ArticleScientific reports2016
miRNA Digger: a comprehensive pipeline for genome-wide novel miRNA mining.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed, 29 citations in OpenAlex.
- Tobacco rattle virus infection alters Arabidopsis gene expression via virus-derived SiRNAs and host MiRNA network disruption.BMC genomics · 2025Article
- An Overview of miRNA and miRNA Target Analysis Tools.Methods in molecular biology (Clifton, N.J.) · 2025Review
- AmiR-P3: An AI-based microRNA prediction pipeline in plants.PloS one · 2024Article
- miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives.International journal of molecular sciences · 2023Review
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa.BMC genomics · 2021Article
- MicroRNAs Regulating Autophagy in Neurodegeneration.Advances in experimental medicine and biology · 2021Article
- The RNA degradome: a precious resource for deciphering RNA processing and regulation codes in plants.RNA biology · 2020Article
- sRNATargetDigger: A bioinformatics software for bidirectional identification of sRNA-target pairs with co-regulatory sRNAs information.PloS one · 2020Article
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- PmiRDiscVali: an integrated pipeline for plant microRNA discovery and validation.BMC genomics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression. The recent advances in high-throughput sequencing (HTS) technique have greatly facilitated large-scale detection of the miRNAs. However, thoroughly discovery of novel miRNAs from the available HTS data sets remains a major challenge. In this study, we observed that Dicer-mediated cleavage sites for the processing of the miRNA precursors could be mapped by using degradome sequencing data in both animals and plants. In this regard, a novel tool, miRNA Digger, was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. To test its sensitivity and reliability, miRNA Digger was applied to discover miRNAs from four organs of Arabidopsis. The results revealed that a majority of already known mature miRNAs along with their miRNA*s expressed in these four organs were successfully recovered. Notably, a total of 30 novel miRNA-miRNA* pairs that have not been registered in miRBase were discovered by miRNA Digger. After target prediction and degradome sequencing data-based validation, eleven miRNA-target interactions involving six of the novel miRNAs were identified. Taken together, miRNA Digger could be applied for sensitive detection of novel miRNAs and it could be freely downloaded from http://www.bioinfolab.cn/miRNA_Digger/index.html.
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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.