Bahiri-Elitzur S, Tuller T. Codon-based indices for modeling gene expression and transcript evolution. Comput Struct Biotechnol J. 2021;19:2646–63.Article
CAS
PubMed
PubMed Central
Google Scholar
Hershberg R, Petrov DA. Selection on codon bias. Annu Rev Genet. 2008;42:287–99.Article
CAS
PubMed
Google Scholar
Parvathy ST, Udayasuriyan V, Bhadana V. Codon usage bias. Mol Biol Rep. 2022;49:539–65.Article
CAS
PubMed
Google Scholar
Liu Y. A code within the genetic code: codon usage regulates co-translational protein folding. Cell Commun Signal. 2020;18:145.Article
CAS
PubMed
PubMed Central
Google Scholar
Athey J, et al. A new and updated resource for codon usage tables. BMC Bioinf. 2017;18:391.Article
Google Scholar
Quax TEF, Claassens NJ, Söll D, van der Oost J. Codon bias as a means to fine-tune gene expression. Mol Cell. 2015;59:149–61.Article
CAS
PubMed
PubMed Central
Google Scholar
Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol. 1986;24:28–38.Article
CAS
PubMed
Google Scholar
Wright F. The ‘effective number of codons’ used in a gene. Gene. 1990;87:23–9.Article
CAS
PubMed
Google Scholar
Satapathy SS, Sahoo AK, Ray SK, Ghosh TC. Codon degeneracy and amino acid abundance influence the measures of codon usage bias: improved Nc ( N̂ c ) and ENCprime ( N̂ ′ c ) measures. Genes Cells. 2017;22:277–83.Article
CAS
PubMed
Google Scholar
Roymondal U, Das S, Sahoo S. Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome. DNA Res. 2009;16:13–30.Article
CAS
PubMed
PubMed Central
Google Scholar
Sabi R, Tuller T. Modelling the efficiency of codon–tRNA interactions based on codon usage bias. DNA Res. 2014;21:511–26.Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Z, et al. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinf. 2012;13:43.Article
Google Scholar
Supek F, Vlahoviček K. Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. BMC Bioinf. 2005;6:182.Article
Google Scholar
Freire-Picos MA, et al. Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes. Gene. 1994;139:43–9.Article
CAS
PubMed
Google Scholar
Wan X-F, Xu D, Kleinhofs A, Zhou J. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol. 2004;4:19.Article
PubMed
PubMed Central
Google Scholar
Wan X-F, Zhou J, Xu D. CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes. Int J Gen Syst. 2006;35:109–25.Article
Google Scholar
Suzuki H, Saito R, Tomita M. The ‘weighted sum of relative entropy’: a new index for synonymous codon usage bias. Gene. 2004;335:19–23.Article
CAS
PubMed
Google Scholar
Gribskov M, Devereux J, Burgess RR. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res. 1984;12:539–49.Article
CAS
PubMed
PubMed Central
Google Scholar
Urrutia AO, Hurst LD. Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics. 2001;159:1191–9.Article
CAS
PubMed
PubMed Central
Google Scholar
Sharp PM, Li WH. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987;15:1281–95.Article
CAS
PubMed
PubMed Central
Google Scholar
Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 1981;151, 389–409.Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. J Mol Biol. 1982;158:573–97.Article
CAS
PubMed
Google Scholar
Bourret J, Alizon S, Bravo IG. COUSIN (COdon usage similarity INdex): a normalized measure of codon usage preferences. Genome Biol Evol. 2019;11:3523–8.Article
CAS
PubMed
PubMed Central
Google Scholar
Bennetzen JL, Hall BD. Codon selection in yeast. J Biol Chem. 1982;257:3026–31.Article
CAS
PubMed
Google Scholar
Suzuki H, Saito R, Tomita M. Measure of synonymous codon usage diversity among genes in bacteria. BMC Bioinf. 2009;10:167.Article
Google Scholar
Fox JM, Erill I. Relative codon adaptation: a generic codon bias index for prediction of gene expression. DNA Res. 2010;17:185–96.Article
CAS
PubMed
PubMed Central
Google Scholar
Diament A, Pinter RY, Tuller T. Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function. Nat Commun. 2014;5:5876.Article
CAS
PubMed
Google Scholar
Karlin S, Mrázek J, Campbell AM. Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol. 1998;29:1341–55.Article
CAS
PubMed
Google Scholar
Reis Md. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 2004;32, 5036–5044.Anwar AM, et al. gtAI: an improved species-specific tRNA adaptation index using the genetic algorithm. Front Mol Biosci. 2023;10:1218518.Article
CAS
PubMed
PubMed Central
Google Scholar
Gouy M, Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982;10:7055–74.Article
CAS
PubMed
PubMed Central
Google Scholar
Stenico M, Lloyd AT, Sharp PM. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res. 1994;22:2437–46.Article
CAS
PubMed
PubMed Central
Google Scholar
Alexaki A, et al. Codon and codon-pair usage tables (CoCoPUTs): facilitating genetic variation analyses and recombinant gene design. J Mol Biol. 2019;431:2434–41.Article
CAS
PubMed
Google Scholar
Kunec D, Osterrieder N. Codon pair bias is a direct consequence of dinucleotide bias. Cell Rep. 2016;14:55–67.Article
CAS
PubMed
Google Scholar
Coleman JR, et al. Virus attenuation by genome-scale changes in codon pair bias. Science. 2008;320:1784–7.Article
CAS
PubMed
PubMed Central
Google Scholar
Plotkin JB, Dushoff J, Fraser HB. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature 428, 942–945 (2004).Ghaemmaghami S, et al. Global analysis of protein expression in yeast. Nature. 2003;425:737–41.Article
CAS
PubMed
Google Scholar
Baycin-Hizal D, et al. Proteomic analysis of Chinese hamster ovary cells. J Proteome Res. 2012;11:5265–76.Article
CAS
PubMed
PubMed Central
Google Scholar
Lu P, Vogel C, Wang R, Yao X, Marcotte EM. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol. 2007;25:117–24.Article
CAS
PubMed
Google Scholar
Schwanhäusser B, et al. Global quantification of mammalian gene expression control. Nature. 2011;473:337–42.Article
PubMed
Google Scholar
Welch M, et al. Design parameters to control synthetic gene expression in Escherichia coli. PLoS ONE. 2009;4: e7002.Article
PubMed
PubMed Central
Google Scholar
Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009;324:255–8.Article
CAS
PubMed
PubMed Central
Google Scholar
Friberg M, von Rohr P, Gonnet G. Limitations of codon adaptation index and other coding DNA-based features for prediction of protein expression inSaccharomyces cerevisiae. Yeast. 2004;21:1083–93.Article
CAS
PubMed
Google Scholar