ArticleJournal of cheminformatics2019
DNAmod: the DNA modification database.
Article in Journal of cheminformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 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
57 citing papers in PubMed.
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- Discovery and biosynthesis of a novel diaminopropane-modified thymine in phage DNA.Nucleic acids research · 2026Article
- Epigenetic regulation in atherosclerosis and its therapeutic potential.Nature reviews. Cardiology · 2026Review
- A pair of DNA glucosyltransferases elevate counter-defense in bacteriophage T4.Nucleic acids research · 2026Article
- Metabolic isotopic labeling of (deoxy)ribose enables dual neutral loss scanning for profiling nucleic acid modifications.Nucleic acids research · 2026Article
- Carboxymethylcytosine is a natural base modification and a handle for bacteriophage DNA hypermodification.Nature communications · 2025Article
- Amplification-free cancer diagnosis based on inhibition of Cas12a activity by site-specific 5mC-modified cfDNA.Nucleic acids research · 2025Article
- Direct detection of 8-oxo-dG using nanopore sequencing.Nature communications · 2025Article
- ReQuant: improved base modification calling by k-mer value imputation.Nucleic acids research · 2025Article
- De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level.Nature communications · 2025Article
- Training data diversity enhances the basecalling of novel RNA modification-induced nanopore sequencing readouts.Nature communications · 2025Article
- Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering.Nucleic acids research · 2025Article
- Air Pollution as an Environmental Risk Factor for Alzheimer's Disease and Related Dementias.Medical research archives · 2024Article
- Lipid nanoparticle technology-mediated therapeutic gene manipulation in the eyes.Molecular therapy. Nucleic acids · 2024Review
- Training Data Diversity Enhances the Basecalling of Novel RNA Modification-Induced Nanopore Sequencing Readouts.bioRxiv : the preprint server for biology · 2024Article
- β-Aminobutyric acid promotes stress tolerance, physiological adjustments, as well as broad epigenetic changes at DNA and RNA nucleobases in field elms (Ulmus minor).BMC plant biology · 2024Article
- Qualitative and Quantitative Analytical Techniques of Nucleic Acid Modification Based on Mass Spectrometry for Biomarker Discovery.International journal of molecular sciences · 2024Review
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins.Accounts of chemical research · 2023Article
- SWAMNA: a comprehensive platform for analysis of nucleic acid modifications.Chemical communications (Cambridge, England) · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Covalent DNA modifications, such as 5-methylcytosine (5mC), are increasingly the focus of numerous research programs. In eukaryotes, both 5mC and 5-hydroxymethylcytosine (5hmC) are now recognized as stable epigenetic marks, with diverse functions. Bacteria, archaea, and viruses contain various other modified DNA nucleobases. Numerous databases describe RNA and histone modifications, but no database specifically catalogues DNA modifications, despite their broad importance in epigenetic regulation. To address this need, we have developed DNAmod: the DNA modification database. DNAmod is an open-source database ( https://dnamod.hoffmanlab.org ) that catalogues DNA modifications and provides a single source to learn about their properties. DNAmod provides a web interface to easily browse and search through these modifications. The database annotates the chemical properties and structures of all curated modified DNA bases, and a much larger list of candidate chemical entities. DNAmod includes manual annotations of available sequencing methods, descriptions of their occurrence in nature, and provides existing and suggested nomenclature. DNAmod enables researchers to rapidly review previous work, select mapping techniques, and track recent developments concerning modified bases of interest.
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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.