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Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics
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Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/cbic.201500013openalex-snapshot
Formation and Abundance of 5‐Hydroxymethylcytosine in RNA
inferredcites →https://doi.org/10.1002/hep.29683openalex-snapshot
RNA N6‐methyladenosine methyltransferase‐like 3 promotes liver cancer progression through YTHDF2‐dependent posttranscriptional silencing of SOCS2
inferredcites →https://doi.org/10.1002/wrna.1319openalex-snapshot
To edit or not to edit: regulation of ADAR editing specificity and efficiency
inferredcites →https://doi.org/10.1002/wrna.1586openalex-snapshot
A molecular‐level perspective on the frequency, distribution, and consequences of messenger RNA modifications
inferredcites →https://doi.org/10.1002/wrna.1595openalex-snapshot
Naturally occurring modified ribonucleosides
inferredcites →https://doi.org/10.1007/978-1-4939-6807-7_11openalex-snapshot
Statistical Methods for Transcriptome-Wide Analysis of RNA Methylation by Bisulfite Sequencing
inferredcites →https://doi.org/10.1007/978-3-030-33607-3_32openalex-snapshot
CNNPSP: Pseudouridine Sites Prediction Based on Deep Learning
inferredcites →https://doi.org/10.1007/s00438-016-1243-7openalex-snapshot
Identifying N 6-methyladenosine sites in the Arabidopsis thaliana transcriptome
inferredcites →https://doi.org/10.1007/s00438-019-01600-9openalex-snapshot
XG-PseU: an eXtreme Gradient Boosting based method for identifying pseudouridine sites
inferredcites →https://doi.org/10.1007/s11011-014-9486-7openalex-snapshot
The fat mass and obesity-associated FTO rs9939609 polymorphism is associated with elevated homocysteine levels in patients with multiple sclerosis screened for vascular risk factors
inferredcites →https://doi.org/10.1007/s11103-018-0698-9openalex-snapshot
RFAthM6A: a new tool for predicting m6A sites in Arabidopsis thaliana
inferredcites →https://doi.org/10.1007/s11704-018-8094-9openalex-snapshot
iRNA-PseTNC: identification of RNA 5-methylcytosine sites using hybrid vector space of pseudo nucleotide composition
inferredcites →https://doi.org/10.1007/s40484-018-0149-2openalex-snapshot
A Bayesian hierarchical model for analyzing methylated RNA immunoprecipitation sequencing data
inferredcites →https://doi.org/10.1016/0092-8674(82)90206-9openalex-snapshot
Gene evolution in the chicken β-globin cluster
inferredcites →https://doi.org/10.1016/j.ab.2015.08.021openalex-snapshot
iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition
inferredcites →https://doi.org/10.1016/j.ab.2015.12.017openalex-snapshot
pRNAm-PC: Predicting N6-methyladenosine sites in RNA sequences via physical–chemical properties
inferredcites →https://doi.org/10.1016/j.ab.2016.01.014openalex-snapshot
DRME: Count-based differential RNA methylation analysis at small sample size scenario
inferredcites →https://doi.org/10.1016/j.ab.2016.06.012openalex-snapshot
RNA-MethylPred: A high-accuracy predictor to identify N6-methyladenosine in RNA
inferredcites →https://doi.org/10.1016/j.ab.2018.03.027openalex-snapshot
Accurate RNA 5-methylcytosine site prediction based on heuristic physical-chemical properties reduction and classifier ensemble
inferredcites →https://doi.org/10.1016/j.ab.2018.09.002openalex-snapshot
iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition
inferredcites →https://doi.org/10.1016/j.ab.2019.01.002openalex-snapshot
EPAI-NC: Enhanced prediction of adenosine to inosine RNA editing sites using nucleotide compositions
inferredcites →https://doi.org/10.1016/j.brainres.2013.12.011openalex-snapshot
The molecular link between inefficient GluA2 Q/R site-RNA editing and TDP-43 pathology in motor neurons of sporadic amyotrophic lateral sclerosis patients
inferredcites →https://doi.org/10.1016/j.canlet.2020.01.021openalex-snapshot
Writers, readers and erasers of RNA modifications in cancer
inferredcites →https://doi.org/10.1016/j.ccell.2015.08.013openalex-snapshot
The Genomic Landscape and Clinical Relevance of A-to-I RNA Editing in Human Cancers
inferredcites →https://doi.org/10.1016/j.ccell.2016.11.017openalex-snapshot
FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N 6 -Methyladenosine RNA Demethylase
inferredcites →https://doi.org/10.1016/j.ccell.2017.02.013openalex-snapshot
m 6 A Demethylase ALKBH5 Maintains Tumorigenicity of Glioblastoma Stem-like Cells by Sustaining FOXM1 Expression and Cell Proliferation Program
inferredcites →https://doi.org/10.1016/j.ccell.2018.03.026openalex-snapshot
A-to-I RNA Editing Contributes to Proteomic Diversity in Cancer
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.2013.03.024openalex-snapshot
ADAR1 Forms a Complex with Dicer to Promote MicroRNA Processing and RNA-Induced Gene Silencing
inferredcites →https://doi.org/10.1016/j.cell.2013.10.026openalex-snapshot
RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock
inferredcites →https://doi.org/10.1016/j.cell.2013.10.047openalex-snapshot
High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis
inferredcites →https://doi.org/10.1016/j.cell.2014.08.028openalex-snapshot
Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA
inferredcites →https://doi.org/10.1016/j.cell.2015.05.014openalex-snapshot
N6-methyladenosine Modulates Messenger RNA Translation Efficiency
inferredcites →https://doi.org/10.1016/j.cell.2015.08.011openalex-snapshot
HNRNPA2B1 Is a Mediator of m6A-Dependent Nuclear RNA Processing Events
inferredcites →https://doi.org/10.1016/j.cell.2015.10.012openalex-snapshot
5′ UTR m6A Promotes Cap-Independent Translation
inferredcites →https://doi.org/10.1016/j.cell.2016.09.038openalex-snapshot
ALKBH1-Mediated tRNA Demethylation Regulates Translation
inferredcites →https://doi.org/10.1016/j.cell.2017.05.003openalex-snapshot
The U6 snRNA m 6 A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
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.cell.2017.09.003openalex-snapshot
Temporal Control of Mammalian Cortical Neurogenesis by m6A Methylation
inferredcites →https://doi.org/10.1016/j.cell.2017.11.031openalex-snapshot
R-2HG Exhibits Anti-tumor Activity by Targeting FTO/m6A/MYC/CEBPA Signaling
inferredcites →https://doi.org/10.1016/j.cell.2018.03.008openalex-snapshot
Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2018.11.037openalex-snapshot
N4-acetylation of Cytidine in mRNA by NAT10 Regulates Stability and Translation
inferredcites →https://doi.org/10.1016/j.celrep.2014.05.048openalex-snapshot
Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites
inferredcites →https://doi.org/10.1016/j.chemolab.2019.103811openalex-snapshot
iN6-Methyl (5-step): Identifying RNA N6-methyladenosine sites using deep learning mode via Chou's 5-step rules and Chou's general PseKNC
inferredcites →https://doi.org/10.1016/j.chom.2019.07.005openalex-snapshot
Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression
inferredcites →https://doi.org/10.1016/j.cmet.2012.11.004openalex-snapshot
Circadian Oscillations of Protein-Coding and Regulatory RNAs in a Highly Dynamic Mammalian Liver Epigenome
inferredcites →https://doi.org/10.1016/j.compbiolchem.2016.09.003openalex-snapshot
BS-RNA: An efficient mapping and annotation tool for RNA bisulfite sequencing data
inferredcites →https://doi.org/10.1016/j.csbj.2020.04.015openalex-snapshot
Computational identification of N6-methyladenosine sites in multiple tissues of mammals
inferredcites →https://doi.org/10.1016/j.devcel.2020.03.009openalex-snapshot
OsNSUN2-Mediated 5-Methylcytosine mRNA Modification Enhances Rice Adaptation to High Temperature
inferredcites →https://doi.org/10.1016/j.gpb.2013.01.002openalex-snapshot
MeRIP-PF: An Easy-to-Use Pipeline for High-Resolution Peak-Finding in MeRIP-Seq Data
inferredcites →https://doi.org/10.1016/j.jaut.2019.102329openalex-snapshot
Increased adenosine-to-inosine RNA editing in rheumatoid arthritis
inferredcites →https://doi.org/10.1016/j.jtbi.2018.04.037openalex-snapshot
Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou's PseKNC
inferredcites →https://doi.org/10.1016/j.jtbi.2018.07.018openalex-snapshot
iMethyl-STTNC: Identification of N6-methyladenosine sites by extending the idea of SAAC into Chou's PseAAC to formulate RNA sequences
inferredcites →https://doi.org/10.1016/j.jtbi.2018.12.034openalex-snapshot
iRNA-PseKNC(2methyl): Identify RNA 2'-O-methylation sites by convolution neural network and Chou's pseudo components
inferredcites →https://doi.org/10.1016/j.jtbi.2019.01.035openalex-snapshot
Identifying N6-methyladenosine sites using extreme gradient boosting system optimized by particle swarm optimizer
inferredcites →https://doi.org/10.1016/j.molcel.2012.10.015openalex-snapshot
ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility
inferredcites →https://doi.org/10.1016/j.molcel.2016.01.012openalex-snapshot
Nuclear m6A Reader YTHDC1 Regulates mRNA Splicing
inferredcites →https://doi.org/10.1016/j.molcel.2016.03.021openalex-snapshot
The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells
inferredcites →https://doi.org/10.1016/j.molcel.2019.06.033openalex-snapshot
RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay
inferredcites →https://doi.org/10.1016/j.molmed.2015.07.001openalex-snapshot
RNA rewriting, recoding, and rewiring in human disease
inferredcites →https://doi.org/10.1016/j.neucom.2018.04.082openalex-snapshot
Integration of deep feature representations and handcrafted features to improve the prediction of N6-methyladenosine sites
inferredcites →https://doi.org/10.1016/j.omtn.2017.03.006openalex-snapshot
iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC
inferredcites →https://doi.org/10.1016/j.omtn.2018.03.012openalex-snapshot
iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites
inferredcites →https://doi.org/10.1016/j.omtn.2018.07.004openalex-snapshot
M6APred-EL: A Sequence-Based Predictor for Identifying N6-methyladenosine Sites Using Ensemble Learning
inferredcites →https://doi.org/10.1016/j.omtn.2019.03.010openalex-snapshot
iPseU-CNN: Identifying RNA Pseudouridine Sites Using Convolutional Neural Networks
inferredcites →https://doi.org/10.1016/j.omtn.2019.08.022openalex-snapshot
iRNA-m7G: Identifying N7-methylguanosine Sites by Fusing Multiple Features
inferredcites →https://doi.org/10.1016/j.omtn.2019.08.023openalex-snapshot
iRNA-m2G: Identifying N2-methylguanosine Sites Based on Sequence-Derived Information
inferredcites →https://doi.org/10.1016/j.omtn.2019.10.001openalex-snapshot
A Linear Regression Predictor for Identifying N6-Methyladenosine Sites Using Frequent Gapped K-mer Pattern
inferredcites →https://doi.org/10.1016/j.omtn.2019.10.008openalex-snapshot
RNAm5CPred: Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition
inferredcites →https://doi.org/10.1016/j.ygeno.2016.05.003openalex-snapshot
Identifying 2′-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions
inferredcites →https://doi.org/10.1016/j.ygeno.2019.10.017openalex-snapshot
Advances in methods and software for RNA cytosine methylation analysis
inferredcites →https://doi.org/10.1016/j.ymeth.2014.06.008openalex-snapshot
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package
inferredcites →https://doi.org/10.1016/j.ymeth.2018.10.019openalex-snapshot
RNA modifications in structure prediction – Status quo and future challenges
inferredcites →https://doi.org/10.1038/cr.2017.55openalex-snapshot
5-methylcytosine promotes mRNA export — NSUN2 as the methyltransferase and ALYREF as an m5C reader
inferredcites →https://doi.org/10.1038/leu.2014.16openalex-snapshot
WTAP is a novel oncogenic protein in acute myeloid leukemia
inferredcites →https://doi.org/10.1038/mtna.2016.37openalex-snapshot
iRNA-PseU: Identifying RNA pseudouridine sites
inferredcites →https://doi.org/10.1038/nature09489openalex-snapshot
2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members
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/nature12730openalex-snapshot
N6-methyladenosine-dependent regulation of messenger RNA stability
inferredcites →https://doi.org/10.1038/nature13802openalex-snapshot
Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells
inferredcites →https://doi.org/10.1038/nature14234openalex-snapshot
N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions
inferredcites →https://doi.org/10.1038/nature14281openalex-snapshot
N6-methyladenosine marks primary microRNAs for processing
inferredcites →https://doi.org/10.1038/nature15377openalex-snapshot
Dynamic m6A mRNA methylation directs translational control of heat shock response
inferredcites →https://doi.org/10.1038/nature16998openalex-snapshot
The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
inferredcites →https://doi.org/10.1038/nature18282openalex-snapshot
Stem cell function and stress response are controlled by protein synthesis
inferredcites →https://doi.org/10.1038/nature19342openalex-snapshot
m6A RNA methylation promotes XIST-mediated transcriptional repression
inferredcites →https://doi.org/10.1038/nature21022openalex-snapshot
Reversible methylation of m6Am in the 5′ cap controls mRNA stability
inferredcites →https://doi.org/10.1038/nature21355openalex-snapshot
m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition
inferredcites →https://doi.org/10.1038/nature21671openalex-snapshot
RNA m6A methylation regulates the ultraviolet-induced DNA damage response
inferredcites →https://doi.org/10.1038/nature23450openalex-snapshot
m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways
inferredcites →https://doi.org/10.1038/nature23883openalex-snapshot
m6A modulates haematopoietic stem and progenitor cell specification
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/nature25784openalex-snapshot
The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency
inferredcites →https://doi.org/10.1038/nbt.3682openalex-snapshot
Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation
inferredcites →https://doi.org/10.1038/nbt996openalex-snapshot
Systematic identification of abundant A-to-I editing sites in the human transcriptome
inferredcites →https://doi.org/10.1038/ncb3110openalex-snapshot
Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis
inferredcites →https://doi.org/10.1038/nchembio.482openalex-snapshot
Grand Challenge Commentary: RNA epigenetics?
inferredcites →https://doi.org/10.1038/nchembio.687openalex-snapshot
N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO
inferredcites →https://doi.org/10.1038/ncomms16027openalex-snapshot
Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells
inferredcites →https://doi.org/10.1038/ng2048openalex-snapshot
Variation in FTO contributes to childhood obesity and severe adult obesity
inferredcites →https://doi.org/10.1038/nm.4416openalex-snapshot
The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot
HISAT: a fast spliced aligner with low memory requirements
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/nprot.2012.148openalex-snapshot
Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing
inferredcites →https://doi.org/10.1038/nsmb.2357openalex-snapshot
RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis
inferredcites →https://doi.org/10.1038/nsmb.2911openalex-snapshot
An expanding universe of mRNA modifications
inferredcites →https://doi.org/10.1038/s41388-020-1248-xopenalex-snapshot
ADAR1-mediated RNA editing is a novel oncogenic process in thyroid cancer and regulates miR-200 activity
inferredcites →https://doi.org/10.1038/s41422-018-0117-4openalex-snapshot
Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase
inferredcites →https://doi.org/10.1038/s41556-019-0319-0openalex-snapshot
RNA modifications regulating cell fate in cancer
inferredcites →https://doi.org/10.1038/s41556-019-0361-yopenalex-snapshot
5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs
inferredcites →https://doi.org/10.1038/s41580-019-0168-5openalex-snapshot
Reading, writing and erasing mRNA methylation
inferredcites →https://doi.org/10.1038/s41586-018-0538-8openalex-snapshot
mRNA circularization by METTL3–eIF3h enhances translation and promotes oncogenesis
inferredcites →https://doi.org/10.1038/s41586-018-0666-1openalex-snapshot
m6A facilitates hippocampus-dependent learning and memory through YTHDF1
inferredcites →https://doi.org/10.1038/s41586-018-0841-4openalex-snapshot
FTSJ3 is an RNA 2′-O-methyltransferase recruited by HIV to avoid innate immune sensing
inferredcites →https://doi.org/10.1038/s41586-019-0916-xopenalex-snapshot
Anti-tumour immunity controlled through mRNA m6A methylation and YTHDF1 in dendritic cells
inferredcites →https://doi.org/10.1038/s41586-019-1016-7openalex-snapshot
Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally
inferredcites →https://doi.org/10.1038/s41594-019-0218-xopenalex-snapshot
Genome-wide identification of mRNA 5-methylcytosine in mammals
inferredcites →https://doi.org/10.1038/s41598-018-35502-4openalex-snapshot
RNAm5Cfinder: A Web-server for Predicting RNA 5-methylcytosine (m5C) Sites Based on Random Forest
inferredcites →https://doi.org/10.1038/s41598-019-47594-7openalex-snapshot
PACES: prediction of N4-acetylcytidine (ac4C) modification sites in mRNA
inferredcites →https://doi.org/10.1038/s41698-019-0085-2openalex-snapshot
RNAMethyPro: a biologically conserved signature of N6-methyladenosine regulators for predicting survival at pan-cancer level
inferredcites →https://doi.org/10.1038/srep13859openalex-snapshot
Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome
inferredcites →https://doi.org/10.1038/srep24345openalex-snapshot
Increased N6-methyladenosine in Human Sperm RNA as a Risk Factor for Asthenozoospermia
inferredcites →https://doi.org/10.1038/srep31080openalex-snapshot
RAMPred: identifying the N1-methyladenosine sites in eukaryotic transcriptomes
inferredcites →https://doi.org/10.1038/srep35123openalex-snapshot
PAI: Predicting adenosine to inosine editing sites by using pseudo nucleotide compositions
inferredcites →https://doi.org/10.1038/srep40242openalex-snapshot
Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines
inferredcites →https://doi.org/10.1038/srep46757openalex-snapshot
Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine
inferredcites →https://doi.org/10.1039/c4mb00604fopenalex-snapshot
Decomposition of RNA methylome reveals co-methylation patterns induced by latent enzymatic regulators of the epitranscriptome
inferredcites →https://doi.org/10.1039/c6mb00471gopenalex-snapshot
Identifying RNA 5-methylcytosine sites via pseudo nucleotide compositions
inferredcites →https://doi.org/10.1039/c6mb00536eopenalex-snapshot
AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.1602883113openalex-snapshot
Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m 6 A-demethylation of NANOG mRNA
inferredcites →https://doi.org/10.1073/pnas.1820574116openalex-snapshot
Structural insights into FTO’s catalytic mechanism for the demethylation of multiple RNA substrates
inferredcites →https://doi.org/10.1073/pnas.1910862117openalex-snapshot
Drosophila YBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5-methylcytosine RNAs
inferredcites →https://doi.org/10.1074/jbc.tm118.004166openalex-snapshot
Adenosine deaminase acting on RNA (ADAR1), a suppressor of double-stranded RNA–triggered innate immune responses
inferredcites →https://doi.org/10.1080/07391102.2016.1157761openalex-snapshot
MethyRNA: a web server for identification of N6-methyladenosine sites
inferredcites →https://doi.org/10.1089/cmb.2018.0004openalex-snapshot
iRNA-2OM: A Sequence-Based Predictor for Identifying 2′-O-Methylation Sites in Homo sapiens
inferredcites →https://doi.org/10.1093/bib/bbx068openalex-snapshot
OPATs: OmnibusP-value association tests
inferredcites →https://doi.org/10.1093/bib/bbz112openalex-snapshot
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btaa178openalex-snapshot
m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human
inferredcites →https://doi.org/10.1093/bioinformatics/btt171openalex-snapshot
Exome-based analysis for RNA epigenome sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv366openalex-snapshot
PPUS: a web server to predict PUS-specific pseudouridine sites
inferredcites →https://doi.org/10.1093/bioinformatics/btv647openalex-snapshot
meRanTK: methylated RNA analysis ToolKit
inferredcites →https://doi.org/10.1093/bioinformatics/btw281openalex-snapshot
A novel algorithm for calling mRNA m 6 A peaks by modeling biological variances in MeRIP-seq data
inferredcites →https://doi.org/10.1093/bioinformatics/btx002openalex-snapshot
MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites
inferredcites →https://doi.org/10.1093/bioinformatics/btz358openalex-snapshot
iRNAD: a computational tool for identifying D modification sites in RNA sequence
inferredcites →https://doi.org/10.1093/bioinformatics/btz900openalex-snapshot
Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite
inferredcites →https://doi.org/10.1093/gigascience/giy035openalex-snapshot
m6ASNP: a tool for annotating genetic variants by m6A function
inferredcites →https://doi.org/10.1093/nar/13.23.8339openalex-snapshot
Conformation of yeast 18S rRNA. Direct chemical probing of the 5′ domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible sites
inferredcites →https://doi.org/10.1093/nar/27.1.196openalex-snapshot
The RNA Modification Database: 1999 update
inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot
dbSNP: the NCBI database of genetic variation
inferredcites →https://doi.org/10.1093/nar/gkp1117openalex-snapshot
5-methylcytosine in RNA: detection, enzymatic formation and biological functions
inferredcites →https://doi.org/10.1093/nar/gkq1028openalex-snapshot
The RNA modification database, RNAMDB: 2011 update
inferredcites →https://doi.org/10.1093/nar/gks1007openalex-snapshot
MODOMICS: a database of RNA modification pathways—2013 update
inferredcites →https://doi.org/10.1093/nar/gks144openalex-snapshot
Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA
inferredcites →https://doi.org/10.1093/nar/gkt996openalex-snapshot
RADAR: a rigorously annotated database of A-to-I RNA editing
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MeT-DB: a database of transcriptome methylation in mammalian cells
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RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data
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ClinVar: public archive of interpretations of clinically relevant variants
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The reverse transcription signature ofN-1-methyladenosine in RNA-Seq is sequence dependent
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MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome
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N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein
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m6AVar: a database of functional variants involved in m6A modification
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RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data
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Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth
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Integrative network analysis identifies cell-specific trans regulators of m6A
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RNAmod: an integrated system for the annotation of mRNA modifications
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SICM6A: Identifying m 6 A Site across Species by Transposed GRU Network
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RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage
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iRNA-m5C_NB: A Novel Predictor to Identify RNA 5-Methylcytosine Sites Based on the Naive Bayes Classifier
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Model-based Analysis of ChIP-Seq (MACS)
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Bioinformatics approaches for Biomedical Research
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Role of m5C methylation in digestive system tumors (Review)
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Additional file 1 of 5-Methylcytosine profiles in mouse transcriptomes suggest the randomness of m5C formation catalyzed by RNA methyltransferase
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Additional file 2 of 5-Methylcytosine profiles in mouse transcriptomes suggest the randomness of m5C formation catalyzed by RNA methyltransferase
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