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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}
}
@inproceedings{DBLP:conf/recomb/BourySHPY25,
author = {Th{\'{e}}o Boury and
Leonhard Sidl and
Ivo L. Hofacker and
Yann Ponty and
Hua{-}Ting Yao},
title = {Old Dog, New Tricks: Exact Seeding Strategy Improves {RNA} Design
Performances},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {15647},
pages = {134--152},
publisher = {Springer},
year = {2025}
}
@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}
}
@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}
}
@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},
title = {Color Coding for the Fragment-Based Docking, Design and Equilibrium
Statistics of Protein-Binding ssRNAs},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {14758},
pages = {147--163},
publisher = {Springer},
year = {2024}
}
@inproceedings{DBLP:conf/wabi/BoehmerBWP24,
author = {Kimon Boehmer and
Sarah J. Berkemer and
Sebastian Will and
Yann Ponty},
title = {{RNA} Triplet Repeats: Improved Algorithms for Structure Prediction
and Interactions},
booktitle = {{WABI}},
series = {LIPIcs},
volume = {312},
pages = {18:1--18:23},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2024}
}
@inproceedings{DBLP:conf/wabi/BouryBP24,
author = {Th{\'{e}}o Boury and
Laurent Bulteau and
Yann Ponty},
title = {{RNA} Inverse Folding Can Be Solved in Linear Time for Structures
Without Isolated Stacks or Base Pairs},
booktitle = {{WABI}},
series = {LIPIcs},
volume = {312},
pages = {19:1--19:23},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2024}
}
@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.}
}
@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}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/wabi/BouryPR23,
author = {Th{\'{e}}o Boury and
Yann Ponty and
Vladimir Reinharz},
title = {Automatic Exploration of the Natural Variability of {RNA} Non-Canonical
Geometric Patterns with a Parameterized Sampling Technique},
booktitle = {{WABI}},
series = {LIPIcs},
volume = {273},
pages = {20:1--20:22},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2023}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/wabi/MarchandWBBP22,
author = {Bertrand Marchand and
Sebastian Will and
Sarah J. Berkemer and
Laurent Bulteau and
Yann Ponty},
title = {Automated Design of Dynamic Programming Schemes for {RNA} Folding
with Pseudoknots},
booktitle = {{WABI}},
series = {LIPIcs},
volume = {242},
pages = {7:1--7:24},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2022}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/cocoon/KhalifePB21,
author = {Sammy Khalife and
Yann Ponty and
Laurent Bulteau},
title = {Sequence Graphs Realizations and Ambiguity in Language Models},
booktitle = {{COCOON}},
series = {Lecture Notes in Computer Science},
volume = {13025},
pages = {153--163},
publisher = {Springer},
year = {2021}
}
@inproceedings{DBLP:conf/iwpec/BulteauMP21,
author = {Laurent Bulteau and
Bertrand Marchand and
Yann Ponty},
title = {A New Parametrization for Independent Set Reconfiguration and Applications
to {RNA} Kinetics},
booktitle = {{IPEC}},
series = {LIPIcs},
volume = {214},
pages = {11:1--11:15},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2021}
}
@inproceedings{DBLP:conf/wabi/MarchandPB21,
author = {Bertrand Marchand and
Yann Ponty and
Laurent Bulteau},
title = {Tree Diet: Reducing the Treewidth to Unlock {FPT} Algorithms in {RNA}
Bioinformatics},
booktitle = {{WABI}},
series = {LIPIcs},
volume = {201},
pages = {7:1--7:23},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2021}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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},
title = {Stochastic Sampling of Structural Contexts Improves the Scalability
and Accuracy of {RNA} 3D Module Identification},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {12074},
pages = {186--201},
publisher = {Springer},
year = {2020}
}
@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}
}
@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}
}
@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 = {3DV},
pages = {47--56},
publisher = {{IEEE}},
year = {2019}
}
@inproceedings{DBLP:conf/bcb/YaoCRP19,
author = {Hua{-}Ting Yao and
C{\'{e}}dric Chauve and
Mireille R{\'{e}}gnier and
Yann Ponty},
title = {Exponentially Few {RNA} Structures are Designable},
booktitle = {{BCB}},
pages = {289--298},
publisher = {{ACM}},
year = {2019}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/recomb/HammerPWW18,
author = {Stefan Hammer and
Yann Ponty and
Wei Wang and
Sebastian Will},
title = {Fixed-Parameter Tractable Sampling for {RNA} Design with Multiple
Target Structures},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {10812},
pages = {256--258},
publisher = {Springer},
year = {2018}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/alcob/ChauveCP16,
author = {C{\'{e}}dric Chauve and
Julien Courtiel and
Yann Ponty},
title = {Counting, Generating and Sampling Tree Alignments},
booktitle = {AlCoB},
series = {Lecture Notes in Computer Science},
volume = {9702},
pages = {53--64},
publisher = {Springer},
year = {2016}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/cpm/HalesMPS15,
author = {Jozef Hales and
J{\'{a}}n Manuch and
Yann Ponty and
Ladislav Stacho},
title = {Combinatorial {RNA} Design: Designability and Structure-Approximating
Algorithm},
booktitle = {{CPM}},
series = {Lecture Notes in Computer Science},
volume = {9133},
pages = {231--246},
publisher = {Springer},
year = {2015}
}
@inproceedings{DBLP:conf/isbra/RajaramanCP15,
author = {Ashok Rajaraman and
C{\'{e}}dric Chauve and
Yann Ponty},
title = {Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods
from Reconciled Phylogenies: Supplementary Material},
booktitle = {{ISBRA}},
series = {Lecture Notes in Computer Science},
volume = {9096},
pages = {260--271},
publisher = {Springer},
year = {2015}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/wob/ChauvePZ14,
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},
booktitle = {{BSB}},
series = {Lecture Notes in Computer Science},
volume = {8826},
pages = {49--56},
publisher = {Springer},
year = {2014}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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},
title = {Flexible {RNA} design under structure and sequence constraints using
formal languages},
booktitle = {{BCB}},
pages = {229},
publisher = {{ACM}},
year = {2013}
}
@inproceedings{DBLP:conf/recomb/ReinharzPW13,
author = {Vladimir Reinharz and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {A Linear Inside-Outside Algorithm for Correcting Sequencing Errors
in Structured RNAs},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {7821},
pages = {199--211},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/recomb/SenterSDPC13,
author = {Evan Senter and
Saad Sheikh and
Iv{\'{a}}n Dot{\'{u}} and
Yann Ponty and
Peter Clote},
title = {Abstract: Using the Fast Fourier Transform to Accelerate the Computational
Search for {RNA} Conformational Switches},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {7821},
pages = {264--265},
publisher = {Springer},
year = {2013}
}
@inproceedings{DBLP:conf/analco/BanderierBPB12,
author = {Cyril Banderier and
Olivier Bodini and
Yann Ponty and
Hanane Tafat Bouzid},
title = {Biodiversity of Pattern Distributions in Combinatorial Ecosystems},
booktitle = {{ANALCO}},
pages = {107--115},
publisher = {{SIAM}},
year = {2012}
}
@inproceedings{DBLP:conf/cpm/SheikhBP12,
author = {Saad Sheikh and
Rolf Backofen and
Yann Ponty},
title = {Impact of the Energy Model on the Complexity of {RNA} Folding with
Pseudoknots},
booktitle = {{CPM}},
series = {Lecture Notes in Computer Science},
volume = {7354},
pages = {321--333},
publisher = {Springer},
year = {2012}
}
@inproceedings{DBLP:conf/wabi/RinaudoPBD12,
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 - (Extended
Abstract)},
booktitle = {{WABI}},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {149--164},
publisher = {Springer},
year = {2012}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/recomb/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},
booktitle = {{RECOMB}},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {501--515},
publisher = {Springer},
year = {2011}
}
@inproceedings{DBLP:conf/wabi/PontyS11,
author = {Yann Ponty and
C{\'{e}}dric Saule},
title = {A Combinatorial Framework for Designing (Pseudoknotted) {RNA} Algorithms},
booktitle = {{WABI}},
series = {Lecture Notes in Computer Science},
volume = {6833},
pages = {250--269},
publisher = {Springer},
year = {2011}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@inproceedings{DBLP:conf/bibe/KucherovNP04,
author = {Gregory Kucherov and
Laurent No{\'{e}} and
Yann Ponty},
title = {Estimating Seed Sensitivity on Homogeneous Alignments},
booktitle = {{BIBE}},
pages = {387--394},
publisher = {{IEEE} Computer Society},
year = {2004}
}
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