ArticleOsteoarthritis and cartilage open2021
A bioinformatics approach to microRNA-sequencing analysis.
Article in Osteoarthritis and cartilage open, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 3 syntheses or guidelines pooled it, 69 citations in OpenAlex.
- A Practical Guideline for MicroRNA Sequencing Data Analysis in Chronic Lymphocytic Leukemia.Methods in molecular biology (Clifton, N.J.) · 2025Guideline
- Prognostic molecular biomarkers in chordomas: A systematic review and identification of clinically usable biomarker panels.Frontiers in oncology · 2022Pooled it
- Next-Generation and Single-Cell Sequencing Approaches to Study Atherosclerosis and Vascular Inflammation Pathophysiology: A Systematic Review.Frontiers in cardiovascular medicine · 2022Pooled it
- Responders vs. non-responders to mesenchymal stromal cells in knee osteoarthritis: Mechanistic correlates of donor cell and patient features.Stem cell reports · 2026Trial
- MicroRNome analysis generates a blood-based signature for endometriosis.Scientific reports · 2022Trial
- MiRQuery: a user-friendly web app for the interactive analysis and visualization of microRNA sequencing data.BMC bioinformatics · 2026Article
- An Exploratory Study on Transcriptomic Profiling of Circulating miRNA Associated with Hub Genes in the Development of Polycystic Ovary Syndrome.Non-coding RNA · 2026Article
- Skeletal Muscle miRNA Patterns in High-Altitude Trekkers: Exploratory Identification of Molecular Signatures of Cellular and Endocrine Adaptation.Biomolecules · 2026Article
- Rewiring miR-22/SNAI1 via CRISPR-based edge editing destabilizes the epithelial phenotype.NPJ systems biology and applications · 2026Article
- Bioinformatics analyses of a potential miRNA‒mRNA regulatory axis in lumbar degenerative disc disease.BMC medical genomics · 2026Article
- Connecting HTT intermediate alleles and microRNA dysregulation to enhanced tauopathy in late-onset Alzheimer's disease.Alzheimer's research & therapy · 2026Article
- Article
- MicroRNAs in neurodegenerative diseases: from molecular mechanisms to clinical biomarkers, detection methods and therapeutic strategies-advances and challenges.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2025Review
- A Bioinformatic Study of Genetics Involved in Determining Mild Traumatic Brain Injury Severity and Recovery.Biomedicines · 2025Article
- QMRInternational journal of molecular sciences · 2025Article
- From mechanism to medicine: The progress and potential of epigenetics in osteoarthritis.Osteoarthritis and cartilage open · 2025Review
- Transcriptome-based screening in TARDBP/TDP-43 knock-in motor neurons identifies the NEDD8-activating enzyme inhibitor MLN4924.Scientific reports · 2025Article
- Circulating microRNA profiles in early-stage osteoarthritis and rheumatoid arthritis.Scientific reports · 2025Article
- Re-Analyses of Samples From Amyotrophic Lateral Sclerosis Patients and Controls Identify Many Novel Small RNAs With Diagnostic And Prognostic Potential.Molecular neurobiology · 2025Article
- Identification of miR-190a-5p and miR-26b-5p as Potential microRNA Biomarkers for Psoriatic Arthritis.ACR open rheumatology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid expansion of Next Generation Sequencing (NGS) data availability has made exploration of appropriate bioinformatics analysis pipelines a timely issue. Since there are multiple tools and combinations thereof to analyze any dataset, there can be uncertainty in how to best perform an analysis in a robust and reproducible manner. This is especially true for newer omics applications, such as miRNomics, or microRNA-sequencing (miRNA-sequencing). As compared to transcriptomics, there have been far fewer miRNA-sequencing studies performed to date, and those that are reported seldom provide detailed description of the bioinformatics analysis, including aspects such as Unique Molecular Identifiers (UMIs). In this article, we attempt to fill the gap and help researchers understand their miRNA-sequencing data and its analysis. This article will specifically discuss a customizable miRNA bioinformatics pipeline that was developed using miRNA-sequencing datasets generated from human osteoarthritis plasma samples. We describe quality assessment of raw sequencing data files, reference-based alignment, counts generation for miRNA expression levels, and novel miRNA discovery. This report is expected to improve clarity and reproducibility of the bioinformatics portion of miRNA-sequencing analysis, applicable across any sample type, to promote sharing of detailed protocols in the NGS field.
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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.