{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T20:50:21Z","timestamp":1784148621555,"version":"3.55.0"},"reference-count":81,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,26]],"date-time":"2025-05-26T00:00:00Z","timestamp":1748217600000},"content-version":"vor","delay-in-days":25,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170681"],"award-info":[{"award-number":["32170681"]}],"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":["32470717"],"award-info":[{"award-number":["32470717"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sub-project of National Key Research and Development Program","award":["2024YFD1201301-2"],"award-info":[{"award-number":["2024YFD1201301-2"]}]},{"name":"Key Research and Development Program of Shaanxi Province","award":["2024NC2-GJHX-16"],"award-info":[{"award-number":["2024NC2-GJHX-16"]}]},{"DOI":"10.13039\/501100005236","name":"Chinese Universities Scientific Fund","doi-asserted-by":"publisher","award":["Z1090224030"],"award-info":[{"award-number":["Z1090224030"]}],"id":[{"id":"10.13039\/501100005236","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Methylated RNA m6A immunoprecipitation sequencing (m6A-Seq) is a powerful technique for investigating transcriptome-wide m6A modification. However, most of the existing m6A-Seq protocols rely on reference genomes, limiting their use in species lacking sequenced genomes. Here, we introduce mlPEA, a user-friendly, multi-functional platform specifically tailored to the streamlined processing of m6A-Seq data in a reference genome-free manner. mlPEA provides a comprehensive collection of functions required for performing transcriptome-wide m6A identification and analysis, where the reference\u2014de novo assembled transcriptome\u2014is built solely using m6A-Seq data. By taking advantage of machine learning (ML) algorithms, mlPEA enhances m6A-Seq data analysis by constructing robust computational models for identifying high-quality transcripts and high-confidence m6A-modified regions. These functions and ML models have been integrated into a web-based Galaxy framework. This ensures that mlPEA has powerful data interaction and visualization capabilities, with flexibility, traceability, and reproducibility throughout the analytical process. mlPEA also has high compatibility and portability as it employs advanced packaging technology, dramatically simplifying its large-scale application in various species. Validated through case studies of Arabidopsis, maize, and wheat, mlPEA has demonstrated its utility and robustness regarding reference genome-free m6A-Seq data analysis for plants of various genomic complexities. mlPEA is freely available via GitHub: https:\/\/github.com\/cma2015\/mlPEA.<\/jats:p>","DOI":"10.1093\/bib\/bbaf235","type":"journal-article","created":{"date-parts":[[2025,5,26]],"date-time":"2025-05-26T07:43:47Z","timestamp":1748245427000},"source":"Crossref","is-referenced-by-count":3,"title":["Machine learning\u2013augmented m6A-Seq analysis without a reference genome"],"prefix":"10.1093","volume":"26","author":[{"given":"Jing","family":"Yang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minggui","family":"Song","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Bu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haonan","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenghui","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chujun","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shutu","family":"Xu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Maize Engineering & Technology Research Centre , College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuang","family":"Ma","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Resistance and High-Efficiency Production , College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region , Ministry of Agriculture, Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]},{"name":"Center of Bioinformatics , Northwest A&F University, Shaanxi, Yangling 712100,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,5,26]]},"reference":[{"key":"2025052702075408000_ref1","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/s13059-023-02947-4","article-title":"m6A readers ECT2\/ECT3\/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis","volume":"24","author":"Song","year":"2023","journal-title":"Genome Biol"},{"key":"2025052702075408000_ref2","doi-asserted-by":"publisher","first-page":"2569","DOI":"10.1111\/jipb.13575","article-title":"The m6A reader SiYTH1 enhances drought tolerance by affecting the messenger RNA stability of genes related to stomatal closure and reactive oxygen species scavenging in Setaria italica","volume":"65","author":"Luo","year":"2023","journal-title":"J Integr Plant Biol"},{"key":"2025052702075408000_ref3","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1016\/j.celrep.2018.10.020","article-title":"N6-methyladenosine inhibits local ribonucleolytic cleavage to stabilize mRNAs in Arabidopsis","volume":"25","author":"Anderson","year":"2018","journal-title":"Cell Rep"},{"key":"2025052702075408000_ref4","doi-asserted-by":"publisher","first-page":"e31311","DOI":"10.7554\/eLife.31311","article-title":"YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs","volume":"6","author":"Roundtree","year":"2017","journal-title":"elife"},{"key":"2025052702075408000_ref5","doi-asserted-by":"publisher","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":"2025052702075408000_ref6","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1038\/s41477-024-01638-7","article-title":"N6-methyladenosine-mediated feedback regulation of abscisic acid perception via phase-separated ECT8 condensates in Arabidopsis","volume":"10","author":"Wu","year":"2024","journal-title":"Nat Plants"},{"key":"2025052702075408000_ref7","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref8","doi-asserted-by":"publisher","first-page":"1294","DOI":"10.1111\/nph.18069","article-title":"MdMTA-mediated m6A modification enhances drought tolerance by promoting mRNA stability and translation efficiency of genes involved in lignin deposition and oxidative stress","volume":"234","author":"Hou","year":"2022","journal-title":"New Phytol"},{"key":"2025052702075408000_ref9","doi-asserted-by":"publisher","first-page":"2908","DOI":"10.1093\/plcell\/koae149","article-title":"The m6A reader ECT8 is an abiotic stress sensor that accelerates mRNA decay in Arabidopsis","volume":"36","author":"Cai","year":"2024","journal-title":"Plant Cell"},{"key":"2025052702075408000_ref10","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref11","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref12","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref13","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref14","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref15","doi-asserted-by":"publisher","first-page":"656302","DOI":"10.3389\/fmicb.2021.656302","article-title":"Transcriptome-wide N6-methyladenosine (m6A) profiling of susceptible and esistant wheat varieties reveals the involvement of variety-specific m6A modification involved in virus-host interaction pathways","volume":"12","author":"Zhang","year":"2021","journal-title":"Front Microbiol"},{"key":"2025052702075408000_ref16","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1111\/nph.19568","article-title":"Dynamic N6-methyladenosine RNA modification regulates peanut resistance to bacterial wilt","volume":"242","author":"Zhao","year":"2024","journal-title":"New Phytol"},{"key":"2025052702075408000_ref17","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref18","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref19","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref20","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref21","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref22","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref23","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\u2032 UTRs and near stop codons","volume":"149","author":"Meyer","year":"2012","journal-title":"Cell"},{"key":"2025052702075408000_ref24","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":"2025052702075408000_ref25","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\u2032 UTR regulation","volume":"29","author":"Ke","year":"2015","journal-title":"Genes Dev"},{"key":"2025052702075408000_ref26","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1038\/nmeth.3898","article-title":"m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome","volume":"13","author":"Molinie","year":"2016","journal-title":"Nat Methods"},{"key":"2025052702075408000_ref27","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":"2025052702075408000_ref28","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref29","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref30","doi-asserted-by":"publisher","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":"2025052702075408000_ref31","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref32","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1093\/plphys\/kiaa008","article-title":"deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data","volume":"185","author":"Zhai","year":"2020","journal-title":"Plant Physiol"},{"key":"2025052702075408000_ref33","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1186\/s13059-019-1915-9","article-title":"RADAR: differential analysis of MeRIP-seq data with a random effect model","volume":"20","author":"Zhang","year":"2019","journal-title":"Genome Biol"},{"key":"2025052702075408000_ref34","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref35","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref36","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2025052702075408000_ref37","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref38","doi-asserted-by":"publisher","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis","volume":"8","author":"Haas","year":"2013","journal-title":"Nat Protoc"},{"key":"2025052702075408000_ref39","doi-asserted-by":"publisher","first-page":"giz100","DOI":"10.1093\/gigascience\/giz100","article-title":"rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data","volume":"8","author":"Bushmanova","year":"2019","journal-title":"GigaScience"},{"key":"2025052702075408000_ref40","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/nmeth.1517","article-title":"De novo assembly and analysis of RNA-seq data","volume":"7","author":"Robertson","year":"2010","journal-title":"Nat Methods"},{"key":"2025052702075408000_ref41","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1186\/s13059-019-1690-7","article-title":"TransLiG: a de novo transcriptome assembler that uses line graph iteration","volume":"20","author":"Liu","year":"2019","journal-title":"Genome Biol"},{"key":"2025052702075408000_ref42","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinfomatics"},{"key":"2025052702075408000_ref43","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1186\/1471-2164-14-328","article-title":"Optimizing de novo assembly of short-read RNA-seq data for phylogenomics","volume":"14","author":"Yang","year":"2013","journal-title":"BMC Genomics"},{"key":"2025052702075408000_ref44","doi-asserted-by":"publisher","first-page":"e110","DOI":"10.1093\/nar\/gkad929","article-title":"A task-specific encoding algorithm for RNAs and RNA-associated interactions based on convolutional autoencoder","volume":"51","author":"Wang","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025052702075408000_ref45","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat Biotechnol"},{"key":"2025052702075408000_ref46","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4939-6658-5_1","article-title":"Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data","volume":"1533","author":"Bolser","year":"2017","journal-title":"Methods Mol Biol"},{"key":"2025052702075408000_ref47","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/j.patrec.2013.06.010","article-title":"A bagging SVM to learn from positive and unlabeled examples","volume":"37","author":"Mordelet","year":"2014","journal-title":"Pattern Recogn Lett"},{"key":"2025052702075408000_ref48","first-page":"2825","article-title":"Scikit-learn: machine learning in python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J Mach Learn Res"},{"key":"2025052702075408000_ref49","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1105\/tpc.113.121913","article-title":"Machine learning\u2013based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis","volume":"26","author":"Ma","year":"2014","journal-title":"Plant Cell"},{"key":"2025052702075408000_ref50","doi-asserted-by":"publisher","first-page":"2590","DOI":"10.1093\/bioinformatics\/btl441","article-title":"PSoL: a positive sample only learning algorithm for finding non-coding RNA genes","volume":"22","author":"Wang","year":"2006","journal-title":"Bioinformatics"},{"key":"2025052702075408000_ref51","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2025052702075408000_ref52","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025052702075408000_ref53","doi-asserted-by":"publisher","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2025052702075408000_ref54","doi-asserted-by":"publisher","first-page":"1200","DOI":"10.1093\/plphys\/kiae120","article-title":"PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants","volume":"195","author":"Song","year":"2024","journal-title":"Plant Physiol"},{"key":"2025052702075408000_ref55","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref56","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkaf277","article-title":"Analysis of RNA translation with a deep learning architecture provides new insight into translation control","volume-title":"Nucleic Acids Res","author":"Fan"},{"key":"2025052702075408000_ref57","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol Cell"},{"key":"2025052702075408000_ref58","doi-asserted-by":"publisher","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025052702075408000_ref59","doi-asserted-by":"publisher","first-page":"2115","DOI":"10.1093\/molbev\/msx148","article-title":"Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper","volume":"34","author":"Huerta-Cepas","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2025052702075408000_ref60","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1186\/s12859-017-1808-4","article-title":"QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model","volume":"18","author":"Liu","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"2025052702075408000_ref61","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"2025052702075408000_ref62","doi-asserted-by":"publisher","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"Li","year":"2021","journal-title":"Bioinformatics"},{"key":"2025052702075408000_ref63","doi-asserted-by":"publisher","first-page":"e323","DOI":"10.1002\/cpz1.323","article-title":"BUSCO: assessing genomic data quality and beyond","volume":"1","author":"Manni","year":"2021","journal-title":"Curr Protoc"},{"key":"2025052702075408000_ref64","doi-asserted-by":"publisher","first-page":"2210","DOI":"10.1093\/bioinformatics\/btw218","article-title":"rnaQUAST: a quality assessment tool for de novo transcriptome assemblies","volume":"32","author":"Bushmanova","year":"2016","journal-title":"Bioinformatics"},{"key":"2025052702075408000_ref65","doi-asserted-by":"publisher","first-page":"4881","DOI":"10.1038\/s41467-024-48941-7","article-title":"Quantitative profiling of m6A at single base resolution across the life cycle of rice and Arabidopsis","volume":"15","author":"Wang","year":"2024","journal-title":"Nat Commun"},{"key":"2025052702075408000_ref66","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":"2025052702075408000_ref67","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref68","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref69","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1105\/tpc.17.00934","article-title":"The m6A reader ECT2 controls trichome morphology by affecting mRNA stability in Arabidopsis","volume":"30","author":"Wei","year":"2018","journal-title":"Plant Cell"},{"key":"2025052702075408000_ref70","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1038\/nature22971","article-title":"Improved maize reference genome with single-molecule technologies","volume":"546","author":"Jiao","year":"2017","journal-title":"Nature"},{"key":"2025052702075408000_ref71","doi-asserted-by":"publisher","first-page":"2476","DOI":"10.1093\/plphys\/kiae451","article-title":"N6-methyladenosine transcriptome-wide profiles of maize kernel development","volume":"196","author":"Wu","year":"2024","journal-title":"Plant Physiol"},{"key":"2025052702075408000_ref72","doi-asserted-by":"publisher","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"},{"key":"2025052702075408000_ref73","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1105\/tpc.114.135657","article-title":"RNA sequencing of laser-capture microdissected compartments of the maize kernel identifies regulatory modules associated with endosperm cell differentiation","volume":"27","author":"Zhan","year":"2015","journal-title":"Plant Cell"},{"key":"2025052702075408000_ref74","doi-asserted-by":"publisher","first-page":"2384","DOI":"10.1111\/nph.17754","article-title":"ZmCTLP1 is required for the maintenance of lipid homeostasis and the basal endosperm transfer layer in maize kernels","volume":"232","author":"Hu","year":"2021","journal-title":"New Phytol"},{"key":"2025052702075408000_ref75","doi-asserted-by":"publisher","first-page":"1574","DOI":"10.1111\/tpj.16548","article-title":"Dynamic transcriptome landscape of maize pericarp development","volume":"117","author":"Zhang","year":"2024","journal-title":"Plant J"},{"key":"2025052702075408000_ref76","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1016\/j.molp.2021.11.013","article-title":"The O2-ZmGRAS11 transcriptional regulatory network orchestrates the coordination of endosperm cell expansion and grain filling in maize","volume":"15","author":"Ji","year":"2022","journal-title":"Mol Plant"},{"key":"2025052702075408000_ref77","doi-asserted-by":"crossref","first-page":"eaar7191","DOI":"10.1126\/science.aar7191","article-title":"Shifting the limits in wheat research and breeding using a fully annotated reference genome","volume":"361","author":"The International Wheat Genome Sequencing Consortium (IWGSC)","year":"2018","journal-title":"Science"},{"key":"2025052702075408000_ref78","doi-asserted-by":"publisher","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":"2025052702075408000_ref79","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1038\/s41587-022-01565-y","article-title":"Accurate isoform discovery with IsoQuant using long reads","volume":"41","author":"Prjibelski","year":"2023","journal-title":"Nat Biotechnol"},{"key":"2025052702075408000_ref80","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1186\/s12859-021-04206-4","article-title":"EDLm6APred: ensemble deep learning approach for mRNA m6A site prediction","volume":"22","author":"Zhang","year":"2021","journal-title":"BMC Bioinformatics"},{"key":"2025052702075408000_ref81","doi-asserted-by":"publisher","first-page":"4830","DOI":"10.1093\/nar\/gkae280","article-title":"m6ACali: machine learning-powered calibration for accurate m6A detection in MeRIP-Seq","volume":"52","author":"Ye","year":"2024","journal-title":"Nucleic Acids Res"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/3\/bbaf235\/63353031\/bbaf235.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/3\/bbaf235\/63353031\/bbaf235.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T06:08:06Z","timestamp":1748326086000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf235\/8148922"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,1]]},"references-count":81,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf235","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,5]]},"published":{"date-parts":[[2025,5,1]]},"article-number":"bbaf235"}}