Yann Ponty
118
Documents
Publications
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Old dog, new tricks: Exact seeding strategy improves RNA design performancesRECOMB 2025 - 29th International Conference of Research in Computational Molecular Biology, 2025, Seoul, South Korea
Conference papers
hal-04756160v1
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Compressed indexing of (ultra) large viral alignmentsSEQBIM 2024 - Journées du groupe de travail Séquences en Bioinformatique, Nov 2024, Rennes, France
Conference papers
hal-04773755v1
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Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling techniqueJOBIM 2024 - Journées Ouvertes en Biologie, Informatique, et Mathématiques 2024, Jun 2024, Toulouse, France
Conference papers
hal-04575263v1
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Color Coding for the Fragment-Based Docking, Design and Equilibrium Statistics of Protein-Binding ssRNAsRECOMB 2024 - 28th International Conference of Research in Computational Molecular Biology, Apr 2024, Boston, United States
Conference papers
hal-03816423v3
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RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairsSEQBIM 2024 - Journées du groupe de travail Séquences en Bioinformatique, Nov 2024, Rennes, France
Conference papers
hal-04773768v1
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RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairsWABI 2024 - 24th Workshop on Algorithms in Bioinformatics, 2024, London, United Kingdom
Conference papers
hal-04589901v2
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RNA Triplet Repeats: Improved Algorithms for Structure Prediction and InteractionsWABI 2024 - 24th Workshop on Algorithms in Bioinformatics, 2024, London, United Kingdom
Conference papers
hal-04589903v2
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Automatic exploration of the natural variability of RNA non-canonical geometric patterns with a parameterized sampling techniqueWABI 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
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Automated design of dynamic programming schemes for RNA folding with pseudoknotsWABI 2022 - 22nd Workshop on Algorithms in Bioinformatics, Sep 2022, Potsdam, Germany
Conference papers
hal-03676377v2
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Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNARECOMB 2021 - 25th international conference on research in computational molecular biology, Apr 2021, Padova, France
Conference papers
hal-02987566v2
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Sequence graphs realizations and ambiguity in language modelsCOCOON 2021 - 27th International Computing and Combinatorics Conference, Oct 2021, Tainan, Taiwan. ⟨10.1007/978-3-030-89543-3_13⟩
Conference papers
hal-02495333v4
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Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA BioinformaticsWABI 2021 - 21st Workshop on Algorithms in Bioinformatics, 2021, Paris, France
Conference papers
hal-03206132v1
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A new parametrization for independent set reconfiguration and applications to RNA kineticsIPEC 2021 - 16th International Symposium on Parameterized and Exact Computation, Sep 2021, Lisbon, Portugal. ⟨10.4230/lipics.ipec.2021.11⟩
Conference papers
hal-03272963v2
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IndelsRNAmute: Predicting deleterious multiple point substitutions and indels mutationsISBRA 2020 - 16th International Symposium on Bioinformatics Research and Applications, Dec 2020, Moscow, Russia
Conference papers
hal-02936276v1
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Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Modules IdentificationRECOMB 2020 - 24th Annual International Conference on Research in Computational Molecular Biology, May 2020, Padova, Italy
Conference papers
hal-02354733v1
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Effective Rotation-invariant Point CNN with Spherical Harmonics kernels3DV - International Conference on 3D Vision - 2019, Sep 2019, Québec City, Canada
Conference papers
hal-02167454v2
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Exponentially few RNA structures are designableACM-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
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Forbidden substrings and the connectivity of the Hamming graph of RNA sequences: Partial disconnectivity testsSEQBIM 2019 - Séquences en Bioinformatique, Informatique et Mathématiques, Dec 2019, Marne-la-Vallée, France
Conference papers
hal-02403517v1
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A hybrid combinatorial method for docking single stranded RNAs in a protein pockect at the thermodynamic equilibriumJOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques), Jul 2018, Marseille, France
Conference papers
hal-02394529v1
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Nucleic Acids design targeting integer-valued features: FPT counting and uniform samplingWEPA 2018 - 2nd International Workshop on Enumeration Problems and Applications, Nov 2018, Pisa, Italy
Conference papers
hal-01911878v1
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Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target StructuresRECOMB - 22nd Annual International Conference on Research in Computational Molecular Biology - 2018, Apr 2018, Paris, France
Conference papers
hal-01631277v2
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An integrative approach for predicting the RNA secondary structure for the HIV–1 Gag UTR using probing dataJOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2017, Jul 2017, Lille, France. pp.102
Conference papers
hal-01534587v1
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An EM algorithm for mapping short reads in multiple RNA structure probing experimentsMatbio2017, King's College London Sep 2017, London, United Kingdom
Conference papers
hal-01590528v1
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Efficient approximations of RNA kinetics landscape using non-redundant samplingISMB/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
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Counting, generating and sampling tree alignmentsALCOB - 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
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Taming reluctant random walks in the positive quadrantGASCOM - 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
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Homology modeling of complex structural RNAsJOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France
Conference papers
hal-01332642v1
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Towards structural models for the Ebola UTR regions using experimental SHAPE probing dataJOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2016, Jun 2016, Lyon, France
Conference papers
hal-01332469v1
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RNA Bioinformatics and ensemble dynamic programming5th biennial Canadian Discrete and Algorithmic Mathematics Conference - CanaDAM 2015, Jun 2015, Saskatoon, Canada
Conference papers
hal-01569852v1
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Towards firm foundations for the rational design of RNA moleculesColloque de Bioinformatique Moléculaire (GdR BIM), Oct 2015, Paris, France
Conference papers
hal-01570180v1
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Résultats algorithmiques pour le design d’ARN avec contraintes de séquenceSeqBio 2015, Nov 2015, Orsay, France. pp.26-31
Conference papers
hal-01266096v1
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Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogeniesISBRA - 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
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Combinatorial RNA Design: Designability and Structure-Approximating AlgorithmCPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy
Conference papers
hal-01115349v2
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Evolution of genes neighborhood within reconciled phylogenies: an ensemble approachBSB - Brazilian Symposium on Bioinformatics - 2014, Oct 2014, Belo Horizonte, Brazil. pp.49--56, ⟨10.1007/978-3-319-12418-6⟩
Conference papers
hal-01056140v2
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Using the Fast Fourier Transform to accelerate the computational search for RNA conformational switches (extended abstract)RECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China
Conference papers
hal-00766780v1
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A linear inside-outside algorithm for correcting sequencing errors in structured RNA sequencesRECOMB - 17th Annual International Conference on Research in Computational Molecular Biology - 2013, Apr 2013, Beijing, China
Conference papers
hal-00766781v1
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Flexible RNA design under structure and sequence constraints using formal languagesACM-BCB - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics - 2013, Sep 2013, Bethesda, Washigton DC, United States
Conference papers
hal-00823279v2
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A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotides distributionISMB/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
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Can Probabilistic Model Checking Explore Ribo-Nucleic Acid Folding Space?IWBDA - 4th International Workshop on Bio-Design Automation - 2012, Jun 2012, San Francisco, United States
Conference papers
hal-00712557v1
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Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknotsWABI - 12th Workshop on Algorithms in Bioinformatics - 2012, University of Ljubljana, Sep 2012, Ljubljana, Slovenia
Conference papers
hal-00708580v2
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Impact Of The Energy Model On The Complexity Of RNA Folding With PseudoknotsCPM - 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
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Visualizing 2D & 3D Structures of RNAVIZBI - 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
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The weighted words collectorAOFA - 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
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On the diversity of pattern distributions in rational languageANALCO - 12th Meeting on Analytic Algorithmics and Combinatorics - 2012, Jan 2012, Kyoto, Japan. pp.107--116
Conference papers
hal-00643598v1
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A Combinatorial Framework for Designing (Pseudoknotted) RNA AlgorithmsWABI - 11th Workshop on Algorithms in Bioinformatics - 2011, 2011, Saarbrucken, Germany
Conference papers
inria-00601060v1
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Investigating the RFAM paradox: The pseudoknot explanationFifth Indo-French Bioinformatics Meeting, Mar 2011, Hyderabad, India
Conference papers
hal-00585647v1
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An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressureRECOMB - 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
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Multi-dimensional Boltzmann Sampling of Languages21st 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
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Weighted random generation of context-free languages: Analysis of collisions in random urn occupancy modelsGASCOM - 8th conference on random generation of combinatorial structures - 2010, LACIM, UQAM, Sep 2010, Montréal, Canada. 14pp
Conference papers
inria-00543150v1
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Non-redundant random generation from weighted context-free languagesGASCOM - 7th conference on random generation of combinatorial structures - 2008, 2008, Bibbiena, Italy. 12pp
Conference papers
hal-00548877v1
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Estimating seed sensitivity on homogeneous alignments4th Symposium on Bioinformatics and bioengineering - BIBE'2004, May 2004, Taichung, Taiwan. pp.387-394, ⟨10.1109/BIBE.2004.1317369⟩
Conference papers
inria-00001163v1
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Clustering strings with mutations using an expectation-maximization algorithm In the context of RNA structure prediction34th Clemson Mini-Conference on Discrete Mathematics and Algorithms, Oct 2019, Clemson, United States
Conference poster
hal-02332313v1
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A hybrid combinatorial method for docking single stranded RNA on proteins at the thermodynamic equilibriumRECOMB 2018 - 22nd Annual International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France
Conference poster
hal-01925083v1
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Computational methods for comparing and integrating multiple probing assays to predict RNA secondary structureDoctorial journey Interface, Ecole polytechnique, Palaiseau, Nov 2016, Palaiseau, France. 10
Conference poster
hal-01558227v1
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Evolution of genes neighborhood within reconciled phylogenies: an ensemble approachConference poster hal-01216782v1 |
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Developing complex RNA design applications in the Infrared frameworkRNA Folding - Methods and Protocols, 2726, Springer US, pp.285-313, 2024, Methods in Molecular Biology, ⟨10.1007/978-1-0716-3519-3_12⟩
Book sections
hal-03711828v2
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RNA secondary structure modelling following the IPANEMAP workflowRNA 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⟩
Book sections
hal-02324783v1
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RNA FoldingFrom text to graphs: Discrete structures and methods for Bioinformatics, ISTE, 2022
Book sections
hal-03614168v1
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Advanced design of structural RNAs using RNARedPrintErnesto 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
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Repliement de l'ARNAnnie Chateau; Mikaël Salson. Du texte aux graphes : méthodes et structures discrètes pour la bioinformatique, inPress
Book sections
hal-02864246v1
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Preface.Computational methods for Structural RNAs (CMSR'14), 22 (3), Mary Ann Liebert, pp.189, 2015, Journal of Computational Biology
Book sections
hal-01136745v1
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Drawing and Editing the Secondary Structure(s) of RNA.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
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Bio-algorithmique des ARN : petite promenade aux interfacesEric Sopena. 1024 - Bulletin de la société informatique de France, 4, SIF, pp.23--53, 2014
Book sections
hal-01077506v3
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Introduction to RNA secondary structure comparison.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
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CREMSA: Compressed indexing of (ultra) large alignments2025
Preprints, Working Papers, ...
hal-04910677v1
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Non-Redundant Sampling and Statistical Estimators for RNA Structural Properties at the Thermodynamic Equilibrium2024
Preprints, Working Papers, ...
hal-02288811v2
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RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs2024
Preprints, Working Papers, ...
hal-04761629v1
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RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions2024
Preprints, Working Papers, ...
hal-04766560v1
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Independent set reconfiguration: general and RNA-focused parameterized algorithms2023
Preprints, Working Papers, ...
hal-04094405v1
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Designing molecular RNA switches with Restricted Boltzmann machines2023
Preprints, Working Papers, ...
hal-04294884v1
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Rule-weighted and terminal-weighted context-free grammars have identical expressivity[Research Report] 2012
Reports
hal-00693600v1
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Estimating seed sensitivity on homogeneous alignments[Research Report] RR-5047, INRIA. 2003, pp.17
Reports
inria-00071536v1
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Modélisation de séquences génomiques structurées, génération aléatoire et applicationsMathématiques [math]. Université Paris Sud - Paris XI, 2006. Français. ⟨NNT : ⟩
Theses
tel-00144130v2
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Ensemble Algorithms and Analytic Combinatorics in RNA Bioinformatics and BeyondBioinformatics [q-bio.QM]. Université Paris-Saclay, 2020
Accreditation to supervise research
tel-03219977v2
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Etudes combinatoire et génération aléatoire des structures secondaires d'ARNBio-informatique [q-bio.QM]. 2003
Master thesis
hal-01261068v1
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