ArticleBMC genomics2019
miRkwood: a tool for the reliable identification of microRNAs in plant genomes.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed, 22 citations in OpenAlex.
- miRNA408 fromBiomolecules · 2025Article
- Review
- Detection of Ethylene Signaling Using Bioinformatics Tools in Plants.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Potential role of the regulatoryFrontiers in plant science · 2023Article
- Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- Integrated sRNA-seq and RNA-seq Analyses Reveal a microRNA Regulation Network Involved in Cold Response inGenes · 2022Article
- The Multiverse of Plant Small RNAs: How Can We Explore It?International journal of molecular sciences · 2022Review
- Evaluation and application of tools for the identification of known microRNAs in plants.Applications in plant sciences · 2021Review
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundMicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited.
resultsHere, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data. Deep-sequencing data of Argonaute associated small RNAs showed that miRkwood is able to identify a large diversity of plant miRNAs and limits false positive predictions. Moreover, it outperforms current tools such as ShortStack and contrary to ShortStack, miRkwood provides a quality score allowing users to rank miRNA predictions.
conclusionmiRkwood is a very efficient tool for the annotation of miRNAs in plant genomes. It is available as a web server, as a standalone version, as a docker image and as a Galaxy tool: http://bioinfo.cristal.univ-lille.fr/mirkwood.
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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.