ArticleRNA (New York, N.Y.)2016
Evaluation of microRNA alignment techniques.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 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.
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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.
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Who cites it
41 citing papers in PubMed.
- Total RNA and MicroRNA Transcriptomic Responses of Human Retinal Müller Glial Cells to Infection withOphthalmology science · 2026Article
- Integrated transcriptomic profiling reveals oncogenic pathways and chimeric transcripts in equine sarcoid lesions with predominant BPV1 detection.Frontiers in molecular biosciences · 2026Article
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- Extracellular vesicles carry transcriptional 'dark matter' revealing tissue-specific information.Journal of extracellular vesicles · 2024Article
- Utilizing multimodal approach to identify candidate pathways and biomarkers and predicting frailty syndrome in individuals from UK Biobank.GeroScience · 2024Article
- miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives.International journal of molecular sciences · 2023Review
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- Putting the "mi" in omics: discovering miRNA biomarkers for pediatric precision care.Pediatric research · 2023Review
- Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq.Functional & integrative genomics · 2022Review
- srnaMapper: an optimal mapping tool for sRNA-Seq reads.BMC bioinformatics · 2022Article
- Analysis of Expression Pattern of snoRNAs in Human Cells A549 Infected by Influenza A Virus.International journal of molecular sciences · 2022Article
- BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data.GigaScience · 2022Article
- Article
- GWAS identifies candidate susceptibility loci and microRNA biomarkers for acute encephalopathy with biphasic seizures and late reduced diffusion.Scientific reports · 2022Article
- Role of ribosomal RNA released from red cells in blood coagulation in zebrafish and humans.Blood advances · 2021Article
- Exosomes in Epilepsy of Tuberous Sclerosis Complex: Carriers of Pro-Inflammatory MicroRNAs.Non-coding RNA · 2021Article
- AASRA: an anchor alignment-based small RNA annotation pipeline†.Biology of reproduction · 2021Article
- Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus.Parasites & vectors · 2021Article
- Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing.
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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.