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De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing

https://doi.org/10.1101/094672
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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N6‐methyladenine functions as a potential epigenetic mark in eukaryotes
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DNA Base-Calling from a Nanopore Using a Viterbi Algorithm
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An Adenine Code for DNA: A Second Life for N6-Methyladenine
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Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape
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Recognition sequence of the dam methylase of Escherichia coli K12 and mode of cleavage of Dpn I endonuclease.
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Differentiation of Short, Single-Stranded DNA Homopolymers in Solid-State Nanopores
inferredcites →https://doi.org/10.1038/nbt.2432openalex-snapshot
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/ncomms11307openalex-snapshot
Fast and sensitive mapping of nanopore sequencing reads with GraphMap
inferredcites →https://doi.org/10.1038/ncomms1878openalex-snapshot
Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription
inferredcites →https://doi.org/10.1038/ncomms8438openalex-snapshot
Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes
inferredcites →https://doi.org/10.1038/nmeth.1459openalex-snapshot
Direct detection of DNA methylation during single-molecule, real-time sequencing
inferredcites →https://doi.org/10.1038/nmeth.2798openalex-snapshot
Protein nanopores to detect DNA methylation
inferredcites →https://doi.org/10.1038/nmeth.3290openalex-snapshot
Improved data analysis for the MinION nanopore sequencer
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
inferredcites →https://doi.org/10.1038/nmeth.4184openalex-snapshot
Detecting DNA cytosine methylation using nanopore sequencing
inferredcites →https://doi.org/10.1038/nmeth.4189openalex-snapshot
Mapping DNA methylation with high-throughput nanopore sequencing
inferredcites →https://doi.org/10.1038/nrm4076openalex-snapshot
DNA N6-methyladenine: a new epigenetic mark in eukaryotes?
inferredcites →https://doi.org/10.1073/pnas.1310240110openalex-snapshot
Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
inferredcites →https://doi.org/10.1073/pnas.1310615110openalex-snapshot
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands
inferredcites →https://doi.org/10.1093/ajcp/15.11.552bopenalex-snapshot
Statistical Methods for Research Workers
inferredcites →https://doi.org/10.1093/bioinformatics/btn209openalex-snapshot
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
inferredcites →https://doi.org/10.1093/bioinformatics/btw237openalex-snapshot
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
inferredcites →https://doi.org/10.1093/bioinformatics/btw569openalex-snapshot
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
inferredcites →https://doi.org/10.1093/nar/gkr1146openalex-snapshot
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
inferredcites →https://doi.org/10.1099/mgen.0.000085openalex-snapshot
Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1128/jb.114.3.1143-1150.1973openalex-snapshot
Isolation of Deoxyribonucleic Acid Methylase Mutants of Escherichia coli K-12
inferredcites →https://doi.org/10.1186/1471-2105-9-303openalex-snapshot
A unified approach to false discovery rate estimation
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A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer
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Erratum: A reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore sequencer
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On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other
inferredcites →https://doi.org/10.12688/f1000research.7201.1openalex-snapshot
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1002935openalex-snapshot
Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic
inferredcites →https://doi.org/10.1371/journal.pone.0178751openalex-snapshot
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction
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Single-molecule direct RNA sequencing reveals the shaping of epitranscriptome across multiple species
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Direct high-throughput deconvolution of non-canonical bases via nanopore sequencing and bootstrapped learning
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Nanopore sequencing of intact aminoacylated tRNAs
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Nanopore sequencing at Mars, Europa, and microgravity conditions
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Nanopore- and AI-empowered microbial viability inference
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Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping
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In silico λ-dynamics predicts protein binding specificities to modified RNAs
inferred← citeshttps://doi.org/10.1093/nar/gkaf323openalex-snapshot
ReQuant: improved base modification calling by k-mer value imputation
inferred← citeshttps://doi.org/10.1093/nar/gkaf873openalex-snapshot
WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing
inferred← citeshttps://doi.org/10.1093/nar/gkag023openalex-snapshot
Unlocking the full potential of nanopore sequencing: tips, tricks, and advanced data analysis techniques
inferred← citeshttps://doi.org/10.1093/nargab/lqaa074openalex-snapshot
Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol
inferred← citeshttps://doi.org/10.1093/ve/veae088openalex-snapshot
Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence
inferred← citeshttps://doi.org/10.1098/rsob.230449openalex-snapshot
Effective training of nanopore callers for epigenetic marks with limited labelled data
inferred← citeshttps://doi.org/10.1099/acmi.0.000363openalex-snapshot
Analysis of the long-read sequencing data using computational tools confirms the presence of 5-methylcytosine in the Saccharomyces cerevisiae genome
inferred← citeshttps://doi.org/10.1099/mgen.0.001327openalex-snapshot
Uncovering the transcriptome-wide RNA modifications in Acinetobacter baumannii
inferred← citeshttps://doi.org/10.1101/132274openalex-snapshot
Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore direct RNA sequencing
inferred← citeshttps://doi.org/10.1101/133058openalex-snapshot
BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal
inferred← citeshttps://doi.org/10.1101/165928openalex-snapshot
Fantastic beasts and how to sequence them: genomic approaches for obscure model organisms
inferred← citeshttps://doi.org/10.1101/2019.12.18.880849openalex-snapshot
Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing
inferred← citeshttps://doi.org/10.1101/2019.12.27.885319openalex-snapshot
Nanopore sequencing of native adeno-associated virus (AAV) single-stranded DNA using a transposase-based rapid protocol
inferred← citeshttps://doi.org/10.1101/2020.02.27.967695openalex-snapshot
Short and Long-read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and its Host
inferred← citeshttps://doi.org/10.1101/2020.03.09.982934openalex-snapshot
TagSeqTools: a flexible and comprehensive analysis pipeline for NAD tagSeq data
inferred← citeshttps://doi.org/10.1101/2020.04.13.040246openalex-snapshot
High-frequency phase-switching of modB methylase is associated with phenotypic ceftriaxone susceptibility in Neisseria gonorrhoeae
inferred← citeshttps://doi.org/10.1101/2020.07.18.204362openalex-snapshot
The landscape of SARS-CoV-2 RNA modifications
inferred← citeshttps://doi.org/10.1101/2020.07.25.220855openalex-snapshot
NanoReviser: An Error-correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm
inferred← citeshttps://doi.org/10.1101/2020.09.13.295089openalex-snapshot
nanoDoc: RNA modification detection using Nanopore raw reads with Deep One-Class Classification
inferred← citeshttps://doi.org/10.1101/2020.11.09.374165openalex-snapshot
An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer
inferred← citeshttps://doi.org/10.1101/2021.05.05.442849openalex-snapshot
DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation
inferred← citeshttps://doi.org/10.1101/2021.05.20.444035openalex-snapshot
Whole human genome 5’-mC methylation analysis using long read nanopore sequencing
inferred← citeshttps://doi.org/10.1101/2021.06.14.448286openalex-snapshot
Insights into rRNA processing and modification mapping in Archaea using Nanopore-based RNA sequencing
inferred← citeshttps://doi.org/10.1101/2021.06.15.448494openalex-snapshot
Yanocomp: robust prediction of m 6 A modifications in individual nanopore direct RNA reads
inferred← citeshttps://doi.org/10.1101/2021.06.17.448800openalex-snapshot
Nanopore callers for epigenetics from limited supervised data
inferred← citeshttps://doi.org/10.1101/2021.08.13.456275openalex-snapshot
Using Oxford Nanopore Technology direct RNA sequencing to identify depurination events induced by ricin and other ribosome inactivating proteins
inferred← citeshttps://doi.org/10.1101/2021.11.23.469791openalex-snapshot
Nanopore-based genome-wide DNA methylation sequencing data of Nosema ceranae -inoculated and un-inoculated eastern honeybee workers’ midguts
inferred← citeshttps://doi.org/10.1101/2022.03.14.484124openalex-snapshot
Prediction of m6A and m5C at single-molecule resolution reveals a cooccurrence of RNA modifications across the transcriptome
inferred← citeshttps://doi.org/10.1101/2022.05.29.493267openalex-snapshot
Direct detection of RNA repair by nanopore sequencing
inferred← citeshttps://doi.org/10.1101/2023.03.12.532289openalex-snapshot
Nanopore sequencing for the 17 modification types in 36 locations in E. coli ribosomal RNA enables monitoring of stress-dependent changes
inferred← citeshttps://doi.org/10.1101/2023.03.17.533149openalex-snapshot
PAPET: a collection of performant algorithms to identify 5-methyl cytosine from PacBio SequelII data
inferred← citeshttps://doi.org/10.1101/2023.07.11.548559openalex-snapshot
Spatial reorganization of Escherichia coli chromosome contextualizes triclosan stress-related genetic, epigenetic and transcriptome changes
inferred← citeshttps://doi.org/10.1101/2023.07.13.548926openalex-snapshot
Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection
inferred← citeshttps://doi.org/10.1101/2023.11.13.566931openalex-snapshot
MicrobeMod: A computational toolkit for identifying prokaryotic methylation and restriction-modification with nanopore sequencing
inferred← citeshttps://doi.org/10.1101/2023.11.28.568965openalex-snapshot
Enhanced detection of RNA modifications and mappability with high-accuracy nanopore RNA basecalling models
inferred← citeshttps://doi.org/10.1101/2023.12.19.572431openalex-snapshot
Adapting Nanopore Sequencing Basecalling Models for Modification Detection via Incremental Learning and Anomaly Detection
inferred← citeshttps://doi.org/10.1101/2024.02.27.582347openalex-snapshot
Discovery of a pentose as a cytosine nucleobase modification in Shewanella phage Thanatos-1 genomic DNA mediating enhanced resistance towards host restriction systems
inferred← citeshttps://doi.org/10.1101/2024.06.10.598221openalex-snapshot
Nanopore- and AI-empowered microbial viability inference
inferred← citeshttps://doi.org/10.1101/2024.07.11.603105openalex-snapshot
Nanopore-based native RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between RNA regulatory features
inferred← citeshttps://doi.org/10.1101/2024.09.26.615132openalex-snapshot
A qualitative review of Oxford Nanopore Sequencing datasets for RNA modifications
inferred← citeshttps://doi.org/10.1101/2024.12.02.625113openalex-snapshot
Direct high-throughput deconvolution of unnatural bases via nanopore sequencing and bootstrapped learning
inferred← citeshttps://doi.org/10.1101/2025.06.29.662079openalex-snapshot
NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing
inferred← citeshttps://doi.org/10.1101/2025.07.06.663400openalex-snapshot
RNA structural heterogeneity in a eukaryotic cell influences its heat shock response
inferred← citeshttps://doi.org/10.1101/2025.08.04.668591openalex-snapshot
Accurate detection and quantification of single-base m6A RNA modification using nanopore signals with multi-view deep learning
inferred← citeshttps://doi.org/10.1101/260166openalex-snapshot
Genome-wide epigenetic profiling of 5-hydroxymethylcytosine by long-read optical mapping
inferred← citeshttps://doi.org/10.1101/469338openalex-snapshot
The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that direct genome-wide DNA methylation
inferred← citeshttps://doi.org/10.1101/483693openalex-snapshot
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
inferred← citeshttps://doi.org/10.1101/491456openalex-snapshot
Searching and mapping genomic subsequences in nanopore raw signals through novel dynamic time warping algorithms
inferred← citeshttps://doi.org/10.1101/694919openalex-snapshot
Nanopore base-calling from a perspective of instance segmentation
inferred← citeshttps://doi.org/10.1101/843136openalex-snapshot
RNA modifications detection by comparative Nanopore direct RNA sequencing
inferred← citeshttps://doi.org/10.1101/gr.247064.118openalex-snapshot
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
inferred← citeshttps://doi.org/10.1101/gr.251512.119openalex-snapshot
Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
inferred← citeshttps://doi.org/10.1101/gr.278849.123openalex-snapshot
Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
inferred← citeshttps://doi.org/10.1109/bibm47256.2019.8983231openalex-snapshot
An attention-based neural network basecaller for Oxford Nanopore sequencing data
inferred← citeshttps://doi.org/10.1109/bibm49941.2020.9313290openalex-snapshot
An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer
inferred← citeshttps://doi.org/10.1109/bibm52615.2021.9669841openalex-snapshot
On the application of BERT models for nanopore methylation detection
inferred← citeshttps://doi.org/10.1111/1755-0998.13624openalex-snapshot
An ecologist's guide for studying DNA methylation variation in wild vertebrates
inferred← citeshttps://doi.org/10.1111/mec.16679openalex-snapshot
Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software
inferred← citeshttps://doi.org/10.1126/science.abe4882openalex-snapshot
A widespread pathway for substitution of adenine by diaminopurine in phage genomes
inferred← citeshttps://doi.org/10.1128/aem.01333-25openalex-snapshot
A pentose, as a cytosine nucleobase modification in Shewanella phage Thanatos genomic DNA, mediates enhanced resistance toward host restriction systems
inferred← citeshttps://doi.org/10.1128/jvi.01342-18openalex-snapshot
Going the Distance: Optimizing RNA-Seq Strategies for Transcriptomic Analysis of Complex Viral Genomes
inferred← citeshttps://doi.org/10.1128/mbio.01067-21openalex-snapshot
Methyltransferase-like 3 Modulates Severe Acute Respiratory Syndrome Coronavirus-2 RNA N6-Methyladenosine Modification and Replication
inferred← citeshttps://doi.org/10.1128/mbio.01289-23openalex-snapshot
Differential adenine methylation analysis reveals increased variability in 6mA in the absence of methyl-directed mismatch repair
inferred← citeshttps://doi.org/10.1128/mbio.03702-21openalex-snapshot
Nanopore-Based Detection of Viral RNA Modifications
inferred← citeshttps://doi.org/10.1128/msphere.00464-23openalex-snapshot
Distinct epigenetic signatures of classical and hypervirulent Klebsiella pneumoniae
inferred← citeshttps://doi.org/10.1128/msystems.01163-23openalex-snapshot
Utilization of nanopore direct RNA sequencing to analyze viral RNA modifications
inferred← citeshttps://doi.org/10.1128/msystems.01193-22openalex-snapshot
Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
inferred← citeshttps://doi.org/10.1128/spectrum.02624-22openalex-snapshot
Identification and Mechanism of Action of the Global Secondary Metabolism Regulator SaraC in Stereum hirsutum
inferred← citeshttps://doi.org/10.1134/s0006350920060056openalex-snapshot
The Efficiency of 5-Methylcytosine Identification in DNA of Escherichia coli Cells that Carry Bacterial DNA Methyltransferase Genes Using an Oxford Nanopore Device
inferred← citeshttps://doi.org/10.1145/3466752.3480117openalex-snapshot
SquiggleFilter: An Accelerator for Portable Virus Detection
inferred← citeshttps://doi.org/10.1186/s12859-019-2860-zopenalex-snapshot
NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
inferred← citeshttps://doi.org/10.1186/s12859-020-03856-0openalex-snapshot
High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing
inferred← citeshttps://doi.org/10.1186/s12859-020-3459-0openalex-snapshot
Nanopore basecalling from a perspective of instance segmentation
inferred← citeshttps://doi.org/10.1186/s12859-023-05193-4openalex-snapshot
nPoRe: n-polymer realigner for improved pileup-based variant calling
inferred← citeshttps://doi.org/10.1186/s12864-018-5372-8openalex-snapshot
NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data
inferred← citeshttps://doi.org/10.1186/s12864-020-07033-8openalex-snapshot
Accurate prediction of DNA N4-methylcytosine sites via boost-learning various types of sequence features
inferred← citeshttps://doi.org/10.1186/s12864-021-07535-zopenalex-snapshot
Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T
inferred← citeshttps://doi.org/10.1186/s12864-021-07736-6openalex-snapshot
DNAscent v2: detecting replication forks in nanopore sequencing data with deep learning
inferred← citeshttps://doi.org/10.1186/s12864-023-09331-3openalex-snapshot
Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species
inferred← citeshttps://doi.org/10.1186/s12864-023-09783-7openalex-snapshot
DNA methylation on C5-Cytosine and N6-Adenine in the Bursaphelenchus xylophilus genome
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