Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning
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DOI: 10.1038/s41467-021-26278-9
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References listed on IDEAS
- Ian R. Henderson & Steven E. Jacobsen, 2007. "Epigenetic inheritance in plants," Nature, Nature, vol. 447(7143), pages 418-424, May.
- Zaka Wing-Sze Yuen & Akanksha Srivastava & Runa Daniel & Dennis McNevin & Cameron Jack & Eduardo Eyras, 2021. "Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
- Shawn J. Cokus & Suhua Feng & Xiaoyu Zhang & Zugen Chen & Barry Merriman & Christian D. Haudenschild & Sriharsa Pradhan & Stanley F. Nelson & Matteo Pellegrini & Steven E. Jacobsen, 2008. "Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning," Nature, Nature, vol. 452(7184), pages 215-219, March.
- Zhengming Wang & David C. Baulcombe, 2020. "Transposon age and non-CG methylation," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
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- Tuomas Hämälä & Christopher Moore & Laura Cowan & Matthew Carlile & David Gopaulchan & Marie K. Brandrud & Siri Birkeland & Matthew Loose & Filip Kolář & Marcus A. Koch & Levi Yant, 2024. "Impact of whole-genome duplications on structural variant evolution in Cochlearia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
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