Laboratoire d'informatique de l'École polytechnique

Yann Ponty

Directeur de recherche, Cnrs

Contact information

Email ponty
Web page
Office 2005


[1] C. Singhal, Y. Ponty, and I. Chauvot de Beauchêne, A hybrid combinatorial method for docking single stranded RNAs in a protein pockect at the thermodynamic equilibrium, in JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), 2018 [Online]. Available:

[2] C. Chauve, Y. Ponty, and M. Wallner, Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models, Journal of Mathematical Biology, vol. 80, no. 5, pp. 1353–1388, 2019 [Online]. Available:

[3] J. Lumbroso, M. Mishna, and Y. Ponty, Taming reluctant random walks in the positive quadrant, in GASCOM - 10th conference on random generation of combinatorial structures - 2016, 2016, vol. 59, pp. 99–114 [Online]. Available:

[4] C. Chauve, J. Courtiel, and Y. Ponty, Counting, generating and sampling tree alignments, in ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, 2016, vol. 9702, pp. 53–64 [Online]. Available:

[5] F. Jossinet, Y. Ponty, and J. Waldispühl, Proceedings of the 1st workshop on Computational Methods for Structural RNAs. McGill University, 2014, p. 76 [Online]. Available:

[6] E. Jacox, C. Chauve, G. J. Szöllősi, Y. Ponty, and C. Scornavacca, ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony, Bioinformatics, vol. 32, no. 13, pp. 2056–2058, Jul. 2016 [Online]. Available:

[7] M. D. Retwitzer, V. Reinharz, A. Churkin, Y. Ponty, J. Waldispühl, and D. Barash, IncaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs, Bioinformatics, vol. 36, no. 9, pp. 2910–2922, May 2020 [Online]. Available:

[8] A. Saaidi, Y. Ponty, and B. Sargueil, An integrative approach for predicting the RNA secondary structure for the HIV–1 Gag UTR using probing data, in JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2017, 2017, p. 102 [Online]. Available:

[9] Y. Ponty and C. Saule, A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms, in WABI - 11th Workshop on Algorithms in Bioinformatics - 2011, 2011 [Online]. Available:

[10] V. Reinharz, Y. Ponty, and J. Waldispühl, A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences, in RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, 2013 [Online]. Available:

[11] Y. Ponty, Rule-weighted and terminal-weighted context-free grammars have identical expressivity, Research Report, 2012 [Online]. Available:

[12] J. Waldispühl and Y. Ponty, An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure., Journal of Computational Biology, vol. 18, no. 11, pp. 1465–79, Nov. 2011 [Online]. Available:

[13] P. Clote, Y. Ponty, and J.-M. Steyaert, Expected distance between terminal nucleotides of RNA secondary structures., Journal of Mathematical Biology, vol. 65, no. 3, pp. 581–99, Sep. 2012 [Online]. Available:

[14] W. A. Lorenz, P. Clote, and Y. Ponty, Asymptotics of RNA shapes, Journal of Computational Biology, vol. 15, no. 1, pp. 31–63, 2008 [Online]. Available:

[15] Y. Ponty, RNA Bioinformatics and ensemble dynamic programming, in 5th biennial Canadian Discrete and Algorithmic Mathematics Conference - CanaDAM 2015, 2015 [Online]. Available: