ArticleFrontiers in plant science2017
isomiR2Function: An Integrated Workflow for Identifying MicroRNA Variants in Plants.
Article in Frontiers in plant science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
- Prediction of miRNA Targets in Plants.Methods in molecular biology (Clifton, N.J.) · 2025Article
- An Overview of miRNA and miRNA Target Analysis Tools.Methods in molecular biology (Clifton, N.J.) · 2025Review
- athisomiRDB: A comprehensive database of Arabidopsis isomiRs.Database : the journal of biological databases and curation · 2024Article
- Article
- The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in bioinformatics · 2023Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- The Multiverse of Plant Small RNAs: How Can We Explore It?International journal of molecular sciences · 2022Review
- MicroRNA-mediated bioengineering for climate-resilience in crops.Bioengineered · 2021Review
- Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing.Briefings in bioinformatics · 2021Article
- MicroRNAs Regulating Autophagy in Neurodegeneration.Advances in experimental medicine and biology · 2021Article
- Trends in the development of miRNA bioinformatics tools.Briefings in bioinformatics · 2019Review
- Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants.Scientific reports · 2019Article
- Identifying and characterizing functional 3' nucleotide addition in the miRNA pathway.Methods (San Diego, Calif.) · 2019Review
- Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants.Frontiers in plant science · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://github.com/347033139/isomiR2Function.
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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.