ArticleRNA (New York, N.Y.)2019
OPTIMIR, a novel algorithm for integrating available genome-wide genotype data into miRNA sequence alignment analysis.
Article in RNA (New York, N.Y.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders.Cardiovascular research · 2023Review
- Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis.BMC bioinformatics · 2021Article
- isomiRs-Hidden Soldiers in the miRNA Regulatory Army, and How to Find Them?Biomolecules · 2020Review
- Bayesian network analysis of plasma microRNA sequencing data in patients with venous thrombosis.European heart journal supplements : journal of the European Society of Cardiology · 2020Article
- Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.Bioinformatics (Oxford, England) · 2020Article
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Authors and funding
9 authors.
Funding
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Abstract
Next-generation sequencing is an increasingly popular and efficient approach to characterize the full set of microRNAs (miRNAs) present in human biosamples. MiRNAs' detection and quantification still remain a challenge as they can undergo different posttranscriptional modifications and might harbor genetic variations (polymiRs) that may impact on the alignment step. We present a novel algorithm, OPTIMIR, that incorporates biological knowledge on miRNA editing and genome-wide genotype data available in the processed samples to improve alignment accuracy. OPTIMIR was applied to 391 human plasma samples that had been typed with genome-wide genotyping arrays. OPTIMIR was able to detect genotyping errors, suggested the existence of novel miRNAs and highlighted the allelic imbalance expression of polymiRs in heterozygous carriers. OPTIMIR is written in python, and freely available on the GENMED website (http://www.genmed.fr/index.php/fr/) and on Github (github.com/FlorianThibord/OptimiR).
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Registered trials
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