ArticlePloS one2015
miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Functional Genomic Evidence for Candidate Small Viral RNA-Mediated Epigenetic Interference in SARS-CoV-1 and SARS-CoV-2.Computational and structural biotechnology journal · 2026Article
- miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs.Genome biology · 2025Article
- Mesenchymal stem cell-derived small extracellular vesicles alleviate the immunometabolic dysfunction in murine septic encephalopathy.iScience · 2024Article
- Comparative Analysis of Published Database Predicting MicroRNA Binding in 3'UTR of mRNA in Diverse Species.MicroRNA (Shariqah, United Arab Emirates) · 2024Review
- MicroRNA Expression Profile in Early-Stage Breast Cancers.MicroRNA (Shariqah, United Arab Emirates) · 2024Article
- Article
- Dysregulated miRNA and mRNA Expression Affect Overlapping Pathways in a Huntington's Disease Model.International journal of molecular sciences · 2023Article
- Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita.BMC genomics · 2023Article
- Reassessing the Abundance of miRNAs in the Human Pancreas and Rodent Cell Lines and Its Implication.Non-coding RNA · 2023Article
- Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System.International journal of molecular sciences · 2023Article
- The hitchhikers' guide to RNA sequencing and functional analysis.Briefings in bioinformatics · 2023Article
- Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome ofFrontiers in genetics · 2023Article
- Small RNA-Seq Reveals Similar miRNA Transcriptome in Children and Young Adults with T-ALL and Indicates miR-143-3p as Novel Candidate Tumor Suppressor in This Leukemia.International journal of molecular sciences · 2022Article
- Global MicroRNA Profiling of Vascular Endothelial Cells.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Article
- miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.NAR genomics and bioinformatics · 2021Article
- IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets.Bioinformatics (Oxford, England) · 2021Article
- Mycobacterium tuberculosis Infection Drives Mitochondria-Biased Dysregulation of Host Transfer RNA-Derived Fragments.The Journal of infectious diseases · 2021Article
- Molecular characterization of atherosclerosis in HIV positive persons.Scientific reports · 2021Article
- MicroRNAs Regulating Autophagy in Neurodegeneration.Advances in experimental medicine and biology · 2021Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small RNA RNA-seq for microRNAs (miRNAs) is a rapidly developing field where opportunities still exist to create better bioinformatics tools to process these large datasets and generate new, useful analyses. We built miRge to be a fast, smart small RNA-seq solution to process samples in a highly multiplexed fashion. miRge employs a Bayesian alignment approach, whereby reads are sequentially aligned against customized mature miRNA, hairpin miRNA, noncoding RNA and mRNA sequence libraries. miRNAs are summarized at the level of raw reads in addition to reads per million (RPM). Reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA) are provided, which is useful for identifying potential contaminants and optimizing small RNA purification strategies. miRge was designed to optimally identify miRNA isomiRs and employs an entropy based statistical measurement to identify differential production of isomiRs. This allowed us to identify decreasing entropy in isomiRs as stem cells mature into retinal pigment epithelial cells. Conversely, we show that pancreatic tumor miRNAs have similar entropy to matched normal pancreatic tissues. In a head-to-head comparison with other miRNA analysis tools (miRExpress 2.0, sRNAbench, omiRAs, miRDeep2, Chimira, UEA small RNA Workbench), miRge was faster (4 to 32-fold) and was among the top-two methods in maximally aligning miRNAs reads per sample. Moreover, miRge has no inherent limits to its multiplexing. miRge was capable of simultaneously analyzing 100 small RNA-Seq samples in 52 minutes, providing an integrated analysis of miRNA expression across all samples. As miRge was designed for analysis of single as well as multiple samples, miRge is an ideal tool for high and low-throughput users. miRge is freely available at http://atlas.pathology.jhu.edu/baras/miRge.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.