ArticleBriefings in bioinformatics2015
Optimization of miRNA-seq data preprocessing.
Article in Briefings in bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 1 of them a synthesis that pooled it.
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Who cites it
86 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Epigenetic changes in healthy human skeletal muscle following exercise- a systematic review.Epigenetics · 2019Pooled it
- Evaluating miRNA Sequencing and Integrative Proteomics for Identifying Plasma miRNAs as Potential Pharmacodynamic Biomarkers of IFNβ-1a Biologics.Clinical and translational science · 2025Trial
- A high-throughput, end-to-end pipeline for extracellular miRNA biomarker discovery from human biofluids.Cell reports methods · 2026Article
- Comparative analysis of microRNAs in bovine colostrum and neonatal calf blood.Journal of the science of food and agriculture · 2026Article
- Bioinformatics analyses of a potential miRNA‒mRNA regulatory axis in lumbar degenerative disc disease.BMC medical genomics · 2026Article
- Thermal Plasticity is Regulated by a Key MicroRNA During Range Expansion of an Invasive Fruit Fly.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- MicroRNA‑microbiome cross‑kingdom networks drive inflammatory bowel disease through dynamic regulatory ecosystems (Review).International journal of molecular medicine · 2026Review
- Article
- Functional properties of skeletal myotube-derived extracellular vesicles based on microRNA profiles: a comparative analysis with mesenchymal stem cell-derived extracellular vesicles.Scientific reports · 2026Article
- NBSR: a Negative Binomial Softmax Regression model for microRNA-seq data analysis.Biostatistics (Oxford, England) · 2026Article
- Liquid biopsy using circulating miRNAs for the identification of recurrence-associated biomarkers in glioblastoma CNS WHO grade 4.Frontiers in oncology · 2026Article
- Identification of miRNAs in Response to Cold Stress in 'Chaling' Common Wild Rice (Life (Basel, Switzerland) · 2025Article
- Standardization of preclinical methodologies for discovery and validation of circulating microRNA biomarkers for post-traumatic epileptogenesis - Lessons learned from the EpiBioS4Rx Project 1.Epilepsy research · 2025Article
- A Comprehensive Review: Molecular Diagnostics and Multi-Omics Approaches to Understanding Bovine Respiratory Disease.Veterinary sciences · 2025Review
- Eight quick tips for biologically and medically informed machine learning.PLoS computational biology · 2025Article
- miRNA expression signatures induced by pasteurella multocida infection in goats lung.Scientific reports · 2024Article
- Article
- Dynamic changes in extracellular vesicle-associated miRNAs elicited by ultrasound in inflammatory bowel disease patients.Scientific reports · 2024Article
- Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs.Nucleic acids research · 2024Article
- Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells.Frontiers in bioinformatics · 2024Article
26 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The past two decades of microRNA (miRNA) research has solidified the role of these small non-coding RNAs as key regulators of many biological processes and promising biomarkers for disease. The concurrent development in high-throughput profiling technology has further advanced our understanding of the impact of their dysregulation on a global scale. Currently, next-generation sequencing is the platform of choice for the discovery and quantification of miRNAs. Despite this, there is no clear consensus on how the data should be preprocessed before conducting downstream analyses. Often overlooked, data preprocessing is an essential step in data analysis: the presence of unreliable features and noise can affect the conclusions drawn from downstream analyses. Using a spike-in dilution study, we evaluated the effects of several general-purpose aligners (BWA, Bowtie, Bowtie 2 and Novoalign), and normalization methods (counts-per-million, total count scaling, upper quartile scaling, Trimmed Mean of M, DESeq, linear regression, cyclic loess and quantile) with respect to the final miRNA count data distribution, variance, bias and accuracy of differential expression analysis. We make practical recommendations on the optimal preprocessing methods for the extraction and interpretation of miRNA count data from small RNA-sequencing experiments.
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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.