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RNA modifications detection by comparative Nanopore direct RNA sequencing
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/0471142727.mb0425s112openalex-snapshot
Transcriptome‐Wide Identification of Pseudouridine Modifications Using Pseudo‐seq
inferredcites →https://doi.org/10.1016/j.cell.2012.05.003openalex-snapshot
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
inferredcites →https://doi.org/10.1016/j.cell.2017.05.045openalex-snapshot
Dynamic RNA Modifications in Gene Expression Regulation
inferredcites →https://doi.org/10.1016/j.chembiol.2013.10.015openalex-snapshot
Posttranscriptional RNA Modifications: Playing Metabolic Games in a Cell’s Chemical Legoland
inferredcites →https://doi.org/10.1016/j.molcel.2019.01.033openalex-snapshot
P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress
inferredcites →https://doi.org/10.1016/j.spl.2004.11.028openalex-snapshot
A simple approximation for the distribution of the weighted combination of non-independent or independent probabilities
inferredcites →https://doi.org/10.1016/j.stem.2017.11.016openalex-snapshot
METTL14 Inhibits Hematopoietic Stem/Progenitor Differentiation and Promotes Leukemogenesis via mRNA m6A Modification
inferredcites →https://doi.org/10.1038/nature11112openalex-snapshot
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
inferredcites →https://doi.org/10.1038/nature24678openalex-snapshot
Promoter-bound METTL3 maintains myeloid leukaemia by m6A-dependent translation control
inferredcites →https://doi.org/10.1038/nmeth.1267openalex-snapshot
Detecting microRNA binding and siRNA off-target effects from expression data
inferredcites →https://doi.org/10.1038/nmeth.3453openalex-snapshot
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
inferredcites →https://doi.org/10.1038/nmeth.4110openalex-snapshot
Epitranscriptome sequencing technologies: decoding RNA modifications
inferredcites →https://doi.org/10.1038/nmeth.4184openalex-snapshot
Detecting DNA cytosine methylation using nanopore sequencing
inferredcites →https://doi.org/10.1038/nmeth.4577openalex-snapshot
Highly parallel direct RNA sequencing on an array of nanopores
inferredcites →https://doi.org/10.1038/nrg.2016.169openalex-snapshot
Detecting RNA modifications in the epitranscriptome: predict and validate
inferredcites →https://doi.org/10.1038/s41467-019-10168-2openalex-snapshot
Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data
inferredcites →https://doi.org/10.1038/s41467-019-11713-9openalex-snapshot
Accurate detection of m6A RNA modifications in native RNA sequences
inferredcites →https://doi.org/10.1038/s41556-019-0319-0openalex-snapshot
RNA modifications regulating cell fate in cancer
inferredcites →https://doi.org/10.1038/s41589-019-0327-1openalex-snapshot
Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates
inferredcites →https://doi.org/10.1038/s41592-019-0617-2openalex-snapshot
Nanopore native RNA sequencing of a human poly(A) transcriptome
inferredcites →https://doi.org/10.1038/sj.onc.1205599openalex-snapshot
Gene silencing in mammalian cells and the spread of DNA methylation
inferredcites →https://doi.org/10.1039/c5an01797aopenalex-snapshot
Mass spectrometry of modified RNAs: recent developments
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq247openalex-snapshot
Repitools: an R package for the analysis of enrichment-based epigenomic data
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btx364openalex-snapshot
UpSetR: an R package for the visualization of intersecting sets and their properties
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/nar/gkq660openalex-snapshot
HEXIM1 targets a repeated GAUC motif in the riboregulator of transcription 7SK and promotes base pair rearrangements
inferredcites →https://doi.org/10.1093/nar/gkv1191openalex-snapshot
csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows
inferredcites →https://doi.org/10.1093/nar/gkx1030openalex-snapshot
MODOMICS: a database of RNA modification pathways. 2017 update
inferredcites →https://doi.org/10.1101/094672openalex-snapshot
De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1126/sciadv.aax0250openalex-snapshot
Single-base mapping of m 6 A by an antibody-independent method
inferredcites →https://doi.org/10.1126/science.aad8711openalex-snapshot
Messenger RNA modifications: Form, distribution, and function
inferredcites →https://doi.org/10.1158/2159-8290.cd-16-1292openalex-snapshot
The Epitranscriptome of Noncoding RNAs in Cancer
inferredcites →https://doi.org/10.1186/1471-2105-12-3openalex-snapshot
R2R - software to speed the depiction of aesthetic consensus RNA secondary structures
inferredcites →https://doi.org/10.1186/gb-2012-13-10-175openalex-snapshot
The birth of the Epitranscriptome: deciphering the function of RNA modifications
inferredcites →https://doi.org/10.1261/rna.072785.119openalex-snapshot
Direct RNA sequencing enables m 6 A detection in endogenous transcript isoforms at base-specific resolution
inferredcites →https://doi.org/10.12688/wellcomeopenres.14663.1openalex-snapshot
‘Read–through marking’ reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP
inferredcites →https://doi.org/10.1371/journal.pone.0216709openalex-snapshot
Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing
inferredcites →https://doi.org/10.15252/embr.201642682openalex-snapshot
Pseudouridylation of 7SK snRNA promotes 7SK snRNP formation to suppress HIV‐1 transcription and escape from latency
inferredcites →https://doi.org/10.21105/joss.01228openalex-snapshot
Bedparse: feature extraction from BED files
inferredcites →https://doi.org/10.21105/joss.01236openalex-snapshot
pycoQC, interactive quality control for Oxford Nanopore Sequencing
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/cpmc.99openalex-snapshot
Using Direct RNA Nanopore Sequencing to Deconvolute Viral Transcriptomes
inferred← citeshttps://doi.org/10.1002/eji.202250226openalex-snapshot
Prmt5 deficient mouse B cells display RNA processing complexity and slower colorectal tumor progression
inferred← citeshttps://doi.org/10.1002/mas.21798openalex-snapshot
Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic code
inferred← citeshttps://doi.org/10.1002/yea.3925openalex-snapshot
Budding yeast as an ideal model for elucidating the role of N 6 ‐methyladenosine in regulating gene expression
inferred← citeshttps://doi.org/10.1007/978-3-030-71612-7_8openalex-snapshot
Regulation of RNA Stability Through RNA Modification
inferred← citeshttps://doi.org/10.1007/978-3-030-71612-7_9openalex-snapshot
Deciphering RNA Methylation in Cancer
inferred← citeshttps://doi.org/10.1007/s12185-023-03576-0openalex-snapshot
RNA modifications in hematological malignancies
inferred← citeshttps://doi.org/10.1016/j.crmeth.2021.100081openalex-snapshot
Global approaches for profiling transcription initiation
inferred← citeshttps://doi.org/10.1016/j.csbj.2022.10.023openalex-snapshot
Detecting RNA modification using direct RNA sequencing: A systematic review
inferred← citeshttps://doi.org/10.1016/j.isci.2022.104861openalex-snapshot
Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition
inferred← citeshttps://doi.org/10.1016/j.tibtech.2020.06.002openalex-snapshot
New Twists in Detecting mRNA Modification Dynamics
inferred← citeshttps://doi.org/10.1016/j.tig.2021.09.001openalex-snapshot
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data
inferred← citeshttps://doi.org/10.1016/j.xgen.2022.100097openalex-snapshot
Direct detection of RNA modifications and structure using single-molecule nanopore sequencing
inferred← citeshttps://doi.org/10.1016/j.xinn.2021.100153openalex-snapshot
Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era
inferred← citeshttps://doi.org/10.1021/acscentsci.0c01094openalex-snapshot
meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation
inferred← citeshttps://doi.org/10.1021/acscentsci.1c00788openalex-snapshot
Nanopore Dwell Time Analysis Permits Sequencing and Conformational Assignment of Pseudouridine in SARS-CoV-2
inferred← citeshttps://doi.org/10.1038/s12276-022-00821-0openalex-snapshot
Detection technologies for RNA modifications
inferred← citeshttps://doi.org/10.1038/s41467-020-19787-6openalex-snapshot
Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing
inferred← citeshttps://doi.org/10.1038/s41467-020-20340-8openalex-snapshot
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
inferred← citeshttps://doi.org/10.1038/s41467-021-26929-xopenalex-snapshot
Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
inferred← citeshttps://doi.org/10.1038/s41467-024-48437-4openalex-snapshot
Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing
inferred← citeshttps://doi.org/10.1038/s41467-024-51639-5openalex-snapshot
Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection
inferred← citeshttps://doi.org/10.1038/s41467-024-54368-xopenalex-snapshot
Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites
inferred← citeshttps://doi.org/10.1038/s41557-023-01322-xopenalex-snapshot
Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics
inferred← citeshttps://doi.org/10.1038/s41564-024-01638-5openalex-snapshot
Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As
inferred← citeshttps://doi.org/10.1038/s41568-022-00541-7openalex-snapshot
RNA splicing dysregulation and the hallmarks of cancer
inferred← citeshttps://doi.org/10.1038/s41569-022-00804-8openalex-snapshot
RNA modifications in cardiovascular health and disease
inferred← citeshttps://doi.org/10.1038/s41576-020-0236-xopenalex-snapshot
Long-read human genome sequencing and its applications
inferred← citeshttps://doi.org/10.1038/s41576-023-00645-2openalex-snapshot
RNA modifications in physiology and disease: towards clinical applications
inferred← citeshttps://doi.org/10.1038/s41587-021-00915-6openalex-snapshot
Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing
inferred← citeshttps://doi.org/10.1038/s41587-021-00936-1openalex-snapshot
The RNA Atlas expands the catalog of human non-coding RNAs
inferred← citeshttps://doi.org/10.1038/s41587-021-00949-wopenalex-snapshot
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore
inferred← citeshttps://doi.org/10.1038/s41587-021-01108-xopenalex-snapshot
Nanopore sequencing technology, bioinformatics and applications
inferred← citeshttps://doi.org/10.1038/s41587-022-01580-zopenalex-snapshot
Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design
inferred← citeshttps://doi.org/10.1038/s41587-024-02135-0openalex-snapshot
Simultaneous nanopore profiling of mRNA m6A and pseudouridine reveals translation coordination
inferred← citeshttps://doi.org/10.1038/s41592-022-01513-3openalex-snapshot
Direct identification of A-to-I editing sites with nanopore native RNA sequencing
inferred← citeshttps://doi.org/10.1038/s41592-022-01666-1openalex-snapshot
Detection of m6A from direct RNA sequencing using a multiple instance learning framework
inferred← citeshttps://doi.org/10.1038/s42255-023-00764-4openalex-snapshot
Epitranscriptomics in metabolic disease
inferred← citeshttps://doi.org/10.1042/bst20190492openalex-snapshot
Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies
inferred← citeshttps://doi.org/10.1080/15476286.2021.1978215openalex-snapshot
Computational methods for RNA modification detection from nanopore direct RNA sequencing data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab539openalex-snapshot
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data
inferred← citeshttps://doi.org/10.1097/moh.0000000000000636openalex-snapshot
The N6-methyladenosine RNA modification in acute myeloid leukemia
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/10.1101/2020.07.18.204362openalex-snapshot
The landscape of SARS-CoV-2 RNA modifications
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
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Yanocomp: robust prediction of m 6 A modifications in individual nanopore direct RNA reads
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/10.1101/2023.03.17.533105openalex-snapshot
Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples
inferred← citeshttps://doi.org/10.1101/2025.04.25.650674openalex-snapshot
Genomic in vitro transcription and Nanopore direct RNA sequencing of a human B-Lymphocyte cell line
inferred← citeshttps://doi.org/10.1101/864322openalex-snapshot
Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning
inferred← citeshttps://doi.org/10.1101/gr.278960.124openalex-snapshot
Detecting m6A RNA modification from nanopore sequencing using a semisupervised learning framework
inferred← citeshttps://doi.org/10.1128/mbio.02131-20openalex-snapshot
It’s the Little Things (in Viral RNA)
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NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs
inferred← citeshttps://doi.org/10.1261/rna.078898.121openalex-snapshot
Synthesis of modified nucleotide polymers by the poly(U) polymerase Cid1: application to direct RNA sequencing on nanopores
inferred← citeshttps://doi.org/10.18388/pb.2020_362openalex-snapshot
Zgłębiając zawiłości struktur, funkcji i lekowalności cis motywów RNA u koronawirusów
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Harnessing Genetic Code: Futuristic Approach of Next-Generation Sequencing for Sustainable Future
inferred← citeshttps://doi.org/10.32657/10356/164272openalex-snapshot
DNA/RNA structure and processing in vitro and in cells: from probing to prediction
inferred← citeshttps://doi.org/10.33540/480openalex-snapshot
Leveraging technological opportunities in cancer genomics
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MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets
inferred← citeshttps://doi.org/10.3389/fgene.2020.00394openalex-snapshot
Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts
inferred← citeshttps://doi.org/10.3389/fgene.2020.00398openalex-snapshot
How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets
inferred← citeshttps://doi.org/10.3389/fgene.2021.672804openalex-snapshot
Cancer Biomarkers Discovery of Methylation Modification With Direct High-Throughput Nanopore Sequencing
inferred← citeshttps://doi.org/10.3390/biology10111131openalex-snapshot
Oxford Nanopore MinION Direct RNA-Seq for Systems Biology
inferred← citeshttps://doi.org/10.3390/genes11121478openalex-snapshot
The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock
inferred← citeshttps://doi.org/10.3390/toxins14070470openalex-snapshot
RIPpore: A Novel Host-Derived Method for the Identification of Ricin Intoxication through Oxford Nanopore Direct RNA Sequencing
inferred← citeshttps://doi.org/10.4103/1673-5374.385858openalex-snapshot
Dysregulation of RNA modification systems in clinical populations with neurocognitive disorders
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Improving SWATH-MS data analysis using multi-omics approach
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Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling
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