The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Detecting DNA cytosine methylation using nanopore sequencing
Open accessAbstract
In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.
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Cites
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Human DNA methylomes at base resolution show widespread epigenomic differences
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DNA methylation arrays as surrogate measures of cell mixture distribution
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ChIP–seq: advantages and challenges of a maturing technology
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The NIH Roadmap Epigenomics Mapping Consortium
Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt1010-1045 · Cited by 1,892
Direct detection of DNA methylation during single-molecule, real-time sequencing
Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460
DNA methylation on N6-adenine in mammalian embryonic stem cells
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Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
Laszlo, A. H., Derrington, I. M., Brinkerhoff, H., Langford, K. W., Nova, I. C., Samson, J. M., Bartlett, J. J., Pavlenok, M., & Gundlach, J. H. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1310240110 · Cited by 321
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Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
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Cited by
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
Opportunities and challenges in long-read sequencing data analysis
Amarasinghe, S. L., Su, S., Dong, X., Zappia, L., Ritchie, M. E., & Gouil, Q. (2020) · Genome Biology · doi:10.1186/s13059-020-1935-5 · Cited by 2,530
Nanopore sequencing and assembly of a human genome with ultra-long reads
Jain, M., Koren, S., Miga, K. H., Quick, J., Rand, A. C., Sasani, T. A., Tyson, J. R., Beggs, A. D., Dilthey, A. T., Fiddes, I. T., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4060 · Cited by 1,892
Self-citationThe Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
Jain, M., Olsen, H. E., Paten, B., & Akeson, M. (2016) · Genome Biology · doi:10.1186/s13059-016-1103-0 · Cited by 1,588
The Third Revolution in Sequencing Technology
van Dijk, E. L., Jaszczyszyn, Y., Naquin, D., & Thermes, C. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.05.008 · Cited by 1,057
Metadata
- Authors
- Simpson, J. T., Workman, R. E., Zuzarte, P. C., David, M., Dursi, L. J., & Timp, W.
- Venue
- Nature Methods
- Published
- 2017-02-20
- Volume
- 14
- Issue
- 4
- Pages
- 407-410
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2591367881
- Cited by
- 1,136
- References
- 10
- FWCI
- 36.66
- Type
- journal article
- Language
- en
- Open access
- green
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- Simpson, J. T., Workman, R. E., Zuzarte, P. C., David, M., Dursi, L. J., & Timp, W. (2017). Detecting DNA cytosine methylation using nanopore sequencing. Nature Methods. https://doi.org/10.1038/nmeth.4184
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