{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T20:49:37Z","timestamp":1784148577034,"version":"3.55.0"},"reference-count":108,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,10,3]],"date-time":"2020-10-03T00:00:00Z","timestamp":1601683200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31671373"],"award-info":[{"award-number":["31671373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"XJTLU Key Program Special Fund","award":["KSF-E-51"],"award-info":[{"award-number":["KSF-E-51"]}]},{"name":"Key Programme Special Fund","award":["KSF-P-02"],"award-info":[{"award-number":["KSF-P-02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Deciphering the biological impacts of millions of single nucleotide variants remains a major challenge. Recent studies suggest that RNA modifications play versatile roles in essential biological mechanisms, and are closely related to the progression of various diseases including multiple cancers. To comprehensively unveil the association between disease-associated variants and their epitranscriptome disturbance, we built RMDisease, a database of genetic variants that can affect RNA modifications. By integrating the prediction results of 18 different RNA modification prediction tools and also 303,426 experimentally-validated RNA modification sites, RMDisease identified a total of 202,307 human SNPs that may affect (add or remove) sites of eight types of RNA modifications (m6A, m5C, m1A, m5U, \u03a8, m6Am, m7G and Nm). These include 4,289 disease-associated variants that may imply disease pathogenesis functioning at the epitranscriptome layer. These SNPs were further annotated with essential information such as post-transcriptional regulations (sites for miRNA binding, interaction with RNA-binding proteins and alternative splicing) revealing putative regulatory circuits. A convenient graphical user interface was constructed to support the query, exploration and download of the relevant information. RMDisease should make a useful resource for studying the epitranscriptome impact of genetic variants via multiple RNA modifications with emphasis on their potential disease relevance. RMDisease is freely accessible at: www.xjtlu.edu.cn\/biologicalsciences\/rmd.<\/jats:p>","DOI":"10.1093\/nar\/gkaa790","type":"journal-article","created":{"date-parts":[[2020,9,11]],"date-time":"2020-09-11T11:12:29Z","timestamp":1599822749000},"page":"D1396-D1404","source":"Crossref","is-referenced-by-count":88,"title":["RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6025-8957","authenticated-orcid":false,"given":"Kunqi","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bowen","family":"Song","sequence":"additional","affiliation":[{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK"},{"name":"Department of Mathematical Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujiao","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Wei","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingru","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jionglong","family":"Su","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jo\u00e3o Pedro","family":"de\u00a0Magalh\u00e3es","sequence":"additional","affiliation":[{"name":"Institute of Ageing & Chronic Disease, University of Liverpool, L7 8TX Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J","family":"Rigden","sequence":"additional","affiliation":[{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3455-205X","authenticated-orcid":false,"given":"Jia","family":"Meng","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L7 8TX Liverpool, UK"},{"name":"AI University Research Centre, Xi\u2019an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,3]]},"reference":[{"key":"2021010313132025500_B1","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/nrg3051","article-title":"Understanding the contribution of synonymous mutations to human disease","volume":"12","author":"Sauna","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2021010313132025500_B2","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msv251","article-title":"Determinants of the usage of splice-associated cis-motifs predict the distribution of human pathogenic SNPs","volume":"33","author":"Wu","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"2021010313132025500_B3","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gkv1308","article-title":"RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins","volume":"44","author":"Mao","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B4","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.1371\/journal.pcbi.0040005","article-title":"In silico detection of sequence variations modifying transcriptional regulation","volume":"4","author":"Andersen","year":"2008","journal-title":"PLoS Comput. Biol."},{"key":"2021010313132025500_B5","doi-asserted-by":"crossref","first-page":"e06397","DOI":"10.7554\/eLife.06397","article-title":"Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE","volume":"4","author":"Riley","year":"2015","journal-title":"Elife"},{"key":"2021010313132025500_B6","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1093\/nar\/gkn1008","article-title":"Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases","volume":"37","author":"Ryu","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B7","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1074\/mcp.M900273-MCP200","article-title":"PhosSNP for systematic analysis of genetic polymorphisms that influence protein phosphorylation","volume":"9","author":"Ren","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2021010313132025500_B8","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1755-8794-8-S2-S7","article-title":"Detection and analysis of disease-associated single nucleotide polymorphism influencing post-translational modification","volume":"8","author":"Kim","year":"2015","journal-title":"BMC Med Genomics"},{"key":"2021010313132025500_B9","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/nmeth.3396","article-title":"MIMP: predicting the impact of mutations on kinase-substrate phosphorylation","volume":"12","author":"Wagih","year":"2015","journal-title":"Nat. Methods"},{"key":"2021010313132025500_B10","doi-asserted-by":"crossref","first-page":"10900","DOI":"10.1038\/srep10900","article-title":"Systematic analysis of the genetic variability that impacts SUMO conjugation and their involvement in human diseases","volume":"5","author":"Xu","year":"2015","journal-title":"Sci. Rep."},{"key":"2021010313132025500_B11","doi-asserted-by":"crossref","first-page":"D901","DOI":"10.1093\/nar\/gkx973","article-title":"ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins","volume":"46","author":"Krassowski","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B12","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1093\/bioinformatics\/btx072","article-title":"PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation","volume":"33","author":"Patrick","year":"2017","journal-title":"Bioinformatics"},{"key":"2021010313132025500_B13","first-page":"7099","article-title":"DeepCLIP: Predicting the effect of mutations on protein-RNA binding with deep learning","volume":"48","author":"Groenning","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B14","doi-asserted-by":"crossref","first-page":"715","DOI":"10.3389\/fgene.2019.00715","article-title":"Precise prediction of calpain cleavage sites and their aberrance caused by mutations in cancer","volume":"10","author":"Liu","year":"2019","journal-title":"Front. Genet."},{"key":"2021010313132025500_B15","first-page":"D111","article-title":"LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation","volume":"48","author":"Wang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B16","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gkz793","article-title":"SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers","volume":"48","author":"Yang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B17","doi-asserted-by":"crossref","first-page":"D139","DOI":"10.1093\/nar\/gkx895","article-title":"m6AVar: a database of functional variants involved in m6A modification","volume":"46","author":"Zheng","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B18","doi-asserted-by":"crossref","first-page":"3528","DOI":"10.1093\/bioinformatics\/btaa178","article-title":"m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human","volume":"36","author":"Song","year":"2020","journal-title":"Bioinformatics"},{"key":"2021010313132025500_B19","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1038\/nchembio.482","article-title":"Grand challenge commentary: RNA epigenetics","volume":"6","author":"He","year":"2010","journal-title":"Nat. Chem. Biol."},{"key":"2021010313132025500_B20","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1186\/gb-2012-13-10-175","article-title":"The birth of the Epitranscriptome: deciphering the function of RNA modifications","volume":"13","author":"Saletore","year":"2012","journal-title":"Genome Biol."},{"key":"2021010313132025500_B21","doi-asserted-by":"crossref","first-page":"e1595","DOI":"10.1002\/wrna.1595","article-title":"Naturally occurring modified ribonucleosides","volume":"n\/a","author":"McCown","year":"2020","journal-title":"WIREs RNA"},{"key":"2021010313132025500_B22","doi-asserted-by":"crossref","first-page":"e1586","DOI":"10.1002\/wrna.1586","article-title":"A molecular-level perspective on the frequency, distribution, and consequences of messenger RNA modifications","volume":"n\/a","author":"Jones","year":"2020","journal-title":"WIREs RNA"},{"key":"2021010313132025500_B23","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.canlet.2020.01.021","article-title":"Writers, readers and erasers of RNA modifications in cancer","volume":"474","author":"Esteve-Puig","year":"2020","journal-title":"Cancer Lett."},{"key":"2021010313132025500_B24","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1038\/s41588-020-0644-z","article-title":"Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability","volume":"52","author":"Zhang","year":"2020","journal-title":"Nat. Genet."},{"key":"2021010313132025500_B25","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1016\/j.cell.2013.10.026","article-title":"RNA-methylation-dependent RNA processing controls the speed of the circadian clock","volume":"155","author":"Fustin","year":"2013","journal-title":"Cell"},{"key":"2021010313132025500_B26","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nature12730","article-title":"N6-methyladenosine-dependent regulation of messenger RNA stability","volume":"505","author":"Wang","year":"2014","journal-title":"Nature"},{"key":"2021010313132025500_B27","doi-asserted-by":"crossref","first-page":"2782","DOI":"10.1038\/s41467-019-10669-0","article-title":"m(6)A mRNA demethylase FTO regulates melanoma tumorigenicity and response to anti-PD-1 blockade","volume":"10","author":"Yang","year":"2019","journal-title":"Nat. Commun."},{"key":"2021010313132025500_B28","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s12943-019-1004-4","article-title":"RNA N6-methyladenosine demethylase FTO promotes breast tumor progression through inhibiting BNIP3","volume":"18","author":"Niu","year":"2019","journal-title":"Mol. Cancer"},{"key":"2021010313132025500_B29","doi-asserted-by":"crossref","first-page":"2065","DOI":"10.1038\/s41467-019-09865-9","article-title":"RNA m(6)A methylation regulates the epithelial mesenchymal transition of cancer cells and translation of Snail","volume":"10","author":"Lin","year":"2019","journal-title":"Nat. Commun."},{"key":"2021010313132025500_B30","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/s41556-019-0318-1","article-title":"Stage-specific requirement for Mettl3-dependent m(6)A mRNA methylation during haematopoietic stem cell differentiation","volume":"21","author":"Lee","year":"2019","journal-title":"Nat. Cell Biol."},{"key":"2021010313132025500_B31","doi-asserted-by":"crossref","first-page":"1872","DOI":"10.1016\/j.cell.2018.10.030","article-title":"Acetylation of Cytidine in mRNA promotes translation efficiency","volume":"175","author":"Arango","year":"2018","journal-title":"Cell"},{"key":"2021010313132025500_B32","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1038\/s41586-018-0841-4","article-title":"FTSJ3 is an RNA 2\u2032-O-methyltransferase recruited by HIV to avoid innate immune sensing","volume":"565","author":"Ringeard","year":"2019","journal-title":"Nature"},{"key":"2021010313132025500_B33","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","article-title":"Comprehensive analysis of mRNA methylation reveals enrichment in 3\u2032 UTRs and near stop codons","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"key":"2021010313132025500_B34","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1038\/nature11112","article-title":"Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq","volume":"485","author":"Dominissini","year":"2012","journal-title":"Nature"},{"key":"2021010313132025500_B35","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1002\/anie.201410647","article-title":"High-resolution N(6) -methyladenosine (m(6) A) map using photo-crosslinking-assisted m(6) A sequencing","volume":"54","author":"Chen","year":"2015","journal-title":"Angew. Chem. Int. Ed. Engl."},{"key":"2021010313132025500_B36","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/nmeth.3453","article-title":"Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome","volume":"12","author":"Linder","year":"2015","journal-title":"Nat. Methods"},{"key":"2021010313132025500_B37","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/nature14252","article-title":"Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer\/'s disease","volume":"518","author":"Gjoneska","year":"2015","journal-title":"Nature"},{"key":"2021010313132025500_B38","first-page":"bbz112","article-title":"Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences","author":"Chen","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2021010313132025500_B39","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1093\/bib\/bbz048","article-title":"Evaluation of different computational methods on 5-methylcytosine sites identification","volume":"21","author":"Lv","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2021010313132025500_B40","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.ab.2015.08.021","article-title":"iRNA-Methyl: identifying N 6-methyladenosine sites using pseudo nucleotide composition","volume":"490","author":"Chen","year":"2015","journal-title":"Anal. Biochem."},{"key":"2021010313132025500_B41","doi-asserted-by":"crossref","first-page":"e91","DOI":"10.1093\/nar\/gkw104","article-title":"SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features","volume":"44","author":"Zhou","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B42","doi-asserted-by":"crossref","first-page":"e41","DOI":"10.1093\/nar\/gkz074","article-title":"WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach","volume":"47","author":"Chen","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B43","first-page":"367","article-title":"A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae","volume":"19","author":"Zhu","year":"2019","journal-title":"Brief. Funct. Genomics"},{"key":"2021010313132025500_B44","doi-asserted-by":"crossref","first-page":"D281","DOI":"10.1093\/nar\/gkx1080","article-title":"MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome","volume":"46","author":"Liu","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B45","doi-asserted-by":"crossref","first-page":"168","DOI":"10.3390\/cells8020168","article-title":"CVm6A: a visualization and exploration database for m(6)As in cell lines","volume":"8","author":"Han","year":"2019","journal-title":"Cells"},{"key":"2021010313132025500_B46","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/s13059-020-02012-4","article-title":"REPIC: a database for exploring &lt;em&gt;N&lt;\/em&gt;&lt;sup&gt;6&lt;\/sup&gt;-methyladenosine methylome","volume":"21","author":"Liu","year":"2019","journal-title":"Genome Biol."},{"key":"2021010313132025500_B47","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/s41594-019-0218-x","article-title":"Genome-wide identification of mRNA 5-methylcytosine in mammals","volume":"26","author":"Huang","year":"2019","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2021010313132025500_B48","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1016\/j.cell.2019.06.013","article-title":"Deciphering the \u201cm(6)A Code\" via antibody-independent quantitative profiling","volume":"178","author":"Garcia-Campos","year":"2019","journal-title":"Cell"},{"key":"2021010313132025500_B49","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.cell.2014.08.028","article-title":"Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA","volume":"159","author":"Schwartz","year":"2014","journal-title":"Cell"},{"key":"2021010313132025500_B50","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/nature13802","article-title":"Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells","volume":"515","author":"Carlile","year":"2014","journal-title":"Nature"},{"key":"2021010313132025500_B51","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/nchembio.1836","article-title":"Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome","volume":"11","author":"Li","year":"2015","journal-title":"Nat. Chem. Biol."},{"key":"2021010313132025500_B52","doi-asserted-by":"crossref","first-page":"6784","DOI":"10.1073\/pnas.1817334116","article-title":"Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution","volume":"116","author":"Khoddami","year":"2019","journal-title":"PNAS"},{"key":"2021010313132025500_B53","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1016\/j.molcel.2017.10.019","article-title":"Base-resolution mapping reveals distinct m(1)A methylome in nuclear- and mitochondrial-encoded transcripts","volume":"68","author":"Li","year":"2017","journal-title":"Mol. Cell"},{"key":"2021010313132025500_B54","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/nature24456","article-title":"The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution","volume":"551","author":"Safra","year":"2017","journal-title":"Nature"},{"key":"2021010313132025500_B55","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1038\/nbt.2566","article-title":"Identification of direct targets and modified bases of RNA cytosine methyltransferases","volume":"31","author":"Khoddami","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2021010313132025500_B56","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/cr.2017.55","article-title":"5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m(5)C reader","volume":"27","author":"Yang","year":"2017","journal-title":"Cell Res."},{"key":"2021010313132025500_B57","doi-asserted-by":"crossref","first-page":"e113","DOI":"10.1093\/nar\/gkz658","article-title":"FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA","volume":"47","author":"Carter","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B58","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1038\/nmeth.4294","article-title":"Nm-seq maps 2\u2032-O-methylation sites in human mRNA with base precision","volume":"14","author":"Dai","year":"2017","journal-title":"Nat. Methods"},{"key":"2021010313132025500_B59","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1016\/j.molcel.2019.03.036","article-title":"Transcriptome-wide mapping of internal N(7)-Methylguanosine methylome in mammalian mRNA","volume":"74","author":"Zhang","year":"2019","journal-title":"Mol. Cell"},{"key":"2021010313132025500_B60","doi-asserted-by":"crossref","first-page":"927","DOI":"10.1038\/s41422-019-0230-z","article-title":"Dynamic methylome of internal mRNA N(7)-methylguanosine and its regulatory role in translation","volume":"29","author":"Malbec","year":"2019","journal-title":"Cell Res."},{"key":"2021010313132025500_B61","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1186\/s12859-018-2321-0","article-title":"PseUI: Pseudouridine sites identification based on RNA sequence information","volume":"19","author":"He","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2021010313132025500_B62","doi-asserted-by":"crossref","first-page":"6231","DOI":"10.3934\/mbe.2019310","article-title":"DeepMRMP: A new predictor for multiple types of RNA modification sites using deep learning","volume":"16","author":"Sun","year":"2019","journal-title":"Math. Biosci. Eng.: MBE"},{"key":"2021010313132025500_B63","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1016\/j.omtn.2019.03.010","article-title":"iPseU-CNN: Identifying RNA pseudouridine sites using convolutional neural networks","volume":"16","author":"Tahir","year":"2019","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2021010313132025500_B64","doi-asserted-by":"crossref","first-page":"2394","DOI":"10.1109\/EMBC.2018.8512780","volume-title":"2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","author":"Mostavi","year":"2018"},{"key":"2021010313132025500_B65","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1186\/s12859-019-2840-3","article-title":"m6Acomet: large-scale functional prediction of individual m(6)A RNA methylation sites from an RNA co-methylation network","volume":"20","author":"Wu","year":"2019","journal-title":"BMC Bioinformatics"},{"key":"2021010313132025500_B66","doi-asserted-by":"crossref","first-page":"e91","DOI":"10.1093\/nar\/gkw104","article-title":"SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features","volume":"44","author":"Zhou","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B67","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1016\/j.omtn.2018.03.012","article-title":"iRNA-3typeA: identifying three types of modification at RNA's adenosine sites","volume":"11","author":"Chen","year":"2018","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2021010313132025500_B68","doi-asserted-by":"crossref","first-page":"3336","DOI":"10.1093\/bioinformatics\/btaa155","article-title":"iMRM:a platform for simultaneously identifying multiple kinds of RNA modifications","volume":"36","author":"Liu","year":"2020","journal-title":"Bioinformatics"},{"key":"2021010313132025500_B69","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1089\/cmb.2018.0004","article-title":"iRNA-2OM: A sequence-based predictor for identifying 2\u2032-O-Methylation sites in homo sapiens","volume":"25","author":"Yang","year":"2018","journal-title":"J. Comput. Biol."},{"key":"2021010313132025500_B70","doi-asserted-by":"crossref","first-page":"982","DOI":"10.1093\/bib\/bbz048","article-title":"Evaluation of different computational methods on 5-methylcytosine sites identification","volume":"21","author":"Lv","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2021010313132025500_B71","doi-asserted-by":"crossref","first-page":"31080","DOI":"10.1038\/srep31080","article-title":"RAMPred: identifying the N(1)-methyladenosine sites in eukaryotic transcriptomes","volume":"6","author":"Chen","year":"2016","journal-title":"Sci. Rep."},{"key":"2021010313132025500_B72","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.omtn.2017.03.006","article-title":"iRNA-PseColl: identifying the occurrence sites of different RNA modifications by incorporating collective effects of nucleotides into PseKNC","volume":"7","author":"Feng","year":"2017","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2021010313132025500_B73","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.omtn.2019.08.022","article-title":"iRNA-m7G: identifying N(7)-methylguanosine sites by fusing multiple features","volume":"18","author":"Chen","year":"2019","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2021010313132025500_B74","doi-asserted-by":"crossref","first-page":"3528","DOI":"10.1093\/bioinformatics\/btaa178","article-title":"m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human","volume":"36","author":"Song","year":"2020","journal-title":"Bioinformatics"},{"key":"2021010313132025500_B75","first-page":"e332","article-title":"iRNA-PseU: Identifying RNA pseudouridine sites","volume":"5","author":"Chen","year":"2016","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"2021010313132025500_B76","doi-asserted-by":"crossref","first-page":"88","DOI":"10.3389\/fgene.2020.00088","article-title":"PIANO: a web server for pseudouridine-site (\u03a8) identification and functional annotation","volume":"11","author":"Song","year":"2020","journal-title":"Front. Genet."},{"key":"2021010313132025500_B77","doi-asserted-by":"crossref","first-page":"81971","DOI":"10.1109\/ACCESS.2020.2991070","article-title":"ISGm1A: integration of sequence features and genomic features to improve the prediction of human m1A RNA methylation sites","volume":"8","author":"Lian","year":"2020","journal-title":"IEEE Access"},{"key":"2021010313132025500_B78","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/nprot.2009.86","article-title":"Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm","volume":"4","author":"Kumar","year":"2009","journal-title":"Nat. Protoc."},{"key":"2021010313132025500_B79","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. Methods"},{"key":"2021010313132025500_B80","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1101\/gr.092619.109","article-title":"Identification of deleterious mutations within three human genomes","volume":"19","author":"Chun","year":"2009","journal-title":"Genome Res."},{"key":"2021010313132025500_B81","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1002\/humu.22225","article-title":"Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models","volume":"34","author":"Shihab","year":"2013","journal-title":"Hum. Mutat."},{"key":"2021010313132025500_B82","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B83","doi-asserted-by":"crossref","first-page":"D203","DOI":"10.1093\/nar\/gky830","article-title":"POSTAR2: deciphering the post-transcriptional regulatory logics","volume":"47","author":"Zhu","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B84","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"eLife"},{"key":"2021010313132025500_B85","doi-asserted-by":"crossref","first-page":"D92","DOI":"10.1093\/nar\/gkt1248","article-title":"starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein\u2013RNA interaction networks from large-scale CLIP-Seq data","volume":"42","author":"Li","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B86","doi-asserted-by":"crossref","first-page":"D1005","DOI":"10.1093\/nar\/gky1120","article-title":"The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019","volume":"47","author":"Buniello","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B87","doi-asserted-by":"crossref","first-page":"D862","DOI":"10.1093\/nar\/gkv1222","article-title":"ClinVar: public archive of interpretations of clinically relevant variants","volume":"44","author":"Landrum","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B88","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1471-2350-10-6","article-title":"An open access database of genome-wide association results","volume":"10","author":"Johnson","year":"2009","journal-title":"BMC Med. Genet."},{"key":"2021010313132025500_B89","first-page":"bbz142","article-title":"RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data","author":"Dong","year":"2019","journal-title":"Brief. Bioinform."},{"key":"2021010313132025500_B90","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol."},{"key":"2021010313132025500_B91","doi-asserted-by":"crossref","first-page":"D303","DOI":"10.1093\/nar\/gkx1030","article-title":"MODOMICS: a database of RNA modification pathways. 2017 update","volume":"46","author":"Boccaletto","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2021010313132025500_B92","doi-asserted-by":"crossref","first-page":"1176934320925752","DOI":"10.1177\/1176934320925752","article-title":"PSI-MOUSE: predicting mouse pseudouridine sites from sequence and genome-derived features","volume":"16","author":"Song","year":"2020","journal-title":"Evolutionary Bioinformatics"},{"key":"2021010313132025500_B93","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.omtn.2019.08.022","article-title":"iRNA-m7G: identifying N7-methylguanosine sites by fusing multiple features","volume":"18","author":"Chen","year":"2019","journal-title":"Mol\/ Ther\/ - Nucleic Acids"},{"key":"2021010313132025500_B94","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1016\/S0092-8674(00)81308-2","article-title":"Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs","volume":"85","author":"Kiss-L\u00e1szl\u00f3","year":"1996","journal-title":"Cell"},{"key":"2021010313132025500_B95","doi-asserted-by":"crossref","first-page":"1549","DOI":"10.1017\/S1355838298980761","article-title":"Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX\/ACA-motif snoRNPs and constitute a common bipartite structure","volume":"4","author":"Watkins","year":"1998","journal-title":"RNA"},{"key":"2021010313132025500_B96","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1126\/science.283.5405.1168","article-title":"A computational screen for methylation guide snoRNAs in yeast","volume":"283","author":"Lowe","year":"1999","journal-title":"Science"},{"key":"2021010313132025500_B97","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1261\/rna.5240503","article-title":"A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast","volume":"9","author":"Badis","year":"2003","journal-title":"RNA"},{"key":"2021010313132025500_B98","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1002\/wrna.79","article-title":"RNA nucleotide methylation","volume":"2","author":"Motorin","year":"2011","journal-title":"Wiley Interdiscip\/ Rev.: RNA"},{"key":"2021010313132025500_B99","doi-asserted-by":"crossref","first-page":"35123","DOI":"10.1038\/srep35123","article-title":"PAI: predicting adenosine to inosine editing sites by using pseudo nucleotide compositions","volume":"6","author":"Chen","year":"2016","journal-title":"Sci. Rep."},{"key":"2021010313132025500_B100","article-title":"Is there any sequence feature in the RNA pseudouridine modification prediction problem","volume":"19","author":"Dou","year":"2019","journal-title":"Mol. Ther. - Nucleic Acids"},{"key":"2021010313132025500_B101","doi-asserted-by":"crossref","first-page":"88","DOI":"10.3389\/fgene.2020.00088","article-title":"PIANO: a web server for pseudouridine-site (\u03a8) identification and functional annotation","volume":"11","author":"Song","year":"2020","journal-title":"Frontiers in Genetics"},{"key":"2021010313132025500_B102","doi-asserted-by":"crossref","first-page":"545","DOI":"10.3389\/fgene.2020.00545","article-title":"LITHOPHONE: improving lncRNA methylation site prediction using an ensemble predictor","volume":"11","author":"Liu","year":"2020","journal-title":"Frontiers in Genetics"},{"key":"2021010313132025500_B103","doi-asserted-by":"crossref","first-page":"67","DOI":"10.2174\/1389202921666200211104140","article-title":"WITMSG: large-scale prediction of human intronic m6A RNA methylation sites from sequence and genomic features","volume":"21","author":"Liu","year":"2020","journal-title":"Curr. Genomics"},{"key":"2021010313132025500_B104","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1016\/j.bbagrm.2018.11.002","article-title":"Post-transcriptional pseudouridylation in mRNA as well as in some major types of noncoding RNAs","volume":"1862","author":"Adachi","year":"2018","journal-title":"Biochim. Biophys. Acta (BBA)-Gene Regul. Mech."},{"key":"2021010313132025500_B105","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1016\/j.ymeth.2016.03.001","article-title":"Pseudouridylation meets next-generation sequencing","volume":"107","author":"Zaringhalam","year":"2016","journal-title":"Methods"},{"key":"2021010313132025500_B106","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1186\/gb4143","article-title":"Characterizing 5-methylcytosine in the mammalian epitranscriptome","volume":"14","author":"Hussain","year":"2013","journal-title":"Genome Biol."},{"key":"2021010313132025500_B107","doi-asserted-by":"crossref","first-page":"398","DOI":"10.3389\/fgene.2020.00398","article-title":"How do you identify m6 a methylation in transcriptomes at high resolution? a comparison of recent datasets","volume":"11","author":"Capitanchik","year":"2020","journal-title":"Front. Genet."},{"key":"2021010313132025500_B108","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1080\/07391102.2016.1157761","article-title":"MethyRNA: a web server for identification of N(6)-methyladenosine sites","volume":"35","author":"Chen","year":"2017","journal-title":"J. Biomol. Struct. Dyn."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/D1\/D1396\/35364568\/gkaa790.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/49\/D1\/D1396\/35364568\/gkaa790.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,7]],"date-time":"2023-10-07T06:30:53Z","timestamp":1696660253000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/49\/D1\/D1396\/5917656"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,10,3]]},"references-count":108,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2020,10,3]]},"published-print":{"date-parts":[[2021,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa790","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,1,8]]},"published":{"date-parts":[[2020,10,3]]}}}