ArticleNucleic acids research2009
MODOMICS: a database of RNA modification pathways. 2008 update.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
116 citing papers in PubMed, 27 citations in OpenAlex.
- 23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures.Nucleic acids research · 2026Article
- MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary.Nucleic acids research · 2026Article
- The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA.Journal of molecular evolution · 2024Review
- Perturbation of METTL1-mediated tRNA NNature communications · 2024Article
- Ribosomal RNA modification enzymes stimulate large ribosome subunit assembly in E. coli.Nucleic acids research · 2024Article
- Interconnections between mLife science alliance · 2024Review
- TRMT6 promotes hepatocellular carcinoma progression through the PI3K/AKT signaling pathway.European journal of medical research · 2023Article
- Nucleic acid adductomics - The next generation of adductomics towards assessing environmental health risks.The Science of the total environment · 2023Article
- The landscape of implantation and placentation: deciphering the function of dynamic RNA methylation at the maternal-fetal interface.Frontiers in endocrinology · 2023Review
- Genome-Wide Identification of mGenes · 2022Article
- RNA modifications stabilize the tertiary structure of tRNAfMet by locally increasing conformational dynamics.Nucleic acids research · 2022Article
- "Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code.Life (Basel, Switzerland) · 2022Review
- Epitranscriptomics of cardiovascular diseases (Review).International journal of molecular medicine · 2022Review
- Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC.Scientific reports · 2021Article
- tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast.RNA biology · 2021Article
- Article
- The Latest Research Progress of mFrontiers in cell and developmental biology · 2021Review
- Structural and Energetic Effects of O2'-Ribose Methylation of Protonated Pyrimidine Nucleosides.Journal of the American Society for Mass Spectrometry · 2019Article
- Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins.Free radical biology & medicine · 2019Review
- Ncl1-mediated metabolic rewiring critical during metabolic stress.Life science alliance · 2019Article
56 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MODOMICS, a database devoted to the systems biology of RNA modification, has been subjected to substantial improvements. It provides comprehensive information on the chemical structure of modified nucleosides, pathways of their biosynthesis, sequences of RNAs containing these modifications and RNA-modifying enzymes. MODOMICS also provides cross-references to other databases and to literature. In addition to the previously available manually curated tRNA sequences from a few model organisms, we have now included additional tRNAs and rRNAs, and all RNAs with 3D structures in the Nucleic Acid Database, in which modified nucleosides are present. In total, 3460 modified bases in RNA sequences of different organisms have been annotated. New RNA-modifying enzymes have been also added. The current collection of enzymes includes mainly proteins for the model organisms Escherichia coli and Saccharomyces cerevisiae, and is currently being expanded to include proteins from other organisms, in particular Archaea and Homo sapiens. For enzymes with known structures, links are provided to the corresponding Protein Data Bank entries, while for many others homology models have been created. Many new options for database searching and querying have been included. MODOMICS can be accessed at http://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.