Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework Article Swipe
Haotian Teng
,
Marcus H. Stoiber
,
Ziv Bar‐Joseph
,
Carl Kingsford
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/gr.278960.124
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/gr.278960.124
Direct nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of modified bases. A key challenge is the scarcity of adequate training data with known methylation modifications. We present Xron, a hybrid encoder–decoder framework that delivers a direct methylation-distinguishing basecaller by training on synthetic RNA data and immunoprecipitation (IP)-based experimental data in two steps. First, we generate data with more diverse modification combinations through in silico cross-linking. Second, we use this data set to train an end-to-end neural network basecaller followed by fine-tuning on IP-based experimental data with label smoothing. The trained neural network basecaller outperforms existing methylation detection methods on both read-level and site-level prediction scores. Xron is a standalone, end-to-end m6A-distinguishing basecaller capable of detecting methylated bases directly from raw sequencing signals, enabling de novo methylome assembly.
Related Topics
Concepts
Biology
Computational biology
Methylation
In silico
RNA
RNA methylation
Computer science
Artificial intelligence
Machine learning
Gene
Genetics
Methyltransferase
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1101/gr.278960.124
- https://genome.cshlp.org/content/early/2024/10/10/gr.278960.124.full.pdf
- OA Status
- hybrid
- Cited By
- 9
- References
- 57
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4403415582
All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W4403415582Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/gr.278960.124Digital Object Identifier
- Title
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Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning frameworkWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2024Year of publication
- Publication date
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2024-10-15Full publication date if available
- Authors
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Haotian Teng, Marcus H. Stoiber, Ziv Bar‐Joseph, Carl KingsfordList of authors in order
- Landing page
-
https://doi.org/10.1101/gr.278960.124Publisher landing page
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https://genome.cshlp.org/content/early/2024/10/10/gr.278960.124.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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hybridOpen access status per OpenAlex
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https://genome.cshlp.org/content/early/2024/10/10/gr.278960.124.full.pdfDirect OA link when available
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Biology, Computational biology, Methylation, In silico, RNA, RNA methylation, Computer science, Artificial intelligence, Machine learning, Gene, Genetics, MethyltransferaseTop concepts (fields/topics) attached by OpenAlex
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9Total citation count in OpenAlex
- Citations by year (recent)
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2025: 7, 2024: 2Per-year citation counts (last 5 years)
- References (count)
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57Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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