ArticleNucleic acids research2022
PmiREN2.0: from data annotation to functional exploration of plant microRNAs.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- What Do We Know about Barley miRNAs?International journal of molecular sciences · 2022Pooled it
- Genome-phenome association prediction using weighted deep matrix factorization with a multisource graph attention network.Quantitative biology (Beijing, China) · 2026Article
- Article
- Photoperiodic patterns in miRNA-mRNA pairs and tRNA fragments revealed by time-course co-sequencing in Arabidopsis.PLoS genetics · 2026Article
- Embedding multilayer RNA networks for lncRNA-miRNA interaction prediction via LMI-MHGAT.BMC biology · 2026Article
- Ethylene signaling and metabolite reprogramming in salt tolerance of Triticum aestivum.Scientific reports · 2026Article
- Under heavy metal stress: genomic characterization and expression profiles of miRNA families in Phaseolus vulgaris.BMC plant biology · 2026Article
- Genome-Wide Identification of miRNAs and Pollen-Associated miRNA-Target Relationships inPlants (Basel, Switzerland) · 2026Article
- Genome-wide analysis of Phaseolus vulgaris L. miR172 gene family members under heavy metal stress.BMC genomics · 2026Article
- Allopolyploidization-driven short-term evolution of miRNAs in Brassica A genome.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Application of Artificial Intelligence Technology in Plant MicroRNA Research: Progress, Challenges, and Prospects.International journal of molecular sciences · 2025Review
- MITE Annotation and Landscape in 207 Plant Genomes Reveal Their Evolutionary Dynamics and Functional Roles.Molecular ecology resources · 2025Article
- Genome-wide identification and analysis of miR396 family members and their target GRF genes in rubber tree (Hevea brasiliensis).BMC genomics · 2025Article
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- MicroRNA528 and Its Regulatory Roles in Monocotyledonous Plants.International journal of molecular sciences · 2025Review
- Hyssopus officinalis: MicroRNA-mediated regulation of terpenoid biosynthesis and defense metabolites.Planta · 2025Article
- Review
- Multi-omics-Based Construction of ncRNA-Gene-Metabolite Networks Provides New Insights Into Metabolic Regulation Under Salt Stress in Rice.Rice (New York, N.Y.) · 2025Article
- WP-MOD: A multi-omics and taxonomy database for woody plants.Plant communications · 2025Article
- The Emerging Applications of Artificial MicroRNA-Mediated Gene Silencing in Plant Biotechnology.Non-coding RNA · 2025Review
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named 'PmiREN Community' was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.
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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.