ArticleBMC bioinformatics2018
miRge 2.0 for comprehensive analysis of microRNA sequencing data.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- NBSR: a Negative Binomial Softmax Regression model for microRNA-seq data analysis.Biostatistics (Oxford, England) · 2026Article
- TSG-6 Activated MSC-derived Extracellular Vesicles Present Altered micro-RNA Contents and Ameliorate the Inflammatory Phenotype of Macrophages in Vitro.Inflammation · 2026Article
- Interplay Between Dysregulated Immune System and the Footprints of Blood-Borne miRNAs in Treatment Naive Crohn's Disease and Ulcerative Colitis Patients.International journal of molecular sciences · 2025Article
- MicroRNA profiling identifies novel regulators of stem cell function in the adult Drosophila intestine.Scientific reports · 2025Article
- MicroRNA bioinformatics in precision oncology: an integrated pipeline from NGS to AI-based target discovery.Journal of applied genetics · 2025Review
- Neutrophil degranulation is increased at seven days after human intracerebral hemorrhage, but not at 72 h, and correlates with decreased miR-3613 and miR-3690.BMC neurology · 2025Article
- Extracellular vesicles, RNA sequencing, and bioinformatic analyses: Challenges, solutions, and recommendations.Journal of extracellular vesicles · 2024Review
- Identification of brain region-specific landscape and functions of clustered circRNAs in Alzheimer's disease using circMeta2.Communications biology · 2024Article
- Genome-Wide Transcriptional Response of Avocado toPlants (Basel, Switzerland) · 2024Article
- Extracellular vesicles carry transcriptional 'dark matter' revealing tissue-specific information.Journal of extracellular vesicles · 2024Article
- Beyond CSF and Neuroimaging Assessment: Evaluating Plasma miR-145-5p as a Potential Biomarker for Mild Cognitive Impairment and Alzheimer's Disease.ACS chemical neuroscience · 2024Article
- Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species.MicroRNA (Shariqah, United Arab Emirates) · 2024Review
- Identification of serum miR-1246 and miR-150-5p as novel diagnostic biomarkers for high-grade serous ovarian cancer.Scientific reports · 2023Article
- Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts.Bioinformatics (Oxford, England) · 2023Article
- Reassessing the Abundance of miRNAs in the Human Pancreas and Rodent Cell Lines and Its Implication.Non-coding RNA · 2023Article
- MicroRNA-eQTLs in the developing human neocortex link miR-4707-3p expression to brain size.eLife · 2023Article
- Pan-Cancer Analysis of Canonical and Modified miRNAs Enhances the Resolution of the Functional miRNAome in Cancer.Cancer research · 2022Article
- Review
- Unique circulating microRNA profiles in epidemic Kaposi's sarcoma.Non-coding RNA research · 2022Article
- Circulating microRNA sequencing revealed miRNome patterns in hematology and oncology patients aiding the prognosis of invasive aspergillosis.Scientific reports · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundmiRNAs play important roles in the regulation of gene expression. The rapidly developing field of microRNA sequencing (miRNA-seq; small RNA-seq) needs comprehensive, robust, user-friendly and standardized bioinformatics tools to analyze these large datasets. We present miRge 2.0, in which multiple enhancements were made towards these goals.
resultsmiRge 2.0 has become more comprehensive with increased functionality including a novel miRNA detection method, A-to-I editing analysis, integrated standardized GFF3 isomiR reporting, and improved alignment to miRNAs. The novel miRNA detection method uniquely uses both miRNA hairpin sequence structure and composition of isomiRs resulting in higher specificity for potential miRNA identification. Using known miRNA data, our support vector machine (SVM) model predicted miRNAs with an average Matthews correlation coefficient (MCC) of 0.939 over 32 human cell datasets and outperformed miRDeep2 and miRAnalyzer regarding phylogenetic conservation. The A-to-I editing detection strongly correlated with a reference dataset with adjusted R
conclusionsmiRge 2.0 is a redesigned, leading miRNA RNA-seq aligner with several improvements and novel utilities. miRge 2.0 is freely available at: https://github.com/mhalushka/miRge .
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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.