[HTML][HTML] DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation

Y Liu, W Rosikiewicz, Z Pan, N Jillette, P Wang… - Genome biology, 2021 - Springer
… DNA methylation from nanopore long-read sequencing data … per-site performance of CpG
methylation prediction across different … We show that the methylation prediction at regions with …

[HTML][HTML] Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing

ZWS Yuen, A Srivastava, R Daniel, D McNevin… - Nature …, 2021 - nature.com
… Although there are multiple tools that enable its detection from Nanopore sequencing, …
methylation from Nanopore sequencing using individual reads, control mixtures of methylated and …

Latest techniques to study DNA methylation

Q Gouil, A Keniry - Essays in biochemistry, 2019 - portlandpress.com
… in detecting base modifications in native DNA and highlight the respective strengths and
weaknesses of PacBio and Nanopore sequencing for this application. Although analysing …

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing

A Tourancheau, EA Mead, XS Zhang, G Fang - Nature methods, 2021 - nature.com
… In this work, we observed that a nanopore sequencing signal displays complex … methylation
events of the same type. To enable nanopore sequencing for broadly applicable methylation

[HTML][HTML] Cancer biomarkers discovery of methylation modification with direct high-throughput nanopore sequencing

J Zhang, S Xie, J Xu, H Liu, S Wan - Frontiers in Genetics, 2021 - frontiersin.org
… advances of nanopore sequencing techniques for detecting methylation modifications and
… The emergence of nanopore sequencing analysis has enabled direct methylation readout …

[HTML][HTML] A signal processing and deep learning framework for methylation detection using Oxford Nanopore sequencing

MU Ahsan, A Gouru, J Chan, W Zhou… - Nature Communications, 2024 - nature.com
Nanopore flowcells and signal data formats. We perform whole-genome Nanopore sequencing
of the NIH3T3 cell line (a widely used mouse reference cell line for methylation studies) …

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

I Lee, R Razaghi, T Gilpatrick, M Molnar, A Gershman… - Nature …, 2020 - nature.com
… , we use nanopore sequencing to evaluate CpG methylation and … We performed nanopore
sequencing of nucleosome … Long-read sequencing makes it possible to robustly assign reads …

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

P Ni, N Huang, Z Zhang, DP Wang, F Liang… - …, 2019 - academic.oup.com
… detect DNA methylation states from Nanopore sequencing reads. Testing on Nanopore reads
… level on detecting 6 mA and 5mC methylation states comparing to previous hidden Markov …

Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays

R Flynn, S Washer, AR Jeffries… - Human Molecular …, 2022 - academic.oup.com
Nanopore sequencing for epidemiology by performing a comparison with DNA methylation
… -Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA …

Robust methylation‐based classification of brain tumours using nanopore sequencing

LP Kuschel, J Hench, S Frank, IB Hench… - Neuropathology and …, 2023 - Wiley Online Library
… In conclusion, nanopore sequencing allows robust and rapid methylation-based classification
across the full spectrum of brain tumours. Platform-specific confidence scores facilitate …