Number of documents

79

Yann's CV


Journal articles32 documents

  • Defne Surujon, Yann Ponty, Peter Clote. Small-world networks and RNA secondary structures. Journal of computational biology : a journal of computational molecular cell biology, Mary Ann Liebert 2019, 26 (1), pp.16--26. ⟨10.1089/cmb.2018.0125⟩. ⟨hal-01424452v2⟩
  • 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⟩
  • 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), In press. ⟨hal-02169271⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • Edwin Jacox, Cedric Chauve, Gergely J Szöllősi, Yann Ponty, Celine Scornavacca. ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.. Bioinformatics (Oxford, England), 2016, pp.2056-8. ⟨hal-01276903⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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, ⟨https://interstices.info/jcms/int_67800/mieux-comprendre-certaines-molecules-biologiques-grace-a-l-informatique⟩. ⟨hal-01350181⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • Mireille Bousquet-Mélou, Yann Ponty. Culminating paths. Discrete Mathematics and Theoretical Computer Science, DMTCS, 2008, 10 (2), pp.125--152. ⟨hal-00151979v2⟩
  • 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⟩

Conference papers34 documents

  • 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. ⟨hal-02141853⟩
  • Adrien Poulenard, Marie-Julie Rakotosaona, Yann Ponty, Maks Ovsjanikov. Effective Rotation-invariant Point CNN with Spherical Harmonics kernels. 3DV 2019 - International Conference on 3D Vision, Sep 2019, Québec City, Canada. ⟨hal-02167454v2⟩
  • Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will. Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. RECOMB 2018 – 22nd Annual International Conference on Research in Computational Molecular Biology, 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • Yann Ponty. RNA Bioinformatics and ensemble dynamic programming. 5th biennial Canadian Discrete and Algorithmic Mathematics Conference - CanaDAM 2015, Jun 2015, Saskatoon, Canada. ⟨hal-01569852⟩
  • Yann Ponty. Towards firm foundations for the rational design of RNA molecules. Colloque de Bioinformatique Moléculaire (GdR BIM), Oct 2015, Paris, France. ⟨hal-01570180⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • 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. ⟨hal-00666399v2⟩
  • Jérôme Waldispühl, Yann Ponty. An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure. Bafna, Vineet and Sahinalp, S. RECOMB - 15th Annual International Conference on Research in Computational Molecular Biology - 2011, Mar 2011, Vancouver, Canada. Springer Berlin / Heidelberg, 6577, pp.501-515, 2011, Lecture Notes in Computer Science. 〈10.1007/978-3-642-20036-6_45〉. 〈hal-00546847〉
  • 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⟩
  • 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⟩
  • 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⟩
  • 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. ⟨hal-00450763v4⟩
  • 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⟩

Poster communications3 documents

  • 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. ⟨http://cs.nyu.edu/~parida/RECOMB-CG2014/⟩. ⟨hal-01216782⟩

Book sections4 documents

Directions of work or proceedings1 document

Preprints, Working Papers, ...1 document

  • 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⟩

Reports2 documents

  • 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⟩

Theses1 document

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

Master thesis1 document

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