ArticleNucleic acids research2025
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- In silico unwinding ofRNA biology · 2026Article
- MiRQuery: a user-friendly web app for the interactive analysis and visualization of microRNA sequencing data.BMC bioinformatics · 2026Article
- Integrated Analyses of mRNA and microRNA Regulatory Networks at Different Soil Moisture in Tropical EarthwormBiology · 2026Article
- DICER1-related tumour predisposition mutations increase 3p-miRNA function and HERVH activity.Nature communications · 2026Article
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- microRNAs bidirectionally regulate FUT1 to modulate α-1,2-fucosylation and cancer-associated biology.The Journal of biological chemistry · 2026Article
- Target-site dynamics explain a large share of apparent microRNA differential expression.RNA (New York, N.Y.) · 2026Article
- Genomic context of mutations in MIR142 in blood cancers: summary and integrative analysis.Cellular & molecular biology letters · 2026Review
- A lncRNA drives developmentally timed decay of all members of an essential microRNA family.Genes & development · 2026Article
- mirtronDB 2.0: enhanced database with novel mirtron discoveries.Bioinformatics (Oxford, England) · 2026Article
- Article
- Small and Large Extracellular Vesicles in Circulation of Diffuse Large B-Cell Lymphoma Patients Originate From Different Cell Types of the Tumor Microenvironment.Journal of extracellular vesicles · 2026Article
- Separable roles for Microprocessor and its cofactors, ERH and SAFB1/2, during microRNA cluster assistance.Genes & development · 2026Article
- mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth.Genes & development · 2026Article
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Nanoparticle-delivered miR-486-5p inhibits HNanoscale advances · 2026Article
- MiRNAs shape mouse age-independent tissue adaptation to spaceflight via ECM and developmental pathways.Nature communications · 2026Article
- bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.Nucleic acids research · 2026Article
- Development of Dirofilaria immitis adult worms in NSG mice, detection of parasite-derived microRNA and comparative analysis of laboratory isolates.Scientific reports · 2026Article
- An intrinsically disordered region of Drosha selectively promotes miRNA biogenesis independent of tissue-specific Microprocessor condensates.Genes & development · 2026Article
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22 authors.
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Abstract
We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA genes (5160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB's phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely available at mirgenedb.org.
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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.