ArticleBMC bioinformatics2017
QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Canonical microRNA loss drives tumor development, implicating therapeutic efficacy of enoxacin in angiosarcoma.RNA (New York, N.Y.) · 2026Article
- Advancing Extracellular Vesicle Research: A Review of Systems Biology and Multiomics Perspectives.Proteomics · 2026Review
- Canonical microRNA loss drives tumor development implicating therapeutic efficacy of enoxacin in angiosarcoma.bioRxiv : the preprint server for biology · 2025Article
- Dorsal root ganglion toxicity after AAV intra-CSF delivery of a RNAi expression construct into non-human primates and mice.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Small RNA-Seq and real time rt-qPCR reveal islet miRNA released under stress conditions.Islets · 2024Article
- Hormonal regulation of miRNA during mammary gland development.Biology open · 2024Article
- RNA-RNA interactions between respiratory syncytial virus and miR-26 and miR-27 are associated with regulation of cell cycle and antiviral immunity.Nucleic acids research · 2024Article
- miR-7 is recruited to the high molecular weight RNA-induced silencing complex in CD8RNA (New York, N.Y.) · 2023Article
- Efficacy and safety of a SOD1-targeting artificial miRNA delivered by AAV9 in mice are impacted by miRNA scaffold selection.Molecular therapy. Nucleic acids · 2023Article
- MicroRNAs in atrial fibrillation target genes in structural remodelling.Cell and tissue research · 2023Article
- Chicken miR-148a-3p regulates immune responses against AIV by targeting the MAPK signalling pathway and IFN-γ.Veterinary research · 2023Article
- Article
- Myocardial RNA Sequencing Reveals New Potential Therapeutic Targets in Heart Failure with Preserved Ejection Fraction.Biomedicines · 2023Article
- MicroRNA expression profiling in the lungs of genetically different Ri chicken lines against the highly pathogenic avian influenza H5N1 virus.Journal of animal science and technology · 2023Article
- Diversity and Differential Expression of MicroRNAs in the Human Skeletal Muscle with Distinct Fiber Type Composition.Life (Basel, Switzerland) · 2023Article
- Insights into male androgenetic alopecia using comparative transcriptome profiling: hypoxia-inducible factor-1 and Wnt/β-catenin signalling pathways.The British journal of dermatology · 2022Article
- The Impact of the Anticoagulant Type in Blood Collection Tubes on Circulating Extracellular Plasma MicroRNA Profiles Revealed by Small RNA Sequencing.International journal of molecular sciences · 2022Article
- dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms.Genomics, proteomics & bioinformatics · 2022Article
- Article
- The Multiverse of Plant Small RNAs: How Can We Explore It?International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset. We implemented a pipeline called QuickMIRSeq for accurate quantification of known miRNAs and miRNA isoforms (isomiRs) from multiple samples simultaneously.
resultsQuickMIRSeq considers the unique nature of miRNAs and combines many important features into its implementation. First, it takes advantage of high redundancy of miRNA reads and introduces joint mapping of multiple samples to reduce computational time. Second, it incorporates the strand information in the alignment step for more accurate quantification. Third, reads potentially arising from background noise are filtered out to improve the reliability of miRNA detection. Fourth, sequences aligned to miRNAs with mismatches are remapped to a reference genome to further reduce false positives. Finally, QuickMIRSeq generates a rich set of QC metrics and publication-ready plots.
conclusionsThe rich visualization features implemented allow end users to interactively explore the results and gain more insights into miRNA-seq data analyses. The high degree of automation and interactivity in QuickMIRSeq leads to a substantial reduction in the time and effort required for miRNA-seq data analysis.
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Registered trials
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