ArticleVirology2020
New insights into the evolutionary features of viral overlapping genes by discriminant analysis.
Article in Virology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 36 citations in OpenAlex.
- Pooled it
- Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes.Journal of molecular evolution · 2026Article
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- Creation of the HIV-1 antisense geneMicrobiology spectrum · 2024Article
- ORF3c is expressed in SARS-CoV-2-infected cells and inhibits innate sensing by targeting MAVS.EMBO reports · 2023Article
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- Homology-based classification of accessory proteins in coronavirus genomes uncovers extremely dynamic evolution of gene content.Molecular ecology · 2022Article
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
- Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective.Cancer metastasis reviews · 2022Review
- Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications.Current opinion in virology · 2022Review
- Article
- Genetic diversity of SARS-CoV-2 in South America: demographic history and structuration signals.Archives of virology · 2021Article
- Article
- Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.Virology · 2021Article
- The HIV-1 Antisense Gene ASP: The New Kid on the Block.Vaccines · 2021Review
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.Nature communications · 2021Article
- Coronavirus, the King Who Wanted More Than a Crown: From Common to the Highly Pathogenic SARS-CoV-2, Is the Key in the Accessory Genes?Frontiers in microbiology · 2021Review
- Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications.Frontiers in molecular biosciences · 2021Article
- The diagnostic and prognostic role of myocardial injury biomarkers in hospitalized patients with COVID-19.Clinica chimica acta; international journal of clinical chemistry · 2020Article
- Quantitative phylogenomic evidence reveals a spatially structured SARS-CoV-2 diversity.Virology · 2020Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Overlapping genes originate by a mechanism of overprinting, in which nucleotide substitutions in a pre-existing frame induce the expression of a de novo protein from an alternative frame. In this study, I assembled a dataset of 319 viral overlapping genes, which included 82 overlaps whose expression is experimentally known and the respective 237 homologs. Principal component analysis revealed that overlapping genes have a common pattern of nucleotide and amino acid composition. Discriminant analysis separated overlapping from non-overlapping genes with an accuracy of 97%. When applied to overlapping genes with known genealogy, it separated ancestral from de novo frames with an accuracy close to 100%. This high discriminant power was crucial to computationally design variants of de novo viral proteins known to possess selective anticancer toxicity (apoptin) or protection against neurodegeneration (X protein), as well as to detect two new potential overlapping genes in the genome of the new coronavirus SARS-CoV-2.
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