2024
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Runge, Frederic; Hutter, Frank Machine Learning for RNA Design: LEARNA Book Chapter In: Churkin, Alexander; Barash, Danny (Ed.): RNA Design: Methods and Protocols, Chapter 5, pp. 63–93, Springer US, New York, NY, 1, 2024, ISBN: 978-1-0716-4079-1. @inbook{nokey,
title = {Machine Learning for RNA Design: LEARNA},
author = {Frederic Runge and Frank Hutter},
editor = {Alexander Churkin and Danny Barash},
doi = {10.1007/978-1-0716-4079-1_5},
year = {2024},
isbn = {978-1-0716-4079-1},
booktitle = {RNA Design: Methods and Protocols},
pages = {63--93},
publisher = {Springer US},
address = {New York, NY},
edition = {1},
chapter = {5},
series = {Methods in Molecular Biology},
keywords = {}
}
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Runge, Frederic; Franke, Jörg K. H.; Fertmann, Daniel; Backofen, Rolf; Hutter, Frank Partial RNA Design Journal Article In: Bioinformatics, vol. 40, no. Supplement_1, pp. i437–i445, 2024, (Oral Presentation at ISMB'24). @article{nokey,
title = {Partial RNA Design},
author = {Frederic Runge and Jörg K.H. Franke and Daniel Fertmann and Rolf Backofen and Frank Hutter},
doi = {https://doi.org/10.1093/bioinformatics/btae222},
year = {2024},
journal = {Bioinformatics},
volume = {40},
number = {Supplement_1},
pages = {i437--i445},
publisher = {Oxford University Press},
keywords = {}
}
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Patil, Sharat; Runge, Frederic; Franke, Jörg K. H.; Hutter, Frank Towards Generative RNA Design with Tertiary Interactions Workshop The Generative and Experimental perspectives in bioMolecular design (GEM) workshop (ICLR 2024), 2024, (Oral Presentation). @workshop{nokey,
title = {Towards Generative RNA Design with Tertiary Interactions},
author = {Sharat Patil and Frederic Runge and Jörg K. H. Franke and Frank Hutter},
year = {2024},
booktitle = {The Generative and Experimental perspectives in bioMolecular design (GEM) workshop (ICLR 2024)},
keywords = {}
}
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Matus, Dominika; Runge, Frederic; Franke, Jörg K. H.; Gerne, Lars; Uhl, Michael; Hutter, Frank; Backofen, Rolf RNA-Protein Interaction Prediction via Sequence Embeddings Workshop The Generative and Experimental perspectives in bioMolecular design (GEM) workshop (ICLR 2024), 2024. @workshop{nokey,
title = {RNA-Protein Interaction Prediction via Sequence Embeddings},
author = {Dominika Matus and Frederic Runge and Jörg K. H. Franke and Lars Gerne and Michael Uhl and Frank Hutter and Rolf Backofen},
year = {2024},
booktitle = {The Generative and Experimental perspectives in bioMolecular design (GEM) workshop (ICLR 2024)},
keywords = {}
}
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Franke, Jörg K. H.; Runge, Frederic; Köksal, Ryan; Backofen, Rolf; Hutter, Frank RNAformer: A Simple Yet Effective Deep Learning Model for RNA Secondary Structure Prediction Miscellaneous 2024. @misc{nokey,
title = {RNAformer: A Simple Yet Effective Deep Learning Model for RNA Secondary Structure Prediction},
author = {Jörg K.H. Franke and Frederic Runge and Ryan Köksal and Rolf Backofen and Frank Hutter},
year = {2024},
keywords = {}
}
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Runge, Frederic; Farid, Karim; Franke, Jörg K. H.; Hutter, Frank RNABench: A Comprehensive Library for In Silico RNA Modelling Miscellaneous 2024. @misc{nokey,
title = {RNABench: A Comprehensive Library for In Silico RNA Modelling},
author = {Frederic Runge and Karim Farid and Jörg K.H. Franke and Frank Hutter},
year = {2024},
keywords = {}
}
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2023
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Runge, Frederic; Franke, Jörg K. H.; Fertmann, Daniel; Hutter, Frank Rethinking Performance Measures of RNA Secondary Structure Problems Workshop Machine Learning for Structural Biology Workshop, (NeruIPS 2023), 2023. @workshop{runge2023rethinking,
title = {Rethinking Performance Measures of RNA Secondary Structure Problems},
author = {Frederic Runge and Jörg K. H. Franke and Daniel Fertmann and Frank Hutter},
year = {2023},
booktitle = {Machine Learning for Structural Biology Workshop, (NeruIPS 2023)},
keywords = {}
}
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Runge, Frederic; Franke, Jörg K. H.; Hutter, Frank Towards Automated Design of Riboswitches Workshop The 2023 ICML Workshop on Computational Biology, 2023. @workshop{runge2023towards,
title = {Towards Automated Design of Riboswitches},
author = {Frederic Runge and Jörg K. H. Franke and Frank Hutter},
year = {2023},
booktitle = {The 2023 ICML Workshop on Computational Biology},
keywords = {}
}
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Franke, Jörg K. H.; Runge, Frederic; Hutter, Frank Scalable Deep Learning for RNA Secondary Structure Prediction Workshop The 2023 ICML Workshop on Computational Biology, 2023. @workshop{nokey,
title = {Scalable Deep Learning for RNA Secondary Structure Prediction},
author = {Jörg K.H. Franke and Frederic Runge and Frank Hutter},
year = {2023},
booktitle = {The 2023 ICML Workshop on Computational Biology},
keywords = {}
}
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2022
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Franke, Jörg; Runge, Frederic; Hutter, Frank Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule Design Inproceedings In: Oh, Alice H.; Agarwal, Alekh; Belgrave, Danielle; Cho, Kyunghyun (Ed.): Advances in Neural Information Processing Systems (NeurIPS 2022), 2022. @inproceedings{franke2022probabilistic,
title = {Probabilistic Transformer: Modelling Ambiguities and Distributions for RNA Folding and Molecule Design},
author = {Jörg Franke and Frederic Runge and Frank Hutter},
editor = {Alice H. Oh and Alekh Agarwal and Danielle Belgrave and Kyunghyun Cho},
year = {2022},
booktitle = {Advances in Neural Information Processing Systems (NeurIPS 2022)},
keywords = {}
}
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2019
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Runge, Frederic; Stoll, Danny; Falkner, Stefan; Hutter, Frank Learning to Design RNA Inproceedings In: International Conference on Learning Representations, 2019. @inproceedings{runge2019learning,
title = {Learning to Design RNA},
author = {Frederic Runge and Danny Stoll and Stefan Falkner and Frank Hutter},
year = {2019},
booktitle = {International Conference on Learning Representations},
keywords = {}
}
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