Ribonanza: deep learning of RNA structure through dual crowdsourcing Article Swipe
Shujun He
,
Rui Huang
,
Jill Townley
,
Rachael C. Kretsch
,
Thomas G. Karagianes
,
David Cox
,
H. Blair
,
Dmitry Penzar
,
Valeriy Vyaltsev
,
Elizaveta Aristova
,
Arsenii Zinkevich
,
Artemy Bakulin
,
Hoyeol Sohn
,
Daniel Krstevski
,
Takaaki Fukui
,
Fumiya Tatematsu
,
Yusuke Uchida
,
Donghoon Jang
,
Jun Seong Lee
,
Roger Shieh
,
Tom Ma
,
E.S. Martynov
,
Maxim V. Shugaev
,
Habib S.T. Bukhari
,
Kazuki Fujikawa
,
Kazuki Onodera
,
Christof Henkel
,
Sampada Ron
,
Jonathan Romano
,
John J. Nicol
,
Nye G
,
Yuan Wu
,
Christian A. Choe
,
Walter Reade
,
Rhiju Das
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.02.24.581671
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.02.24.581671
Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequences collected through Eterna and other crowdsourced initiatives. Ribonanza measurements enabled solicitation, training, and prospective evaluation of diverse deep neural networks through a Kaggle challenge, followed by distillation into a single, self-contained model called RibonanzaNet. When fine tuned on auxiliary datasets, RibonanzaNet achieves state-of-the-art performance in modeling experimental sequence dropout, RNA hydrolytic degradation, and RNA secondary structure, with implications for modeling RNA tertiary structure.
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Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.02.24.581671
- https://www.biorxiv.org/content/biorxiv/early/2024/02/27/2024.02.24.581671.full.pdf
- OA Status
- green
- Cited By
- 19
- References
- 68
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4392236160
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4392236160Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/2024.02.24.581671Digital Object Identifier
- Title
-
Ribonanza: deep learning of RNA structure through dual crowdsourcingWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-02-27Full publication date if available
- Authors
-
Shujun He, Rui Huang, Jill Townley, Rachael C. Kretsch, Thomas G. Karagianes, David Cox, H. Blair, Dmitry Penzar, Valeriy Vyaltsev, Elizaveta Aristova, Arsenii Zinkevich, Artemy Bakulin, Hoyeol Sohn, Daniel Krstevski, Takaaki Fukui, Fumiya Tatematsu, Yusuke Uchida, Donghoon Jang, Jun Seong Lee, Roger Shieh, Tom Ma, E.S. Martynov, Maxim V. Shugaev, Habib S.T. Bukhari, Kazuki Fujikawa, Kazuki Onodera, Christof Henkel, Sampada Ron, Jonathan Romano, John J. Nicol, Nye G, Yuan Wu, Christian A. Choe, Walter Reade, Rhiju DasList of authors in order
- Landing page
-
https://doi.org/10.1101/2024.02.24.581671Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/02/27/2024.02.24.581671.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/02/27/2024.02.24.581671.full.pdfDirect OA link when available
- Concepts
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RNA, Deep learning, Artificial intelligence, Computer science, Nucleic acid structure, Dual (grammatical number), Sequence (biology), Dropout (neural networks), Crowdsourcing, Computational biology, Machine learning, Biology, Gene, Genetics, World Wide Web, Art, LiteratureTop concepts (fields/topics) attached by OpenAlex
- Cited by
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19Total citation count in OpenAlex
- Citations by year (recent)
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2025: 13, 2024: 6Per-year citation counts (last 5 years)
- References (count)
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68Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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