ArticleNucleic acids research2024
RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- A token-pruning framework enables efficient representation of the human genome for RNA modification analysis.Bioinformatics (Oxford, England) · 2026Article
- DirectASRM: uncovering allele-specific post-transcriptional RNA modifications through direct RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- MoRNiNG: A Database of RNA Modification Sites Associated with RNA Secondary Structure Dynamics.Genomics, proteomics & bioinformatics · 2026Article
- Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome.Genomics, proteomics & bioinformatics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- A novel biclustering algorithm for mining m6A co-methylation patterns based on beta-binomial distribution and data screening strategy.PLoS computational biology · 2026Article
- Mapping the rRNA methylome reveals contributions of methyltransferases to ribosome function and antibiotic sensitivity.bioRxiv : the preprint server for biology · 2026Article
- ac4C modification sites prediction in human mRNA: a complete review.Briefings in bioinformatics · 2026Review
- Graph-based RNA structural representation reveals determinants of subcellular localization.Briefings in bioinformatics · 2026Article
- EvoRMD: integrating biological context and evolutionary RNA language models for interpretable prediction of RNA modifications.Genome biology · 2026Article
- Isoform-specific m6A deposition and coordinated splicing shape mammalian transcriptome evolution.Nature communications · 2026Article
- Unbiased profiling of translational landscape reveals TNFR2 as a translation-dependent vulnerability in colorectal cancer.Journal of experimental & clinical cancer research : CR · 2026Article
- The epigenetic and epitranscriptomic regulation of Brd4-Mettl3 axis on STING mediated vascular calcification.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Mitochondrial uncoupling inhibits serine catabolismCancer biology & medicine · 2026Article
- TRMT6-directed mNPJ precision oncology · 2026Article
- Comprehensive Profiling of NAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- RMzyme: regulations of RNA-modifying enzymes in humans.Signal transduction and targeted therapy · 2026Article
- Accelerate the Highly Efficient Development of mRNA Vaccines Through Advanced Computational Methods.MedComm · 2026Review
- Regulation of Translation of ATF4 mRNA: A Focus on Translation Initiation Factors and RNA-Binding Proteins.Cells · 2026Review
- Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.Nature communications · 2026Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the 'RNA Modifications' module reveals the map of 73 RNA modifications of 62 species. the 'Genes' module allows to retrieve RNA modification profiles and clusters by gene and transcript. The 'Mechanisms' module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The 'Co-localization' module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The 'RMP' module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The 'Interactome' integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The 'Motif' illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The 'Tools' introduces a novel web-based 'modGeneTool' for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.
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Registered trials
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 Socratic graph.