Yann's CV

Bertrand Marchand, Yann Ponty, Laurent Bulteau. Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. Algorithms for Molecular Biology, BioMed Central, 2022. ⟨hal-03608412v2⟩

Gregor Entzian, Ivo Hofacker, Yann Ponty, Ronny Lorenz, Andrea Tanzer. RNAxplorer: Harnessing the Power of Guiding Potentials to Sample RNA Landscapes. Bioinformatics, Oxford University Press (OUP), 2021. ⟨hal-02889448v3⟩

Dehe Wang, Ao Jiang, Jiangpeng Feng, Guangnan Li, Dong Guo, et al.. The SARS-CoV-2 Subgenome Landscape and its Novel Regulatory Features. Molecular Cell, Cell Press, In press, ⟨10.1016/j.molcel.2021.02.036⟩. ⟨hal-03154155v2⟩

Ha Nguyen, Haoliang Xue, Virginie Firlej, Yann Ponty, Mélina Gallopin, et al.. Reference-free transcriptome signatures for prostate cancer prognosis. BMC Cancer, BioMed Central, 2021, 21 (394), ⟨10.1186/s12885-021-08021-1⟩. ⟨hal-02948844⟩

Grégoire de Bisschop, Delphine Allouche, Elisa Frezza, Benoît Masquida, Yann Ponty, et al.. Progress Toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. Non-Coding RNA, MDPI, 2021, 7 (4), pp.71. ⟨10.3390/ncrna7040071⟩. ⟨hal-03413594⟩

Matan Drory Retwitzer, Vladimir Reinharz, Alexander Churkin, Yann Ponty, Jérôme Waldispühl, et al.. IncaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs. Bioinformatics, Oxford University Press (OUP), 2020, 36 (9), pp.2910--2922. ⟨10.1093/bioinformatics/btaa039⟩. ⟨hal-02423237⟩

Afaf Saaidi, Delphine Allouche, Mireille Regnier, Bruno Sargueil, Yann Ponty. IPANEMAP: Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles. Nucleic Acids Research, Oxford University Press, 2020, 48 (15), pp.8276--8289. ⟨10.1093/nar/gkaa607⟩. ⟨hal-02889041v3⟩

Cedric Chauve, Yann Ponty, Michael Wallner. Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models. Journal of Mathematical Biology, Springer Verlag (Germany), 2019, 80 (5), pp.1353--1388. ⟨10.1007/s00285-019-01465-x⟩. ⟨hal-02169271⟩

Stefan Hammer, Wei Wang, Sebastian Will, Yann Ponty. Fixed-parameter tractable sampling for RNA design with multiple target structures. BMC Bioinformatics, BioMed Central, 2019, 20 (1), pp.209. ⟨10.1186/s12859-019-2784-7⟩. ⟨hal-02112888⟩

Defne Surujon, Yann Ponty, Peter Clote. Small-world networks and RNA secondary structures. Journal of Computational Biology, Mary Ann Liebert, 2019, 26 (1), pp.16--26. ⟨10.1089/cmb.2018.0125⟩. ⟨hal-01424452v2⟩

Alexander Churkin, Matan Drory Retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, et al.. Design of RNAs: comparing programs for inverse RNA folding.. Briefings in Bioinformatics, Oxford University Press (OUP), 2018, 19 (2), pp.350--358. ⟨10.1093/bib/bbw120⟩. ⟨hal-01392958⟩

Cedric Chauve, Julien Courtiel, Yann Ponty. Counting, generating, analyzing and sampling tree alignments. International Journal of Foundations of Computer Science, World Scientific Publishing, 2018, 29 (5), pp.741--767. ⟨hal-01500116⟩

Nika Abdollahi, Alexandre Albani, Eric Anthony, Agnes Baud, Mélissa Cardon, et al.. Meet-U: educating through research immersion. PLoS Computational Biology, Public Library of Science, 2018, 14 (3), pp.1-10. ⟨10.1371/journal.pcbi.1005992⟩. ⟨hal-01722019⟩

Benedikt Löwes, Cedric Chauve, Yann Ponty, Robert Giegerich. The BRaliBase dent - a tale of benchmark design and interpretation.. Briefings in Bioinformatics, Oxford University Press (OUP), 2017, 18 (2), pp.306--311. ⟨10.1093/bib/bbw022⟩. ⟨hal-01273406⟩

Jozef Haleš, Alice Héliou, Ján Maňuch, Yann Ponty, Ladislav Stacho. Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models. Algorithmica, Springer Verlag, 2017, 79 (3), pp.835--856. ⟨10.1007/s00453-016-0196-x⟩. ⟨hal-01285499v2⟩

Jules Deforges, Sylvain de Breyne, Melissa Ameur, Nathalie Ulryck, Nathalie Chamond, et al.. Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame. Nucleic Acids Research, Oxford University Press, 2017, 45 (12), pp.7382--7400. ⟨10.1093/nar/gkx303⟩. ⟨hal-01505282⟩

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, et al.. DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2017, 9 (5), pp.1312-1319. ⟨10.1093/gbe/evx069⟩. ⟨hal-01503766v2⟩

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces. Nucleic Acids Research, Oxford University Press, 2016, 44 (11), pp.e104 - e104. ⟨10.1093/nar/gkw217⟩. ⟨hal-01291754⟩

Edwin Jacox, Cedric Chauve, Gergely J Szöllősi, Yann Ponty, Celine Scornavacca. ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony. Bioinformatics, Oxford University Press (OUP), 2016, 32 (13), pp.2056-2058. ⟨10.1093/bioinformatics/btw105⟩. ⟨hal-01276903⟩

Matan Drory retwitzer, Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl, Danny Barash. incaRNAfbinv : a web server for the fragment-based design of RNA sequences. Nucleic Acids Research, Oxford University Press, 2016, 44 (W1), pp.W308 - W314. ⟨10.1093/nar/gkw440⟩. ⟨hal-01319682⟩

Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BMC Bioinformatics, BioMed Central, 2015, 16 (Suppl 19), pp.S6. ⟨10.1186/1471-2105-16-S19-S6⟩. ⟨hal-01245495⟩

Andy Lorenz, Yann Ponty. Non-redundant random generation algorithms for weighted context-free languages. Theoretical Computer Science, Elsevier, 2013, Generation of Combinatorial Structures, 502, pp.177-194. ⟨10.1016/j.tcs.2013.01.006⟩. ⟨inria-00607745v2⟩

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs.. Journal of Computational Biology, Mary Ann Liebert, 2013, 20 (11), pp.905-19. ⟨10.1089/cmb.2013.0085⟩. ⟨hal-00828062⟩

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.. Bioinformatics, Oxford University Press (OUP), 2013, 29 (13), pp.i308-15. ⟨10.1093/bioinformatics/btt217⟩. ⟨hal-00840260⟩

Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, et al.. Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information. PLoS Computational Biology, Public Library of Science, 2013, 9 (12), pp.e1003369. ⟨10.1371/journal.pcbi.1003369⟩. ⟨hal-00875116⟩

Yang Zhang, Yann Ponty, Mathieu Blanchette, Eric Lecuyer, Jérôme Waldispühl. SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.. Nucleic Acids Research, Oxford University Press, 2013, Web Server Issue, 41 (Web Server issue), pp.W480-5. ⟨10.1093/nar/gkt461⟩. ⟨hal-00819017⟩

Yann Ponty, Joanna Jongwane. Mieux comprendre certaines molécules biologiques grâce à l’informatique. Interstices, INRIA, 2012. ⟨hal-01350181⟩

Peter Clote, Yann Ponty, Jean-Marc Steyaert. Expected distance between terminal nucleotides of RNA secondary structures.. Journal of Mathematical Biology, Springer Verlag (Germany), 2012, 65 (3), pp.581-99. ⟨10.1007/s00285-011-0467-8⟩. ⟨inria-00619921⟩

Alex Levin, Mieszko Lis, Yann Ponty, Charles W O'Donnell, Srinivas Devadas, et al.. A global sampling approach to designing and reengineering RNA secondary structures.. Nucleic Acids Research, Oxford University Press, 2012, 40 (20), pp.10041-10052. ⟨10.1093/nar/gks768⟩. ⟨hal-00733924⟩

Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote. Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches. PLoS ONE, Public Library of Science, 2012, 7 (12), pp.e50506. ⟨10.1371/journal.pone.0050506⟩. ⟨hal-00769740⟩

Jérôme Waldispühl, Yann Ponty. An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.. Journal of Computational Biology, Mary Ann Liebert, 2011, 18 (11), pp.1465-79. ⟨10.1089/cmb.2011.0181⟩. ⟨hal-00681928⟩

Alain Denise, Yann Ponty, Michel Termier. Controlled non uniform random generation of decomposable structures. Theoretical Computer Science, Elsevier, 2010, 411 (40-42), pp.3527-3552. ⟨10.1016/j.tcs.2010.05.010⟩. ⟨hal-00483581v2⟩

Kévin Darty, Alain Denise, Yann Ponty. VARNA: Interactive drawing and editing of the RNA secondary structure.. Bioinformatics, Oxford University Press (OUP), 2009, 25 (15), pp.1974-5. ⟨10.1093/bioinformatics/btp250⟩. ⟨hal-00432548⟩

Mireille Bousquet-Mélou, Yann Ponty. Culminating paths. Discrete Mathematics and Theoretical Computer Science, DMTCS, 2008, 10 (2), pp.125--152. ⟨hal-00151979v2⟩

William Andrew Lorenz, Peter Clote, Yann Ponty. Asymptotics of RNA shapes. Journal of Computational Biology, Mary Ann Liebert, 2008, 15 (1), pp.31--63. ⟨10.1089/cmb.2006.0153⟩. ⟨inria-00548861⟩

Yann Ponty, R. Istrate, E. Porcelli, Peter Clote. LocalMove: computing on-lattice fits for biopolymers. Nucleic Acids Research, Oxford University Press, 2008, 36 (2), pp.W216-W222. ⟨10.1093/nar/gkn367⟩. ⟨inria-00548867⟩

Yann Ponty. Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method. Journal of Mathematical Biology, Springer Verlag (Germany), 2008, 56 (1-2), pp.107--127. ⟨10.1007/s00285-007-0137-z⟩. ⟨inria-00548863⟩

Ferrè Fabrizzio, Yann Ponty, William Lorenz, Peter 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, Oxford University Press, 2007, 35 (Web server issue), pp.W659--668. ⟨10.1093/nar/gkm334⟩. ⟨inria-00548870⟩

Yann Ponty, Michel Termier, Alain Denise. GenRGenS: Software for Generating Random Genomic Sequences and Structures. Bioinformatics, Oxford University Press (OUP), 2006, 22 (12), pp.1534--1535. ⟨10.1093/bioinformatics/btl113⟩. ⟨inria-00548871⟩

Hua-Ting Yao, Jérôme Waldispühl, Yann Ponty, Sebastian Will. Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA. RECOMB 2021 - 25th international conference on research in computational molecular biology, Apr 2021, Padova, France. ⟨hal-02987566v2⟩

Bertrand Marchand, Yann Ponty, Laurent Bulteau. Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. WABI 2021 - 21st Workshop on Algorithms in Bioinformatics, 2021, Paris, France. ⟨hal-03206132⟩

Sammy Khalife, Yann Ponty, Laurent Bulteau. Sequence graphs realizations and ambiguity in language models. COCOON 2021 - 27th International Computing and Combinatorics Conference, Oct 2021, Tainan, Taiwan. ⟨hal-02495333v3⟩

Laurent Bulteau, Bertrand Marchand, Yann Ponty. A new parametrization for independent set reconfiguration and applications to RNA kinetics. IPEC 2021 - 16th International Symposium on Parameterized and Exact Computation, Sep 2021, Lisbon, Portugal. ⟨hal-03272963v2⟩

Roman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos Oliver, Yann Ponty, et al.. Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules Identification. RECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology, May 2020, Padova, Italy. ⟨hal-02354733⟩

Alexander Churkin, Yann Ponty, Danny Barash. IndelsRNAmute: Predicting deleterious multiple point substitutions and indels mutations. ISBRA 2020 - 16th International Symposium on Bioinformatics Research and Applications, Dec 2020, Moscow, Russia. ⟨hal-02936276⟩

Hua-Ting Yao, Cedric Chauve, Mireille Regnier, Yann Ponty. Exponentially few RNA structures are designable. ACM-BCB 2019 - 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Sep 2019, Niagara-Falls, United States. pp.289-298, ⟨10.1145/3307339.3342163⟩. ⟨hal-02141853v2⟩

Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov. Effective Rotation-invariant Point CNN with Spherical Harmonics kernels. 3DV - International Conference on 3D Vision - 2019, Sep 2019, Québec City, Canada. ⟨hal-02167454v2⟩

Maher Mallem, Alain Denise, Yann Ponty. Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity tests. SEQBIM 2019 - Séquences en Bioinformatique, Informatique et Mathématiques, Dec 2019, Marne-la-Vallée, France. ⟨hal-02403517⟩

Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB - 22nd Annual International Conference on Research in Computational Molecular Biology - 2018, Apr 2018, Paris, France. ⟨hal-01631277v2⟩

Yann Ponty, Sebastian Will, Stefan Hammer. Nucleic Acids design targeting integer-valued features: FPT counting and uniform sampling. WEPA 2018 - 2nd International Workshop on Enumeration Problems and Applications, Nov 2018, Pisa, Italy. ⟨hal-01911878⟩

Chinmay Singhal, Yann Ponty, Isaure Chauvot de Beauchêne. A hybrid combinatorial method for docking single stranded RNAs in a protein pockect at the thermodynamic equilibrium. JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2018, Marseille, France. ⟨hal-02394529⟩

Juraj Michálik, Hélène Touzet, Yann Ponty. Efficient approximations of RNA kinetics landscape using non-redundant sampling. ISMB/ECCB - 25th Annual international conference on Intelligent Systems for Molecular Biology/16th European Conference on Computational Biology - 2017, Jul 2017, Prague, Czech Republic. pp.i283 - i292, ⟨10.1093/bioinformatics/btx269⟩. ⟨hal-01500115⟩

Afaf Saaidi, Yann Ponty, Bruno Sargueil. An integrative approach for predicting the RNA secondary structure for the HIV–1 Gag UTR using probing data. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2017, Jul 2017, Lille, France. pp.102. ⟨hal-01534587⟩

Afaf Saaidi, Yann Ponty, Mathieu Blanchette, Mireille Regnier, Bruno Sargueil. An EM algorithm for mapping short reads in multiple RNA structure probing experiments. Matbio2017, King's College London Sep 2017, London, United Kingdom. ⟨hal-01590528⟩

Cedric Chauve, Julien Courtiel, Yann Ponty. Counting, generating and sampling tree alignments. ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. pp.53--64, ⟨10.1007/978-3-319-38827-4_5⟩. ⟨hal-01154030v3⟩

Jeremie Lumbroso, Marni Mishna, Yann Ponty. Taming reluctant random walks in the positive quadrant. GASCOM - 10th conference on random generation of combinatorial structures - 2016, Jun 2016, Bastia, France. pp.99 -- 114, ⟨10.1016/j.endm.2017.05.008⟩. ⟨hal-01291164⟩

Afaf Saaidi, Delphine Allouche, Bruno Sargueil, Yann Ponty. Towards structural models for the Ebola UTR regions using experimental SHAPE probing data. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France. ⟨hal-01332469⟩

Wei Wang​, Matthieu Barba​, Philippe Rinaudo​, Alain Denise, Yann Ponty. Homology ­modeling of complex structural RNAs. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France. ⟨hal-01332642⟩

Ashok Rajaraman, Cedric Chauve, Yann Ponty. Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies. ISBRA - 11th International Symposium on Bioinformatics Research and Applications - 2015, Jun 2015, Norfolk, Virginia, United States. pp.260--271, ⟨10.1007/978-3-319-19048-8_22⟩. ⟨hal-01104587v3⟩

Yann Ponty. RNA Bioinformatics and ensemble dynamic programming. 5th biennial Canadian Discrete and Algorithmic Mathematics Conference - CanaDAM 2015, Jun 2015, Saskatoon, Canada. ⟨hal-01569852⟩

Jozef Haleš, Ján Maňuch, Yann Ponty, Ladislav Stacho. Combinatorial RNA Design: Designability and Structure-Approximating Algorithm. CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. ⟨hal-01115349v2⟩

Yann Ponty. Towards firm foundations for the rational design of RNA molecules. Colloque de Bioinformatique Moléculaire (GdR BIM), Oct 2015, Paris, France. ⟨hal-01570180⟩

Vincent Le Gallic, Alain Denise, Yann Ponty. Résultats algorithmiques pour le design d’ARN avec contraintes de séquence. SeqBio 2015, Nov 2015, Orsay, France. pp.26-31. ⟨hal-01266096⟩

Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. BSB - Brazilian Symposium on Bioinformatics - 2014, Oct 2014, Belo Horizonte, Brazil. pp.49--56, ⟨10.1007/978-3-319-12418-6⟩. ⟨hal-01056140v2⟩

Yu Zhou, Yann Ponty, Stéphane Vialette, Jérôme Waldispühl, Yi Zhang, et al.. Flexible RNA design under structure and sequence constraints using formal languages. ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States. ⟨hal-00823279v2⟩

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences. RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China. ⟨hal-00766781⟩

Vladimir Reinharz, Yann Ponty, Jérôme Waldispühl. A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution. ISMB/ECCB - 21st Annual international conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology - 2013, Jul 2013, Berlin, Germany. ⟨hal-00811607⟩

Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty, Peter Clote. Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract). RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China. ⟨hal-00766780⟩

Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise. Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots. WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, University of Ljubljana, Sep 2012, Ljubljana, Slovenia. ⟨hal-00708580v2⟩

Yann Ponty. Visualizing 2D & 3D Structures of RNA. VIZBI - 3rd international meeting on Visualizing Biological Data - 2012, Jim, Procter (U-Dundee, Scotland) and Sean O'Donoghue (CMIS, Australia), Mar 2012, Heidelberg, Germany. ⟨hal-00723351⟩

Cyril Banderier, Olivier Bodini, Yann Ponty, Hanane Tafat. On the diversity of pattern distributions in rational language. ANALCO - 12th Meeting on Analytic Algorithmics and Combinatorics - 2012, Jan 2012, Kyoto, Japan. pp.107--116. ⟨hal-00643598⟩

Saad Sheikh, Rolf Backofen, Yann Ponty. Impact Of The Energy Model On The Complexity Of RNA Folding With Pseudoknots. CPM - 23rd Annual Symposium on Combinatorial Pattern Matching - 2012, Juha Kärkkäinen, Jul 2012, Helsinki, Finland. pp.321--333, ⟨10.1007/978-3-642-31265-6_26⟩. ⟨hal-00670232v3⟩

Jérémie Du Boisberranger, Danièle Gardy, Yann Ponty. The weighted words collector. AOFA - 23rd International Meeting on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms - 2012, Nicolas, Broutin (INRIA, France) and Luc, Devroye (McGill, Canada), Jun 2012, Montreal, Canada. pp.243--264, ⟨10.46298/dmtcs.2998⟩. ⟨hal-00666399v2⟩

Stefan Janssen, Loïc Paulevé, Yann Ponty, Balaji Raman, Matthias Zytnicki. Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?. IWBDA - 4th International Workshop on Bio-Design Automation - 2012, Jun 2012, San Francisco, United States. ⟨hal-00712557⟩

Stefan Janssen, Yann Ponty, Balaji Raman, Saad Sheikh, Jean-Marc Steyaert, et al.. Investigating the RFAM paradox: The pseudoknot explanation. Fifth Indo-French Bioinformatics Meeting, Mar 2011, Hyderabad, India. ⟨hal-00585647⟩

Jérôme Waldispühl, Yann Ponty. An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure. RECOMB - 15th Annual International Conference on Research in Computational Molecular Biology - 2011, Mar 2011, Vancouver, Canada. pp.501-515, ⟨10.1007/978-3-642-20036-6_45⟩. ⟨hal-00546847⟩

Yann Ponty, Cédric Saule. A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms. WABI - 11th Workshop on Algorithms in Bioinformatics - 2011, 2011, Saarbrucken, Germany. ⟨inria-00601060⟩

Olivier Bodini, Yann Ponty. Multi-dimensional Boltzmann Sampling of Languages. 21st International Meeting on Probabilistic, Combinatorial, and Asymptotic Methods in the Analysis of Algorithms (AofA'10), Jun 2010, Vienna, Austria. pp.49-64, ⟨10.46298/dmtcs.2793⟩. ⟨hal-00450763v4⟩

Danièle Gardy, Yann Ponty. Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models. GASCOM - 8th conference on random generation of combinatorial structures - 2010, LACIM, UQAM, Sep 2010, Montréal, Canada. 14pp. ⟨inria-00543150⟩

Yann Ponty. Non-redundant random generation from weighted context-free languages. GASCOM - 7th conference on random generation of combinatorial structures - 2008, 2008, Bibbiena, Italy. 12pp. ⟨hal-00548877⟩

Gregory Kucherov, Laurent Noé, Yann Ponty. Estimating seed sensitivity on homogeneous alignments. 4th Symposium on Bioinformatics and bioengineering - BIBE'2004, May 2004, Taichung, Taiwan. pp.387-394, ⟨10.1109/BIBE.2004.1317369⟩. ⟨inria-00001163⟩

Afaf Saaidi, Yann Ponty, Mireille Regnier. Clustering strings with mutations using an expectation-maximization algorithm In the context of RNA structure prediction. 34th Clemson Mini-Conference on Discrete Mathematics and Algorithms, Oct 2019, Clemson, United States. ⟨hal-02332313⟩

Chinmay Singhal, Yann Ponty, Isaure Chauvot de Beauchêne. A hybrid combinatorial method for docking single stranded RNA on proteins at the thermodynamic equilibrium. RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France. ⟨hal-01925083⟩

Afaf Saaidi, Delphine Allouche, Yann Ponty, Bruno Sargueil, Mireille Regnier. Computational methods for comparing and integrating multiple probing assays to predict RNA secondary structure . Doctorial journey Interface, Ecole polytechnique, Palaiseau, Nov 2016, Palaiseau, France. 10. ⟨hal-01558227⟩

Cedric Chauve, Yann Ponty, João Paulo Pereira Zanetti. Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach. RECOMB-CG'14, Oct 2014, Cold Spring HArbour, United States. ⟨hal-01216782⟩

Yann Ponty, Vladimir Reinharz. RNA Folding. From text to graphs: Discrete structures and methods for Bioinformatics, ISTE, 2022. ⟨hal-03614168⟩

Yann Ponty, Stefan Hammer, Hua-Ting Yao, Sebastian Will. Advanced design of structural RNAs using RNARedPrint. Ernesto Picardi. RNA Bioinformatics, 2284, pp.1--15, 2021, Methods in Molecular Biology, 978-1-0716-1306-1. ⟨10.1007/978-1-0716-1307-8_1⟩. ⟨hal-02990264⟩

Yann Ponty, Vladimir Reinharz. Repliement de l'ARN. Annie Chateau; Mikaël Salson. Du texte aux graphes : méthodes et structures discrètes pour la bioinformatique, A paraître. ⟨hal-02864246⟩

Delphine Allouche, Grégoire de Bisschop, Afaf Saaidi, Yann Ponty, Sargueil Bruno. RNA secondary structure modelling following the IPANEMAP workflow. RNA Folding - Methods and Protocols, Springer Nature, In press, Methods in Molecular Biology. ⟨hal-02324783⟩

Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl. Preface.: Extended versions of selected papers presented at Computational methods for Structural RNAs (CMSR'14). Computational methods for Structural RNAs (CMSR'14), 22 (3), Mary Ann Liebert, pp.189, 2015, Journal of Computational Biology. ⟨hal-01136745⟩

Yann Ponty, Fabrice Leclerc. Drawing and Editing the Secondary Structure(s) of RNA.. Ernesto Picardi. RNA Bioinformatics, 1269, Springer New York, pp.63-100, 2015, Methods in Molecular Biology, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_5⟩. ⟨hal-01079893⟩

Yann Ponty. Bio-algorithmique des ARN : petite promenade aux interfaces. Eric Sopena. 1024 - Bulletin de la société informatique de France, 4, SIF, pp.23--53, 2014. ⟨hal-01077506v3⟩

Stefanie Schirmer, Yann Ponty, Robert Giegerich. Introduction to RNA secondary structure comparison.. Gorodkin, Jan and Ruzzo, Walter L. RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods, 1097, Springer, pp.247-73, 2013, Methods in molecular biology, ISBN 978-1-62703-708-2. ⟨10.1007/978-1-62703-709-9_12⟩. ⟨hal-00846818⟩

Fabrice Jossinet, Yann Ponty, Jérôme Waldispühl. Proceedings of the 1st workshop on Computational Methods for Structural RNAs. Jossinet, Fabrice; Ponty, Yann; Waldispühl, Jérôme. France. McGill University, pp.76, 2014, 978-2-9550187-0-5. ⟨10.15455/CMSR.2014.0000⟩. ⟨hal-01071417⟩

Bertrand Marchand, Sebastian Will, Sarah Berkemer, Laurent Bulteau, Yann Ponty. Automated design of dynamic programming schemes for RNA folding with pseudoknots. 2022. ⟨hal-03676377⟩

Christelle Rovetta, Juraj Michálik, Ronny Lorenz, Andrea Tanzer, Yann Ponty. Non-Redundant Sampling and Statistical Estimators for RNA Structural Properties at the Thermodynamic Equilibrium. 2019. ⟨hal-02288811⟩

Yann Ponty. Rule-weighted and terminal-weighted context-free grammars have identical expressivity. [Research Report] 2012. ⟨hal-00693600⟩

Gregory Kucherov, Laurent Noé, Yann Ponty. Estimating seed sensitivity on homogeneous alignments. [Research Report] RR-5047, INRIA. 2003, pp.17. ⟨inria-00071536⟩

Yann Ponty. Modélisation de séquences génomiques structurées, génération aléatoire et applications. Mathématiques [math]. Université Paris Sud - Paris XI, 2006. Français. ⟨tel-00144130v2⟩

Yann Ponty. Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond. Bioinformatics [q-bio.QM]. Université Paris-Saclay, 2020. ⟨tel-03219977v2⟩

Yann Ponty. Etudes combinatoire et génération aléatoire des structures secondaires d'ARN. Bio-informatique [q-bio.QM]. 2003. ⟨hal-01261068⟩