{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T03:20:56Z","timestamp":1778210456870,"version":"3.51.4"},"reference-count":54,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,8,1]],"date-time":"2024-08-01T00:00:00Z","timestamp":1722470400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100006683","name":"Xi\u2019an Jiaotong-Liverpool University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006683","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Methods"],"published-print":{"date-parts":[[2024,8]]},"DOI":"10.1016\/j.ymeth.2024.05.009","type":"journal-article","created":{"date-parts":[[2024,5,18]],"date-time":"2024-05-18T06:29:49Z","timestamp":1716013789000},"page":"30-37","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":10,"special_numbering":"C","title":["Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data"],"prefix":"10.1016","volume":"228","author":[{"given":"Shenglun","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jia","family":"Meng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuxin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.ymeth.2024.05.009_b0005","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1002\/jcp.1040990208","article-title":"Pyrimidine nucleoside, pseudouridine, and modified nucleoside excretion by growing and resting fibroblasts","volume":"99","author":"Uziel","year":"1979","journal-title":"J. Cell. Physiol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0010","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1261\/rna.049866.115","article-title":"RNA modification: the Golden Period 1995\u20132015","volume":"21","author":"Grosjean","year":"2015","journal-title":"RNA"},{"key":"10.1016\/j.ymeth.2024.05.009_b0015","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.cell.2017.05.045","article-title":"Dynamic RNA Modifications in Gene Expression Regulation","volume":"169","author":"Roundtree","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.ymeth.2024.05.009_b0020","unstructured":"Clark, W. (2016) Dynamic tRNA Modification Landscape."},{"key":"10.1016\/j.ymeth.2024.05.009_b0025","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1038\/nmeth.3508","article-title":"ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments","volume":"12","author":"Cozen","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ymeth.2024.05.009_b0030","doi-asserted-by":"crossref","first-page":"2484","DOI":"10.1038\/s41467-022-30210-0","article-title":"Developmental mRNA m(5)C landscape and regulatory innovations of massive m(5)C modification of maternal mRNAs in animals","volume":"13","author":"Liu","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ymeth.2024.05.009_b0035","doi-asserted-by":"crossref","first-page":"e14122","DOI":"10.1371\/journal.pone.0014122","article-title":"Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human","volume":"5","author":"Pu","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.ymeth.2024.05.009_b0040","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":"10.1016\/j.ymeth.2024.05.009_b0045","doi-asserted-by":"crossref","first-page":"14695","DOI":"10.1074\/jbc.M117.798298","article-title":"Three distinct 3-methylcytidine (m(3)C) methyltransferases modify tRNA and mRNA in mice and humans","volume":"292","author":"Xu","year":"2017","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.ymeth.2024.05.009_b0050","doi-asserted-by":"crossref","first-page":"6251","DOI":"10.1093\/nar\/gkaa347","article-title":"Dynamic landscape and evolution of m6A methylation in human","volume":"48","author":"Zhang","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0055","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":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0060","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1261\/rna.063503.117","article-title":"The RNA modification landscape in human disease","volume":"23","author":"Jonkhout","year":"2017","journal-title":"RNA"},{"key":"10.1016\/j.ymeth.2024.05.009_b0065","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":"10.1016\/j.ymeth.2024.05.009_b0070","doi-asserted-by":"crossref","first-page":"135","DOI":"10.3389\/fnmol.2017.00135","article-title":"Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders","volume":"10","author":"Bedn\u00e1\u0159ov\u00e1","year":"2017","journal-title":"Front. Mol. Neurosci."},{"key":"10.1016\/j.ymeth.2024.05.009_b0075","doi-asserted-by":"crossref","unstructured":"Motorin, Y. and Helm, M. (2019) Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies. Genes (Basel), 10.","DOI":"10.3390\/genes10010035"},{"key":"10.1016\/j.ymeth.2024.05.009_b0080","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1021\/acs.accounts.3c00529","article-title":"General Principles and Limitations for Detection of RNA Modifications by Sequencing","volume":"57","author":"Motorin","year":"2024","journal-title":"Acc. Chem. Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0085","doi-asserted-by":"crossref","first-page":"14908","DOI":"10.1038\/s41598-019-51470-9","article-title":"Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules","volume":"9","author":"Sessegolo","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ymeth.2024.05.009_b0090","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.ymeth.2018.10.011","article-title":"Misincorporation signatures for detecting modifications in mRNA: Not as simple as it sounds","volume":"156","author":"Sas-Chen","year":"2019","journal-title":"Methods"},{"key":"10.1016\/j.ymeth.2024.05.009_b0095","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.1261\/rna.079404.122","article-title":"Exploring the epitranscriptome by native RNA sequencing","volume":"28","author":"Begik","year":"2022","journal-title":"RNA"},{"key":"10.1016\/j.ymeth.2024.05.009_b0100","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-0716-1374-0_1","article-title":"RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework","volume":"2298","author":"Manfredonia","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0105","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":"10.1016\/j.ymeth.2024.05.009_b0110","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":"10.1016\/j.ymeth.2024.05.009_b0115","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1261\/rna.041178.113","article-title":"Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA","volume":"19","author":"Liu","year":"2013","journal-title":"RNA"},{"key":"10.1016\/j.ymeth.2024.05.009_b0120","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1016\/j.ymeth.2014.06.008","article-title":"A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R\/Bioconductor package","volume":"69","author":"Meng","year":"2014","journal-title":"Methods"},{"key":"10.1016\/j.ymeth.2024.05.009_b0125","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0130","doi-asserted-by":"crossref","unstructured":"Athanasopoulou, K., Boti, M.A., Adamopoulos, P.G., Skourou, P.C. and Scorilas, A. (2021) Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life (Basel), 12.","DOI":"10.3390\/life12010030"},{"key":"10.1016\/j.ymeth.2024.05.009_b0135","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1093\/bib\/bbx129","article-title":"Elucidating the editome: bioinformatics approaches for RNA editing detection","volume":"20","author":"Diroma","year":"2019","journal-title":"Brief. Bioinform."},{"key":"10.1016\/j.ymeth.2024.05.009_b0140","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/978-1-0716-0787-9_12","article-title":"High-Throughput Sequencing to Detect DNA-RNA Changes","volume":"2181","author":"Lo Giudice","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0145","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/978-1-0716-1307-8_14","article-title":"RNA Editing Detection in HPC Infrastructures","volume":"2284","author":"Lo Giudice","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0150","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/j.gpb.2016.05.004","article-title":"Oxford Nanopore MinION Sequencing and Genome Assembly","volume":"14","author":"Lu","year":"2016","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"10.1016\/j.ymeth.2024.05.009_b0155","doi-asserted-by":"crossref","first-page":"e0116323","DOI":"10.1128\/msystems.01163-23","article-title":"Utilization of Nanopore Direct RNA Sequencing to Analyze Viral RNA Modifications","volume":"9","author":"Tan","year":"2024","journal-title":"mSystems"},{"key":"10.1016\/j.ymeth.2024.05.009_b0160","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1007\/s12275-022-2324-4","article-title":"Analyzing viral epitranscriptomes using nanopore direct RNA sequencing","volume":"60","author":"Hong","year":"2022","journal-title":"J. Microbiol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0165","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/978-1-0716-2257-5_5","article-title":"Direct Sequencing of RNA and RNA Modification Identification Using Nanopore","volume":"2477","author":"Wongsurawat","year":"2022","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0170","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1261\/rna.078937.121","article-title":"Nanopore sequencing of RNA and cDNA molecules in Escherichia coli","volume":"28","author":"Gr\u00fcnberger","year":"2022","journal-title":"RNA"},{"key":"10.1016\/j.ymeth.2024.05.009_b0175","doi-asserted-by":"crossref","first-page":"e104","DOI":"10.1093\/nar\/gkad810","article-title":"Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data","volume":"51","author":"Liu","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0180","doi-asserted-by":"crossref","first-page":"7700","DOI":"10.1093\/nar\/gkaa588","article-title":"New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs","volume":"48","author":"Zhang","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0185","doi-asserted-by":"crossref","first-page":"253","DOI":"10.3389\/fgene.2019.00253","article-title":"Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing","volume":"10","author":"Zhao","year":"2019","journal-title":"Front. Genet."},{"key":"10.1016\/j.ymeth.2024.05.009_b0190","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.111317","article-title":"m(1)A and m(6)A modifications function cooperatively to facilitate rapid mRNA degradation","volume":"40","author":"Boo","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.ymeth.2024.05.009_b0195","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijbiomac.2023.126773","article-title":"The functions and mechanisms of post-translational modification in protein regulators of RNA methylation: Current status and future perspectives","volume":"253","author":"Chen","year":"2023","journal-title":"Int. J. Biol. Macromol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0200","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2021.767668","article-title":"Role of Main RNA Methylation in Hepatocellular Carcinoma: N6-Methyladenosine, 5-Methylcytosine, and N1-Methyladenosine","volume":"9","author":"Xu","year":"2021","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0205","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/s12876-023-02776-6","article-title":"The m6A\/m5C\/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma","volume":"23","author":"Liu","year":"2023","journal-title":"BMC Gastroenterol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0210","article-title":"The m6A\/m5C\/m1A Regulated Gene Signature Predicts the Prognosis and Correlates With the Immune Status of Hepatocellular Carcinoma","volume":"13","author":"Li","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0215","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1126\/science.aau1646","article-title":"RNA modifications modulate gene expression during development","volume":"361","author":"Frye","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.ymeth.2024.05.009_b0220","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1186\/s12864-023-09876-3","article-title":"Exploration and validation of a combined Hypoxia and m6A\/m5C\/m1A regulated gene signature for prognosis prediction of liver cancer","volume":"24","author":"Ren","year":"2023","journal-title":"BMC Genomics"},{"key":"10.1016\/j.ymeth.2024.05.009_b0225","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1186\/s12964-023-01357-0","article-title":"Non-coding RNA methylation modifications in hepatocellular carcinoma: interactions and potential implications","volume":"21","author":"Shi","year":"2023","journal-title":"Cell Commun. Signal"},{"key":"10.1016\/j.ymeth.2024.05.009_b0230","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1186\/s12920-023-01611-x","article-title":"Development and validation of a novel prognostic signature based on m6A\/m5C\/m1A-related genes in hepatocellular carcinoma","volume":"16","author":"Xiao","year":"2023","journal-title":"BMC Med. Genomics"},{"key":"10.1016\/j.ymeth.2024.05.009_b0235","first-page":"5868","article-title":"The prognostic value and immune landscapes of m1A\/m5C\/m6A-associated lncRNA signature in osteosarcoma","volume":"26","author":"Wu","year":"2022","journal-title":"Eur. Rev. Med. Pharmacol. Sci."},{"key":"10.1016\/j.ymeth.2024.05.009_b0240","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2022.903117","article-title":"An m6A\/m5C\/m1A\/m7G-Related Long Non-coding RNA Signature to Predict Prognosis and Immune Features of Glioma","volume":"13","author":"Shao","year":"2022","journal-title":"Front. Genet."},{"key":"10.1016\/j.ymeth.2024.05.009_b0245","doi-asserted-by":"crossref","first-page":"e7","DOI":"10.1093\/nar\/gkaa620","article-title":"Decoding the epitranscriptional landscape from native RNA sequences","volume":"49","author":"Jenjaroenpun","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0250","doi-asserted-by":"crossref","first-page":"2236","DOI":"10.1080\/15476286.2021.1898160","article-title":"Accurate identification of RNA D modification using multiple features","volume":"18","author":"Dou","year":"2021","journal-title":"RNA Biol."},{"key":"10.1016\/j.ymeth.2024.05.009_b0255","doi-asserted-by":"crossref","first-page":"W317","DOI":"10.1093\/nar\/gkab447","article-title":"KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis","volume":"49","author":"Bu","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0260","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ymeth.2024.05.009_b0265","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1021\/acschembio.9b00655","article-title":"YTHDF2 Recognition of N(1)-Methyladenosine (m(1)A)-Modified RNA Is Associated with Transcript Destabilization","volume":"15","author":"Seo","year":"2020","journal-title":"ACS Chem. Biol."},{"issue":"D1","key":"10.1016\/j.ymeth.2024.05.009_bib266","doi-asserted-by":"crossref","first-page":"D106","DOI":"10.1093\/nar\/gkac1061","article-title":"DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology","volume":"51","author":"Zhang","year":"2023","journal-title":"Nucleic. Acids. Res."}],"container-title":["Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1046202324001257?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1046202324001257?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,5,21]],"date-time":"2024-05-21T04:59:15Z","timestamp":1716267555000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1046202324001257"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,8]]},"references-count":54,"alternative-id":["S1046202324001257"],"URL":"https:\/\/doi.org\/10.1016\/j.ymeth.2024.05.009","relation":{},"ISSN":["1046-2023"],"issn-type":[{"value":"1046-2023","type":"print"}],"subject":[],"published":{"date-parts":[[2024,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data","name":"articletitle","label":"Article Title"},{"value":"Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ymeth.2024.05.009","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}