Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty. RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 18:1-18:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{boehmer_et_al:LIPIcs.WABI.2024.18, author = {Boehmer, Kimon and Berkemer, Sarah J. and Will, Sebastian and Ponty, Yann}, title = {{RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {18:1--18:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.18}, URN = {urn:nbn:de:0030-drops-206625}, doi = {10.4230/LIPIcs.WABI.2024.18}, annote = {Keywords: RNA folding, RNA interactions, triplet repeats, dynamic programming, NP-hardness} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Théo Boury, Laurent Bulteau, and Yann Ponty. RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 19:1-19:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{boury_et_al:LIPIcs.WABI.2024.19, author = {Boury, Th\'{e}o and Bulteau, Laurent and Ponty, Yann}, title = {{RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {19:1--19:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.19}, URN = {urn:nbn:de:0030-drops-206632}, doi = {10.4230/LIPIcs.WABI.2024.19}, annote = {Keywords: RNA structure, String Design, Parameterized Complexity, Uniform Sampling} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Théo Boury, Yann Ponty, and Vladimir Reinharz. Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 20:1-20:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{boury_et_al:LIPIcs.WABI.2023.20, author = {Boury, Th\'{e}o and Ponty, Yann and Reinharz, Vladimir}, title = {{Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {20:1--20:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-294-5}, ISSN = {1868-8969}, year = {2023}, volume = {273}, editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.20}, URN = {urn:nbn:de:0030-drops-186460}, doi = {10.4230/LIPIcs.WABI.2023.20}, annote = {Keywords: Subgraph Isomorphism, 3D RNA, Parameterized Complexity, Tree Decomposition, Boltzmann sampling, Neighborhood metrics, Kink-Turn family} }
Published in: Dagstuhl Reports, Volume 12, Issue 9 (2023)
Sven Findeiß, Christoph Flamm, and Yann Ponty. Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). In Dagstuhl Reports, Volume 12, Issue 9, pp. 121-149, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@Article{findei_et_al:DagRep.12.9.121, author = {Findei{\ss}, Sven and Flamm, Christoph and Ponty, Yann}, title = {{Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381)}}, pages = {121--149}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2023}, volume = {12}, number = {9}, editor = {Findei{\ss}, Sven and Flamm, Christoph and Ponty, Yann}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagRep.12.9.121}, URN = {urn:nbn:de:0030-drops-178110}, doi = {10.4230/DagRep.12.9.121}, annote = {Keywords: RNA, RNA design, Inverse folding, RNA structure, mRNA design, RNA sensors, Co-transcriptional folding, Molecular evolution, Distant homology, Drug design} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, and Yann Ponty. Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 7:1-7:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{marchand_et_al:LIPIcs.WABI.2022.7, author = {Marchand, Bertrand and Will, Sebastian and Berkemer, Sarah J. and Bulteau, Laurent and Ponty, Yann}, title = {{Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {7:1--7:24}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.7}, URN = {urn:nbn:de:0030-drops-170414}, doi = {10.4230/LIPIcs.WABI.2022.7}, annote = {Keywords: RNA folding, treewidth, dynamic programming} }
Published in: LIPIcs, Volume 214, 16th International Symposium on Parameterized and Exact Computation (IPEC 2021)
Laurent Bulteau, Bertrand Marchand, and Yann Ponty. A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics. In 16th International Symposium on Parameterized and Exact Computation (IPEC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 214, pp. 11:1-11:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{bulteau_et_al:LIPIcs.IPEC.2021.11, author = {Bulteau, Laurent and Marchand, Bertrand and Ponty, Yann}, title = {{A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics}}, booktitle = {16th International Symposium on Parameterized and Exact Computation (IPEC 2021)}, pages = {11:1--11:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-216-7}, ISSN = {1868-8969}, year = {2021}, volume = {214}, editor = {Golovach, Petr A. and Zehavi, Meirav}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2021.11}, URN = {urn:nbn:de:0030-drops-153946}, doi = {10.4230/LIPIcs.IPEC.2021.11}, annote = {Keywords: reconfiguration problems - parameterized algorithms - RNA bioinformatics - directed pathwidth} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Bertrand Marchand, Yann Ponty, and Laurent Bulteau. Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{marchand_et_al:LIPIcs.WABI.2021.7, author = {Marchand, Bertrand and Ponty, Yann and Bulteau, Laurent}, title = {{Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {7:1--7:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.7}, URN = {urn:nbn:de:0030-drops-143604}, doi = {10.4230/LIPIcs.WABI.2021.7}, annote = {Keywords: RNA, treewidth, FPT algorithms, RNA design, structure-sequence alignment} }
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