Laboratoire d'informatique de l'École polytechnique

Yann Ponty

Directeur de recherche, Cnrs

Contact information

Email ponty lix.polytechnique.fr
Web page http://www.lix.polytechnique.fr/~ponty
Office 2005

Bibliography

[1] D. M. Allouche, G. de Bisschop, A. Saaidi, Y. Ponty, and S. Bruno, RNA secondary structure modelling following the IPANEMAP workflow, Springer Nature, 2019 [Online]. Available: https://inria.hal.science/hal-02324783

[2] C. Singhal, Y. Ponty, and I. Chauvot de Beauchêne, A hybrid combinatorial method for docking single stranded RNA on proteins at the thermodynamic equilibrium, in RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, 2018 [Online]. Available: https://inria.hal.science/hal-01925083

[3] F. Fabrizzio, Y. Ponty, W. A. Lorenz, and P. Clote, DIAL: A web server for the pairwise alignment of two RNA 3-dimensional structures using nucleotide, dihedral angle and base pairing similarities, Nucleic Acids Research, vol. 35, no. Web server issue, pp. W659–668, 2007 [Online]. Available: https://inria.hal.science/inria-00548870

[4] M. Drory retwitzer, V. Reinharz, Y. Ponty, J. Waldispühl, and D. Barash, incaRNAfbinv : a web server for the fragment-based design of RNA sequences, Nucleic Acids Research, vol. 44, no. W1, pp. W308–W314, 2016 [Online]. Available: https://inria.hal.science/hal-01319682

[5] A. Saaidi, D. Allouche, B. Sargueil, and Y. Ponty, Towards structural models for the Ebola UTR regions using experimental SHAPE probing data, in JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, 2016 [Online]. Available: https://inria.hal.science/hal-01332469

[6] C. Chauve, Y. Ponty, and J. P. P. Zanetti, Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach, in BSB - Brazilian Symposium on Bioinformatics - 2014, 2014, vol. 8826, pp. 49–56 [Online]. Available: https://inria.hal.science/hal-01056140

[7] S. Findeiß, C. Flamm, and Y. Ponty, Preface/Executive summary, vol. 12. Dagstuhl publishing, 2023, pp. 121–149 [Online]. Available: https://inria.hal.science/hal-04058064

[8] Y. Ponty, Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond, Habilitation à diriger des recherches, Université Paris-Saclay, 2020 [Online]. Available: https://theses.hal.science/tel-03219977

[9] Y. Ponty and V. Reinharz, RNA Folding, ISTE, 2022 [Online]. Available: https://hal.science/hal-03614168

[10] R. Sarrazin-Gendron, H.-T. Yao, V. Reinharz, C. G. Oliver, Y. Ponty, and J. Waldispühl, Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules Identification, in RECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology, 2020 [Online]. Available: https://inria.hal.science/hal-02354733

[11] H. T. Nguyen, H. Xue, V. Firlej, Y. Ponty, M. Gallopin, and D. Gautheret, Reference-free transcriptome signatures for prostate cancer prognosis, BMC Cancer, vol. 21, no. 394, 2021 [Online]. Available: https://inria.hal.science/hal-02948844

[12] W. Wang​, M. Barba​, P. Rinaudo​, A. Denise, and Y. Ponty, Homology ­modeling of complex structural RNAs, in JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, 2016 [Online]. Available: https://inria.hal.science/hal-01332642

[13] S. Schirmer, Y. Ponty, and R. Giegerich, Introduction to RNA secondary structure comparison., vol. 1097, Gorodkin, Jan, Ruzzo, and W. L., Eds. Springer, 2013, pp. 247–73 [Online]. Available: https://inria.hal.science/hal-00846818

[14] V. Reinharz, Y. Ponty, and J. Waldispühl, A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution., Bioinformatics, vol. 29, no. 13, pp. i308–15, Jul. 2013 [Online]. Available: https://inria.hal.science/hal-00840260

[15] 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: https://hal.science/hal-02394529