ArticleCell genomics2023
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Article
- Social isolation is associated with microRNA expression changes in the visual system of poison frog tadpoles.bioRxiv : the preprint server for biology · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Copy number evolution of conserved noncoding RNA gene families across mammals.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- First insights into the miRNA landscape of Tursiops truncatus milk reveal shared dominant microRNA families with terrestrial mammals.PloS one · 2026Article
- Interpretation of RNA Universe and Coding Potential Using IntRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- miRScore: A rapid and precise microRNA validation tool.PLoS computational biology · 2025Article
- The complete genome of a songbird.bioRxiv : the preprint server for biology · 2025Article
- Repeated emergence of giant microRNA hairpins across invertebrates.Cell reports · 2025Article
- A genome resource for the marine annelid Platynereis spp.BMC genomics · 2025Article
- Substantial Hierarchical Reductions of Genetic and Morphological Traits in the Evolution of Rotiferan Parasites.Genome biology and evolution · 2025Article
- The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with a reduced posterior tagma.BMC biology · 2025Article
- Unraveling the miRNA landscape in tsetse fly saliva and salivary glands duringNAR molecular medicine · 2025Article
- Differentially expressed miRNAs offer new perspective into cave adaptation of Astyanax mexicanus.Annals of the New York Academy of Sciences · 2025Article
- Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.Cell genomics · 2025Article
- MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models.Nucleic acids research · 2025Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- Article
- Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences.Nature ecology & evolution · 2024Article
- Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy.iScience · 2024Article
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7 authors.
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Abstract
The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
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