Yann Ponty

123

Documents

Publications

Bipartite Independent Set Reconfiguration: General and RNA-Inspired Parameterized Algorithms

Théo Boury , Laurent Bulteau , Bertrand Marchand , Yann Ponty

Algorithmica, 2026, 88 (2), 59 p. ⟨10.1007/s00453-026-01371-x⟩

Article dans une revue hal-04094405v5

Undesignable motifs in structural RNAs and combinatorial consequences

Hua-Ting Yao , Cedric Chauve , Mireille Regnier , Yann Ponty

Journal of Mathematical Biology, 2026, 92 (4), pp.49. ⟨10.1007/s00285-026-02358-6⟩

Article dans une revue hal-05067902v2

RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions

Kimon Boehmer , Sarah Berkemer , Sebastian Will , Yann Ponty

Algorithms for Molecular Biology, 2026, 21 (1), pp.4. ⟨10.1186/s13015-025-00292-8⟩

Article dans une revue hal-04766560v1

CParty: Hierarchically Constrained Partition Function of RNA Pseudoknots

Mateo Gray , Luke Trinity , Ulrike Stege , Yann Ponty , Sebastian Will et al.

Bioinformatics, 2025, 41 (1), ⟨10.1093/bioinformatics/btae748⟩

Article dans une revue hal-04821969v1

RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs

Théo Boury , Samuel Gardelle , Laurent Bulteau , Yann Ponty

Algorithms for Molecular Biology, 2025, 20 (1), pp.20. ⟨10.1186/s13015-025-00278-6⟩

Article dans une revue hal-04761629v3

IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling

Pierre Hardouin , Nan Pan , Francois-Xavier Lyonnet Du Moutier , Nathalie Chamond , Yann Ponty et al.

NAR Genomics and Bioinformatics, In press

Article dans une revue hal-04966010v2

Designing molecular RNA switches with Restricted Boltzmann machines

Jorge Fernandez-De-Cossio-Diaz , Pierre Hardouin , Francois-Xavier Lyonnet Du Moutier , Andrea Di Gioacchino , Bertrand Marchand et al.

Nature Communications, 2025, 16, pp.11223. ⟨10.1038/s41467-025-66265-y⟩

Article dans une revue hal-04294884v1

Infrared: a declarative tree decomposition-powered framework for bioinformatics

Hua-Ting Yao , Bertrand Marchand , Sarah Berkemer , Yann Ponty , Sebastian Will

Algorithms for Molecular Biology, 2024, 19 (1), pp.13. ⟨10.1186/s13015-024-00258-2⟩

Article dans une revue hal-04211173v2

Automated design of dynamic programming schemes for RNA folding with pseudoknots

Bertrand Marchand , Sebastian Will , Sarah Berkemer , Yann Ponty , Laurent Bulteau

Algorithms for Molecular Biology, 2023, 18 (1), pp.18. ⟨10.1186/s13015-023-00229-z⟩

Article dans une revue hal-04103565v1

Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics

Bertrand Marchand , Yann Ponty , Laurent Bulteau

Algorithms for Molecular Biology, 2022, 17 (1), pp.8. ⟨10.1186/s13015-022-00213-z⟩

Article dans une revue hal-03608412v2

IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations

Alexander Churkin , Yann Ponty , Danny Barash

BMC Bioinformatics, 2022, 23 (S8), pp.424. ⟨10.1186/s12859-022-04943-0⟩

Article dans une revue hal-03815555v1

The SARS-CoV-2 Subgenome Landscape and its Novel Regulatory Features

Dehe Wang , Ao Jiang , Jiangpeng Feng , Guangnan Li , Dong Guo et al.

Molecular Cell, 2021, 81 (10), pp.2135-2147.e5. ⟨10.1016/j.molcel.2021.02.036⟩

Article dans une revue hal-03154155v2

Progress Toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure

Grégoire de Bisschop , Delphine Allouche , Elisa Frezza , Benoît Masquida , Yann Ponty et al.

Non-Coding RNA, 2021, 7 (4), pp.71. ⟨10.3390/ncrna7040071⟩

Article dans une revue hal-03413594v1

RNAxplorer: Harnessing the Power of Guiding Potentials to Sample RNA Landscapes

Gregor Entzian , Ivo Hofacker , Yann Ponty , Ronny Lorenz , Andrea Tanzer

Bioinformatics, 2021, 37 (15), pp.2126-2133. ⟨10.1093/bioinformatics/btab066⟩

Article dans une revue hal-02889448v3

Reference-free transcriptome signatures for prostate cancer prognosis

Ha Tn Nguyen , Haoliang Xue , Virginie Firlej , Yann Ponty , Mélina Gallopin et al.

BMC Cancer, 2021, 21 (394), ⟨10.1186/s12885-021-08021-1⟩

Article dans une revue hal-02948844v1

IPANEMAP: Integrative Probing Analysis of Nucleic Acids Empowered by Multiple Accessibility Profiles

Afaf Saaidi , Delphine M Allouche , Mireille Regnier , Bruno Sargueil , Yann Ponty

Nucleic Acids Research, 2020, 48 (15), pp.8276--8289. ⟨10.1093/nar/gkaa607⟩

Article dans une revue hal-02889041v3

IncaRNAfbinv 2.0 - A webserver and software with motif control for fragment-based design of RNAs

Matan Drory Retwitzer , Vladimir Reinharz , Alexander Churkin , Yann Ponty , Jérôme Waldispühl et al.

Bioinformatics, 2020, 36 (9), pp.2910--2922. ⟨10.1093/bioinformatics/btaa039⟩

Article dans une revue hal-02423237v1

Fixed-parameter tractable sampling for RNA design with multiple target structures

Stefan Hammer , Wei Wang , Sebastian Will , Yann Ponty

BMC Bioinformatics, 2019, 20 (1), pp.209. ⟨10.1186/s12859-019-2784-7⟩

Article dans une revue hal-02112888v1

Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models

Cedric Chauve , Yann Ponty , Michael Wallner

Journal of Mathematical Biology, 2019, 80 (5), pp.1353--1388. ⟨10.1007/s00285-019-01465-x⟩

Article dans une revue hal-02169271v1

Small-world networks and RNA secondary structures

Defne Surujon , Yann Ponty , Peter Clote

Journal of Computational Biology, 2019, 26 (1), pp.16--26. ⟨10.1089/cmb.2018.0125⟩

Article dans une revue hal-01424452v2

Design of RNAs: comparing programs for inverse RNA folding.

Alexander Churkin , Matan Drory Retwitzer , Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl et al.

Briefings in Bioinformatics, 2018, 19 (2), pp.350--358. ⟨10.1093/bib/bbw120⟩

Article dans une revue hal-01392958v1

Meet-U: educating through research immersion

Nika Abdollahi , Alexandre Albani , Eric Anthony , Agnes Baud , Mélissa Cardon et al.

PLoS Computational Biology, 2018, 14 (3), pp.1-10. ⟨10.1371/journal.pcbi.1005992⟩

Article dans une revue hal-01722019v1

Counting, generating, analyzing and sampling tree alignments

Cedric Chauve , Julien Courtiel , Yann Ponty

International Journal of Foundations of Computer Science, 2018, 29 (5), pp.741--767

Article dans une revue hal-01500116v1

The BRaliBase dent - a tale of benchmark design and interpretation.

Benedikt Löwes , Cedric Chauve , Yann Ponty , Robert Giegerich

Briefings in Bioinformatics, 2017, 18 (2), pp.306--311. ⟨10.1093/bib/bbw022⟩

Article dans une revue hal-01273406v1

Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame

Jules Deforges , Sylvain de Breyne , Melissa Ameur , Nathalie Ulryck , Nathalie Chamond et al.

Nucleic Acids Research, 2017, 45 (12), pp.7382--7400. ⟨10.1093/nar/gkx303⟩

Article dans une revue hal-01505282v1

DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies

Wandrille Duchemin , Yoann Anselmetti , Murray Patterson , Yann Ponty , Sèverine Bérard et al.

Genome Biology and Evolution, 2017, 9 (5), pp.1312-1319. ⟨10.1093/gbe/evx069⟩

Article dans une revue hal-01503766v2

Combinatorial RNA Design

Jozef Haleš , Alice Héliou , Ján Maňuch , Yann Ponty , Ladislav Stacho

Algorithmica, 2017, 79 (3), pp.835--856. ⟨10.1007/s00453-016-0196-x⟩

Article dans une revue hal-01285499v2

ecceTERA: Comprehensive gene tree-species tree reconciliation using parsimony

Edwin Jacox , Cedric Chauve , Gergely J Szöllősi , Yann Ponty , Celine Scornavacca

Bioinformatics, 2016, 32 (13), pp.2056-2058. ⟨10.1093/bioinformatics/btw105⟩

Article dans une revue hal-01276903v1

Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces

Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl

Nucleic Acids Research, 2016, 44 (11), pp.e104 - e104. ⟨10.1093/nar/gkw217⟩

Article dans une revue hal-01291754v1

incaRNAfbinv : a web server for the fragment-based design of RNA sequences

Matan Drory retwitzer , Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl , Danny Barash

Nucleic Acids Research, 2016, 44 (W1), pp.W308 - W314. ⟨10.1093/nar/gkw440⟩

Article dans une revue hal-01319682v1

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve , Yann Ponty , João Paulo Pereira Zanetti

BMC Bioinformatics, 2015, 16 (Suppl 19), pp.S6. ⟨10.1186/1471-2105-16-S19-S6⟩

Article dans une revue hal-01245495v1

SPARCS: a web server to analyze (un)structured regions in coding RNA sequences.

Yang Zhang , Yann Ponty , Mathieu Blanchette , Eric Lecuyer , Jérôme Waldispühl

Nucleic Acids Research, 2013, Web Server Issue, 41 (Web Server issue), pp.W480-5. ⟨10.1093/nar/gkt461⟩

Article dans une revue hal-00819017v1

Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding RNAs.

Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl

Journal of Computational Biology, 2013, 20 (11), pp.905-19. ⟨10.1089/cmb.2013.0085⟩

Article dans une revue hal-00828062v1

Protein-protein interactions in a crowded environment: an analysis via cross-docking simulations and evolutionary information

Anne Lopes , Sophie Sacquin-Mora , Viktoriya Dimitrova , Elodie Laine , Yann Ponty et al.

PLoS Computational Biology, 2013, 9 (12), pp.e1003369. ⟨10.1371/journal.pcbi.1003369⟩

Article dans une revue hal-00875116v1

Non-redundant random generation algorithms for weighted context-free languages

Andy Lorenz , Yann Ponty

Theoretical Computer Science, 2013, Generation of Combinatorial Structures, 502, pp.177-194. ⟨10.1016/j.tcs.2013.01.006⟩

Article dans une revue inria-00607745v2

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl

Bioinformatics, 2013, 29 (13), pp.i308-15. ⟨10.1093/bioinformatics/btt217⟩

Article dans une revue hal-00840260v1

Mieux comprendre certaines molécules biologiques grâce à l’informatique

Yann Ponty , Joanna Jongwane

Interstices, 2012

Article dans une revue hal-01350181v1

Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches

Evan Senter , Saad Sheikh , Ivan Dotu , Yann Ponty , Peter Clote

PLoS ONE, 2012, 7 (12), pp.e50506. ⟨10.1371/journal.pone.0050506⟩

Article dans une revue hal-00769740v1

A global sampling approach to designing and reengineering RNA secondary structures.

Alex Levin , Mieszko Lis , Yann Ponty , Charles W O'Donnell , Srinivas Devadas et al.

Nucleic Acids Research, 2012, 40 (20), pp.10041-10052. ⟨10.1093/nar/gks768⟩

Article dans une revue hal-00733924v1

The weighted words collector

Jérémie Du Boisberranger , Danièle Gardy , Yann Ponty

Discrete Mathematics and Theoretical Computer Science, 2012, DMTCS Proceedings vol. AQ, 23rd Intern. Meeting on Probabilistic, Combinatorial, and Asymptotic Methods for the Analysis of Algorithms (AofA'12), pp.243--264. ⟨10.46298/dmtcs.2998⟩

Article dans une revue hal-00666399v2

Expected distance between terminal nucleotides of RNA secondary structures.

Peter Clote , Yann Ponty , Jean-Marc Steyaert

Journal of Mathematical Biology, 2012, 65 (3), pp.581-99. ⟨10.1007/s00285-011-0467-8⟩

Article dans une revue inria-00619921v1

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.

Jérôme Waldispühl , Yann Ponty

Journal of Computational Biology, 2011, 18 (11), pp.1465-79. ⟨10.1089/cmb.2011.0181⟩

Article dans une revue hal-00681928v1

Controlled non uniform random generation of decomposable structures

Alain Denise , Yann Ponty , Michel Termier

Theoretical Computer Science, 2010, 411 (40-42), pp.3527-3552. ⟨10.1016/j.tcs.2010.05.010⟩

Article dans une revue hal-00483581v2

Multi-dimensional Boltzmann Sampling of Languages

Olivier Bodini , Yann Ponty

Discrete Mathematics and Theoretical Computer Science, 2010, DMTCS Proceedings, DMTCS Proceedings vol. AM, 21st International Meeting on Probabilistic, Combinatorial, and Asymptotic Methods in the Analysis of Algorithms (AofA'10), pp.49-64. ⟨10.46298/dmtcs.2793⟩

Article dans une revue hal-00450763v4

VARNA: Interactive drawing and editing of the RNA secondary structure.

Kévin Darty , Alain Denise , Yann Ponty

Bioinformatics, 2009, 25 (15), pp.1974-5. ⟨10.1093/bioinformatics/btp250⟩

Article dans une revue hal-00432548v1

LocalMove: computing on-lattice fits for biopolymers

Yann Ponty , R. Istrate , E. Porcelli , Peter Clote

Nucleic Acids Research, 2008, 36 (2), pp.W216-W222. ⟨10.1093/nar/gkn367⟩

Article dans une revue inria-00548867v1

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: The boustrophedon method

Yann Ponty

Journal of Mathematical Biology, 2008, 56 (1-2), pp.107--127. ⟨10.1007/s00285-007-0137-z⟩

Article dans une revue istex inria-00548863v1

Culminating paths

Mireille Bousquet-Mélou , Yann Ponty

Discrete Mathematics and Theoretical Computer Science, 2008, 10 (2), pp.125--152

Article dans une revue hal-00151979v2

Asymptotics of RNA shapes

William Andrew Lorenz , Peter Clote , Yann Ponty

Journal of Computational Biology, 2008, 15 (1), pp.31--63. ⟨10.1089/cmb.2006.0153⟩

Article dans une revue inria-00548861v1

DIAL: A web server for the pairwise alignment of two RNA 3-dimensional structures using nucleotide, dihedral angle and base pairing similarities

Ferrè Fabrizzio , Yann Ponty , William Andrew Lorenz , Peter Clote

Nucleic Acids Research, 2007, 35 (Web server issue), pp.W659--668. ⟨10.1093/nar/gkm334⟩

Article dans une revue inria-00548870v1

GenRGenS: Software for Generating Random Genomic Sequences and Structures

Yann Ponty , Michel Termier , Alain Denise

Bioinformatics, 2006, 22 (12), pp.1534--1535. ⟨10.1093/bioinformatics/btl113⟩

Article dans une revue inria-00548871v1

FPT Learning of Sparse, Robust and Interpretable Generative models of RNA evolution

Samuel Gardelle , Laurent Bulteau , Yann Ponty

WABI 2026 - 26th Workshop on Algorithms in Bioinformatics, 2026, L'aquila, Italy

Communication dans un congrès hal-05630853v1

RNA inverse folding under stacked base pair maximization

Théo Boury , Laurent Bulteau , Yann Ponty

WABI 2026 - 26th Workshop on Algorithms in Bioinformatics, 2026, L'Aquila, Italy

Communication dans un congrès hal-05510148v4

Old dog, new tricks: Exact seeding strategy improves RNA design performances

Théo Boury , Leonhard Sidl , Ivo L. Hofacker , Yann Ponty , Hua-Ting Yao

RECOMB 2025 - 29th International Conference of Research in Computational Molecular Biology, 2025, Seoul, South Korea

Communication dans un congrès hal-04756160v2

CREMSA: Compressed indexing of (ultra) large multiple sequence alignments

Mikaël Salson , Arthur Boddaert , Awa Bousso Gueye , Laurent Bulteau , Yohan Hernandez--Courbevoie et al.

ISMB/ECCB 2025 - 33rd international conference on Intelligent Systems for Molecular Biology, ISCB, Jul 2025, Liverpool, United Kingdom. pp.i246-i254, ⟨10.1093/bioinformatics/btaf211⟩

Communication dans un congrès hal-04910677v2

Compressed indexing of (ultra) large viral alignments

Mikael Salson , Thomas Baudeau , Arthur Boddaert , Awa Bousso Gueye , Laurent Bulteau et al.

SEQBIM 2024 - Journées du groupe de travail Séquences en Bioinformatique, Nov 2024, Rennes, France

Communication dans un congrès hal-04773755v1

Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAs

Taher Yacoub , Roy González-Alemán , Fabrice Leclerc , Isaure Chauvot de Beauchêne , Yann Ponty

RECOMB 2024 - 28th International Conference of Research in Computational Molecular Biology, Apr 2024, Boston, United States. pp.147-163, ⟨10.1007/978-1-0716-3989-4_10⟩

Communication dans un congrès hal-03816423v3

Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique

Théo Boury , Vladimir Reinharz , Yann Ponty

JOBIM 2024 - Journées Ouvertes en Biologie, Informatique, et Mathématiques 2024, Jun 2024, Toulouse, France

Communication dans un congrès hal-04575263v1

RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs

Théo Boury , Laurent Bulteau , Yann Ponty

SEQBIM 2024 - Journées du groupe de travail Séquences en Bioinformatique, Nov 2024, Rennes, France

Communication dans un congrès hal-04773768v1

RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs

Théo Boury , Laurent Bulteau , Yann Ponty

WABI 2024 - 24th Workshop on Algorithms in Bioinformatics, 2024, London, United Kingdom

Communication dans un congrès hal-04589901v2

RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions

Kimon Boehmer , Sarah J Berkemer , Sebastian Will , Yann Ponty

WABI 2024 - 24th Workshop on Algorithms in Bioinformatics, 2024, London, United Kingdom

Communication dans un congrès hal-04589903v2

Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling technique

Théo Boury , Yann Ponty , Vladimir Reinharz

WABI 2023 - 23rd Workshop on Algorithms in Bioinformatics, Texas A&M University, Sep 2023, Houston, United States. ⟨10.4230/LIPIcs.WABI.2023.20⟩

Communication dans un congrès hal-04094288v2

Automated design of dynamic programming schemes for RNA folding with pseudoknots

Bertrand Marchand , Sebastian Will , Sarah Berkemer , Laurent Bulteau , Yann Ponty

WABI 2022 - 22nd Workshop on Algorithms in Bioinformatics, Sep 2022, Potsdam, Germany

Communication dans un congrès hal-03676377v2

Sequence graphs realizations and ambiguity in language models

Sammy Khalife , Yann Ponty , Laurent Bulteau

COCOON 2021 - 27th International Computing and Combinatorics Conference, Oct 2021, Tainan, Taiwan. ⟨10.1007/978-3-030-89543-3_13⟩

Communication dans un congrès hal-02495333v4

Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA

Hua-Ting Yao , Jérôme Waldispühl , Yann Ponty , Sebastian Will

RECOMB 2021 - 25th international conference on research in computational molecular biology, Apr 2021, Padova, France

Communication dans un congrès hal-02987566v2

A new parametrization for independent set reconfiguration and applications to RNA kinetics

Laurent Bulteau , Bertrand Marchand , Yann Ponty

IPEC 2021 - 16th International Symposium on Parameterized and Exact Computation, Sep 2021, Lisbon, Portugal. ⟨10.4230/lipics.ipec.2021.11⟩

Communication dans un congrès hal-03272963v2

Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics

Bertrand Marchand , Yann Ponty , Laurent Bulteau

WABI 2021 - 21st Workshop on Algorithms in Bioinformatics, 2021, Paris, France

Communication dans un congrès hal-03206132v1

IndelsRNAmute: Predicting deleterious multiple point substitutions and indels mutations

Alexander Churkin , Yann Ponty , Danny Barash

ISBRA 2020 - 16th International Symposium on Bioinformatics Research and Applications, Dec 2020, Moscow, Russia

Communication dans un congrès hal-02936276v1

Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules Identification

Roman Sarrazin-Gendron , Hua-Ting Yao , Vladimir Reinharz , Carlos G Oliver , Yann Ponty et al.

RECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology, May 2020, Padova, Italy

Communication dans un congrès hal-02354733v1

Effective Rotation-invariant Point CNN with Spherical Harmonics kernels

Adrien Poulenard , Marie-Julie Rakotosaona , Yann Ponty , Maks Ovsjanikov

3DV - International Conference on 3D Vision - 2019, Sep 2019, Québec City, Canada

Communication dans un congrès hal-02167454v2

Exponentially few RNA structures are designable

Hua-Ting Yao , Cedric Chauve , Mireille Regnier , Yann Ponty

ACM-BCB 2019 - 10th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Sep 2019, Niagara-Falls, United States. pp.289-298, ⟨10.1145/3307339.3342163⟩

Communication dans un congrès hal-02141853v2

Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity tests

Maher Mallem , Alain Denise , Yann Ponty

SEQBIM 2019 - Séquences en Bioinformatique, Informatique et Mathématiques, Dec 2019, Marne-la-Vallée, France

Communication dans un congrès hal-02403517v1

Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures

Stefan Hammer , Yann Ponty , Wei Wang , Sebastian Will

RECOMB - 22nd Annual International Conference on Research in Computational Molecular Biology - 2018, Apr 2018, Paris, France

Communication dans un congrès hal-01631277v2

A hybrid combinatorial method for docking single stranded RNAs in a protein pockect at the thermodynamic equilibrium

Chinmay Singhal , Yann Ponty , Isaure Chauvot de Beauchêne

JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2018, Marseille, France

Communication dans un congrès hal-02394529v1

Nucleic Acids design targeting integer-valued features: FPT counting and uniform sampling

Yann Ponty , Sebastian Will , Stefan Hammer

WEPA 2018 - 2nd International Workshop on Enumeration Problems and Applications, Nov 2018, Pisa, Italy

Communication dans un congrès hal-01911878v1

Efficient approximations of RNA kinetics landscape using non-redundant sampling

Juraj Michálik , Hélène Touzet , Yann Ponty

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⟩

Communication dans un congrès hal-01500115v1

An EM algorithm for mapping short reads in multiple RNA structure probing experiments

Afaf Saaidi , Yann Ponty , Mathieu Blanchette , Mireille Regnier , Bruno Sargueil

Matbio2017, King's College London Sep 2017, London, United Kingdom

Communication dans un congrès hal-01590528v1

Taming reluctant random walks in the positive quadrant

Jeremie Lumbroso , Marni Mishna , Yann Ponty

GASCOM - 10th conference on random generation of combinatorial structures - 2016, Jun 2016, Bastia, France. pp.99 -- 114, ⟨10.1016/j.endm.2017.05.008⟩

Communication dans un congrès hal-01291164v1

An integrative approach for predicting the RNA secondary structure for the HIV–1 Gag UTR using probing data

Afaf Saaidi , Yann Ponty , Bruno Sargueil

JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2017, Jul 2017, Lille, France. pp.102

Communication dans un congrès hal-01534587v1

Counting, generating and sampling tree alignments

Cedric Chauve , Julien Courtiel , Yann Ponty

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⟩

Communication dans un congrès hal-01154030v3

Towards structural models for the Ebola UTR regions using experimental SHAPE probing data

Afaf Saaidi , Delphine Allouche , Bruno Sargueil , Yann Ponty

JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France

Communication dans un congrès hal-01332469v1

Homology modeling of complex structural RNAs

Wei Wang , Matthieu Barba , Philippe Rinaudo , Alain Denise , Yann Ponty

JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France

Communication dans un congrès hal-01332642v1

Towards firm foundations for the rational design of RNA molecules

Yann Ponty

Colloque de Bioinformatique Moléculaire (GdR BIM), Oct 2015, Paris, France

Communication dans un congrès hal-01570180v1

RNA Bioinformatics and ensemble dynamic programming

Yann Ponty

5th biennial Canadian Discrete and Algorithmic Mathematics Conference - CanaDAM 2015, Jun 2015, Saskatoon, Canada

Communication dans un congrès hal-01569852v1

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

Jozef Haleš , Ján Maňuch , Yann Ponty , Ladislav Stacho

CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy

Communication dans un congrès hal-01115349v2

Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies

Ashok Rajaraman , Cedric Chauve , Yann Ponty

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⟩

Communication dans un congrès hal-01104587v3

Résultats algorithmiques pour le design d’ARN avec contraintes de séquence

Vincent Le Gallic , Alain Denise , Yann Ponty

SeqBio 2015, Nov 2015, Orsay, France. pp.26-31

Communication dans un congrès hal-01266096v1

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve , Yann Ponty , João Paulo Pereira Zanetti

BSB - Brazilian Symposium on Bioinformatics - 2014, Oct 2014, Belo Horizonte, Brazil. pp.49--56, ⟨10.1007/978-3-319-12418-6⟩

Communication dans un congrès hal-01056140v2

Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract)

Evan Senter , Saad Sheikh , Ivan Dotu , Yann Ponty , Peter Clote

RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China

Communication dans un congrès hal-00766780v1

A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequences

Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl

RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China

Communication dans un congrès hal-00766781v1

Flexible RNA design under structure and sequence constraints using formal languages

Yu Zhou , Yann Ponty , Stéphane Vialette , Jérôme Waldispühl , Yi Zhang et al.

ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States

Communication dans un congrès hal-00823279v2

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distribution

Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl

ISMB/ECCB - 21st Annual international conference on Intelligent Systems for Molecular Biology/12th European Conference on Computational Biology - 2013, Jul 2013, Berlin, Germany

Communication dans un congrès hal-00811607v1

Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?

Stefan Janssen , Loïc Paulevé , Yann Ponty , Balaji Raman , Matthias Zytnicki

IWBDA - 4th International Workshop on Bio-Design Automation - 2012, Jun 2012, San Francisco, United States

Communication dans un congrès hal-00712557v1

Impact Of The Energy Model On The Complexity Of RNA Folding With Pseudoknots

Saad Sheikh , Rolf Backofen , Yann Ponty

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⟩

Communication dans un congrès hal-00670232v3

Visualizing 2D & 3D Structures of RNA

Yann Ponty

VIZBI - 3rd international meeting on Visualizing Biological Data - 2012, Jim, Procter (U-Dundee, Scotland) and Sean O'Donoghue (CMIS, Australia), Mar 2012, Heidelberg, Germany

Communication dans un congrès hal-00723351v1

Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots

Philippe Rinaudo , Yann Ponty , Dominique Barth , Alain Denise

WABI - 12th Workshop on Algorithms in Bioinformatics - 2012, University of Ljubljana, Sep 2012, Ljubljana, Slovenia

Communication dans un congrès hal-00708580v2

On the diversity of pattern distributions in rational language

Cyril Banderier , Olivier Bodini , Yann Ponty , Hanane Tafat

ANALCO - 12th Meeting on Analytic Algorithmics and Combinatorics - 2012, Jan 2012, Kyoto, Japan. pp.107--116

Communication dans un congrès hal-00643598v1

Investigating the RFAM paradox: The pseudoknot explanation

Stefan Janssen , Yann Ponty , Balaji Raman , Saad Sheikh , Jean-Marc Steyaert et al.

Fifth Indo-French Bioinformatics Meeting, Mar 2011, Hyderabad, India

Communication dans un congrès hal-00585647v1

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure

Jérôme Waldispühl , Yann Ponty

RECOMB - 15th Annual International Conference on Research in Computational Molecular Biology - 2011, Mar 2011, Vancouver, Canada. pp.501-515, ⟨10.1007/978-3-642-20036-6_45⟩

Communication dans un congrès hal-00546847v1

A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms

Yann Ponty , Cédric Saule

WABI - 11th Workshop on Algorithms in Bioinformatics - 2011, 2011, Saarbrucken, Germany

Communication dans un congrès inria-00601060v1

Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy models

Danièle Gardy , Yann Ponty

GASCOM - 8th conference on random generation of combinatorial structures - 2010, LACIM, UQAM, Sep 2010, Montréal, Canada. 14pp

Communication dans un congrès inria-00543150v1

Non-redundant random generation from weighted context-free languages

Yann Ponty

GASCOM - 7th conference on random generation of combinatorial structures - 2008, 2008, Bibbiena, Italy. 12pp

Communication dans un congrès hal-00548877v1

Estimating seed sensitivity on homogeneous alignments

Gregory Kucherov , Laurent Noé , Yann Ponty

4th Symposium on Bioinformatics and bioengineering - BIBE'2004, May 2004, Taichung, Taiwan. pp.387-394, ⟨10.1109/BIBE.2004.1317369⟩

Communication dans un congrès inria-00001163v1

Old dog, new tricks: Exact seeding strategy improves RNA design performances

Théo Boury , Leonhard Sidl , Ivo Hofacker , Yann Ponty , Hua-Ting Yao

E4H annual forum, Nov 2025, Palaiseau (France), France

Poster de conférence hal-05481882v1

Clustering strings with mutations using an expectation-maximization algorithm In the context of RNA structure prediction

Afaf Saaidi , Yann Ponty , Mireille Regnier

34th Clemson Mini-Conference on Discrete Mathematics and Algorithms, Oct 2019, Clemson, United States

Poster de conférence hal-02332313v1

A hybrid combinatorial method for docking single stranded RNA on proteins at the thermodynamic equilibrium

Chinmay Singhal , Yann Ponty , Isaure Chauvot de Beauchêne

RECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France

Poster de conférence hal-01925083v1

Computational methods for comparing and integrating multiple probing assays to predict RNA secondary structure

Afaf Saaidi , Delphine M Allouche , Yann Ponty , Bruno M Sargueil , Mireille M Regnier

Doctorial journey Interface, Ecole polytechnique, Palaiseau, Nov 2016, Palaiseau, France. 10

Poster de conférence hal-01558227v1

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach

Cedric Chauve , Yann Ponty , João Paulo Pereira Zanetti

RECOMB-CG'14, Oct 2014, Cold Spring HArbour, United States. , 16

Poster de conférence hal-01216782v1

Developing complex RNA design applications in the Infrared framework

Hua-Ting Yao , Yann Ponty , Sebastian Will

RNA Folding - Methods and Protocols, 2726, Springer US, pp.285-313, 2024, Methods in Molecular Biology, ⟨10.1007/978-1-0716-3519-3_12⟩

Chapitre d'ouvrage hal-03711828v2

RNA secondary structure modelling following the IPANEMAP workflow

Delphine M Allouche , Grégoire de Bisschop , Afaf Saaidi , Pierre Hardouin , Francois-Xavier Lyonnet Du Moutier et al.

RNA Folding - Methods and Protocols, 2726, Springer Nature; Springer US, pp.85-104, 2024, Methods in Molecular Biology, ⟨10.1007/978-1-0716-3519-3_4⟩

Chapitre d'ouvrage hal-02324783v1

RNA Folding

Yann Ponty , Vladimir Reinharz

From text to graphs: Discrete structures and methods for Bioinformatics, ISTE, 2022

Chapitre d'ouvrage hal-03614168v1

Advanced design of structural RNAs using RNARedPrint

Yann Ponty , Stefan Hammer , Hua-Ting Yao , Sebastian Will

Ernesto Picardi. RNA Bioinformatics, 2284, pp.1--15, 2021, Methods in Molecular Biology, 978-1-0716-1306-1. ⟨10.1007/978-1-0716-1307-8_1⟩

Chapitre d'ouvrage hal-02990264v1

Repliement de l'ARN

Yann Ponty , Vladimir Reinharz

Annie Chateau; Mikaël Salson. Du texte aux graphes : méthodes et structures discrètes pour la bioinformatique, A paraître

Chapitre d'ouvrage hal-02864246v1

Preface.

Fabrice Jossinet , Yann Ponty , Jérôme Waldispühl

Computational methods for Structural RNAs (CMSR'14), 22 (3), Mary Ann Liebert, pp.189, 2015, Journal of Computational Biology

Chapitre d'ouvrage hal-01136745v1

Drawing and Editing the Secondary Structure(s) of RNA.

Yann Ponty , Fabrice Leclerc

Ernesto Picardi. RNA Bioinformatics, 1269, Springer New York, pp.63-100, 2015, Methods in Molecular Biology, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_5⟩

Chapitre d'ouvrage hal-01079893v1

Bio-algorithmique des ARN : petite promenade aux interfaces

Yann Ponty

Eric Sopena. 1024 - Bulletin de la société informatique de France, 4, SIF, pp.23--53, 2014

Chapitre d'ouvrage hal-01077506v3

Introduction to RNA secondary structure comparison.

Stefanie Schirmer , Yann Ponty , Robert Giegerich

Gorodkin, Jan and Ruzzo, Walter L. RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods, 1097, Springer, pp.247-73, 2013, Methods in molecular biology, ISBN 978-1-62703-708-2. ⟨10.1007/978-1-62703-709-9_12⟩

Chapitre d'ouvrage hal-00846818v1