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  1. DeepMP is a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a read is methylated or not. DeepMP's architecture consists of two different modules. First, the sequence module involves 6 1D convolutional layers with 256 1x4 filters.

    DeepMP is a computational tool to detect DNA modifications in …

    github.com/pepebonet/DeepMP
    github.com/pepebonet/DeepMP
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  2. Oxford Academic
    https://academic.oup.com/bioinformatics/article/38/5/1235/6413628

    DeepMP: a deep learning tool to detect DNA base modifications …

  3. PubMed
    https://pubmed.ncbi.nlm.nih.gov/34718417

    DeepMP: a deep learning tool to detect DNA base modifications …

  4. Github
    https://github.com/pepebonet/DeepMP

    DeepMP is a computational tool to detect DNA modifications in …

  5. Studies of DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data.
  6. ResearchGate
    https://www.researchgate.net/publication/352800581...

    DeepMP: a deep learning tool to detect DNA base modifications …

  7. Europe PMC
    https://europepmc.org/article/MED/34718417

    DeepMP: a deep learning tool to detect DNA base modifications …

  8. researchhub.com
    https://www.researchhub.com/paper/1397012/deepmp-a...

    DeepMP: a deep learning tool to detect DNA base modifications …

  9. People also ask
    How does deepmp detect methylation?
    Here, we present DeepMP, a convolutional neural network-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells.

    DeepMP: a deep learning tool to detect DNA base modifications on

    academic.oup.com
    How does deepmp work?
    DeepMP takes as input two types of information from Nanopore sequencing data ( Fig. 1A ), basecalling errors and raw current signals ( Fig. 1B ). Features from these two types of information are fed into a CNN-based module to identify modified sites in individual reads ( Fig. 1D ).

    DeepMP: a deep learning tool to detect DNA base modifications on

    academic.oup.com
    What datasets were used to evaluate deepmp performance?
    Three datasets, K12 ER2925 ( E.coli ), NA12878 (human) and pUC19 (plasmid DNA) were useed to evaluate the performance and benchmark DeepMP. Supplementary Table S1 summarizes all datasets and the number of reads available for each sample.

    DeepMP: a deep learning tool to detect DNA base modifications on

    academic.oup.com
    Can a neural network detect methylation using nanopore sequencing?
    This study proposes a neural network solution, DeepMP, which utilizes both electric currents and basecalling errors from Nanopore sequencing to deliver high accurate methylation detection. We showed that DeepMP outperforms state-of-the-art methods Megalodon, Guppy, DeepSignal and Nanopolish on E.coli, human and pUC19 datasets.

    DeepMP: a deep learning tool to detect DNA base modifications on

    academic.oup.com
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  10. Semantic Scholar
    https://www.semanticscholar.org/paper/DeepMP:-a...

    DeepMP: a deep learning tool to detect DNA base modifications …

  11. Europe PMC
    https://europepmc.org/article/PPR/PPR362481

    DeepMP: a deep learning tool to detect DNA base modifications …

  12. Oxford Academic
    https://academic.oup.com/view-large/394292119

    DeepMP: a deep learning tool to detect DNA base modifications …

  13. e-Repositori UPF
    https://repositori.upf.edu/handle/10230/51909?locale-attribute=en

    DeepMP: a deep learning tool to detect DNA base modifications …

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