{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T15:49:00Z","timestamp":1783698540825,"version":"3.55.0"},"reference-count":109,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,7,9]],"date-time":"2025-07-09T00:00:00Z","timestamp":1752019200000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"XJTLU Key Program Special Fund","award":["KSF-E-51 and KSF-P-02"],"award-info":[{"award-number":["KSF-E-51 and KSF-P-02"]}]},{"DOI":"10.13039\/501100007956","name":"Nanjing University of Chinese Medicine","doi-asserted-by":"publisher","award":["013038019029"],"award-info":[{"award-number":["013038019029"]}],"id":[{"id":"10.13039\/501100007956","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007956","name":"Nanjing University of Chinese Medicine","doi-asserted-by":"publisher","award":["013038030001"],"award-info":[{"award-number":["013038030001"]}],"id":[{"id":"10.13039\/501100007956","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20240723"],"award-info":[{"award-number":["BK20240723"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005892","name":"China Academy of Chinese Medical Sciences","doi-asserted-by":"publisher","award":["CI2023C042LH"],"award-info":[{"award-number":["CI2023C042LH"]}],"id":[{"id":"10.13039\/501100005892","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U24A20785"],"award-info":[{"award-number":["U24A20785"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U2102201"],"award-info":[{"award-number":["U2102201"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32400527"],"award-info":[{"award-number":["32400527"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32300552"],"award-info":[{"award-number":["32300552"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Precise identification of condition-specific epitranscriptomes is of critical importance for investigating the dynamics and versatile functions of RNA modification under various biological contexts. Existing approaches for predicting condition-specific RNA modification are usually trained on epitranscriptome data obtained from the same condition, which limited their usage, as such data are available only for a small number of conditions due to the technical difficulties and high expenses of epitranscriptome profiling technologies. We present ExpressRM, a multimodal zero-shot learning framework for predicting condition-specific RNA modification sites in previously unseen contexts from genome and RNA-seq data. Different from existing in-condition learning approaches, this method does not rely on matched epitranscriptome data for training, which greatly expands its applicability. On a benchmark dataset comprising epitranscriptomes and matched transcriptomes of 37 human tissues, we demonstrate that ExpressRM can accurately predict epitranscriptomes of previously unseen conditions from their transcriptomes only, and the performance is comparable to existing in-condition learning algorithms that require epitranscriptome data from the same condition. Additionally, the method has the capability of differentiating highly dynamic RNA methylation sites from more static (or house-keeping) ones. With a case study, we show that ExpressRM can uncover N6-methyladenosine RNA methylation sites in glioblastoma using only its RNA-seq data, and unveils novel and previously validated pathological insights. Together, these results suggest that the proposed multimodal zero-shot learning framework can effectively leverage transcriptome knowledge to explore the dynamic roles of RNA modifications in previously unseen experimental setups, providing valuable insights into vast biological contexts where RNA-seq is routinely used but epitranscriptome profiling has not yet been covered.<\/jats:p>","DOI":"10.1093\/bib\/bbaf332","type":"journal-article","created":{"date-parts":[[2025,7,9]],"date-time":"2025-07-09T14:13:50Z","timestamp":1752070430000},"source":"Crossref","is-referenced-by-count":4,"title":["Multimodal zero-shot learning of previously unseen epitranscriptomes from RNA-seq data"],"prefix":"10.1093","volume":"26","author":[{"given":"Yiyou","family":"Song","sequence":"first","affiliation":[{"name":"Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine , 138 Xianlin Avenue, Qixia District, Nanjing 210023 ,","place":["China"]},{"name":"Department of Public Health, School of Medicine, Nanjing University of Chinese Medicine , 138 Xianlin Avenue, Qixia District, Nanjing 210023 ,","place":["China"]},{"name":"Department of Biological Sciences, School of Science, Suzhou Key Laboratory of Cancer Biology and Chronic Diseases, Xi\u2019an Jiaotong-Liverpool University , 111 Ren'ai Road, Suzhou Industrial Park, Suzhou 215123 ,","place":["China"]},{"name":"Department of Computer Sciences, University of Liverpool , Ashton Street, Liverpool L69 3BX ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8586-0573","authenticated-orcid":false,"given":"Bowen","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Public Health, School of Medicine, Nanjing University of Chinese Medicine , 138 Xianlin Avenue, Qixia District, Nanjing 210023 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daiyun","family":"Huang","sequence":"additional","affiliation":[{"name":"Wisdom Lake Academy of Pharmacy, Xi\u2019an Jiaotong-Liverpool University , Suzhou 215123 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anh","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Department of Computer Sciences, University of Liverpool , Ashton Street, Liverpool L69 3BX ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lihong","family":"Hu","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine , 138 Xianlin Avenue, Qixia District, Nanjing 210023 ,","place":["China"]}],"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, School of Science, Suzhou Key Laboratory of Cancer Biology and Chronic Diseases, Xi\u2019an Jiaotong-Liverpool University , 111 Ren'ai Road, Suzhou Industrial Park, Suzhou 215123 ,","place":["China"]},{"name":"AI University Research Centre, Xi\u2019an Jiaotong-Liverpool University , 111 Ren'ai Road, Suzhou Industrial Park, Suzhou 215123 ,","place":["China"]},{"name":"Institute of Systems, Molecular and Integrative Biology, University of Liverpool , Biosciences Building, Crown Street, Liverpool L69 7BE ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6271-6547","authenticated-orcid":false,"given":"Yue","family":"Wang","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine , 138 Xianlin Avenue, Qixia District, Nanjing 210023 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,7,9]]},"reference":[{"key":"2025070910134736800_ref1","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/s41568-020-0253-2","article-title":"Role of RNA modifications in cancer","volume":"20","author":"Barbieri","year":"2020","journal-title":"Nat Rev Cancer"},{"key":"2025070910134736800_ref2","doi-asserted-by":"publisher","first-page":"D262","DOI":"10.1093\/nar\/gks1007","article-title":"MODOMICS: a database of RNA modification pathways\u20142013 update","volume":"41","author":"Machnicka","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref3","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.chembiol.2013.10.015","article-title":"Posttranscriptional RNA modifications: playing metabolic games in a cell's chemical Legoland","volume":"21","author":"Helm","year":"2014","journal-title":"Chem Biol"},{"key":"2025070910134736800_ref4","doi-asserted-by":"publisher","first-page":"e1691","DOI":"10.1002\/wrna.1691","article-title":"RNA nucleotide methylation: 2021 update","volume":"13","author":"Motorin","year":"2022","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2025070910134736800_ref5","doi-asserted-by":"publisher","first-page":"e1618","DOI":"10.1002\/wrna.1618","article-title":"A birds'-eye view of the activity and specificity of the mRNA m(6) A methyltransferase complex","volume":"12","author":"Garcias","year":"2021","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2025070910134736800_ref6","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/s41392-020-00450-x","article-title":"The role of m6A modification in the biological functions and diseases","volume":"6","author":"Jiang","year":"2021","journal-title":"Signal Transduct Target Ther"},{"key":"2025070910134736800_ref7","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1016\/j.cell.2015.10.012","article-title":"5' UTR m(6)A promotes cap-independent translation","volume":"163","author":"Meyer","year":"2015","journal-title":"Cell"},{"key":"2025070910134736800_ref8","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1016\/j.cell.2015.05.014","article-title":"N(6)-methyladenosine modulates messenger RNA translation efficiency","volume":"161","author":"Wang","year":"2015","journal-title":"Cell"},{"key":"2025070910134736800_ref9","doi-asserted-by":"publisher","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":"2025070910134736800_ref10","doi-asserted-by":"publisher","first-page":"482","DOI":"10.1038\/nature14281","article-title":"N6-methyladenosine marks primary microRNAs for processing","volume":"519","author":"Alarcon","year":"2015","journal-title":"Nature"},{"key":"2025070910134736800_ref11","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1038\/nature14234","article-title":"N6-methyladenosine-dependent RNA structural switches regulate RNA\u2013protein interactions","volume":"518","author":"Liu","year":"2015","journal-title":"Nature"},{"key":"2025070910134736800_ref12","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":"2025070910134736800_ref13","doi-asserted-by":"publisher","first-page":"552","DOI":"10.1038\/s41556-019-0319-0","article-title":"RNA modifications regulating cell fate in cancer","volume":"21","author":"Delaunay","year":"2019","journal-title":"Nat Cell Biol"},{"key":"2025070910134736800_ref14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/toxsci\/kfz252","article-title":"ToxPoint: dissecting functional RNA modifications in responses to environmental exposure\u2014mechanistic toxicology research enters a new era","volume":"174","author":"Yang","year":"2020","journal-title":"Toxicol Sci"},{"key":"2025070910134736800_ref15","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1016\/j.cell.2017.05.003","article-title":"The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention","volume":"169","author":"Pendleton","year":"2017","journal-title":"Cell"},{"key":"2025070910134736800_ref16","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/s41586-021-03536-w","article-title":"Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia","volume":"593","author":"Yankova","year":"2021","journal-title":"Nature"},{"key":"2025070910134736800_ref17","doi-asserted-by":"publisher","first-page":"e1702","DOI":"10.1002\/wrna.1702","article-title":"RNA modifications as emerging therapeutic targets","volume":"13","author":"Cayir","year":"2022","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2025070910134736800_ref18","doi-asserted-by":"publisher","first-page":"e105977","DOI":"10.15252\/embj.2020105977","article-title":"m6A RNA methylation: from mechanisms to therapeutic potential","volume":"40","author":"He","year":"2021","journal-title":"EMBO J"},{"key":"2025070910134736800_ref19","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","article-title":"Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"key":"2025070910134736800_ref20","doi-asserted-by":"publisher","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":"2025070910134736800_ref21","doi-asserted-by":"publisher","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":"2025070910134736800_ref22","doi-asserted-by":"publisher","first-page":"2037","DOI":"10.1101\/gad.269415.115","article-title":"A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation","volume":"29","author":"Ke","year":"2015","journal-title":"Genes Dev"},{"key":"2025070910134736800_ref23","doi-asserted-by":"publisher","first-page":"9250","DOI":"10.1093\/nar\/gkaa684","article-title":"METTL4 catalyzes m6Am methylation in U2 snRNA to regulate pre-mRNA splicing","volume":"48","author":"Goh","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref24","doi-asserted-by":"publisher","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":"2025070910134736800_ref25","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1016\/j.cell.2019.06.013","article-title":"Deciphering the \"m(6)A code\" via antibody-independent quantitative profiling","volume":"178","author":"Garcia-Campos","year":"2019","journal-title":"Cell"},{"key":"2025070910134736800_ref26","doi-asserted-by":"publisher","first-page":"D976","DOI":"10.1093\/nar\/gky987","article-title":"ETCM: an encyclopaedia of traditional Chinese medicine","volume":"47","author":"Xu","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref27","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1038\/s41592-019-0570-0","article-title":"DART-seq: an antibody-free method for global m6A detection","volume":"16","author":"Meyer","year":"2019","journal-title":"Nat Methods"},{"key":"2025070910134736800_ref28","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1016\/j.molcel.2021.12.038","article-title":"scDART-seq reveals distinct m6A signatures and mRNA methylation heterogeneity in single cells","volume":"82","author":"Tegowski","year":"2022","journal-title":"Mol Cell"},{"key":"2025070910134736800_ref29","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1038\/s41587-022-01587-6","article-title":"Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination","volume":"41","author":"Xiao","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2025070910134736800_ref30","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1038\/s41596-022-00765-9","article-title":"m6A-SAC-seq for quantitative whole transcriptome m6A profiling","volume":"18","author":"Ge","year":"2023","journal-title":"Nat Protoc"},{"key":"2025070910134736800_ref31","doi-asserted-by":"publisher","first-page":"D239","DOI":"10.1093\/nar\/gkad1083","article-title":"MODOMICS: a database of RNA modifications and related information. 2023 update","volume":"52","author":"Cappannini","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref32","doi-asserted-by":"publisher","first-page":"D273","DOI":"10.1093\/nar\/gkad1070","article-title":"RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications","volume":"52","author":"Xuan","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref33","doi-asserted-by":"publisher","first-page":"D1597","DOI":"10.1093\/nar\/gkad851","article-title":"PRMD: an integrated database for plant RNA modifications","volume":"52","author":"Lang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref34","doi-asserted-by":"publisher","first-page":"D194","DOI":"10.1093\/nar\/gkad691","article-title":"m6A-Atlas v2.0: updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species","volume":"52","author":"Liang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref35","doi-asserted-by":"publisher","first-page":"D1388","DOI":"10.1093\/nar\/gkac750","article-title":"RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication","volume":"51","author":"Song","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref36","doi-asserted-by":"publisher","first-page":"D1333","DOI":"10.1093\/nar\/gkac801","article-title":"M6AREG: m6A-centered regulation of disease development and drug response","volume":"51","author":"Liu","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref37","doi-asserted-by":"publisher","first-page":"D269","DOI":"10.1093\/nar\/gkac945","article-title":"RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications","volume":"51","author":"Bao","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref38","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/nmeth.4577","article-title":"Highly parallel direct RNA sequencing on an array of nanopores","volume":"15","author":"Garalde","year":"2018","journal-title":"Nat Methods"},{"key":"2025070910134736800_ref39","doi-asserted-by":"publisher","first-page":"16642","DOI":"10.1021\/acsnano.1c06488","article-title":"Direct nanopore sequencing of individual full length tRNA strands","volume":"15","author":"Thomas","year":"2021","journal-title":"ACS Nano"},{"key":"2025070910134736800_ref40","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.tibtech.2020.06.002","article-title":"New twists in detecting mRNA modification dynamics","volume":"39","author":"Anreiter","year":"2021","journal-title":"Trends Biotechnol"},{"key":"2025070910134736800_ref41","doi-asserted-by":"publisher","first-page":"4079","DOI":"10.1038\/s41467-019-11713-9","article-title":"Accurate detection of m6A RNA modifications in native RNA sequences","volume":"10","author":"Liu","year":"2019","journal-title":"Nat Commun"},{"key":"2025070910134736800_ref42","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1038\/s41587-021-00915-6","article-title":"Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing","volume":"39","author":"Begik","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2025070910134736800_ref43","doi-asserted-by":"publisher","first-page":"1914","DOI":"10.1093\/nar\/gkad044","article-title":"Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription","volume":"51","author":"Fleming","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref44","doi-asserted-by":"publisher","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"},{"key":"2025070910134736800_ref45","doi-asserted-by":"publisher","first-page":"4110","DOI":"10.1016\/j.csbj.2023.08.021","article-title":"RgnTX: colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity","volume":"21","author":"Wang","year":"2023","journal-title":"Comput Struct Biotechnol J"},{"key":"2025070910134736800_ref46","doi-asserted-by":"publisher","DOI":"10.1016\/j.xgen.2024.100702","article-title":"Statistical modeling of single-cell epitranscriptomics enabled trajectory and regulatory inference of RNA methylation. Cell","volume":"5","author":"Wang","year":"2025","journal-title":"Genomics"},{"key":"2025070910134736800_ref47","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1016\/j.gpb.2013.01.002","article-title":"MeRIP-PF: an easy-to-use pipeline for high-resolution peak-finding in MeRIP-Seq data","volume":"11","author":"Li","year":"2013","journal-title":"Genom Proteom Bioinform"},{"key":"2025070910134736800_ref48","doi-asserted-by":"publisher","first-page":"1565","DOI":"10.1093\/bioinformatics\/btt171","article-title":"Exome-based analysis for RNA epigenome sequencing data","volume":"29","author":"Meng","year":"2013","journal-title":"Bioinformatics"},{"key":"2025070910134736800_ref49","doi-asserted-by":"publisher","first-page":"2818","DOI":"10.1093\/bioinformatics\/btab181","article-title":"Detecting m6A methylation regions from methylated RNA immunoprecipitation sequencing","volume":"37","author":"Guo","year":"2021","journal-title":"Bioinformatics"},{"key":"2025070910134736800_ref50","doi-asserted-by":"publisher","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":"2025070910134736800_ref51","doi-asserted-by":"publisher","first-page":"C447","DOI":"10.1152\/ajpcell.00437.2022","article-title":"Bioinformatic tools for epitranscriptomics","volume":"324","author":"Taguchi","year":"2023","journal-title":"Am J Physiol Cell Physiol"},{"key":"2025070910134736800_ref52","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad163","article-title":"Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning","volume":"24","author":"Acera","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025070910134736800_ref53","doi-asserted-by":"publisher","first-page":"3175","DOI":"10.1016\/j.csbj.2024.08.004","article-title":"Domain-knowledge enabled ensemble learning of 5-formylcytosine (f5C) modification sites","volume":"23","author":"Huang","year":"2024","journal-title":"Comput Struct Biotechnol J"},{"key":"2025070910134736800_ref54","doi-asserted-by":"publisher","DOI":"10.1016\/j.omtn.2024.102376","article-title":"Interpretable deep cross networks unveiled common signatures of dysregulated epitranscriptomes across 12 cancer types","volume":"35","author":"Xia","year":"2024","journal-title":"Mol Ther Nucleic Acids"},{"key":"2025070910134736800_ref55","doi-asserted-by":"publisher","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":"2025070910134736800_ref56","doi-asserted-by":"crossref","first-page":"31080","DOI":"10.1038\/srep31080","article-title":"RAMPred: identifying the N1-methyladenosine sites in eukaryotic transcriptomes","volume":"6","author":"Chen","year":"2016","journal-title":"Sci Rep"},{"key":"2025070910134736800_ref57","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1016\/j.omtn.2019.10.008","article-title":"RNAm5CPred: prediction of RNA 5-methylcytosine sites based on three different kinds of nucleotide composition","volume":"18","author":"Fang","year":"2019","journal-title":"Mol Ther Nucleic Acids"},{"key":"2025070910134736800_ref58","doi-asserted-by":"publisher","first-page":"D203","DOI":"10.1093\/nar\/gkad789","article-title":"m7GHub V2.0: an updated database for decoding the N7-methylguanosine (m7G) epitranscriptome","volume":"52","author":"Wang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref59","doi-asserted-by":"publisher","first-page":"3362","DOI":"10.1093\/bioinformatics\/btv366","article-title":"PPUS: a web server to predict PUS-specific pseudouridine sites","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2025070910134736800_ref60","doi-asserted-by":"publisher","first-page":"4011","DOI":"10.1038\/s41467-021-24313-3","article-title":"Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications","volume":"12","author":"Song","year":"2021","journal-title":"Nat Commun"},{"key":"2025070910134736800_ref61","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac573","article-title":"Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences","volume":"24","author":"Wang","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025070910134736800_ref62","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad105","article-title":"Multi-task adaptive pooling enabled synergetic learning of RNA modification across tissue, type and species from low-resolution epitranscriptomes","volume":"24","author":"Song","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025070910134736800_ref63","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab480","article-title":"NmRF: identification of multispecies RNA 2'-O-methylation modification sites from RNA sequences","volume":"23","author":"Ao","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025070910134736800_ref64","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbad170","article-title":"ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species","volume":"24","author":"Chen","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025070910134736800_ref65","doi-asserted-by":"publisher","first-page":"e1011677","DOI":"10.1371\/journal.pcbi.1011677","article-title":"RMDGCN: prediction of RNA methylation and disease associations based on graph convolutional network with attention mechanism","volume":"19","author":"Liu","year":"2023","journal-title":"PLoS Comput Biol"},{"key":"2025070910134736800_ref66","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1038\/nrm3785","article-title":"The dynamic epitranscriptome: N6-methyladenosine and gene expression control","volume":"15","author":"Meyer","year":"2014","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025070910134736800_ref67","doi-asserted-by":"publisher","first-page":"1156","DOI":"10.1038\/s41588-021-00890-3","article-title":"Genetic drivers of m6A methylation in human brain, lung, heart and muscle","volume":"53","author":"Xiong","year":"2021","journal-title":"Nat Genet"},{"key":"2025070910134736800_ref68","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/nrg3724","article-title":"Gene expression regulation mediated through reversible m6A RNA methylation","volume":"15","author":"Fu","year":"2014","journal-title":"Nat Rev Genet"},{"key":"2025070910134736800_ref69","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1016\/j.molcel.2019.09.032","article-title":"Landscape and regulation of m(6)A and m(6)Am methylome across human and mouse tissues","volume":"77","author":"Liu","year":"2020","journal-title":"Mol Cell"},{"key":"2025070910134736800_ref70","doi-asserted-by":"crossref","first-page":"eaax0250","DOI":"10.1126\/sciadv.aax0250","article-title":"Single-base mapping of m6A by an antibody-independent method","volume":"5","author":"Zhang","year":"2019","journal-title":"Sci Adv"},{"key":"2025070910134736800_ref71","doi-asserted-by":"publisher","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":"2025070910134736800_ref72","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1016\/j.csbj.2020.04.015","article-title":"Computational identification of N6-methyladenosine sites in multiple tissues of mammals","volume":"18","author":"Dao","year":"2020","journal-title":"Comput Struct Biotechnol J"},{"key":"2025070910134736800_ref73","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1016\/j.omtn.2020.07.034","article-title":"im6A-TS-CNN: identifying the N6-methyladenine site in multiple tissues by using the convolutional neural network","volume":"21","author":"Liu","year":"2020","journal-title":"Mol Ther Nucleic Acids"},{"key":"2025070910134736800_ref74","doi-asserted-by":"publisher","first-page":"4619","DOI":"10.1016\/j.csbj.2021.08.014","article-title":"TS-m6A-DL: tissue-specific identification of N6-methyladenosine sites using a universal deep learning model","volume":"19","author":"Abbas","year":"2021","journal-title":"Comput Struct Biotechnol J"},{"key":"2025070910134736800_ref75","doi-asserted-by":"publisher","first-page":"15490","DOI":"10.3390\/ijms232415490","article-title":"Predicting N6-methyladenosine sites in multiple tissues of mammals through ensemble deep learning","volume":"23","author":"Luo","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2025070910134736800_ref76","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1109\/TCBB.2022.3192572","article-title":"DL-m6A: identification of N6-methyladenosine sites in mammals using deep learning based on different encoding schemes","volume":"20","author":"Rehman","year":"2023","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"key":"2025070910134736800_ref77","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1016\/j.gpb.2022.09.001","article-title":"m6A-TSHub: unveiling the context-specific m6A methylation and m6A-affecting mutations in 23 human tissues","volume":"21","author":"Song","year":"2023","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2025070910134736800_ref78","doi-asserted-by":"publisher","first-page":"731","DOI":"10.3390\/sym15030731","article-title":"M6A-BERT-stacking: a tissue-specific predictor for identifying RNA N6-methyladenosine sites based on BERT and stacking strategy","volume":"15","author":"Li","year":"2023","journal-title":"Symmetry"},{"key":"2025070910134736800_ref79","doi-asserted-by":"publisher","first-page":"btad709","DOI":"10.1093\/bioinformatics\/btad709","article-title":"Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues","volume":"39","author":"Zhang","year":"2023","journal-title":"Bioinformatics"},{"key":"2025070910134736800_ref80","doi-asserted-by":"publisher","first-page":"107892","DOI":"10.1016\/j.compbiomed.2023.107892","article-title":"Tissue-specific RNA methylation prediction from gene expression data using sparse regression models","volume":"169","author":"Jiang","year":"2024","journal-title":"Comput Biol Med"},{"key":"2025070910134736800_ref81","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ymeth.2024.03.004","article-title":"Deepm6A-MT: a deep learning-based method for identifying RNA N6-methyladenosine sites in multiple tissues","volume":"226","author":"Huang","year":"2024","journal-title":"Methods"},{"key":"2025070910134736800_ref82","doi-asserted-by":"publisher","first-page":"927","DOI":"10.1038\/nchembio.1654","article-title":"Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain","volume":"10","author":"Xu","year":"2014","journal-title":"Nat Chem Biol"},{"key":"2025070910134736800_ref83","doi-asserted-by":"publisher","first-page":"eabk2709","DOI":"10.1126\/scitranslmed.abk2709","article-title":"Inhibition of METTL3 attenuates renal injury and inflammation by alleviating TAB3 m6A modifications via IGF2BP2-dependent mechanisms","volume":"14","author":"Wang","year":"2022","journal-title":"Sci Transl Med"},{"key":"2025070910134736800_ref84","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1038\/s41419-022-04817-6","article-title":"METTL3-mediated m6A modification of STEAP2 mRNA inhibits papillary thyroid cancer progress by blocking the Hedgehog signaling pathway and epithelial-to-mesenchymal transition","volume":"13","author":"Zhu","year":"2022","journal-title":"Cell Death Dis"},{"key":"2025070910134736800_ref85","doi-asserted-by":"publisher","DOI":"10.1096\/fasebj.2022.36.S1.R3452","article-title":"METTL3 enhances hepatocellular carcinoma progression by regulating polycomb repressive complex 1 (PRC1) components BMI1 and RNF2","volume":"36","author":"Chen","year":"2022","journal-title":"FASEB J"},{"key":"2025070910134736800_ref86","doi-asserted-by":"publisher","first-page":"7155","DOI":"10.1158\/0008-5472.CAN-11-1212","article-title":"Blockade of TGF-\u03b2 signaling by the TGF\u03b2R-I kinase inhibitor LY2109761 enhances radiation response and prolongs survival in glioblastoma","volume":"71","author":"Zhang","year":"2011","journal-title":"Cancer Res"},{"key":"2025070910134736800_ref87","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1038\/s41467-019-08480-y","article-title":"Deciphering the complex role of thrombospondin-1 in glioblastoma development","volume":"10","author":"Daubon","year":"2019","journal-title":"Nat Commun"},{"key":"2025070910134736800_ref88","doi-asserted-by":"publisher","first-page":"175678","DOI":"10.1016\/j.ejphar.2023.175678","article-title":"TGF-\u03b2 signaling pathway: therapeutic targeting and potential for anti-cancer immunity","volume":"947","author":"Ali","year":"2023","journal-title":"Eur J Pharmacol"},{"key":"2025070910134736800_ref89","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s13059-020-02250-6","article-title":"A novel protein encoded by circular SMO RNA is essential for Hedgehog signaling activation and glioblastoma tumorigenicity","volume":"22","author":"Wu","year":"2021","journal-title":"Genome Biol"},{"key":"2025070910134736800_ref90","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1186\/s12935-017-0491-x","article-title":"Hedgehog\/Gli1 signaling pathway regulates MGMT expression and chemoresistance to temozolomide in human glioblastoma","volume":"17","author":"Wang","year":"2017","journal-title":"Cancer Cell Int"},{"key":"2025070910134736800_ref91","doi-asserted-by":"publisher","first-page":"eaal2323","DOI":"10.1126\/scisignal.aal2323","article-title":"Endoplasmic reticulum proteostasis in glioblastoma\u2014from molecular mechanisms to therapeutic perspectives","volume":"10","author":"Obacz","year":"2017","journal-title":"Sci Signal"},{"key":"2025070910134736800_ref92","doi-asserted-by":"publisher","first-page":"1504","DOI":"10.1038\/onc.2015.210","article-title":"Astrocytes promote glioma invasion via the gap junction protein connexin43","volume":"35","author":"Sin","year":"2016","journal-title":"Oncogene"},{"key":"2025070910134736800_ref93","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1158\/1541-7786.MCR-21-0199","article-title":"Glioblastoma\u2013astrocyte connexin 43 gap junctions promote tumor invasion","volume":"20","author":"McCutcheon","year":"2022","journal-title":"Mol Cancer Res"},{"key":"2025070910134736800_ref94","doi-asserted-by":"publisher","first-page":"326","DOI":"10.7555\/JBR.37.20220234","article-title":"HSP90B1-mediated plasma membrane localization of GLUT1 promotes radioresistance of glioblastomas","volume":"37","author":"Li","year":"2023","journal-title":"J Biomed Res"},{"key":"2025070910134736800_ref95","doi-asserted-by":"publisher","first-page":"eaay8826","DOI":"10.1126\/science.aay8826","article-title":"Autosomal dominant VCP hypomorph mutation impairs disaggregation of PHF-tau","volume":"370","author":"Darwich","year":"2020","journal-title":"Science"},{"key":"2025070910134736800_ref96","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1016\/j.nbd.2012.01.014","article-title":"DRPLA transgenic mouse substrains carrying single copy of full-length mutant human DRPLA gene with variable sizes of expanded CAG repeats exhibit CAG repeat length- and age-dependent changes in behavioral abnormalities and gene expression profiles","volume":"46","author":"Suzuki","year":"2012","journal-title":"Neurobiol Dis"},{"key":"2025070910134736800_ref97","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/3324926","article-title":"A survey of zero-shot learning: settings, methods, and applications","volume":"10","author":"Wang","year":"2019","journal-title":"ACM Trans Intell Syst Technol"},{"key":"2025070910134736800_ref98","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1109\/TPAMI.2018.2857768","article-title":"Zero-shot learning\u2014a comprehensive evaluation of the good, the bad and the ugly","volume":"41","author":"Xian","year":"2019","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"key":"2025070910134736800_ref99","doi-asserted-by":"publisher","DOI":"10.1002\/marc.202000124","article-title":"Adaptive pooling is all you need: an empirical study on hyperparameter-insensitive human action recognition using wearable sensors","author":"Abdu-Aguye","year":"2020","journal-title":"2020 International Joint Conference on Neural Networks (IJCNN)"},{"key":"2025070910134736800_ref100","doi-asserted-by":"publisher","first-page":"10290","DOI":"10.1093\/nar\/gkac830","article-title":"Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation","volume":"50","author":"Huang","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025070910134736800_ref101","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2025070910134736800_ref102","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat Methods"},{"key":"2025070910134736800_ref103","doi-asserted-by":"publisher","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"2025070910134736800_ref104","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/s13059-023-03024-6","article-title":"Cross-protein transfer learning substantially improves disease variant prediction","volume":"24","author":"Jagota","year":"2023","journal-title":"Genome Biol"},{"key":"2025070910134736800_ref105","first-page":"Article 2243","article-title":"Language models enable zero-shot prediction of the effects of mutations on protein function","volume-title":"Proceedings of the 35th International Conference on Neural Information Processing Systems","author":"Meier","year":"2021"},{"key":"2025070910134736800_ref106","doi-asserted-by":"publisher","first-page":"7861","DOI":"10.1038\/s41467-023-43597-1","article-title":"ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions","volume":"14","author":"Wang","year":"2023","journal-title":"Nat Commun"},{"key":"2025070910134736800_ref107","doi-asserted-by":"publisher","first-page":"5144","DOI":"10.1038\/s41467-023-40804-x","article-title":"Zero-shot visual reasoning through probabilistic analogical mapping","volume":"14","author":"Webb","year":"2023","journal-title":"Nat Commun"},{"key":"2025070910134736800_ref108","doi-asserted-by":"publisher","first-page":"738","DOI":"10.1038\/s41467-023-36476-2","article-title":"Multilingual translation for zero-shot biomedical classification using BioTranslator","volume":"14","author":"Xu","year":"2023","journal-title":"Nat Commun"},{"key":"2025070910134736800_ref109","doi-asserted-by":"publisher","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME suite: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/4\/bbaf332\/63711484\/bbaf332.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/4\/bbaf332\/63711484\/bbaf332.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,9]],"date-time":"2025-07-09T14:13:53Z","timestamp":1752070433000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf332\/8195345"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":109,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf332","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2025,7]]},"article-number":"bbaf332"}}