{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T19:10:34Z","timestamp":1789067434288,"version":"build-2803163510"},"reference-count":76,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T00:00:00Z","timestamp":1709251200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170681[CM]"],"award-info":[{"award-number":["32170681[CM]"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hundred Talents Program of Shaanxi Province of China"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>N 6-methyladenosine (m6A), which is the mostly prevalent modification in eukaryotic mRNAs, is involved in gene expression regulation and many RNA metabolism processes. Accurate prediction of m6A modification is important for understanding its molecular mechanisms in different biological contexts. However, most existing models have limited range of application and are species-centric. Here we present PEA-m6A, a unified, modularized and parameterized framework that can streamline m6A-Seq data analysis for predicting m6A-modified regions in plant genomes. The PEA-m6A framework builds ensemble learning-based m6A prediction models with statistic-based and deep learning-driven features, achieving superior performance with an improvement of 6.7% to 23.3% in the area under precision-recall curve compared with state-of-the-art regional-scale m6A predictor WeakRM in 12 plant species. Especially, PEA-m6A is capable of leveraging knowledge from pretrained models via transfer learning, representing an innovation in that it can improve prediction accuracy of m6A modifications under small-sample training tasks. PEA-m6A also has a strong capability for generalization, making it suitable for application in within- and cross-species m6A prediction. Overall, this study presents a promising m6A prediction tool, PEA-m6A, with outstanding performance in terms of its accuracy, flexibility, transferability, and generalization ability. PEA-m6A has been packaged using Galaxy and Docker technologies for ease of use and is publicly available at https:\/\/github.com\/cma2015\/PEA-m6A.<\/jats:p>","DOI":"10.1093\/plphys\/kiae120","type":"journal-article","created":{"date-parts":[[2024,3,2]],"date-time":"2024-03-02T01:41:36Z","timestamp":1709343696000},"page":"1200-1213","source":"Crossref","is-referenced-by-count":9,"title":["PEA-m6A: an ensemble learning framework for accurately predicting <i>N<\/i>6-methyladenosine modifications in plants"],"prefix":"10.1093","volume":"195","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4406-3877","authenticated-orcid":false,"given":"Minggui","family":"Song","sequence":"first","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4129-8571","authenticated-orcid":false,"given":"Jiawen","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8601-9289","authenticated-orcid":false,"given":"Chujun","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-8367-0730","authenticated-orcid":false,"given":"Chengchao","family":"Jia","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6386-6088","authenticated-orcid":false,"given":"Jing","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-8553-945X","authenticated-orcid":false,"given":"Haonan","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1535-3103","authenticated-orcid":false,"given":"Jingjing","family":"Zhai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"},{"name":"Institute for Genomic Diversity, Cornell University , Ithaca, NY 14853 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2869-4684","authenticated-orcid":false,"given":"Beilei","family":"Lei","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiheng","family":"Tao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2460-4381","authenticated-orcid":false,"given":"Siqi","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Computer Software, College of Intelligence and Computing, Tianjin University , Tianjin 300072 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5922-0364","authenticated-orcid":false,"given":"Ran","family":"Su","sequence":"additional","affiliation":[{"name":"School of Computer Software, College of Intelligence and Computing, Tianjin University , Tianjin 300072 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9612-7898","authenticated-orcid":false,"given":"Chuang","family":"Ma","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Center of Bioinformatics, College of Life Sciences, Northwest A&F University , Yangling, Shaanxi 712100 , China"},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,3,1]]},"reference":[{"issue":"3","key":"2024053117433240600_kiae120-B1","doi-asserted-by":"crossref","first-page":"bbad163","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 Mateos","year":"2023","journal-title":"Brief Bioinform"},{"key":"2024053117433240600_kiae120-B2","doi-asserted-by":"crossref","first-page":"2623","DOI":"10.1145\/3292500.3330701","article-title":"Optuna: a next-generation hyperparameter optimization framework","author":"Akiba","year":"2019","journal-title":"Proceedings of the 25th ACM SIGKDD international conference on Knowledge Discovery & Data Mining (KDD \u201919); Anchorage, AK, USA. New York (NY): Association for Computing Machinery"},{"issue":"Web Server","key":"2024053117433240600_kiae120-B3","doi-asserted-by":"crossref","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"},{"issue":"1","key":"2024053117433240600_kiae120-B4","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.molcel.2019.07.016","article-title":"N\n            6-methyladenosine modification controls circular RNA immunity","volume":"76","author":"Chen","year":"2019","journal-title":"Mol Cell"},{"key":"2024053117433240600_kiae120-B5","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.ab.2018.09.002","article-title":"iRNA(m6A)-PseDNC: identifying N6-methyladenosine sites using pseudo dinucleotide composition","volume":"561\u2013562","author":"Chen","year":"2018","journal-title":"Anal Biochem"},{"issue":"2","key":"2024053117433240600_kiae120-B6","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bib\/bbz018","article-title":"CAFU: a galaxy framework for exploring unmapped RNA-Seq data","volume":"21","author":"Chen","year":"2020","journal-title":"Brief Bioinform"},{"issue":"7","key":"2024053117433240600_kiae120-B7","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"},{"issue":"5","key":"2024053117433240600_kiae120-B8","doi-asserted-by":"crossref","first-page":"1676","DOI":"10.1093\/bib\/bbz112","article-title":"Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences","volume":"21","author":"Chen","year":"2020","journal-title":"Brief Bioinform"},{"issue":"17","key":"2024053117433240600_kiae120-B9","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"astp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"issue":"2","key":"2024053117433240600_kiae120-B10","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.devcel.2021.12.014","article-title":"RNA N6-methyladenosine modification promotes auxin biosynthesis required for male meiosis in rice","volume":"57","author":"Cheng","year":"2022","journal-title":"Dev Cell"},{"issue":"1","key":"2024053117433240600_kiae120-B11","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1186\/s12284-021-00502-y","article-title":"Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress","volume":"14","author":"Cheng","year":"2021","journal-title":"Rice (N Y)"},{"issue":"D1","key":"2024053117433240600_kiae120-B12","doi-asserted-by":"crossref","first-page":"D18","DOI":"10.1093\/nar\/gkaa1022","article-title":"Database resources of the national genomics data center, China national center for bioinformation in 2021","volume":"49","author":"CNCB-NGDC Members and Partners","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2024053117433240600_kiae120-B13","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1038\/nprot.2012.148","article-title":"Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing","volume":"8","author":"Dominissini","year":"2013","journal-title":"Nat Protoc"},{"issue":"7397","key":"2024053117433240600_kiae120-B14","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"},{"issue":"19","key":"2024053117433240600_kiae120-B15","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"issue":"5","key":"2024053117433240600_kiae120-B16","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1214\/aos\/1013203451","article-title":"Greedy function approximation: a gradient boosting machine","volume":"29","author":"Friedman","year":"2001","journal-title":"Ann Stat"},{"issue":"1","key":"2024053117433240600_kiae120-B17","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1093\/plphys\/kiac272","article-title":"Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa","volume":"190","author":"Gao","year":"2022","journal-title":"Plant Physiol"},{"issue":"D1","key":"2024053117433240600_kiae120-B18","doi-asserted-by":"crossref","first-page":"D1178","DOI":"10.1093\/nar\/gkr944","article-title":"Phytozome: a comparative platform for green plant genomics","volume":"40","author":"Goodstein","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2024053117433240600_kiae120-B19","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1111\/pbi.13733","article-title":"The m6A reader MhYTP2 regulates MdMLO19 mRNA stability and antioxidant genes translation efficiency conferring powdery mildew resistance in apple","volume":"20","author":"Guo","year":"2022","journal-title":"Plant Biotechnol J"},{"issue":"18","key":"2024053117433240600_kiae120-B20","doi-asserted-by":"crossref","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"},{"issue":"1","key":"2024053117433240600_kiae120-B21","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1186\/s40537-020-00369-8","article-title":"CatBoost for big data: an interdisciplinary review","volume":"7","author":"Hancock","year":"2020","journal-title":"J Big Data"},{"issue":"8","key":"2024053117433240600_kiae120-B22","doi-asserted-by":"crossref","first-page":"2856","DOI":"10.1016\/j.ymthe.2022.05.001","article-title":"Deepm5C: a deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy","volume":"30","author":"Hasan","year":"2022","journal-title":"Mol Ther"},{"issue":"6633","key":"2024053117433240600_kiae120-B23","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1126\/science.abj9090","article-title":"Exon architecture controls mRNA m6A suppression and gene expression","volume":"379","author":"He","year":"2023","journal-title":"Science"},{"issue":"D1","key":"2024053117433240600_kiae120-B24","doi-asserted-by":"crossref","first-page":"D689","DOI":"10.1093\/nar\/gkz890","article-title":"Ensembl genomes 2020\u2014enabling non-vertebrate genomic research","volume":"48","author":"Howe","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"Suppl 1","key":"2024053117433240600_kiae120-B25","doi-asserted-by":"crossref","first-page":"i222","DOI":"10.1093\/bioinformatics\/btab278","article-title":"Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data","volume":"37","author":"Huang","year":"2021","journal-title":"Bioinformatics"},{"issue":"8","key":"2024053117433240600_kiae120-B26","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"7","key":"2024053117433240600_kiae120-B27","doi-asserted-by":"crossref","first-page":"1812","DOI":"10.1093\/molbev\/msx116","article-title":"TimeTree: a resource for timelines, timetrees, and divergence times","volume":"34","author":"Kumar","year":"2017","journal-title":"Mol Biol Evol"},{"issue":"D1","key":"2024053117433240600_kiae120-B28","first-page":"D134","article-title":"m6A-Atlas v2.0: updated resources for unraveling the N6-methyladenosine (m6A) epitranscriptome among multiple species","volume":"49","author":"Liang","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2024053117433240600_kiae120-B29","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.ymeth.2021.11.010","article-title":"m6A-Maize: weakly supervised prediction of m6A-carrying transcripts and m6A-affecting mutations in maize (Zea mays)","volume":"203","author":"Liang","year":"2022","journal-title":"Methods"},{"issue":"1","key":"2024053117433240600_kiae120-B30","doi-asserted-by":"crossref","first-page":"4935","DOI":"10.1038\/s41467-023-40426-3","article-title":"Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes","volume":"14","author":"Lin","year":"2023","journal-title":"Nat Commun"},{"issue":"1","key":"2024053117433240600_kiae120-B31","doi-asserted-by":"crossref","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"},{"issue":"1","key":"2024053117433240600_kiae120-B32","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/s41420-022-01050-0","article-title":"The emerging roles of N6-methyladenosine (m6A)-modified long non-coding RNAs in human cancers","volume":"8","author":"Liu","year":"2022","journal-title":"Cell Death Discov"},{"issue":"1","key":"2024053117433240600_kiae120-B33","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/s42256-019-0138-9","article-title":"From local explanations to global understanding with explainable AI for trees","volume":"2","author":"Lundberg","year":"2020","journal-title":"Nat Mach Intell"},{"issue":"1","key":"2024053117433240600_kiae120-B34","doi-asserted-by":"crossref","first-page":"5630","DOI":"10.1038\/ncomms6630","article-title":"Unique features of the m6A methylome in Arabidopsis thaliana","volume":"5","author":"Luo","year":"2014","journal-title":"Nat Commun"},{"issue":"8","key":"2024053117433240600_kiae120-B35","doi-asserted-by":"crossref","first-page":"2933","DOI":"10.1093\/jxb\/erab074","article-title":"Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize","volume":"72","author":"Luo","year":"2021","journal-title":"J Exp Bot"},{"issue":"1","key":"2024053117433240600_kiae120-B36","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1104\/pp.19.00987","article-title":"Natural variation in RNA m6A methylation and its relationship with translational status","volume":"182","author":"Luo","year":"2020","journal-title":"Plant Physiol"},{"issue":"1","key":"2024053117433240600_kiae120-B37","doi-asserted-by":"crossref","first-page":"2720","DOI":"10.1038\/s41467-022-30209-7","article-title":"Deep learning modeling m6A deposition reveals the importance of downstream cis-element sequences","volume":"13","author":"Luo","year":"2022","journal-title":"Nat Commun"},{"issue":"3","key":"2024053117433240600_kiae120-B38","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1101\/gr.212563.116","article-title":"Evolution of transcript modification by N6-methyladenosine in primates","volume":"27","author":"Ma","year":"2017","journal-title":"Genome Res"},{"issue":"1","key":"2024053117433240600_kiae120-B39","doi-asserted-by":"crossref","first-page":"6590","DOI":"10.1038\/s41598-020-63355-3","article-title":"Limits in the detection of m6A changes using MeRIP\/m6A-seq","volume":"10","author":"McIntyre","year":"2020","journal-title":"Sci Rep"},{"issue":"7","key":"2024053117433240600_kiae120-B40","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","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"issue":"1","key":"2024053117433240600_kiae120-B41","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1104\/pp.19.00323","article-title":"Evolution of the RNA N6-methyladenosine methylome mediated by genomic duplication","volume":"182","author":"Miao","year":"2020","journal-title":"Plant Physiol"},{"issue":"1","key":"2024053117433240600_kiae120-B42","doi-asserted-by":"crossref","first-page":"msab299","DOI":"10.1093\/molbev\/msab299","article-title":"Evolutionary implications of the RNA N6-methyladenosine methylome in plants","volume":"39","author":"Miao","year":"2022","journal-title":"Mol Biol Evol"},{"issue":"11","key":"2024053117433240600_kiae120-B43","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1038\/s41587-021-00949-w","article-title":"Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore","volume":"39","author":"Pratanwanich","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2024053117433240600_kiae120-B44","first-page":"6639","article-title":"CatBoost: unbiased boosting with categorical features","author":"Prokhorenkova","year":"2018","journal-title":"Proceedings of the 32nd international conference on Neural Information Processing Systems (NIPS'18); Montr\u00e9al Canada. Red Hook (NY): Curran Associates Inc"},{"issue":"1","key":"2024053117433240600_kiae120-B45","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13059-021-02598-3","article-title":"DENA: training an authentic neural network model using nanopore sequencing data of Arabidopsis transcripts for detection and quantification of N6-methyladenosine on RNA","volume":"23","author":"Qin","year":"2022","journal-title":"Genome Biol"},{"issue":"3","key":"2024053117433240600_kiae120-B46","doi-asserted-by":"crossref","first-page":"bbaa137","DOI":"10.1093\/bib\/bbaa137","article-title":"Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS","volume":"22","author":"Qiu","year":"2021","journal-title":"Brief Bioinform"},{"issue":"1","key":"2024053117433240600_kiae120-B47","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1111\/nph.18117","article-title":"MTA1-mediated RNA m6A modification regulates autophagy and is required for infection of the rice blast fungus","volume":"235","author":"Ren","year":"2022","journal-title":"New Phytol"},{"issue":"4","key":"2024053117433240600_kiae120-B48","doi-asserted-by":"crossref","first-page":"e1249","DOI":"10.1002\/widm.1249","article-title":"Ensemble learning: a survey","volume":"8","author":"Sagi","year":"2018","journal-title":"WIREs Data Mining Knowl Discov"},{"issue":"D1","key":"2024053117433240600_kiae120-B49","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024053117433240600_kiae120-B50","doi-asserted-by":"crossref","first-page":"102047","DOI":"10.1016\/j.pbi.2021.102047","article-title":"N6-methyladenosine modification underlies messenger RNA metabolism and plant development","volume":"63","author":"Shao","year":"2021","journal-title":"Curr Opin Plant Biol"},{"issue":"1","key":"2024053117433240600_kiae120-B51","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s13059-023-02872-6","article-title":"Recent advances in the plant epitranscriptome","volume":"24","author":"Shen","year":"2023","journal-title":"Genome Biol"},{"issue":"1","key":"2024053117433240600_kiae120-B52","doi-asserted-by":"crossref","first-page":"2813","DOI":"10.1038\/s41467-023-38414-8","article-title":"Small-sample learning reveals propionylation in determining global protein homeostasis","volume":"14","author":"Shui","year":"2023","journal-title":"Nat Commun"},{"issue":"1","key":"2024053117433240600_kiae120-B53","doi-asserted-by":"crossref","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":"2024053117433240600_kiae120-B54","doi-asserted-by":"crossref","first-page":"519","DOI":"10.3389\/fpls.2018.00519","article-title":"Transcriptome-wide annotation of m5C RNA modifications using machine learning","volume":"9","author":"Song","year":"2018","journal-title":"Front Plant Sci"},{"issue":"3","key":"2024053117433240600_kiae120-B55","doi-asserted-by":"crossref","first-page":"100546","DOI":"10.1016\/j.xplc.2023.100546","article-title":"Detection, regulation, and functions of RNA N6-methyladenosine modification in plants","volume":"4","author":"Tang","year":"2023","journal-title":"Plant Commun"},{"issue":"D1","key":"2024053117433240600_kiae120-B56","doi-asserted-by":"crossref","first-page":"D134","DOI":"10.1093\/nar\/gkaa692","article-title":"m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome","volume":"49","author":"Tang","year":"2020","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"2024053117433240600_kiae120-B57","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.molcel.2022.12.026","article-title":"Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability","volume":"83","author":"Uzonyi","year":"2023","journal-title":"Mol Cell"},{"key":"2024053117433240600_kiae120-B58","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1016\/j.ymeth.2022.03.001","article-title":"A brief review of machine learning methods for RNA methylation sites prediction","volume":"203","author":"Wang","year":"2022","journal-title":"Methods"},{"issue":"3","key":"2024053117433240600_kiae120-B59","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1007\/s11103-018-0698-9","article-title":"RFAthm6a: a new tool for predicting m6A sites in Arabidopsis thaliana","volume":"96","author":"Wang","year":"2018","journal-title":"Plant Mol Biol"},{"issue":"1","key":"2024053117433240600_kiae120-B60","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13059-022-02612-2","article-title":"FIONA1 is an RNA N6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering","volume":"23","author":"Wang","year":"2022","journal-title":"Genome Biol"},{"issue":"2","key":"2024053117433240600_kiae120-B61","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1111\/nph.17630","article-title":"A deep learning approach to automate whole-genome prediction of diverse epigenomic modifications in plants","volume":"232","author":"Wang","year":"2021","journal-title":"New Phytol"},{"issue":"4","key":"2024053117433240600_kiae120-B62","doi-asserted-by":"crossref","first-page":"2513","DOI":"10.1093\/plphys\/kiad470","article-title":"Global hypermethylation of the N6-methyladenosine RNA modification associated with apple heterografting","volume":"193","author":"Xu","year":"2023","journal-title":"Plant Physiol"},{"key":"2024053117433240600_kiae120-B63","doi-asserted-by":"crossref","first-page":"685189","DOI":"10.3389\/fpls.2021.685189","article-title":"Transcriptome-wide analysis of RNA m6A methylation and gene expression changes among two Arabidopsis ecotypes and their reciprocal hybrids","volume":"12","author":"Xu","year":"2021","journal-title":"Front Plant Sci"},{"issue":"6","key":"2024053117433240600_kiae120-B64","doi-asserted-by":"crossref","first-page":"2103628","DOI":"10.1002\/advs.202103628","article-title":"FIONA1-mediated m6a modification regulates the floral transition in Arabidopsis","volume":"9","author":"Xu","year":"2022","journal-title":"Adv Sci (Weinh)"},{"issue":"4","key":"2024053117433240600_kiae120-B65","first-page":"6550","article-title":"Not all attention is needed: gated attention network for sequence data","volume":"34","author":"Xue","year":"2019","journal-title":"Proceedings of the 34th AAAI Conference on Artificial Intelligence; New York Hilton Midtown, New York, New York, USA. Palo Alto (CA): AAAI Press"},{"issue":"12","key":"2024053117433240600_kiae120-B66","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1038\/s41587-021-00982-9","article-title":"RNA demethylation increases the yield and biomass of rice and potato plants in field trials","volume":"39","author":"Yu","year":"2021","journal-title":"Nat Biotechnol"},{"issue":"2","key":"2024053117433240600_kiae120-B67","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1093\/bfgp\/elaa021","article-title":"The impact of epitranscriptomic marks on post-transcriptional regulation in plants","volume":"20","author":"Yu","year":"2021","journal-title":"Brief Funct Genomics"},{"issue":"21","key":"2024053117433240600_kiae120-B68","doi-asserted-by":"crossref","first-page":"3747","DOI":"10.1093\/bioinformatics\/bty421","article-title":"PEA: an integrated R toolkit for plant epitranscriptome analysis","volume":"34","author":"Zhai","year":"2018","journal-title":"Bioinformatics"},{"issue":"1","key":"2024053117433240600_kiae120-B69","first-page":"29","article-title":"deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data","volume":"185","author":"Zhai","year":"2020","journal-title":"Plant Physiol"},{"issue":"1","key":"2024053117433240600_kiae120-B70","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/s41467-022-28753-3","article-title":"Two zinc finger proteins with functions in m6A writing interact with HAKAI","volume":"13","author":"Zhang","year":"2022","journal-title":"Nat Commun"},{"issue":"9","key":"2024053117433240600_kiae120-B71","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"},{"issue":"1","key":"2024053117433240600_kiae120-B72","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1186\/s13059-021-02410-2","article-title":"The dynamics of N6-methyladenine RNA modification in interactions between rice and plant viruses","volume":"22","author":"Zhang","year":"2021","journal-title":"Genome Biol"},{"issue":"1","key":"2024053117433240600_kiae120-B73","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1186\/s12870-023-04458-7","article-title":"Changes in m6A RNA methylation are associated with male sterility in wolfberry","volume":"23","author":"Zhao","year":"2023","journal-title":"BMC Plant Biol"},{"key":"2024053117433240600_kiae120-B74","doi-asserted-by":"crossref","first-page":"110801","DOI":"10.1016\/j.plantsci.2020.110801","article-title":"Analysis of N6-methyladenosine reveals a new important mechanism regulating the salt tolerance of sweet sorghum","volume":"304","author":"Zheng","year":"2021","journal-title":"Plant Sci"},{"issue":"1","key":"2024053117433240600_kiae120-B75","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1186\/s13059-021-02385-0","article-title":"N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner","volume":"22","author":"Zhou","year":"2021","journal-title":"Genome Biol"},{"issue":"10","key":"2024053117433240600_kiae120-B76","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"}],"container-title":["Plant Physiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/plphys\/advance-article-pdf\/doi\/10.1093\/plphys\/kiae120\/56963975\/kiae120.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/plphys\/article-pdf\/195\/2\/1200\/58035582\/kiae120.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/plphys\/article-pdf\/195\/2\/1200\/58035582\/kiae120.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,31]],"date-time":"2024-05-31T22:17:48Z","timestamp":1717193868000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/plphys\/article\/195\/2\/1200\/7617589"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,1]]},"references-count":76,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2024,3,1]]},"published-print":{"date-parts":[[2024,5,31]]}},"URL":"https:\/\/doi.org\/10.1093\/plphys\/kiae120","relation":{},"ISSN":["0032-0889","1532-2548"],"issn-type":[{"value":"0032-0889","type":"print"},{"value":"1532-2548","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,6]]},"published":{"date-parts":[[2024,3,1]]}}}