[1] Sueoka N. On the genetic basis of variation and heterogeneity of DNA base compositon[J]. Proc Natl Acad Sci U S A, 1962, 48:582- 592.
[2] Novembre J A. Accounting for background nucleotide composition when measuring codon usage bias[J]. Mol Biol Evol, 2002, 19(8): 1390-1394.
[3] Shi Xiu-Fan, Huang Jing-Fei, Liu Shu-Qun, et al. The features of synonymous codon bias and GC- content relationship in human genes[J]. Prog. Biochem. Biophys,2002,29(3):4l1-414.
[4] Wang H C, Hickey D A. Rapid divergence of codon usage patterns within the rice genome[J], BMC Evol Biol,2007,7(S1):S6.
[5] Carlini D B, Chen Y, Stephan W. The relationship between thirdcodon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr [J]. Genetics, 2001, 159(2): 623-633.
[6] Shah P, Gilchrist M A. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias[J]. PLoS Genet, 2010, 6(9): pii: e1001128.
[7] Sharp PM, Bailes E, Grocock RJ, et al. Variation in the strength of selected codon usage bias among bacteria[J]. Nucleic Acids Res, 2005,33(4):1141-1153.
[8] Gupta S K, Majumdar S, Bhattacharya T K, et al. Studies on the relationships between the synonymous codon usage and protein secondary structural units[J]. Biochem Biophys Res Commun, 2000, 269(3):692-696.
[9] Mahdi R N, Rouchka E C. Codon usage bias as a function of generation time and life expectancy[J]. Bioinformation,2012,8(3): 158-162.
[10] Gustafsson C, Govindarajan S, Minshull J. Codon bias and heterologous protein expression[J]. Trends Biotechnol,2004,22(7): 346-353.
[11] Angov E. Codon usage: nature's roadmap to expression and folding of proteins[J]. Biotechnol J,2011,6(6):650-659.
[12] Sueoka N, Kawanishi Y. DNA GC content of the third codon position and codon usage biases of human genes[J], Gene,2000,261 (1):53-62
[13] Stenico M, Lloyd A T, Sharp P M. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases [J]. Nucleic Acids Res,1994,22(13):2437-2446.
[14] Marais G, Duret L. Synonymous codon usage, accuracy of translation, and gene length in elegans[J], J Mol Evol,2001,52(3): 275-280.
[15] Moriyama E N, Powell J R. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli[J]. Nucleic Acids Res,1998,26(13):3188-3193.
[16] Zhou T, Gu W, Ma J, et al. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses[J]. Biosystems,2005,81 (1):77-86.
[17] Li M, Zhao Z, Chen J, et al. Characterization of synonymous codon usage bias in the pseudorabies virus US1 gene[J]. Virologica Sinica, 2012,27(5):303-315.
[18] Satapathy S S, Dutta M, Buragohain A K, et al. Transfer RNA Gene Numbers may not be Completely Responsible for the Codon Usage Bias in Asparagine, Isoleucine, Phenylalanine, and Tyrosine in the High Expression Genes in Bacteria[J]. J Mol Evol,2012,75(1-2):34- 42.
[19] Shao Z Q, Zhang Y M, Feng X Y, et al. Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency[J]. PLoS one,2012,7(3):e33547.
[20] Fan San- Hong, Guo Ai- Guang, Shan Li- Wei, et al. Analysis of genetic code preference in Arabidopsis thaliana [J]. Prog. Biochem. Biophys,2003,30(2):221-225.
[21] Kawabe A, Miyashita N T. Patterns of codon usage bias in three dicot and four monocot plant species[J], Genes Genet Syst,2003,78 (5): 343-352.
[22] Liu Qing-Po., Tan Jun, Xue Qing-Zhong. Synonymous codon usage bias in the rice cultivar 93-11[J]. Acta Genetica Sinica,2003,30(4): 335-340.
[23] Liu Han-Mei, He Rui, Zhao Yao, et al. Analysis of codon usage in maize[J], Journal of Nuclear Agriculture Sciences,2008,22(2):141- 147.
[24] Liu Han- Mei, He Rui, Zhang Huai- Yu, et al. Analysis of Synonymous Codon Bias in Maize[J]. Journal of Agricultural Biotechnology,2010,18(3):456-461.
[25] Qiu S, Bergero R, Zeng K, et al. Patterns of codon usage bias in Silene latifolia[J]. Mol Biology Evol,2011,28(1):771-780.
[26] Muyle A, Serres- Giardi L, Ressayre A, et al. GC- biased gene conversion and selection affect GC content in the Oryza genus (rice) [J]. Mol Biol Evol,2011,28(9):2695-2706.
[27] Zhao Sheng, Zhang Qin, Liao Wei- Xuan, et al. Analysis of code preference of patrly CDS on yak[J], Journal of Southwest University for Nationalities (Natrual Science Edition),2005,31(5): 755-760.
[28] Dass J F, Sudandiradoss C. Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species [J]. Gene,2012,503(1):92-100.
[29] Romero H, Zavala A, Musto H, et al. The influence of translational selection on codon usage in fishes from the family Cyprinidae[J]. Gene,2003,317(1-2):141-147.
[30] Rao Y, Wu G, Wang Z, et al. Mutation bias is the driving force of codon usage in the Gallus gallus genome [J]. DNA Res,2011,18(6): 499-512.
[31] Wright F. The 'effective number of codons' used in a gene[J]. Gene. 1990,87(1):23-29.
[32] Wu Xian-Ming, Wu Song-Feng, Ren Da-Ming, et al. The analysis method and progress in the study of codon bias [J]. HEREDITAS (Beijing), 2007,29(4):420-426.
[33] Sharp P M, Li W H. The codon Adaptation Index——a measure of directional synonymous codon usage bias, and its potential applications[J]. Nucleic Acids Res,1987,15(3):1281-1295.
[34] Carbone A, Zinovyev A, Képès F. Codon adaptation index as a measure of dominating codon bias [J]. Bioinformatics,2003,19(16): 2005-2015.
[35] Puigbò P, Bravo IG, Garcia- Vallve S. CAIcal: a combined set of tools to assess codon usage adaptation [J]. Biol Direct,2008,3:38.
[36] Lavener Y, Kotlar D. Codon bias as a factor in regulating expression via translation rate in the human genome [J]. Gene,2005, 345(1):127-138.
[37] Roymondal U, Das S, Sahoo S. Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome[J]. DNA Res,2009,16(1):13-30.
[38] Zeng K, Charlesworth B. Estimating selection intensity on synonymous codon usage in a nonequilibrium population[J]. Genetics,2009,183(2):651-662.
[39] Fox J M, Erill I. Relative codon adaptation: a generic codon bias index for prediction of gene expression [J].DNA Res,2010,17(3): 185-196.
[40] Lee S, Weon S, Lee S, et al. Relative codon adaptation index, a sensitive measure of codon usage bias[J]. Evol Bioinform Online, 2010,6:47-55.
[41] Sharp P M, Cowe E, Higgins D G, et al. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within- species diversity[J]. Nucleic Acids Res,1988,16(17):8207-8211
[42] Raghavan R, Kelkar Y D, Ochman H. A selective force favoring increased G+C content in bacterial genes [J]. Proc Natl Acad U S A, 2012,109(36):14504-14507.
[43] Wald N, Alroy M, Botzman M, et al. Codon usage bias in prokaryotic pyrimidine- ending codons is associated with the degeneracy of the encoded amino acids[J]. Nucleic Acids Res. 2012, 40(15):7074-7083.
[44] Novoa E M, Ribas de Pouplana L. Speeding with control: codon usage, tRNAs, and ribosomes[J]. Trends Genet,2012,28(11):574- 581.
[45] Palidwor GA, Perkins TJ, Xia X. A general model of codon bias due to GC mutational bias[J]. PLoS one,2010,5(10):e13431.
[46] O'Connell M J, Doyle A M, Juenger T E, et al. In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure [J]. BMC Res Notes,2012,5(1):359.
|