User profiles for Yann Ponty

Yann Ponty

Research director at CNRS & Ecole Polytechnique
Verified email at lix.polytechnique.fr
Cited by 3035

[HTML][HTML] VARNA: Interactive drawing and editing of the RNA secondary structure

K Darty, A Denise, Y Ponty - Bioinformatics, 2009 - ncbi.nlm.nih.gov
VARNA is a tool for the automated drawing, visualization and annotation of the secondary
structure of RNA, designed as a companion software for web servers and databases. Features…

[PDF][PDF] The SARS-CoV-2 subgenome landscape and its novel regulatory features

…, J Feng, G Li, D Guo, M Sajid, K Wu, Q Zhang, Y Ponty… - Molecular cell, 2021 - cell.com
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2), is currently a global pandemic. CoVs are known to generate …

Effective rotation-invariant point cnn with spherical harmonics kernels

A Poulenard, MJ Rakotosaona, Y Ponty… - … Conference on 3D …, 2019 - ieeexplore.ieee.org
We present a novel rotation invariant architecture operating directly on point cloud data. We
demonstrate how rotation invariance can be injected into a recently proposed point-based …

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony

E Jacox, C Chauve, GJ Szöllősi, Y Ponty… - …, 2016 - academic.oup.com
A gene tree-species tree reconciliation explains the evolution of a gene tree within the
species tree given a model of gene-family evolution. We describe ecceTERA, a program that …

Design of RNAs: comparing programs for inverse RNA folding

…, MD Retwitzer, V Reinharz, Y Ponty… - Briefings in …, 2018 - academic.oup.com
Computational programs for predicting RNA sequences with desired folding properties have
been extensively developed and expanded in the past several years. Given a secondary …

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

V Reinharz, Y Ponty, J Waldispühl - Bioinformatics, 2013 - academic.oup.com
Motivations: The design of RNA sequences folding into predefined secondary structures is a
milestone for many synthetic biology and gene therapy studies. Most of the current software …

[HTML][HTML] Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

…, V Dimitrova, E Laine, Y Ponty… - PLoS computational …, 2013 - journals.plos.org
Large-scale analyses of protein-protein interactions based on coarse-grain molecular docking
simulations and binding site predictions resulting from evolutionary sequence analysis, …

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities

F Ferrè, Y Ponty, WA Lorenz, P Clote - Nucleic acids research, 2007 - academic.oup.com
DIAL (dihedral alignment) is a web server that provides public access to a new dynamic
programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic …

DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies

…, Y Anselmetti, M Patterson, Y Ponty… - Genome biology and …, 2017 - academic.oup.com
DeCoSTAR is a software that aims at reconstructing the organization of ancestral genes or
genomes in the form of sets of neighborhood relations (adjacencies) between pairs of …

[PDF][PDF] Multi-dimensional Boltzmann sampling of languages

O Bodini, Y Ponty - Discrete Mathematics & Theoretical …, 2010 - dmtcs.episciences.org
Random generation is the core of the simulation of complex data. It appears in real applicative
domains such as complex networks (biology, Internet or social relationship), or software …