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BibTeX records: Yann Ponty
@article{DBLP:journals/almob/BouryGBP25,
author = {Th{\'{e}}o Boury and
Samuel Gardelle and
Laurent Bulteau and
Yann Ponty},
title = {{RNA} inverse folding can be solved in linear time for structures
without isolated stacks or base pairs},
journal = {Algorithms Mol. Biol.},
volume = {20},
number = {1},
pages = {20},
year = {2025},
url = {https://doi.org/10.1186/s13015-025-00278-6},
doi = {10.1186/S13015-025-00278-6},
timestamp = {Sat, 15 Nov 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/BouryGBP25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BourySHPY25,
author = {Th{\'{e}}o Boury and
Leonhard Sidl and
Ivo L. Hofacker and
Yann Ponty and
Hua{-}Ting Yao},
editor = {Sriram Sankararaman},
title = {Old Dog, New Tricks: Exact Seeding Strategy Improves {RNA} Design
Performances},
booktitle = {Research in Computational Molecular Biology - 29th International Conference,
{RECOMB} 2025, Seoul, South Korea, April 26-29, 2025, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {15647},
pages = {134--152},
publisher = {Springer},
year = {2025},
url = {https://doi.org/10.1007/978-3-031-90252-9\_9},
doi = {10.1007/978-3-031-90252-9\_9},
timestamp = {Sat, 31 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BourySHPY25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/YaoMBPW24,
author = {Hua{-}Ting Yao and
Bertrand Marchand and
Sarah J. Berkemer and
Yann Ponty and
Sebastian Will},
title = {Infrared: a declarative tree decomposition-powered framework for bioinformatics},
journal = {Algorithms Mol. Biol.},
volume = {19},
number = {1},
pages = {13},
year = {2024},
url = {https://doi.org/10.1186/s13015-024-00258-2},
doi = {10.1186/S13015-024-00258-2},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/YaoMBPW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MilenkovicP24,
author = {Tijana Milenkovic and
Yann Ponty},
title = {{ISMB} 2024 Proceedings},
journal = {Bioinform.},
volume = {40},
number = {Supplement{\_}1},
pages = {i1--i2},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae286},
doi = {10.1093/BIOINFORMATICS/BTAE286},
timestamp = {Tue, 28 Oct 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MilenkovicP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/YacoubGLBP24,
author = {Taher Yacoub and
Roy Gonz{\'{a}}lez{-}Alem{\'{a}}n and
Fabrice Leclerc and
Isaure Chauvot de Beauch{\^{e}}ne and
Yann Ponty},
editor = {Jian Ma},
title = {Color Coding for the Fragment-Based Docking, Design and Equilibrium
Statistics of Protein-Binding ssRNAs},
booktitle = {Research in Computational Molecular Biology - 28th Annual International
Conference, {RECOMB} 2024, Cambridge, MA, USA, April 29 - May 2, 2024,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14758},
pages = {147--163},
publisher = {Springer},
year = {2024},
url = {https://doi.org/10.1007/978-1-0716-3989-4\_10},
doi = {10.1007/978-1-0716-3989-4\_10},
timestamp = {Thu, 04 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/YacoubGLBP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BoehmerBWP24,
author = {Kimon Boehmer and
Sarah J. Berkemer and
Sebastian Will and
Yann Ponty},
editor = {Solon P. Pissis and
Wing{-}Kin Sung},
title = {{RNA} Triplet Repeats: Improved Algorithms for Structure Prediction
and Interactions},
booktitle = {24th International Workshop on Algorithms in Bioinformatics, {WABI}
2024, September 2-4, 2024, Royal Holloway, London, United Kingdom},
series = {LIPIcs},
volume = {312},
pages = {18:1--18:23},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2024},
url = {https://doi.org/10.4230/LIPIcs.WABI.2024.18},
doi = {10.4230/LIPICS.WABI.2024.18},
timestamp = {Mon, 26 Aug 2024 16:40:52 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BoehmerBWP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BouryBP24,
author = {Th{\'{e}}o Boury and
Laurent Bulteau and
Yann Ponty},
editor = {Solon P. Pissis and
Wing{-}Kin Sung},
title = {{RNA} Inverse Folding Can Be Solved in Linear Time for Structures
Without Isolated Stacks or Base Pairs},
booktitle = {24th International Workshop on Algorithms in Bioinformatics, {WABI}
2024, September 2-4, 2024, Royal Holloway, London, United Kingdom},
series = {LIPIcs},
volume = {312},
pages = {19:1--19:23},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2024},
url = {https://doi.org/10.4230/LIPIcs.WABI.2024.19},
doi = {10.4230/LIPICS.WABI.2024.19},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BouryBP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@misc{DBLP:data/11/BouryBP24,
author = {Th{\'{e}}o Boury and
Laurent Bulteau and
Yann Ponty},
title = {LinearBPDesign},
publisher = {{DROPS} Artifacts},
year = {2024},
month = nov,
howpublished = {\url{https://doi.org/10.4230/artifacts.22511}},
note = {Accessed on YYYY-MM-DD.},
url = {https://doi.org/10.4230/artifacts.22511},
doi = {10.4230/ARTIFACTS.22511},
timestamp = {Wed, 15 Jan 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/data/11/BouryBP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-08830,
author = {Sammy Khalife and
Yann Ponty and
Laurent Bulteau},
title = {Sequence graphs realizations and ambiguity in language models},
journal = {CoRR},
volume = {abs/2402.08830},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.08830},
doi = {10.48550/ARXIV.2402.08830},
eprinttype = {arXiv},
eprint = {2402.08830},
timestamp = {Mon, 19 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-08830.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MarchandWBPB23,
author = {Bertrand Marchand and
Sebastian Will and
Sarah J. Berkemer and
Yann Ponty and
Laurent Bulteau},
title = {Automated design of dynamic programming schemes for {RNA} folding
with pseudoknots},
journal = {Algorithms Mol. Biol.},
volume = {18},
number = {1},
pages = {18},
year = {2023},
url = {https://doi.org/10.1186/s13015-023-00229-z},
doi = {10.1186/S13015-023-00229-Z},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/MarchandWBPB23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PontyR23,
author = {Yann Ponty and
Sushmita Roy},
title = {{ISMB/ECCB} 2023 proceedings},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {1--2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad319},
doi = {10.1093/BIOINFORMATICS/BTAD319},
timestamp = {Tue, 28 Oct 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PontyR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BouryPR23,
author = {Th{\'{e}}o Boury and
Yann Ponty and
Vladimir Reinharz},
editor = {Djamal Belazzougui and
A{\"{\i}}da Ouangraoua},
title = {Automatic Exploration of the Natural Variability of {RNA} Non-Canonical
Geometric Patterns with a Parameterized Sampling Technique},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics, {WABI}
2023, September 4-6, 2023, Houston, TX, {USA}},
series = {LIPIcs},
volume = {273},
pages = {20:1--20:22},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2023},
url = {https://doi.org/10.4230/LIPIcs.WABI.2023.20},
doi = {10.4230/LIPICS.WABI.2023.20},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BouryPR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MarchandPB22,
author = {Bertrand Marchand and
Yann Ponty and
Laurent Bulteau},
title = {Tree diet: reducing the treewidth to unlock {FPT} algorithms in {RNA}
bioinformatics},
journal = {Algorithms Mol. Biol.},
volume = {17},
number = {1},
pages = {8},
year = {2022},
url = {https://doi.org/10.1186/s13015-022-00213-z},
doi = {10.1186/S13015-022-00213-Z},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/MarchandPB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChurkinPB22,
author = {Alexander Churkin and
Yann Ponty and
Danny Barash},
title = {IndelsRNAmute: predicting deleterious multiple point substitutions
and indels mutations},
journal = {{BMC} Bioinform.},
volume = {23-S},
number = {8},
pages = {424},
year = {2022},
url = {https://doi.org/10.1186/s12859-022-04943-0},
doi = {10.1186/S12859-022-04943-0},
timestamp = {Sun, 13 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChurkinPB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MarchandWBBP22,
author = {Bertrand Marchand and
Sebastian Will and
Sarah J. Berkemer and
Laurent Bulteau and
Yann Ponty},
editor = {Christina Boucher and
Sven Rahmann},
title = {Automated Design of Dynamic Programming Schemes for {RNA} Folding
with Pseudoknots},
booktitle = {22nd International Workshop on Algorithms in Bioinformatics, {WABI}
2022, September 5-7, 2022, Potsdam, Germany},
series = {LIPIcs},
volume = {242},
pages = {7:1--7:24},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2022},
url = {https://doi.org/10.4230/LIPIcs.WABI.2022.7},
doi = {10.4230/LIPICS.WABI.2022.7},
timestamp = {Wed, 21 Aug 2024 22:46:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/MarchandWBBP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dagstuhl-reports/FindeissFP22,
author = {Sven Findei{\ss} and
Christoph Flamm and
Yann Ponty},
title = {Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381)},
journal = {Dagstuhl Reports},
volume = {12},
number = {9},
pages = {121--149},
year = {2022},
url = {https://doi.org/10.4230/DagRep.12.9.121},
doi = {10.4230/DAGREP.12.9.121},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dagstuhl-reports/FindeissFP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EntzianHPLT21,
author = {Gregor Entzian and
Ivo L. Hofacker and
Yann Ponty and
Ronny Lorenz and
Andrea Tanzer},
title = {RNAxplorer: harnessing the power of guiding potentials to sample {RNA}
landscapes},
journal = {Bioinform.},
volume = {37},
number = {15},
pages = {2126--2133},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab066},
doi = {10.1093/BIOINFORMATICS/BTAB066},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/EntzianHPLT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/KhalifePB21,
author = {Sammy Khalife and
Yann Ponty and
Laurent Bulteau},
editor = {Chi{-}Yeh Chen and
Wing{-}Kai Hon and
Ling{-}Ju Hung and
Chia{-}Wei Lee},
title = {Sequence Graphs Realizations and Ambiguity in Language Models},
booktitle = {Computing and Combinatorics - 27th International Conference, {COCOON}
2021, Tainan, Taiwan, October 24-26, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13025},
pages = {153--163},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-89543-3\_13},
doi = {10.1007/978-3-030-89543-3\_13},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cocoon/KhalifePB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwpec/BulteauMP21,
author = {Laurent Bulteau and
Bertrand Marchand and
Yann Ponty},
editor = {Petr A. Golovach and
Meirav Zehavi},
title = {A New Parametrization for Independent Set Reconfiguration and Applications
to {RNA} Kinetics},
booktitle = {16th International Symposium on Parameterized and Exact Computation,
{IPEC} 2021, September 8-10, 2021, Lisbon, Portugal},
series = {LIPIcs},
volume = {214},
pages = {11:1--11:15},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2021},
url = {https://doi.org/10.4230/LIPIcs.IPEC.2021.11},
doi = {10.4230/LIPICS.IPEC.2021.11},
timestamp = {Wed, 21 Aug 2024 22:46:00 +0200},
biburl = {https://dblp.org/rec/conf/iwpec/BulteauMP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MarchandPB21,
author = {Bertrand Marchand and
Yann Ponty and
Laurent Bulteau},
editor = {Alessandra Carbone and
Mohammed El{-}Kebir},
title = {Tree Diet: Reducing the Treewidth to Unlock {FPT} Algorithms in {RNA}
Bioinformatics},
booktitle = {21st International Workshop on Algorithms in Bioinformatics, {WABI}
2021, August 2-4, 2021, Virtual Conference},
series = {LIPIcs},
volume = {201},
pages = {7:1--7:23},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2021},
url = {https://doi.org/10.4230/LIPIcs.WABI.2021.7},
doi = {10.4230/LIPICS.WABI.2021.7},
timestamp = {Wed, 21 Aug 2024 22:46:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/MarchandPB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/hal/Ponty20,
author = {Yann Ponty},
title = {Ensemble Algorithms and Analytic Combinatorics in {RNA} Bioinformatics
and Beyond. (Algorithmes ensemblistes et combinatoire analytique en
Bioinformatique des {ARN)}},
year = {2020},
url = {https://tel.archives-ouvertes.fr/tel-03219977},
timestamp = {Thu, 15 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/hal/Ponty20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RetwitzerRCPWB20,
author = {Matan Drory Retwitzer and
Vladimir Reinharz and
Alexander Churkin and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl and
Danny Barash},
title = {incaRNAfbinv 2.0: a webserver and software with motif control for
fragment-based design of RNAs},
journal = {Bioinform.},
volume = {36},
number = {9},
pages = {2920--2922},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa039},
doi = {10.1093/BIOINFORMATICS/BTAA039},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RetwitzerRCPWB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZulkowerRP20,
author = {Valentin Zulkower and
Susan Rosser and
Yann Ponty},
title = {{DNA} Chisel, a versatile sequence optimizer},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4508--4509},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa558},
doi = {10.1093/BIOINFORMATICS/BTAA558},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZulkowerRP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KochnevHCDP20,
author = {Yuri Kochnev and
Erich Hellemann and
Kevin C. Cassidy and
Jacob D. Durrant and
Yann Ponty},
title = {Webina: an open-source library and web app that runs AutoDock Vina
entirely in the web browser},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4513--4515},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa579},
doi = {10.1093/BIOINFORMATICS/BTAA579},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KochnevHCDP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PuchalaBKDBCDP20,
author = {Weronika Puchala and
Michal Burdukiewicz and
Michal Kistowski and
Katarzyna A. Dabrowska and
Aleksandra E. Badaczewska{-}Dawid and
Dominik Cysewski and
Michal Dadlez and
Yann Ponty},
title = {HaDeX: an {R} package and web-server for analysis of data from hydrogen-deuterium
exchange mass spectrometry experiments},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4516--4518},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa587},
doi = {10.1093/BIOINFORMATICS/BTAA587},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PuchalaBKDBCDP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/Sarrazin-Gendron20,
author = {Roman Sarrazin{-}Gendron and
Hua{-}Ting Yao and
Vladimir Reinharz and
Carlos G. Oliver and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
editor = {Russell Schwartz},
title = {Stochastic Sampling of Structural Contexts Improves the Scalability
and Accuracy of {RNA} 3D Module Identification},
booktitle = {Research in Computational Molecular Biology - 24th Annual International
Conference, {RECOMB} 2020, Padua, Italy, May 10-13, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12074},
pages = {186--201},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-45257-5\_12},
doi = {10.1007/978-3-030-45257-5\_12},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/Sarrazin-Gendron20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HammerWWP19,
author = {Stefan Hammer and
Wei Wang and
Sebastian Will and
Yann Ponty},
title = {Fixed-parameter tractable sampling for {RNA} design with multiple
target structures},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {209:1--209:13},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2784-7},
doi = {10.1186/S12859-019-2784-7},
timestamp = {Tue, 28 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HammerWWP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SurujonPC19,
author = {Defne Surujon and
Yann Ponty and
Peter Clote},
title = {Small-World Networks and {RNA} Secondary Structures},
journal = {J. Comput. Biol.},
volume = {26},
number = {1},
pages = {16--26},
year = {2019},
url = {https://doi.org/10.1089/cmb.2018.0125},
doi = {10.1089/CMB.2018.0125},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/SurujonPC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/3dim/PoulenardRPO19,
author = {Adrien Poulenard and
Marie{-}Julie Rakotosaona and
Yann Ponty and
Maks Ovsjanikov},
title = {Effective Rotation-Invariant Point {CNN} with Spherical Harmonics
Kernels},
booktitle = {2019 International Conference on 3D Vision, 3DV 2019, Qu{\'{e}}bec
City, QC, Canada, September 16-19, 2019},
pages = {47--56},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/3DV.2019.00015},
doi = {10.1109/3DV.2019.00015},
timestamp = {Tue, 05 Nov 2019 17:39:17 +0100},
biburl = {https://dblp.org/rec/conf/3dim/PoulenardRPO19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/YaoCRP19,
author = {Hua{-}Ting Yao and
C{\'{e}}dric Chauve and
Mireille R{\'{e}}gnier and
Yann Ponty},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {Exponentially Few {RNA} Structures are Designable},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {289--298},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3342163},
doi = {10.1145/3307339.3342163},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/YaoCRP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1905-04971,
author = {C{\'{e}}dric Chauve and
Yann Ponty and
Michael Wallner},
title = {Counting and sampling gene family evolutionary histories in the duplication-loss
and duplication-loss-transfer models},
journal = {CoRR},
volume = {abs/1905.04971},
year = {2019},
url = {http://arxiv.org/abs/1905.04971},
eprinttype = {arXiv},
eprint = {1905.04971},
timestamp = {Fri, 01 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1905-04971.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1906-11555,
author = {Adrien Poulenard and
Marie{-}Julie Rakotosaona and
Yann Ponty and
Maks Ovsjanikov},
title = {Effective Rotation-invariant Point {CNN} with Spherical Harmonics
kernels},
journal = {CoRR},
volume = {abs/1906.11555},
year = {2019},
url = {http://arxiv.org/abs/1906.11555},
eprinttype = {arXiv},
eprint = {1906.11555},
timestamp = {Mon, 01 Jul 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1906-11555.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChurkinRRPWB18,
author = {Alexander Churkin and
Matan Drory Retwitzer and
Vladimir Reinharz and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl and
Danny Barash},
title = {Design of RNAs: comparing programs for inverse {RNA} folding},
journal = {Briefings Bioinform.},
volume = {19},
number = {2},
pages = {350--358},
year = {2018},
url = {https://doi.org/10.1093/bib/bbw120},
doi = {10.1093/BIB/BBW120},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ChurkinRRPWB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/ChauveCP18,
author = {C{\'{e}}dric Chauve and
Julien Courtiel and
Yann Ponty},
title = {Counting, Generating, Analyzing and Sampling Tree Alignments},
journal = {Int. J. Found. Comput. Sci.},
volume = {29},
number = {5},
pages = {741--767},
year = {2018},
url = {https://doi.org/10.1142/S0129054118420030},
doi = {10.1142/S0129054118420030},
timestamp = {Tue, 12 Mar 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijfcs/ChauveCP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/AbdollahiAABCCC18,
author = {Nika Abdollahi and
Alexandre Albani and
{\'{E}}ric Anthony and
Agnes Baud and
M{\'{e}}lissa Cardon and
Robert Clerc and
Dariusz Czernecki and
Romain Conte and
Laurent David and
Agathe Delaune and
Samia Djerroud and
Pauline Fourgoux and
Nad{\`{e}}ge Guiglielmoni and
Jeanne Laurentie and
Nathalie Lehmann and
Camille Lochard and
R{\'{e}}mi Montagne and
Vasiliki Myrodia and
Vaitea Opuu and
Elise Parey and
L{\'{e}}lia Polit and
Sylvain Priv{\'{e}} and
Chlo{\'{e}} Quignot and
Maria Ruiz{-}Cuevas and
Mariam Sissoko and
Nicolas Sompairac and
Audrey Vallerix and
Violaine Verrecchia and
Marc Delarue and
Rapha{\"{e}}l Gu{\'{e}}rois and
Yann Ponty and
Sophie Sacquin{-}Mora and
Alessandra Carbone and
Christine Froidevaux and
St{\'{e}}phane Le Crom and
Olivier Lespinet and
Martin Weigt and
Samer Abboud and
Juliana S. Bernardes and
Guillaume Bouvier and
Chlo{\'{e}} Dequeker and
Arnaud Ferr{\'{e}} and
Patrick Fuchs and
Ga{\"{e}}lle Lelandais and
Pierre Poulain and
Hugues Richard and
Hugo Schweke and
Elodie Laine and
Anne Lopes},
title = {Meet-U: Educating through research immersion},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {3},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1005992},
doi = {10.1371/JOURNAL.PCBI.1005992},
timestamp = {Sat, 06 Sep 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/AbdollahiAABCCC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HammerPWW18,
author = {Stefan Hammer and
Yann Ponty and
Wei Wang and
Sebastian Will},
editor = {Benjamin J. Raphael},
title = {Fixed-Parameter Tractable Sampling for {RNA} Design with Multiple
Target Structures},
booktitle = {Research in Computational Molecular Biology - 22nd Annual International
Conference, {RECOMB} 2018, Paris, France, April 21-24, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10812},
pages = {256--258},
publisher = {Springer},
year = {2018},
url = {https://link.springer.com/content/pdf/bbm\%3A978-3-319-89929-9\%2F1.pdf},
timestamp = {Tue, 28 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HammerPWW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/HalesHMPS17,
author = {Jozef Hales and
Alice H{\'{e}}liou and
J{\'{a}}n Manuch and
Yann Ponty and
Ladislav Stacho},
title = {Combinatorial {RNA} Design: Designability and Structure-Approximating
Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models},
journal = {Algorithmica},
volume = {79},
number = {3},
pages = {835--856},
year = {2017},
url = {https://doi.org/10.1007/s00453-016-0196-x},
doi = {10.1007/S00453-016-0196-X},
timestamp = {Fri, 30 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithmica/HalesHMPS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LowesCPG17,
author = {Benedikt L{\"{o}}wes and
C{\'{e}}dric Chauve and
Yann Ponty and
Robert Giegerich},
title = {The BRaliBase dent - a tale of benchmark design and interpretation},
journal = {Briefings Bioinform.},
volume = {18},
number = {2},
pages = {306--311},
year = {2017},
url = {https://doi.org/10.1093/bib/bbw022},
doi = {10.1093/BIB/BBW022},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LowesCPG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MichalikTP17,
author = {Juraj Michalik and
H{\'{e}}l{\`{e}}ne Touzet and
Yann Ponty},
title = {Efficient approximations of {RNA} kinetics landscape using non-redundant
sampling},
journal = {Bioinform.},
volume = {33},
number = {14},
pages = {i283--i292},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx269},
doi = {10.1093/BIOINFORMATICS/BTX269},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MichalikTP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/endm/LumbrosoMP17,
author = {J{\'{e}}r{\'{e}}mie O. Lumbroso and
Marni Mishna and
Yann Ponty},
title = {Taming reluctant random walks in the positive quadrant},
journal = {Electron. Notes Discret. Math.},
volume = {59},
pages = {99--114},
year = {2017},
url = {https://doi.org/10.1016/j.endm.2017.05.008},
doi = {10.1016/J.ENDM.2017.05.008},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/endm/LumbrosoMP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JacoxCSPS16,
author = {Edwin Jacox and
C{\'{e}}dric Chauve and
Gergely J. Sz{\"{o}}llosi and
Yann Ponty and
C{\'{e}}line Scornavacca},
title = {ecceTERA: comprehensive gene tree-species tree reconciliation using
parsimony},
journal = {Bioinform.},
volume = {32},
number = {13},
pages = {2056--2058},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw105},
doi = {10.1093/BIOINFORMATICS/BTW105},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JacoxCSPS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RetwitzerRPWB16,
author = {Matan Drory Retwitzer and
Vladimir Reinharz and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl and
Danny Barash},
title = {incaRNAfbinv: a web server for the fragment-based design of {RNA}
sequences},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Webserver-Issue},
pages = {W308--W314},
year = {2016},
url = {https://doi.org/10.1093/nar/gkw440},
doi = {10.1093/NAR/GKW440},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/RetwitzerRPWB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/ChauveCP16,
author = {C{\'{e}}dric Chauve and
Julien Courtiel and
Yann Ponty},
editor = {Mar{\'{\i}}a Bot{\'{o}}n{-}Fern{\'{a}}ndez and
Carlos Mart{\'{\i}}n{-}Vide and
Sergio Santander{-}Jim{\'{e}}nez and
Miguel A. Vega{-}Rodr{\'{\i}}guez},
title = {Counting, Generating and Sampling Tree Alignments},
booktitle = {Algorithms for Computational Biology - Third International Conference,
AlCoB 2016, Trujillo, Spain, June 21-22, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9702},
pages = {53--64},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-38827-4\_5},
doi = {10.1007/978-3-319-38827-4\_5},
timestamp = {Tue, 14 May 2019 10:00:49 +0200},
biburl = {https://dblp.org/rec/conf/alcob/ChauveCP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChauvePZ15,
author = {C{\'{e}}dric Chauve and
Yann Ponty and
Jo{\~{a}}o Paulo Pereira Zanetti},
title = {Evolution of genes neighborhood within reconciled phylogenies: an
ensemble approach},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S19}},
pages = {S6},
year = {2015},
url = {https://doi.org/10.1186/1471-2105-16-s19-s6},
doi = {10.1186/1471-2105-16-S19-S6},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChauvePZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/JossinetPW15,
author = {Fabrice Jossinet and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {Preface},
journal = {J. Comput. Biol.},
volume = {22},
number = {3},
pages = {189},
year = {2015},
url = {https://doi.org/10.1089/cmb.2015.010P},
doi = {10.1089/CMB.2015.010P},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/JossinetPW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/HalesMPS15,
author = {Jozef Hales and
J{\'{a}}n Manuch and
Yann Ponty and
Ladislav Stacho},
editor = {Ferdinando Cicalese and
Ely Porat and
Ugo Vaccaro},
title = {Combinatorial {RNA} Design: Designability and Structure-Approximating
Algorithm},
booktitle = {Combinatorial Pattern Matching - 26th Annual Symposium, {CPM} 2015,
Ischia Island, Italy, June 29 - July 1, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9133},
pages = {231--246},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-19929-0\_20},
doi = {10.1007/978-3-319-19929-0\_20},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/HalesMPS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/RajaramanCP15,
author = {Ashok Rajaraman and
C{\'{e}}dric Chauve and
Yann Ponty},
editor = {Robert W. Harrison and
Yaohang Li and
Ion I. Mandoiu},
title = {Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods
from Reconciled Phylogenies: Supplementary Material},
booktitle = {Bioinformatics Research and Applications - 11th International Symposium,
{ISBRA} 2015, Norfolk, VA, USA, June 7-10, 2015 Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9096},
pages = {260--271},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-19048-8\_22},
doi = {10.1007/978-3-319-19048-8\_22},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/RajaramanCP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/HalesMPS15,
author = {Jozef Hales and
J{\'{a}}n Manuch and
Yann Ponty and
Ladislav Stacho},
title = {Combinatorial {RNA} Design: Designability and Structure-Approximating
Algorithm},
journal = {CoRR},
volume = {abs/1502.03201},
year = {2015},
url = {http://arxiv.org/abs/1502.03201},
eprinttype = {arXiv},
eprint = {1502.03201},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/HalesMPS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ChauveCP15,
author = {C{\'{e}}dric Chauve and
Julien Courtiel and
Yann Ponty},
title = {An Unambiguous And Complete Dynamic Programming Algorithm For Tree
Alignment},
journal = {CoRR},
volume = {abs/1505.05983},
year = {2015},
url = {http://arxiv.org/abs/1505.05983},
eprinttype = {arXiv},
eprint = {1505.05983},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ChauveCP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/ChauvePZ14,
author = {C{\'{e}}dric Chauve and
Yann Ponty and
Jo{\~{a}}o Paulo Pereira Zanetti},
editor = {S{\'{e}}rgio Vale Aguiar Campos},
title = {Evolution of Genes Neighborhood within Reconciled Phylogenies: An
Ensemble Approach},
booktitle = {Advances in Bioinformatics and Computational Biology - 9th Brazilian
Symposium on Bioinformatics, {BSB} 2014, Belo Horizonte, Brazil, October
28-30, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8826},
pages = {49--56},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-12418-6\_7},
doi = {10.1007/978-3-319-12418-6\_7},
timestamp = {Sun, 23 Jan 2022 21:20:49 +0100},
biburl = {https://dblp.org/rec/conf/wob/ChauvePZ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/eccb/2014cmsr,
editor = {Fabrice Jossinet and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {Proceedings of the 1st Workshop on Computational Methods for Structural
RNAs {(CMSR} 2014), Strasbourg, France, September 7, 2014},
publisher = {McGill University},
year = {2014},
url = {https://doi.org/10.15455/CMSR.2014.0000},
doi = {10.15455/CMSR.2014.0000},
timestamp = {Mon, 08 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/2014cmsr.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ReinharzPW13,
author = {Vladimir Reinharz and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {A weighted sampling algorithm for the design of {RNA} sequences with
targeted secondary structure and nucleotide distribution},
journal = {Bioinform.},
volume = {29},
number = {13},
pages = {308--315},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt217},
doi = {10.1093/BIOINFORMATICS/BTT217},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ReinharzPW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ReinharzPW13,
author = {Vladimir Reinharz and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {Using Structural and Evolutionary Information to Detect and Correct
Pyrosequencing Errors in Noncoding RNAs},
journal = {J. Comput. Biol.},
volume = {20},
number = {11},
pages = {905--919},
year = {2013},
url = {https://doi.org/10.1089/cmb.2013.0085},
doi = {10.1089/CMB.2013.0085},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/ReinharzPW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ZhangPBLW13,
author = {Yang Zhang and
Yann Ponty and
Mathieu Blanchette and
Eric L{\'{e}}cuyer and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {{SPARCS:} a web server to analyze (un)structured regions in coding
{RNA} sequences},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Webserver-Issue},
pages = {480--485},
year = {2013},
url = {https://doi.org/10.1093/nar/gkt461},
doi = {10.1093/NAR/GKT461},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ZhangPBLW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LopesSDLPC13,
author = {Anne Lopes and
Sophie Sacquin{-}Mora and
Viktoriya Dimitrova and
Elodie Laine and
Yann Ponty and
Alessandra Carbone},
title = {Protein-Protein Interactions in a Crowded Environment: An Analysis
via Cross-Docking Simulations and Evolutionary Information},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {12},
year = {2013},
url = {https://doi.org/10.1371/journal.pcbi.1003369},
doi = {10.1371/JOURNAL.PCBI.1003369},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LopesSDLPC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/LorenzP13,
author = {William Andrew Lorenz and
Yann Ponty},
title = {Non-redundant random generation algorithms for weighted context-free
grammars},
journal = {Theor. Comput. Sci.},
volume = {502},
pages = {177--194},
year = {2013},
url = {https://doi.org/10.1016/j.tcs.2013.01.006},
doi = {10.1016/J.TCS.2013.01.006},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/LorenzP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/ZhouPVWZD13,
author = {Yu Zhou and
Yann Ponty and
St{\'{e}}phane Vialette and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl and
Yi Zhang and
Alain Denise},
editor = {Jing Gao},
title = {Flexible {RNA} design under structure and sequence constraints using
formal languages},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {229},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2506623},
doi = {10.1145/2506583.2506623},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/ZhouPVWZD13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ReinharzPW13,
author = {Vladimir Reinharz and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
editor = {Minghua Deng and
Rui Jiang and
Fengzhu Sun and
Xuegong Zhang},
title = {A Linear Inside-Outside Algorithm for Correcting Sequencing Errors
in Structured RNAs},
booktitle = {Research in Computational Molecular Biology - 17th Annual International
Conference, {RECOMB} 2013, Beijing, China, April 7-10, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7821},
pages = {199--211},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-37195-0\_17},
doi = {10.1007/978-3-642-37195-0\_17},
timestamp = {Fri, 07 Mar 2025 20:53:46 +0100},
biburl = {https://dblp.org/rec/conf/recomb/ReinharzPW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SenterSDPC13,
author = {Evan Senter and
Saad Sheikh and
Iv{\'{a}}n Dot{\'{u}} and
Yann Ponty and
Peter Clote},
editor = {Minghua Deng and
Rui Jiang and
Fengzhu Sun and
Xuegong Zhang},
title = {Abstract: Using the Fast Fourier Transform to Accelerate the Computational
Search for {RNA} Conformational Switches},
booktitle = {Research in Computational Molecular Biology - 17th Annual International
Conference, {RECOMB} 2013, Beijing, China, April 7-10, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7821},
pages = {264--265},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-37195-0\_22},
doi = {10.1007/978-3-642-37195-0\_22},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SenterSDPC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/analco/BanderierBPB12,
author = {Cyril Banderier and
Olivier Bodini and
Yann Ponty and
Hanane Tafat Bouzid},
editor = {Conrado Mart{\'{\i}}nez and
Hsien{-}Kuei Hwang},
title = {Biodiversity of Pattern Distributions in Combinatorial Ecosystems},
booktitle = {Proceedings of the 9th Meeting on Analytic Algorithmics and Combinatorics,
{ANALCO} 2012, Kyoto, Japan, January 16, 2012},
pages = {107--115},
publisher = {{SIAM}},
year = {2012},
url = {https://doi.org/10.1137/1.9781611973020.13},
doi = {10.1137/1.9781611973020.13},
timestamp = {Tue, 23 May 2017 01:10:31 +0200},
biburl = {https://dblp.org/rec/conf/analco/BanderierBPB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/SheikhBP12,
author = {Saad Sheikh and
Rolf Backofen and
Yann Ponty},
editor = {Juha K{\"{a}}rkk{\"{a}}inen and
Jens Stoye},
title = {Impact of the Energy Model on the Complexity of {RNA} Folding with
Pseudoknots},
booktitle = {Combinatorial Pattern Matching - 23rd Annual Symposium, {CPM} 2012,
Helsinki, Finland, July 3-5, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7354},
pages = {321--333},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-31265-6\_26},
doi = {10.1007/978-3-642-31265-6\_26},
timestamp = {Tue, 21 Mar 2023 21:02:12 +0100},
biburl = {https://dblp.org/rec/conf/cpm/SheikhBP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/RinaudoPBD12,
author = {Philippe Rinaudo and
Yann Ponty and
Dominique Barth and
Alain Denise},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {Tree Decomposition and Parameterized Algorithms for {RNA} Structure-Sequence
Alignment Including Tertiary Interactions and Pseudoknots - (Extended
Abstract)},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {149--164},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_12},
doi = {10.1007/978-3-642-33122-0\_12},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/RinaudoPBD12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1202-0920,
author = {J{\'{e}}r{\'{e}}mie Du Boisberranger and
Dani{\`{e}}le Gardy and
Yann Ponty},
title = {The weighted words collector},
journal = {CoRR},
volume = {abs/1202.0920},
year = {2012},
url = {http://arxiv.org/abs/1202.0920},
eprinttype = {arXiv},
eprint = {1202.0920},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1202-0920.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1205-0627,
author = {Yann Ponty},
title = {Rule-weighted and terminal-weighted context-free grammars have identical
expressivity},
journal = {CoRR},
volume = {abs/1205.0627},
year = {2012},
url = {http://arxiv.org/abs/1205.0627},
eprinttype = {arXiv},
eprint = {1205.0627},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1205-0627.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1206-3789,
author = {Philippe Rinaudo and
Yann Ponty and
Dominique Barth and
Alain Denise},
title = {Tree decomposition and parameterized algorithms for {RNA} structure-sequence
alignment including tertiary interactions and pseudoknots},
journal = {CoRR},
volume = {abs/1206.3789},
year = {2012},
url = {http://arxiv.org/abs/1206.3789},
eprinttype = {arXiv},
eprint = {1206.3789},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1206-3789.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1211-0303,
author = {W. A. Lorenz and
Yann Ponty},
title = {Non-redundant random generation algorithms for weighted context-free
languages},
journal = {CoRR},
volume = {abs/1211.0303},
year = {2012},
url = {http://arxiv.org/abs/1211.0303},
eprinttype = {arXiv},
eprint = {1211.0303},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1211-0303.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/WaldispuhlP11,
author = {J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl and
Yann Ponty},
title = {An Unbiased Adaptive Sampling Algorithm for the Exploration of {RNA}
Mutational Landscapes Under Evolutionary Pressure},
journal = {J. Comput. Biol.},
volume = {18},
number = {11},
pages = {1465--1479},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0181},
doi = {10.1089/CMB.2011.0181},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/WaldispuhlP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/WaldispuhlP11,
author = {J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl and
Yann Ponty},
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {An Unbiased Adaptive Sampling Algorithm for the Exploration of {RNA}
Mutational Landscapes under Evolutionary Pressure},
booktitle = {Research in Computational Molecular Biology - 15th Annual International
Conference, {RECOMB} 2011, Vancouver, BC, Canada, March 28-31, 2011.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {501--515},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6\_45},
doi = {10.1007/978-3-642-20036-6\_45},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/WaldispuhlP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/PontyS11,
author = {Yann Ponty and
C{\'{e}}dric Saule},
editor = {Teresa M. Przytycka and
Marie{-}France Sagot},
title = {A Combinatorial Framework for Designing (Pseudoknotted) {RNA} Algorithms},
booktitle = {Algorithms in Bioinformatics - 11th International Workshop, {WABI}
2011, Saarbr{\"{u}}cken, Germany, September 5-7, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6833},
pages = {250--269},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-23038-7\_22},
doi = {10.1007/978-3-642-23038-7\_22},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/PontyS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/DenisePT10,
author = {Alain Denise and
Yann Ponty and
Michel Termier},
title = {Controlled non-uniform random generation of decomposable structures},
journal = {Theor. Comput. Sci.},
volume = {411},
number = {40-42},
pages = {3527--3552},
year = {2010},
url = {https://doi.org/10.1016/j.tcs.2010.05.010},
doi = {10.1016/J.TCS.2010.05.010},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/DenisePT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1002-0046,
author = {Olivier Bodini and
Yann Ponty},
title = {Multi-dimensional Boltzmann Sampling of context-free Languages},
journal = {CoRR},
volume = {abs/1002.0046},
year = {2010},
url = {http://arxiv.org/abs/1002.0046},
eprinttype = {arXiv},
eprint = {1002.0046},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1002-0046.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1006-0423,
author = {Alain Denise and
Yann Ponty and
Michel Termier},
title = {Controlled non uniform random generation of decomposable structures},
journal = {CoRR},
volume = {abs/1006.0423},
year = {2010},
url = {http://arxiv.org/abs/1006.0423},
eprinttype = {arXiv},
eprint = {1006.0423},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1006-0423.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1012-1129,
author = {Dani{\`{e}}le Gardy and
Yann Ponty},
title = {Weighted random generation of context-free languages: Analysis of
collisions in random urn occupancy models},
journal = {CoRR},
volume = {abs/1012.1129},
year = {2010},
url = {http://arxiv.org/abs/1012.1129},
eprinttype = {arXiv},
eprint = {1012.1129},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1012-1129.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1012-4560,
author = {Yann Ponty},
title = {Non-redundant random generation from weighted context-free languages},
journal = {CoRR},
volume = {abs/1012.4560},
year = {2010},
url = {http://arxiv.org/abs/1012.4560},
eprinttype = {arXiv},
eprint = {1012.4560},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1012-4560.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DartyDP09,
author = {K{\'{e}}vin Darty and
Alain Denise and
Yann Ponty},
title = {{VARNA:} Interactive drawing and editing of the {RNA} secondary structure},
journal = {Bioinform.},
volume = {25},
number = {15},
pages = {1974--1975},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp250},
doi = {10.1093/BIOINFORMATICS/BTP250},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DartyDP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dmtcs/Bousquet-MelouP08,
author = {Mireille Bousquet{-}M{\'{e}}lou and
Yann Ponty},
title = {Culminating Paths},
journal = {Discret. Math. Theor. Comput. Sci.},
volume = {10},
number = {2},
year = {2008},
url = {https://doi.org/10.46298/dmtcs.438},
doi = {10.46298/DMTCS.438},
timestamp = {Sun, 16 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dmtcs/Bousquet-MelouP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/LorenzPC08,
author = {W. A. Lorenz and
Yann Ponty and
Peter Clote},
title = {Asymptotics of {RNA} Shapes},
journal = {J. Comput. Biol.},
volume = {15},
number = {1},
pages = {31--63},
year = {2008},
url = {https://doi.org/10.1089/cmb.2006.0153},
doi = {10.1089/CMB.2006.0153},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/LorenzPC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PontyIPC08,
author = {Yann Ponty and
R. Istrate and
E. Porcelli and
Peter Clote},
title = {LocalMove: computing on-lattice fits for biopolymers},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Web-Server-Issue},
pages = {216--222},
year = {2008},
url = {https://doi.org/10.1093/nar/gkn367},
doi = {10.1093/NAR/GKN367},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PontyIPC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FerrePLC07,
author = {Fabrizio Ferr{\`{e}} and
Yann Ponty and
W. A. Lorenz and
Peter Clote},
title = {{DIAL:} a web server for the pairwise alignment of two {RNA} three-dimensional
structures using nucleotide, dihedral angle and base-pairing similarities},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Web-Server-Issue},
pages = {659--668},
year = {2007},
url = {https://doi.org/10.1093/nar/gkm334},
doi = {10.1093/NAR/GKM334},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FerrePLC07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/hal/Ponty06,
author = {Yann Ponty},
title = {Mod{\'{e}}lisation de s{\'{e}}quences g{\'{e}}nomiques
structur{\'{e}}es, g{\'{e}}n{\'{e}}ration al{\'{e}}atoire
et applications. (Models for structured genomic sequences, random
generation and applications)},
school = {University of Paris-Sud, Orsay, France},
year = {2006},
url = {https://tel.archives-ouvertes.fr/tel-00144130},
timestamp = {Tue, 21 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/hal/Ponty06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PontyTD06,
author = {Yann Ponty and
Michel Termier and
Alain Denise},
title = {GenRGenS: software for generating random genomic sequences and structures},
journal = {Bioinform.},
volume = {22},
number = {12},
pages = {1534--1535},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl113},
doi = {10.1093/BIOINFORMATICS/BTL113},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PontyTD06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-cs-0603106,
author = {Gregory Kucherov and
Laurent No{\'{e}} and
Yann Ponty},
title = {Estimating seed sensitivity on homogeneous alignments},
journal = {CoRR},
volume = {abs/cs/0603106},
year = {2006},
url = {http://arxiv.org/abs/cs/0603106},
eprinttype = {arXiv},
eprint = {cs/0603106},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-cs-0603106.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/KucherovNP04,
author = {Gregory Kucherov and
Laurent No{\'{e}} and
Yann Ponty},
title = {Estimating Seed Sensitivity on Homogeneous Alignments},
booktitle = {4th {IEEE} International Symposium on BioInformatics and BioEngineering
{(BIBE} 2004), 19-21 March 2004, Taichung, Taiwan},
pages = {387--394},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/BIBE.2004.1317369},
doi = {10.1109/BIBE.2004.1317369},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/KucherovNP04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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