ReviewGenome biology2023
In silico methods for predicting functional synonymous variants.
Review in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Synonymous variants in IRX4 and their association with congenital heart disease: an in-silico functional assessment.Molecular biology reports · 2026Article
- Integrating WGCNA and machine learning to identify and validate key biomarkers in MASLD.BMC gastroenterology · 2026Article
- Causal variants in animal genomes: approaches to identification, phenotypic impact, and implications for selective breeding.BMC genomics · 2026Review
- CDsyn: A comprehensive database for deleterious human synonymous variation prediction.iScience · 2026Article
- SyMetrics: an integrated machine learning model for evaluating the pathogenicity of synonymous variants in the human genome.NAR genomics and bioinformatics · 2026Article
- The SynMall resource for characterizing the functional impact of synonymous variation.Genome research · 2026Article
- PGVDA: a pathway-aggregated genetic dosage framework for interpretable disease classification using machine learning.Briefings in bioinformatics · 2026Article
- Classification of driver and passenger mutations in different cancer types using deep neural networks.Bioinformatics advances · 2026Article
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- TPdsm: a method based on TabPFN for prediction of deleterious synonymous mutations.Bioinformatics advances · 2026Article
- Molecular characterization of a novel synonymous variant in a Mexican patient with Pompe disease.Molecular genetics and metabolism reports · 2025Article
- Investigation of GSDME results in the identification of the first pathogenic synonymous variants and genotype-phenotype correlations.Human genetics · 2025Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- Assessing the performance of 28 pathogenicity prediction methods on rare single nucleotide variants in coding regions.BMC genomics · 2025Article
- PRP: pathogenic risk prediction for rare nonsynonymous single nucleotide variants.Human genetics · 2025Article
- Article
- Unraveling the impact ofIn silico pharmacology · 2025Article
- Integrating next-generation sequencing and artificial intelligence for the identification and validation of pathogenic variants in colorectal cancer.Frontiers in oncology · 2025Article
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Corrections and comments
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be "silent," but mounting evidence has revealed that these variants can cause RNA and protein changes and are implicated in over 85 human diseases and cancers. Recent improvements in computational platforms have led to the development of numerous machine-learning tools, which can be used to advance synonymous SNV research. In this review, we discuss tools that should be used to investigate synonymous variants. We provide supportive examples from seminal studies that demonstrate how these tools have driven new discoveries of functional synonymous SNVs.
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