Yann Ponty

Orcid: 0000-0002-7615-3930

Affiliations:
  • École Polytechnique, Palaiseau, France
  • University of Paris-Sud, Laboratory for Computer Science (LRI), France (former)


According to our database1, Yann Ponty authored at least 64 papers between 2004 and 2023.

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Bibliography

2023
Automated design of dynamic programming schemes for RNA folding with pseudoknots.
Algorithms Mol. Biol., December, 2023

ISMB/ECCB 2023 proceedings.
Bioinform., 2023

Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique.
Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

2022
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381).
Dagstuhl Reports, September, 2022

IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations.
BMC Bioinform., 2022

Tree diet: reducing the treewidth to unlock FPT algorithms in RNA bioinformatics.
Algorithms Mol. Biol., 2022

2021
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes.
Bioinform., 2021

A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics.
Proceedings of the 16th International Symposium on Parameterized and Exact Computation, 2021

Sequence Graphs Realizations and Ambiguity in Language Models.
Proceedings of the Computing and Combinatorics - 27th International Conference, 2021

2020
DNA Chisel, a versatile sequence optimizer.
Bioinform., 2020

incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs.
Bioinform., 2020

HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments.
Bioinform., 2020

Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser.
Bioinform., 2020

Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification.
Proceedings of the Research in Computational Molecular Biology, 2020

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

2019
Small-World Networks and RNA Secondary Structures.
J. Comput. Biol., 2019

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.
CoRR, 2019

Fixed-parameter tractable sampling for RNA design with multiple target structures.
BMC Bioinform., 2019

Exponentially Few RNA Structures are Designable.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

Effective Rotation-Invariant Point CNN with Spherical Harmonics Kernels.
Proceedings of the 2019 International Conference on 3D Vision, 2019

2018
Meet-U: Educating through research immersion.
PLoS Comput. Biol., 2018

Counting, Generating, Analyzing and Sampling Tree Alignments.
Int. J. Found. Comput. Sci., 2018

Design of RNAs: comparing programs for inverse RNA folding.
Briefings Bioinform., 2018

2017
Taming reluctant random walks in the positive quadrant.
Electron. Notes Discret. Math., 2017

Efficient approximations of RNA kinetics landscape using non-redundant sampling.
Bioinform., 2017

The BRaliBase dent - a tale of benchmark design and interpretation.
Briefings Bioinform., 2017

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models.
Algorithmica, 2017

2016
incaRNAfbinv: a web server for the fragment-based design of RNA sequences.
Nucleic Acids Res., 2016

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.
Bioinform., 2016

Counting, Generating and Sampling Tree Alignments.
Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

2015
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.
BMC Bioinform., December, 2015

Preface.
J. Comput. Biol., 2015

An Unambiguous And Complete Dynamic Programming Algorithm For Tree Alignment.
CoRR, 2015

Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods from Reconciled Phylogenies: Supplementary Material.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm.
Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

2013
Non-redundant random generation algorithms for weighted context-free grammars.
Theor. Comput. Sci., 2013

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information.
PLoS Comput. Biol., 2013

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.
Nucleic Acids Res., 2013

Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs.
J. Comput. Biol., 2013

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.
Bioinform., 2013

Abstract: Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches.
Proceedings of the Research in Computational Molecular Biology, 2013

A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNAs.
Proceedings of the Research in Computational Molecular Biology, 2013

Flexible RNA design under structure and sequence constraints using formal languages.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
Non-redundant random generation algorithms for weighted context-free languages
CoRR, 2012

Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots.
CoRR, 2012

Rule-weighted and terminal-weighted context-free grammars have identical expressivity
CoRR, 2012

The weighted words collector
CoRR, 2012

Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots - (Extended Abstract).
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots.
Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

Biodiversity of Pattern Distributions in Combinatorial Ecosystems.
Proceedings of the 9th Meeting on Analytic Algorithmics and Combinatorics, 2012

2011
An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure.
J. Comput. Biol., 2011

A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

2010
Controlled non-uniform random generation of decomposable structures.
Theor. Comput. Sci., 2010

Non-redundant random generation from weighted context-free languages
CoRR, 2010

Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models
CoRR, 2010

Multi-dimensional Boltzmann Sampling of context-free Languages
CoRR, 2010

2009
VARNA: Interactive drawing and editing of the RNA secondary structure.
Bioinform., 2009

2008
LocalMove: computing on-lattice fits for biopolymers.
Nucleic Acids Res., 2008

Asymptotics of RNA Shapes.
J. Comput. Biol., 2008

Culminating Paths.
Discret. Math. Theor. Comput. Sci., 2008

2007
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., 2007

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

GenRGenS: software for generating random genomic sequences and structures.
Bioinform., 2006

2004
Estimating Seed Sensitivity on Homogeneous Alignments.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004


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