ArticleF1000Research2022
miND (miRNA NGS Discovery pipeline): a small RNA-seq analysis pipeline and report generator for microRNA biomarker discovery studies.
Article in F1000Research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Integrated Analysis of mRNA and microRNA Expression in Corneal Impression Cytology Samples from Patients withInternational journal of molecular sciences · 2026Article
- Rapamycin reduces peritendinous fibrosis but has a limited effect on intratendinous healing in a rodent Achilles tendon injury model.Scientific reports · 2026Article
- Human bronchial air-liquid interface responses to nebulised protease exposure.Frontiers in immunology · 2026Article
- Synovial Fluid and Serum MicroRNA Signatures in Equine Osteoarthritis.International journal of molecular sciences · 2025Article
- Synovial Fluid MicroRNA Biomarkers Enable Accurate Diagnosis of Hip and Knee Periprosthetic Joint Infections.The Journal of bone and joint surgery. American volume · 2025Article
- Sepsis-associated acute kidney injury in mice and humans elicits heterogeneous renal microvascular microRNA responses.Scientific reports · 2025Article
- Dexamethasone: a double-edged sword in the treatment of osteoarthritis.Scientific reports · 2025Article
- Extracellular Vesicle-Derived microRNA Crosstalk Between Equine Chondrocytes and Synoviocytes-An In Vitro Approach.International journal of molecular sciences · 2025Article
- Neuron-Derived Extracellular Vesicles miRNA Profiles Identify Children Who Experience Adverse Events after Ketamine Administration for Procedural Sedation.Clinical pharmacology and therapeutics · 2025Article
- Differential microRNA expression patterns between TallyHo/JngJ mice and non-diabetic Swiss Webster Random/Jackson mice.JBMR plus · 2025Article
- Circulating miRNAs are associated with successful bone regeneration.Frontiers in bioengineering and biotechnology · 2025Article
- Distinct miRNA profiles in human amniotic tissue and its vesicular and non-vesicular secretome.Frontiers in cell and developmental biology · 2025Article
- Postmortem analyses of myocardial microRNA expression in sepsis.Scientific reports · 2024Observational
- Longitudinal course of circulating miRNAs in a patient with hypophosphatasia and asfotase alfa treatment: a case report.JBMR plus · 2024Article
- Candidate Signature miRNAs from Secreted miRNAome of Human Lung Microvascular Endothelial Cells in Response to Different Oxygen Conditions: A Pilot Study.International journal of molecular sciences · 2024Article
- MicroRNA expression analysis in peripheral blood and soft-tissue of patients with periprosthetic hip infection.Bone & joint open · 2024Article
- The plasma miRNome and venous thromboembolism in high-grade glioma: miRNA Sequencing of a nested case-control cohort.Journal of cellular and molecular medicine · 2024Article
- Analysis of extracellular vesicle microRNA profiles reveals distinct blood and lymphatic endothelial cell origins.Journal of extracellular biology · 2024Article
- Exploratory miRNA profiling from serum and bone tissue of mice with T1D-induced bone loss.Frontiers in endocrinology · 2024Article
- Unique miRNome and transcriptome profiles underlie microvascular heterogeneity in mouse kidney.American journal of physiology. Renal physiology · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In contrast to traditional methods like real-time polymerase chain reaction, next-generation sequencing (NGS), and especially small RNA-seq, enables the untargeted investigation of the whole small RNAome, including microRNAs (miRNAs) but also a multitude of other RNA species. With the promising application of small RNAs as biofluid-based biomarkers, small RNA-seq is the method of choice for an initial discovery study. However, the presentation of specific quality aspects of small RNA-seq data varies significantly between laboratories and is lacking a common (minimal) standard. The miRNA NGS Discovery pipeline (miND) aims to bridge the gap between wet lab scientist and bioinformatics with an easy to setup configuration sheet and an automatically generated comprehensive report that contains all essential qualitative and quantitative results that should be reported. Besides the standard steps like preprocessing, mapping, visualization, and quantification of reads, the pipeline also incorporates differential expression analysis when given the appropriate information regarding sample groups. Although miND has a focus on miRNAs, other RNA species like tRNAs, piRNA, snRNA, or snoRNA are included and mapping statistics are available for further analysis. miND has been developed and tested on a multitude of data sets with various RNA sources (tissue, plasma, extracellular vesicles, urine, etc.) and different species. miND is a Snakemake based pipeline and thus incorporates all advantages using a flexible workflow management system. Reference databases are downloaded, prepared and built with an included (but separate) workflow and thus can easily be updated to the most recent version but also stored for reproducibility. In conclusion, the miND pipeline aims to streamline the bioinformatics processing of small RNA-seq data by standardizing the processing from raw data to a final, comprehensive and reproducible report.
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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.