Yann Ponty - RankMe

86 papers B 10C 8Misc 1Journal 57Unranked 7

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Bipartite Independent Set Reconfiguration: General and RNA-Inspired Parameterized Algorithms. Algorithmica Théo Boury, Laurent Bulteau, Bertrand Marchand, Yann Ponty
2026	J	`jnl`	RNA triplet repeats: improved algorithms for structure prediction and interactions. Algorithms Mol. Biol. Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty
2025	J	`jnl`	<tt>CREMSA</tt>: compressed indexing of (ultra) large multiple sequence alignments. Bioinform. Mikaël Salson, Arthur Boddaert, Awa Bousso Gueye, Laurent Bulteau, Yohan Hernandez-Courbevoie, Camille Marchet, Nan Pan, Sebastian Will, Yann Ponty
2025	J	`jnl`	CParty: hierarchically constrained partition function of RNA pseudoknots. Bioinform. Mateo Gray, Luke Trinity, Ulrike Stege, Yann Ponty, Sebastian Will, Hosna Jabbari
2025	B	`conf`	Old Dog, New Tricks: Exact Seeding Strategy Improves RNA Design Performances. RECOMB Théo Boury, Leonhard Sidl, Ivo L. Hofacker, Yann Ponty, Hua-Ting Yao
2025	J	`jnl`	RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs. Algorithms Mol. Biol. Théo Boury, Samuel Gardelle, Laurent Bulteau, Yann Ponty
2024	B	`conf`	Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs. RECOMB Taher Yacoub, Roy González-Alemán, Fabrice Leclerc, Isaure Chauvot de Beauchêne, Yann Ponty
2024	J	`jnl`	ISMB 2024 Proceedings. Bioinform. Tijana Milenkovic, Yann Ponty
2024	J	`jnl`	Infrared: a declarative tree decomposition-powered framework for bioinformatics. Algorithms Mol. Biol. Hua-Ting Yao, Bertrand Marchand, Sarah J. Berkemer, Yann Ponty, Sebastian Will
2024	C	`conf`	RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. WABI Théo Boury, Laurent Bulteau, Yann Ponty
2024	C	`conf`	RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. WABI Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, Yann Ponty
2024	J	`jnl`	Sequence graphs realizations and ambiguity in language models. CoRR Sammy Khalife, Yann Ponty, Laurent Bulteau
2023	J	`jnl`	Automated design of dynamic programming schemes for RNA folding with pseudoknots. Algorithms Mol. Biol. Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Yann Ponty, Laurent Bulteau
2023	C	`conf`	Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. WABI Théo Boury, Yann Ponty, Vladimir Reinharz
2023	J	`jnl`	ISMB/ECCB 2023 proceedings. Bioinform. Yann Ponty, Sushmita Roy
2022	C	`conf`	Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. WABI Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, Yann Ponty
2022	J	`jnl`	IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations. BMC Bioinform. Alexander Churkin, Yann Ponty, Danny Barash
2022	J	`jnl`	Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). Dagstuhl Reports Sven Findeiß, Christoph Flamm, Yann Ponty
2022	J	`jnl`	Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics. Algorithms Mol. Biol. Bertrand Marchand, Yann Ponty, Laurent Bulteau
2021	B	`conf`	A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics. IPEC Laurent Bulteau, Bertrand Marchand, Yann Ponty
2021	J	`jnl`	RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. Bioinform. Gregor Entzian, Ivo L. Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer
2021	Misc	`conf`	Sequence Graphs Realizations and Ambiguity in Language Models. COCOON Sammy Khalife, Yann Ponty, Laurent Bulteau
2021	C	`conf`	Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. WABI Bertrand Marchand, Yann Ponty, Laurent Bulteau
2020	J	`jnl`	DNA Chisel, a versatile sequence optimizer. Bioinform. Valentin Zulkower, Susan Rosser, Yann Ponty
2020	—	`book`	Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond. (Algorithmes ensemblistes et combinatoire analytique en Bioinformatique des ARN). Yann Ponty
2020	J	`jnl`	HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments. Bioinform. Weronika Puchala, Michal Burdukiewicz, Michal Kistowski, Katarzyna A. Dabrowska, Aleksandra E. Badaczewska-Dawid, Dominik Cysewski, Michal Dadlez, Yann Ponty
2020	B	`conf`	Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification. RECOMB Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jérôme Waldispühl
2020	J	`jnl`	Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser. Bioinform. Yuri Kochnev, Erich Hellemann, Kevin C. Cassidy, Jacob D. Durrant, Yann Ponty
2020	J	`jnl`	incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs. Bioinform. Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, Danny Barash
2019	J	`jnl`	Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. CoRR Cédric Chauve, Yann Ponty, Michael Wallner
2019	—	`conf`	Effective Rotation-Invariant Point CNN with Spherical Harmonics Kernels. 3DV Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov
2019	J	`jnl`	Effective Rotation-invariant Point CNN with Spherical Harmonics kernels. CoRR Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov
2019	—	`conf`	Exponentially Few RNA Structures are Designable. BCB Hua-Ting Yao, Cédric Chauve, Mireille Régnier, Yann Ponty
2019	J	`jnl`	Fixed-parameter tractable sampling for RNA design with multiple target structures. BMC Bioinform. Stefan Hammer, Wei Wang, Sebastian Will, Yann Ponty
2019	J	`jnl`	Small-World Networks and RNA Secondary Structures. J. Comput. Biol. Defne Surujon, Yann Ponty, Peter Clote
2018	J	`jnl`	Counting, Generating, Analyzing and Sampling Tree Alignments. Int. J. Found. Comput. Sci. Cédric Chauve, Julien Courtiel, Yann Ponty
2018	J	`jnl`	Design of RNAs: comparing programs for inverse RNA folding. Briefings Bioinform. Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
2018	B	`conf`	Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will
2018	J	`jnl`	Meet-U: Educating through research immersion. PLoS Comput. Biol. 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
2017	J	`jnl`	Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models. Algorithmica Jozef Hales, Alice Héliou, Ján Manuch, Yann Ponty, Ladislav Stacho
2017	J	`jnl`	Efficient approximations of RNA kinetics landscape using non-redundant sampling. Bioinform. Juraj Michalik, Hélène Touzet, Yann Ponty
2017	J	`jnl`	Taming reluctant random walks in the positive quadrant. Electron. Notes Discret. Math. Jérémie O. Lumbroso, Marni Mishna, Yann Ponty
2017	J	`jnl`	The BRaliBase dent - a tale of benchmark design and interpretation. Briefings Bioinform. Benedikt Löwes, Cédric Chauve, Yann Ponty, Robert Giegerich
2016	—	`conf`	Counting, Generating and Sampling Tree Alignments. AlCoB Cédric Chauve, Julien Courtiel, Yann Ponty
2016	J	`jnl`	ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. Bioinform. Edwin Jacox, Cédric Chauve, Gergely J. Szöllosi, Yann Ponty, Céline Scornavacca
2016	J	`jnl`	incaRNAfbinv: a web server for the fragment-based design of RNA sequences. Nucleic Acids Res. Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash
2015	J	`jnl`	An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment. CoRR Cédric Chauve, Julien Courtiel, Yann Ponty
2015	—	`conf`	Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material. ISBRA Ashok Rajaraman, Cédric Chauve, Yann Ponty
2015	B	`conf`	Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CPM Jozef Hales, Ján Manuch, Yann Ponty, Ladislav Stacho
2015	J	`jnl`	Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CoRR Jozef Hales, Ján Manuch, Yann Ponty, Ladislav Stacho
2015	J	`jnl`	Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinform. Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti
2015	J	`jnl`	Preface. J. Comput. Biol. Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl
2014	—	`conf`	Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach. BSB Cédric Chauve, Yann Ponty, João Paulo Pereira Zanetti
2014	—	`ed.`	Proceedings of the 1st Workshop on Computational Methods for Structural RNAs (CMSR 2014), Strasbourg, France, September 7, 2014. CMSR@ECCB Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl
2013	B	`conf`	A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs. RECOMB Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2013	J	`jnl`	A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. Bioinform. Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2013	B	`conf`	Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. RECOMB Evan Senter, Saad Sheikh, Iván Dotú, Yann Ponty, Peter Clote
2013	—	`conf`	Flexible RNA design under structure and sequence constraints using formal languages. BCB Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, Alain Denise
2013	J	`jnl`	Non-redundant random generation algorithms for weighted context-free grammars. Theor. Comput. Sci. William Andrew Lorenz, Yann Ponty
2013	J	`jnl`	Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information. PLoS Comput. Biol. Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone
2013	J	`jnl`	SPARCS: a web server to analyze (un)structured regions in coding RNA sequences. Nucleic Acids Res. Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lécuyer, Jérôme Waldispühl
2013	J	`jnl`	Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs. J. Comput. Biol. Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl
2012	—	`conf`	Biodiversity of Pattern Distributions in Combinatorial Ecosystems. ANALCO Cyril Banderier, Olivier Bodini, Yann Ponty, Hanane Tafat Bouzid
2012	B	`conf`	Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots. CPM Saad Sheikh, Rolf Backofen, Yann Ponty
2012	J	`jnl`	Non-redundant random generation algorithms for weighted context-free languages CoRR W. A. Lorenz, Yann Ponty
2012	J	`jnl`	Rule-weighted and terminal-weighted context-free grammars have identical expressivity CoRR Yann Ponty
2012	J	`jnl`	The weighted words collector CoRR Jérémie Du Boisberranger, Danièle Gardy, Yann Ponty
2012	C	`conf`	Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots - (Extended Abstract). WABI Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise
2012	J	`jnl`	Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. CoRR Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise
2011	C	`conf`	A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. WABI Yann Ponty, Cédric Saule
2011	J	`jnl`	An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure. J. Comput. Biol. Jérôme Waldispühl, Yann Ponty
2011	B	`conf`	An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure. RECOMB Jérôme Waldispühl, Yann Ponty
2010	J	`jnl`	Controlled non uniform random generation of decomposable structures CoRR Alain Denise, Yann Ponty, Michel Termier
2010	J	`jnl`	Controlled non-uniform random generation of decomposable structures. Theor. Comput. Sci. Alain Denise, Yann Ponty, Michel Termier
2010	J	`jnl`	Multi-dimensional Boltzmann Sampling of context-free Languages CoRR Olivier Bodini, Yann Ponty
2010	J	`jnl`	Non-redundant random generation from weighted context-free languages CoRR Yann Ponty
2010	J	`jnl`	Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models CoRR Danièle Gardy, Yann Ponty
2009	J	`jnl`	VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinform. Kévin Darty, Alain Denise, Yann Ponty
2008	J	`jnl`	Asymptotics of RNA Shapes. J. Comput. Biol. W. A. Lorenz, Yann Ponty, Peter Clote
2008	J	`jnl`	Culminating Paths. Discret. Math. Theor. Comput. Sci. Mireille Bousquet-Mélou, Yann Ponty
2008	J	`jnl`	LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Res. Yann Ponty, R. Istrate, E. Porcelli, Peter Clote
2007	J	`jnl`	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. Fabrizio Ferrè, Yann Ponty, W. A. Lorenz, Peter Clote
2006	J	`jnl`	Estimating seed sensitivity on homogeneous alignments CoRR Gregory Kucherov, Laurent Noé, Yann Ponty
2006	J	`jnl`	GenRGenS: software for generating random genomic sequences and structures. Bioinform. Yann Ponty, Michel Termier, Alain Denise
2006	—	`—`	Modélisation de séquences génomiques structurées, génération aléatoire et applications. (Models for structured genomic sequences, random generation and applications). Yann Ponty
2004	C	`conf`	Estimating Seed Sensitivity on Homogeneous Alignments. BIBE Gregory Kucherov, Laurent Noé, Yann Ponty