ArticlePloS one2017
NMD Classifier: A reliable and systematic classification tool for nonsense-mediated decay events.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- A novel truncated mutation in folate receptor α (FRα) affecting its glycosylation and affinity for folate in a consanguineous family with progressive encephalopathy: follow up and treatment improvement.Molecular biology reports · 2025Article
- Genetic and Phenotypic Features of 2 Northern Italy Families with Dowling-Degos Disease Type 4.JID innovations : skin science from molecules to population health · 2025Article
- Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons.Genome biology · 2024Article
- Mutations in SAMD7 cause autosomal-recessive macular dystrophy with or without cone dysfunction.American journal of human genetics · 2024Article
- SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms.International journal of molecular sciences · 2024Article
- Homozygous Duplication in theBiomedicines · 2023Article
- rs67047829 genotypes of ERV3-1/ZNF117 are associated with lower body mass index in the Polish population.Scientific reports · 2023Article
- RNA-Based Strategies for Cancer Therapy: In Silico Design and Evaluation of ASOs for Targeted Exon Skipping.International journal of molecular sciences · 2023Article
- Exome sequencing in retinal dystrophy patients reveals a novel candidate gene ER membrane protein complex subunit 3.Heliyon · 2023Article
- EMILIN1 deficiency causes arterial tortuosity with osteopenia and connects impaired elastogenesis with defective collagen fibrillogenesis.American journal of human genetics · 2022Article
- Identification of a Novel de Novo Variant in the CASZ1 Causing a Rare Type of Dilated Cardiomyopathy.International journal of molecular sciences · 2022Article
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- Mutations in RPS19 may affect ribosome function and biogenesis in Diamond Blackfan anemia.FEBS open bio · 2022Article
- Wnt/β-catenin pathway and cell adhesion deregulation in CSDE1-related intellectual disability and autism spectrum disorders.Molecular psychiatry · 2021Article
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- Expansion of NEUROD2 phenotypes to include developmental delay without seizures.American journal of medical genetics. Part A · 2021Article
- A framework for high-resolution phenotyping of candidate male infertility mutants: from human to mouse.Human genetics · 2021Review
- Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area.Journal of clinical medicine · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nonsense-mediated decay (NMD) degrades mRNAs that include premature termination codons to avoid the translation and accumulation of truncated proteins. This mechanism has been found to participate in gene regulation and a wide spectrum of biological processes. However, the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs) have been less studied, partly because of the complexity in analyzing NMD events. Here we report NMD Classifier, a tool for systematic classification of NMD events for either annotated or de novo assembled transcripts. This tool is based on the assumption of minimal evolution/regulation-an event that leads to the least change is the most likely to occur. Our simulation results indicate that NMD Classifier can correctly identify an average of 99.3% of the NMD-causing transcript structural changes, particularly exon inclusions/exclusions and exon boundary alterations. Researchers can apply NMD Classifier to evolutionary and regulatory studies by comparing NMD events of different biological conditions or in different organisms.
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