ArticleGenetica2018
Codon usage and amino acid usage influence genes expression level.
Article in Genetica, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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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Who cites it
13 citing papers in PubMed, 28 citations in OpenAlex.
- Article
- Comparative Genomics and Phylogenetics of Chloroplasts Reveal Lower Rates of Genetic Variation in Mango (Ecology and evolution · 2025Article
- Complete chloroplast genome of two Brachycorythis (Orchidaceae) species from China: comparative analysis and phylogenetic implications.BMC genomics · 2025Article
- Role Analysis of theAnimals : an open access journal from MDPI · 2025Article
- Comparative genomics and phylogenomics of the genusFrontiers in pharmacology · 2024Article
- Chloroplast genome structure analysis ofFrontiers in plant science · 2024Article
- Article
- Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance.BMC genomics · 2022Article
- Strong Selectional Forces Fine-Tune CpG Content in Genes Involved in Neurological Disorders as Revealed by Codon Usage Patterns.Frontiers in neuroscience · 2022Article
- Article
- Identification and phylogenetic analysis of five Crataegus species (Rosaceae) based on complete chloroplast genomes.Planta · 2021Article
- Article
- Directed Evolution of a Homodimeric Laccase fromInternational journal of molecular sciences · 2018Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.
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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.