ArticleNucleic acids research2019
WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.
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132 citing papers in PubMed, 232 citations in OpenAlex.
- A novel method for the identification and quantification of N6-methyladenosine motifs in RNA transcripts.Molecular biology reports · 2026Article
- Sequence determinant and functional relevance of 8-oxoguanine RNA modification unveiled from foundation-model-based predictor.Molecular therapy. Nucleic acids · 2026Article
- mArXiv · 2026Article
- A novel biclustering algorithm for mining m6A co-methylation patterns based on beta-binomial distribution and data screening strategy.PLoS computational biology · 2026Article
- M6AREG 2.0: the landscape of m6A-centered crosstalk with diverse epigenetic regulation.Nucleic acids research · 2026Article
- m6AHD: a new framework for identifying abnormal N6-methyladenosine (m6A) in heart diseases based on sequencing features.Frontiers in genetics · 2026Article
- Functional Prediction of Epitranscriptome.Methods in molecular biology (Clifton, N.J.) · 2026Article
- mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset.Nature communications · 2025Article
- PathoRM: Computational inference of pathogenic RNA methylation sites by incorporating multi-view features.PLoS computational biology · 2025Article
- Deciphering RNA modification and post-transcriptional regulation with NetRNApan.Briefings in bioinformatics · 2025Article
- A robust deep learning framework for RNA 5-methyluridine modification prediction using integrated features.BMC biology · 2025Article
- Block sparse Bayes-based fuzzy system for RNA N6-methyladenosine sites prediction.PLoS computational biology · 2025Article
- Interpretability-guided RNA NCommunications biology · 2025Article
- Article
- HNRNPC promotes progression of non-small cell lung cancer by maintaining TFAP2A mRNA stability.Cancer cell international · 2025Article
- Exploring the methyl-verse: Dynamic interplay of epigenome and m6A epitranscriptome.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- Hybrid representation learning for human mBioinformatics advances · 2025Article
- MLA-ac4C: A N4-Acetylcytidine Site Prediction Model Based on Multi-Layer Attention, Bidirectional GRU, and DenseNet.Current genomics · 2025Article
- AI techniques have facilitated the understanding of epitranscriptome distribution.Cell genomics · 2024Article
- A combined deep learning framework for mammalian m6A site prediction.Cell genomics · 2024Article
72 more citing papers are in PubMed but not listed here.
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10 authors at 2 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
N 6-methyladenosine (m6A) is the most prevalent post-transcriptional modification in eukaryotes, and plays a pivotal role in various biological processes, such as splicing, RNA degradation and RNA-protein interaction. We report here a prediction framework WHISTLE for transcriptome-wide m6A RNA-methylation site prediction. When tested on six independent datasets, our approach, which integrated 35 additional genomic features besides the conventional sequence features, achieved a major improvement in the accuracy of m6A site prediction (average AUC: 0.948 and 0.880 under the full transcript or mature messenger RNA models, respectively) compared to the state-of-the-art computational approaches MethyRNA (AUC: 0.790 and 0.732) and SRAMP (AUC: 0.761 and 0.706). It also out-performed the existing epitranscriptome databases MeT-DB (AUC: 0.798 and 0.744) and RMBase (AUC: 0.786 and 0.736), which were built upon hundreds of epitranscriptome high-throughput sequencing samples. To probe the putative biological processes impacted by changes in an individual m6A site, a network-based approach was implemented according to the 'guilt-by-association' principle by integrating RNA methylation profiles, gene expression profiles and protein-protein interaction data. Finally, the WHISTLE web server was built to facilitate the query of our high-accuracy map of the human m6A epitranscriptome, and the server is freely available at: www.xjtlu.edu.cn/biologicalsciences/whistle and http://whistle-epitranscriptome.com.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.