ArticleNAR genomics and bioinformatics2021
miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 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
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Who cites it
61 citing papers in PubMed, 81 citations in OpenAlex.
- The role of microRNAs in executive functions: a comprehensive review and bioinformatics analysis of human and animal studies.Molecular psychiatry · 2026Review
- MicroRNA Expression Profiles Before and After Neoadjuvant Chemotherapy in Breast Cancer: Correlations with Molecular Subtypes, Pathological Response, and Clinical Timing-A Pilot Translational Study.International journal of molecular sciences · 2026Article
- Profiling miRNAs Involved in Human Oligodendrocyte Precursor Cell Differentiation and Maturation.Cells · 2026Article
- HPV8-E6 drives coordinated transcriptional and epigenetic reprogramming of keratinocytes.Tumour virus research · 2026Article
- Altered sncRNA Signatures in Semen Extracellular Vesicles Between Patients with Benign and Malignant Prostate Disease as Potential Non-Invasive Biomarkers in the PSA Grey Zone.International journal of molecular sciences · 2026Article
- Biochemical insights and microRNA profiling via next-generation sequencing in moderate and severe COVID-19 cases.Clinics (Sao Paulo, Brazil) · 2026Article
- PARiS: Probabilistic Assignment and Repartitioning of isomiR Sequences: A data-driven method for denoising isomiR read count data.bioRxiv : the preprint server for biology · 2026Article
- Sex differences in circulating microRNA profiles in heart failure with preserved and reduced ejection fraction.European heart journal open · 2026Article
- miRNA regulation in brain tissue space: the 3'UTR perspective.RNA (New York, N.Y.) · 2026Review
- Adenosine-to-inosine editing of miR-200b-3p is associated with the progression of high-grade serous ovarian cancer.Molecular oncology · 2026Article
- Identification of candidate microRNA biomarkers of endometriosis in different bodily fluids.Scientific reports · 2026Article
- MIRit: an integrative R framework for the identification of impaired miRNA-mRNA regulatory networks in complex diseases.Bioinformatics advances · 2026Article
- MicroRNAs and Their Profiling via Single-Cell Sequencing Technologies.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Profiling miRNAs involved in Human Oligodendrocyte Precursor Cell Differentiation and Maturation.bioRxiv : the preprint server for biology · 2025Article
- Network-based insights into miRNA regulation of β-cell insulin secretion in type 2 diabetes.iScience · 2025Article
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- Feedforward miR-181d degradation modulates population variance of methyl-guanine methyl transferase and temozolomide resistance.Cell reports · 2025Article
- Robustness of urinary extracellular vesicle-derived MiRNA profiles over multiple days and the impact of urine concentration.Scientific reports · 2025Article
- IsomiR stoichiometry changes as disease biomarkers.Molecular therapy. Nucleic acids · 2025Article
- Article
1 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
2 authors at 1 institution in 1 country.
Funding
Abstract
MicroRNAs and tRFs are classes of small non-coding RNAs, known for their roles in translational regulation of genes. Advances in next-generation sequencing (NGS) have enabled high-throughput small RNA-seq studies, which require robust alignment pipelines. Our laboratory previously developed miRge and miRge2.0, as flexible tools to process sequencing data for annotation of miRNAs and other small-RNA species and further predict novel miRNAs using a support vector machine approach. Although miRge2.0 is a leading analysis tool in terms of speed with unique quantifying and annotation features, it has a few limitations. We present miRge3.0 that provides additional features along with compatibility to newer versions of Cutadapt and Python. The revisions of the tool include the ability to process Unique Molecular Identifiers (UMIs) to account for PCR duplicates while quantifying miRNAs in the datasets, correct erroneous single base substitutions in miRNAs with miREC and an accurate mirGFF3 formatted isomiR tool. miRge3.0 also has speed improvements benchmarked to miRge2.0, Chimira and sRNAbench. Finally, miRge3.0 output integrates into other packages for a streamlined analysis process and provides a cross-platform Graphical User Interface (GUI). In conclusion miRge3.0 is our third generation small RNA-seq aligner with improvements in speed, versatility and functionality over earlier iterations.
Identifiers
What OpenQuestion holds
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.