Access content directly

Yann Ponty

109
Documents

Publications

Image document

Infrared: a declarative tree decomposition-powered framework for bioinformatics

Hua-Ting Yao , Bertrand Marchand , Sarah J. Berkemer , Yann Ponty , Sebastian Will
Algorithms for Molecular Biology, 2024, ⟨10.1186/s13015-024-00258-2⟩
Journal articles hal-04211173v2
Image document

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⟩
Journal articles hal-04103565v1
Image document

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⟩
Journal articles 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⟩
Journal articles hal-03815555v1
Image document

Reference-free transcriptome signatures for prostate cancer prognosis

Ha Tn Nguyen , Haoliang Xue , Virginie Firlej , Yann Ponty , Mélina Gallopin
BMC Cancer, 2021, 21 (394), ⟨10.1186/s12885-021-08021-1⟩
Journal articles hal-02948844v1
Image document

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

Gregor Entzian , Ivo Hofacker , Yann Ponty , Ronny Lorenz , Andrea Tanzer
Bioinformatics, 2021
Journal articles hal-02889448v3
Image document

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

Dehe Wang , Ao Jiang , Jiangpeng Feng , Guangnan Li , Dong Guo
Molecular Cell, inPress, ⟨10.1016/j.molcel.2021.02.036⟩
Journal articles hal-03154155v2
Image document

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

Grégoire de Bisschop , Delphine Allouche , Elisa Frezza , Benoît Masquida , Yann Ponty
Non-Coding RNA, 2021, 7 (4), pp.71. ⟨10.3390/ncrna7040071⟩
Journal articles hal-03413594v1
Image document

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⟩
Journal articles 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
Bioinformatics, 2020, 36 (9), pp.2910--2922. ⟨10.1093/bioinformatics/btaa039⟩
Journal articles hal-02423237v1
Image document

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⟩
Journal articles hal-01424452v2
Image document

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⟩
Journal articles hal-02112888v1
Image document

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⟩
Journal articles hal-02169271v1
Image document

Design of RNAs: comparing programs for inverse RNA folding.

Alexander Churkin , Matan Drory Retwitzer , Vladimir Reinharz , Yann Ponty , Jérôme Waldispühl
Briefings in Bioinformatics, 2018, 19 (2), pp.350--358. ⟨10.1093/bib/bbw120⟩
Journal articles hal-01392958v1
Image document

Meet-U: educating through research immersion

Nika Abdollahi , Alexandre Albani , Eric Anthony , Agnes Baud , Mélissa Cardon
PLoS Computational Biology, 2018, 14 (3), pp.1-10. ⟨10.1371/journal.pcbi.1005992⟩
Journal articles hal-01722019v1
Image document

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
Journal articles hal-01500116v1
Image document

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⟩
Journal articles hal-01273406v1
Image document

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
Nucleic Acids Research, 2017, 45 (12), pp.7382--7400. ⟨10.1093/nar/gkx303⟩
Journal articles hal-01505282v1
Image document

Combinatorial RNA Design: Designability and Structure-Approximating Algorithm in Watson-Crick and Nussinov-Jacobson Energy Models

Jozef Haleš , Alice Héliou , Ján Maňuch , Yann Ponty , Ladislav Stacho
Algorithmica, 2017, 79 (3), pp.835--856. ⟨10.1007/s00453-016-0196-x⟩
Journal articles hal-01285499v2
Image document

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

Wandrille Duchemin , Yoann Anselmetti , Murray Patterson , Yann Ponty , Sèverine Bérard
Genome Biology and Evolution, 2017, 9 (5), pp.1312-1319. ⟨10.1093/gbe/evx069⟩
Journal articles hal-01503766v2
Image document

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⟩
Journal articles hal-01319682v1
Image document

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⟩
Journal articles hal-01291754v1
Image document

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⟩
Journal articles hal-01276903v1

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⟩
Journal articles hal-01245495v1

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⟩
Journal articles hal-00840260v1
Image document

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⟩
Journal articles hal-00819017v1

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
PLoS Computational Biology, 2013, 9 (12), pp.e1003369. ⟨10.1371/journal.pcbi.1003369⟩
Journal articles hal-00875116v1
Image document

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⟩
Journal articles hal-00828062v1
Image document

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⟩
Journal articles inria-00607745v2

Mieux comprendre certaines molécules biologiques grâce à l’informatique

Yann Ponty , Joanna Jongwane
Interstices, 2012
Journal articles 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⟩
Journal articles 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
Nucleic Acids Research, 2012, 40 (20), pp.10041-10052. ⟨10.1093/nar/gks768⟩
Journal articles hal-00733924v1
Image document

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⟩
Journal articles 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⟩
Journal articles hal-00681928v1
Image document

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⟩
Journal articles hal-00483581v2
Image document

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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles inria-00548863v1
Image document

Culminating paths

Mireille Bousquet-Mélou , Yann Ponty
Discrete Mathematics and Theoretical Computer Science, 2008, 10 (2), pp.125--152
Journal articles 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⟩
Journal articles 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⟩
Journal articles inria-00548870v1
Image document

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⟩
Journal articles inria-00548871v1
Image document

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
Conference papers hal-03816423v3
Image document

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⟩
Conference papers hal-04094288v2
Image document

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
Conference papers hal-03676377v2
Image document

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⟩
Conference papers hal-02495333v4
Image document

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
Conference papers hal-02987566v2
Image document

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
Conference papers hal-03206132v1
Image document

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
Conference papers hal-03272963v2
Image document

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
RECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology, May 2020, Padova, Italy
Conference papers hal-02354733v1
Image document

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
Conference papers hal-02936276v1
Image document

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
Conference papers hal-02167454v2
Image document

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⟩
Conference papers hal-02141853v2
Image document

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
Conference papers hal-02403517v1
Image document

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
Conference papers hal-01911878v1
Image document

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
Conference papers hal-01631277v2
Image document

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
Conference papers hal-02394529v1
Image document

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⟩
Conference papers 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
Conference papers hal-01590528v1

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
Conference papers hal-01534587v1
Image document

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
Conference papers hal-01332642v1
Image document

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
Conference papers hal-01332469v1
Image document

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⟩
Conference papers hal-01154030v3
Image document

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⟩
Conference papers hal-01291164v1
Image document

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
Conference papers hal-01115349v2
Image document

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⟩
Conference papers 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
Conference papers hal-01266096v1

Towards firm foundations for the rational design of RNA molecules

Yann Ponty
Colloque de Bioinformatique Moléculaire (GdR BIM), Oct 2015, Paris, France
Conference papers hal-01570180v1

RNA Bioinformatics and ensemble dynamic programming

Yann Ponty
5th biennial Canadian Discrete and Algorithmic Mathematics Conference - CanaDAM 2015, Jun 2015, Saskatoon, Canada
Conference papers hal-01569852v1
Image document

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⟩
Conference papers hal-01056140v2
Image document

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
Conference papers hal-00766780v1
Image document

Flexible RNA design under structure and sequence constraints using formal languages

Yu Zhou , Yann Ponty , Stéphane Vialette , Jérôme Waldispühl , Yi Zhang
ACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States
Conference papers hal-00823279v2
Image document

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
Conference papers hal-00766781v1
Image document

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
Conference papers 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
Conference papers hal-00712557v1
Image document

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
Conference papers hal-00708580v2
Image document

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⟩
Conference papers hal-00670232v3
Image document

The weighted words collector

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

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
Conference papers hal-00723351v1
Image document

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
Conference papers hal-00643598v1
Image document

Investigating the RFAM paradox: The pseudoknot explanation

Stefan Janssen , Yann Ponty , Balaji Raman , Saad Sheikh , Jean-Marc Steyaert
Fifth Indo-French Bioinformatics Meeting, Mar 2011, Hyderabad, India
Conference papers hal-00585647v1
Image document

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⟩
Conference papers hal-00546847v1
Image document

A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms

Yann Ponty , Cédric Saule
WABI - 11th Workshop on Algorithms in Bioinformatics - 2011, 2011, Saarbrucken, Germany
Conference papers inria-00601060v1
Image document

Multi-dimensional Boltzmann Sampling of Languages

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

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
Conference papers inria-00543150v1
Image document

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
Conference papers hal-00548877v1
Image document

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⟩
Conference papers inria-00001163v1
Image document

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
Conference poster hal-02332313v1
Image document

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
Conference poster hal-01925083v1
Image document

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
Conference poster hal-01558227v1
Image document

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
Conference poster hal-01216782v1
Image document

RNA Folding

Yann Ponty , Vladimir Reinharz
From text to graphs: Discrete structures and methods for Bioinformatics, ISTE, 2022
Book sections hal-03614168v1
Image document

Developing complex RNA design applications in the Infrared framework

Hua-Ting Yao , Yann Ponty , Sebastian Will
RNA Folding - Methods and Protocols, 2022
Book sections hal-03711828v2
Image document

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⟩
Book sections hal-02990264v1
Image document

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
Book sections hal-02864246v1
Image document

RNA secondary structure modelling following the IPANEMAP workflow

Delphine M Allouche , Grégoire de Bisschop , Afaf Saaidi , Yann Ponty , Sargueil Bruno
RNA Folding - Methods and Protocols, Springer Nature, inPress, Methods in Molecular Biology
Book sections hal-02324783v1
Image document

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⟩
Book sections hal-01079893v1

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
Book sections hal-01136745v1
Image document

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
Book sections 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⟩
Book sections hal-00846818v1
Image document

Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and Beyond

Yann Ponty
Bioinformatics [q-bio.QM]. Université Paris-Saclay, 2020
Habilitation à diriger des recherches tel-03219977v2