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List of works by Yann Ponty

A global sampling approach to designing and reengineering RNA secondary structures

scientific article

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

scientific article

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure

scientific article published on 28 October 2011

Asymptotics of RNA shapes

scientific article published in January 2008

Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces

scientific article

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

scientific article published on 15 February 2020

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

scientific article published on 13 June 2007

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

scientific article published on 8 April 2017

Design of RNAs: comparing programs for inverse RNA folding

scientific article published on 03 January 2017

Drawing and editing the secondary structure(s) of RNA.

scientific article published on January 2015

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

scientific article published in July 2017

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method

scientific article published on 12 October 2007

Estimating seed sensitivity on homogeneous alignments

article

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

scientific article published on 16 December 2015

Expected distance between terminal nucleotides of RNA secondary structures

scientific article

GenRGenS: software for generating random genomic sequences and structures

scientific article published on 30 March 2006

IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles

scientific article published on 31 July 2020

Impact of the Energy Model on the Complexity of RNA Folding with Pseudoknots

Introduction to RNA secondary structure comparison

scientific article published on January 2014

LocalMove: computing on-lattice fits for biopolymers.

scientific article published on 13 June 2008

Meet-U: Educating through research immersion.

scientific article published on 15 March 2018

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

scientific article (publication date: 2013)

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences

scientific article published on 8 June 2013

Small-World Networks and RNA Secondary Structures

scientific article published on 31 October 2018

The BRaliBase dent-a tale of benchmark design and interpretation

scientific article published on 16 March 2016

Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame

scientific article

Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs

scientific article (publication date: November 2013)

VARNA: Interactive drawing and editing of the RNA secondary structure

scientific article

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony

scientific article published on 26 February 2016

incaRNAfbinv: a web server for the fragment-based design of RNA sequences

scientific article published on 16 May 2016

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