Generative Models of RNA Evolution. | Samuel Gardelle, Laurent Bulteau, Yann Ponty |
| 2025 | RECOMB | Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. | Tho Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao |
| 2024 | RECOMB | Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. | Taher Yacoub, Roy Gonzlez-Alemn, Fabrice Leclerc, Isaure Chauvot de Beauchne, Yann Ponty |
| 2024 | WABI | RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. | Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty |
| 2024 | WABI | RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. | Tho Boury, Laurent Bulteau, Yann Ponty |
| 2023 | WABI | Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. | Tho Boury, Yann Ponty, Vladimir Reinharz |
| 2022 | WABI | Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. | Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, Yann Ponty |
| 2021 | COCOON | Sequence Graphs Realizations and Ambiguity in Language Models. | Sammy Khalife, Yann Ponty, Laurent Bulteau |
| 2021 | WABI | Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. | Bertrand Marchand, Yann Ponty, Laurent Bulteau |
| 2020 | RECOMB | 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, Jrme Waldisphl |
| 2018 | RECOMB | Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. | Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will |
| 2015 | CPM | Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. | Jozef Hales, Jn Manuch, Yann Ponty, Ladislav Stacho |
| 2013 | RECOMB | A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. | Vladimir Reinharz, Yann Ponty, Jrme Waldisphl |
| 2013 | RECOMB | Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. | Evan Senter, Saad Sheikh, Ivn Dot, Yann Ponty, Peter Clote |
| 2012 | CPM | Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. | Saad Sheikh, Rolf Backofen, Yann Ponty |
| 2012 | WABI | 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 |
| 2011 | RECOMB | An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. | Jrme Waldisphl, Yann Ponty |
| 2011 | WABI | A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. | Yann Ponty, Cdric Saule |
| 2004 | BIBE | Estimating Seed Sensitivity on Homogeneous Alignments. | Gregory Kucherov, Laurent No, Yann Ponty |