The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications
Open accessAbstract
A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.
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“The codon optimization applied to BNT-162b2 and mRNA-1273 leads to a much increased codon adaptation index (CAI) [21,22] and index of translation efficiency (ITE) [11,36] for the two vaccine mRNAs.”
From Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines (2021) · cites this paper as [21]
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“Usually, the frequencies of the peptides displayed on phages are not even in the library. There were some reasons for the heterogenous phage amount, such as biases in library construction, variance in the use of cryptography,45,46 the different growth rates of phages and peptide degradation by protease.47”
From Identification of heptapeptides targeting a lethal bacterial strain in septic mice through an integrative approach (2022) · cites this paper as [45]
Experimental — accuracy not yet measuredIn the citing paper
“Codon preference varies extensively in different organisms,249 therefore adjusting the balance between codon usage frequency and host tRNA availability can significantly improve translation efficiency and in vivo expression of the target antigen.250,251”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [249]
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Citations
Cites
The Neutral Theory of Molecular Evolution
Kimura, M. (1979) · Scientific American · doi:10.1038/scientificamerican1179-98 · Cited by 7,687
Codon usage and tRNA content in unicellular and multicellular organisms.
Ikemura, T. (1985) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040335 · Cited by 1,710
Bennetzen, J. L., & Hall, B. D. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)81068-2 · Cited by 1,584
The neutral theory of molecular evolution
Dover, G. A. (1984) · Endeavour · doi:10.1016/0160-9327(84)90064-4 · Cited by 1,394
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
Sharp, P. M., Tuohy, T. M. F., & Mosurski, K. (1986) · Nucleic Acids Research · doi:10.1093/nar/14.13.5125 · Cited by 1,206
Self-citationCodon usage in bacteria: correlation with gene expressivity.
Gouy, M., & Gautier, C. (1982) · Nucleic Acids Research · doi:10.1093/nar/10.22.7055 · Cited by 1,182
Codon catalog usage is a genome strategy modulated for gene expressivity
Grantham, R. L., Gautier, C., Gouy, M., Jacobzone, M., & Mercier, R. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.1.213-b · Cited by 939
Ikemura, T. (1981) · Journal of Molecular Biology · doi:10.1016/0022-2836(81)90363-6 · Cited by 875
The mosaic genome of warm-blooded vertebrates
Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M., & Rodier, F. (1985) · Science · doi:10.1126/science.4001930 · Cited by 875
Ikemura, T. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90250-9 · Cited by 605
Research works printed but not linked: 5
- Toh, H. (1986) FEBS Letters 194, 245-248.
- Miyata, T. and Hayashida, H. (1981) Proc. Natl. Acad. Sci. USA 78, 5739- 5743.
- Sharp, P.M. and Li, W-H. (1986) J. Mol. Evol. (in press)
- Li, W-H. (1987) J. Mol. Evol. (in press)
- Ochman, H. and Selander, R.K. (1984) Proc. Natl. Acad. Sci. USA 81, 198- 201.
Cited by
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Items 1,001–1,006 of 1,006
Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias
Lee, S., Weon, S., Lee, S., & Kang, C. (2010) · Evolutionary Bioinformatics · doi:10.4137/ebo.s4608 · Cited by 68
Terai, G., Kamegai, S., & Asai, K. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btv678 · Cited by 36
A code for transcription elongation speed
Cohen, E., Zafrir, Z., & Tuller, T. (2018) · RNA Biology · doi:10.1080/15476286.2017.1384118 · Cited by 29
The improvement of amorpha-4,11-diene production by a yeast-conform variant
Jiang-Qiang, K., Wei, W., Li-Na, W., Xiao-Dong, Z., Ke-Di, C., & Ping, Z. (2009) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2008.04063.x · Cited by 22
Zhang, X., Li, S., Luo, H., He, S., Yang, H., Li, L., Tian, T., Han, Q., Ye, J., Huang, C., et al. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01035-6 · Cited by 14
Codon-triplet context unveils unique features of the Candida albicans protein coding genome
Moura, G. R., Lousado, J. P., Pinheiro, M., Carreto, L., Silva, R. M., Oliveira, J. L., & Santos, M. A. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-444 · Cited by 9
Metadata
- Authors
- Sharp, P. M., & Li, W.-H.
- Affiliations
- The University of Texas System (US)
- Corresponding author
- Sharp, Paul M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 1987
- Volume
- 15
- Issue
- 3
- Pages
- 1281-1295
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC340524
- OpenAlex
- W2018590530
- Cited by
- 3,992
- References
- 30
- Citations by year
- 2026: 223 · 2025: 203 · 2024: 205 · 2023: 177 · 2022: 198 · 2021: 239 · 2020: 212 · 2019: 147 · 2018: 155 · 2017: 120 · 2016: 133 · 2015: 112 · 2014: 147 · 2013: 145 · 2012: 137
- FWCI
- 7.58
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM30998)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- codon adaptation index, codon usage bias, codon usage, gene expression prediction, heterologous expression, highly expressed genes, natural selection
- MeSH terms
- Animals, Base Sequence, Cattle, Codon, Escherichia coli, Biological Evolution, Genes, Genes, Bacterial, Genes, Fungal, Humans, Mathematics, Models, Genetic, RNA, Messenger, Saccharomyces cerevisiae
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