ArticleNucleic acids research2026
MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Computational prediction of RNA modification site-disease associations: a systematic review.Briefings in bioinformatics · 2026Pooled it
- Production of MarathonRT and its comparison with commercial reverse transcriptases for tRNA sequencing library preparation.RNA biology · 2026Article
- Polyphenism Through RNA Chemical Modifications.Molecular ecology · 2026Review
- qMAP decodes RNA fragmentation dynamics in development and disease.Molecular systems biology · 2026Article
- Defining cell surface and glycosylated RNAs.Trends in genetics : TIG · 2026Review
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Article
- How Epitranscriptomic Machinery Senses Environmental Cues.Advanced biology · 2026Review
- Mechanistic Insights Into the Oxidative Reactivity of 2-Selenouridine in tRNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Identification of Rice mPlants (Basel, Switzerland) · 2026Article
- Multi-omics-driven precision medicine.iMeta · 2026Review
- Guanosine 10 methylation by TRMT11-TRMT112 optimizes human mitochondrial tRNAs for efficient translation.Nucleic acids research · 2026Article
- RNAViruses · 2026Review
- ModiCal: A Targeted Calibration Workflow for Site-Specific mACS chemical biology · 2026Article
- Prediction of Ligand Binding to Transthyretin Using Machine Learning Algorithms and Low-Dimensional Molecular Descriptors: A Tox24 Challenge Study.Chemical research in toxicology · 2026Article
- Mapping the rRNA methylome reveals contributions of methyltransferases to ribosome function and antibiotic sensitivity.bioRxiv : the preprint server for biology · 2026Article
- NanoCortex: A Unified Agentic System for Nanopore Sequencing Analysis.bioRxiv : the preprint server for biology · 2026Article
- Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State inbioRxiv : the preprint server for biology · 2026Article
- The Evolution of the First Code.Genes · 2026Review
- Mechanism of 30S subunit recognition and modification by the conserved bacterial ribosomal RNA methyltransferase RsmI.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
MODOMICS is the reference database of RNA modifications and related information, integrating chemical, biochemical, structural, and functional data. In this 2025 update, marking the 20th anniversary of MODOMICS, the database has been significantly expanded in scope and depth. The RNA sequence section now includes transcriptome-wide data generated in collaboration with Sci-ModoM, a quantitative resource of high-throughput epitranscriptomic datasets, enabling the representation of >48 000 transcripts with high-confidence modification annotations. The catalog of modified residues was improved with systematic curation, and addition of new computational descriptors derived from quantum mechanical calculations. An all-versus-all similarity analysis of chemical structures was performed, and the results are provided as an interactive similarity graph to explore chemical relationships among modifications. The protein section has been updated with newly characterized enzymes and expanded annotations of modification pathways, supported by an improved evidence and reliability framework. Together, these advances further strengthen MODOMICS as a comprehensive and reliable community resource, serving as both a reference and a platform for discovery in the rapidly developing field of epitranscriptomics. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.
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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 OpenQuestion graph.