1. Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 1985;2:13-34.
2. 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.
4. Sharp PM, Li WH. An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 1986;24:28-38.
5. Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in
Caenorhabditis, Drosophila, and
Arabidopsis. Proc Natl Acad Sci USA 1999;96:4482-4487.
7. Kliman RM, Hey J. Hill-Robertson interference in
Drosophila melanogaster: reply to Marais, Mouchiroud and Duret. Genet Res 2003;81:89-90.
8. Vinogradov AE. Intron length and codon usage. J Mol Evol 2001;52:2-5.
9. Romero H, Zavala A, Musto H. Codon usage in
Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res 2000;28:2084-2090.
10. Kane JF. Effects of rare codon clusters on high-level expression of heterologous proteins in
Escherichia coli. Curr Opin Biotechnol 1995;6:494-500.
11. Naya H, Romero H, Carels N, Zavala A, Musto H. Translational selection shapes codon usage in the GC-rich genome of
Chlamydomonas reinhardtii. FEBS Lett 2001;501:127-130.
12. Lin K, Kuang Y, Joseph JS, Kolatkar PR. Conserved codon composition of ribosomal protein coding genes in
Escherichia coli, Mycobacterium tuberculosis and
Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res 2002;30:2599-2607.
13. Salamov AA, Solovyev VV. Ab initio gene finding in
Drosophila genomic DNA. Genome Res 2000;10:516-522.
14. Kliman RM, Irving N, Santiago M. Selection conflicts, gene expression, and codon usage trends in yeast. J Mol Evol 2003;57:98-109.
15. Lafay B, Sharp PM. Synonymous codon usage variation among
Giardia lamblia genes and isolates. Mol Biol Evol 1999;16:1484-1495.
16. McInerney JO. Replicational and transcriptional selection on codon usage in
Borrelia burgdorferi. Proc Natl Acad Sci USA 1998;95:10698-10703.
17. Flisser A, Sarti E, Lightowlers M, Schantz P. Neurocysticercosis: regional status, epidemiology, impact and control measures in the Americas. Acta Trop 2003;87:43-51.
18. Kanaya S, Yamada Y, Kinouchi M, Kudo Y, Ikemura T. Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. J Mol Evol 2001;53:290-298.
20. Greenacre MJ. Theory and applications of correspondence analysis. Información General. Academic Press. 1984.
22. Liu Q. Analysis of codon usage pattern in the radioresistant bacterium
Deinococcus radiodurans. Biosystems 2006;85:99-106.
23. Chen L, Liu T, Yang D, Nong X, Xie Y, Xie Y, Fu Y, Wu X, Huang X, Gu X, Wang S, Peng X, Yang G. Analysis of codon usage patterns in Taenia pisiformis through annotated
transcriptome data. Biochem Biophys Res Commun 2013;430:1344-1348.
24. Zhong J, Li Y, Zhao S, Liu S, Zhang Z. Mutation pressure shapes codon usage in the GC-rich genome of foot-and-mouth disease virus. Virus Genes 2007;35:767-776.
25. Sau K, Sau S, Mandal SC, Ghosh TC. Factors influencing the synonymous codon and amino acid usage bias in AT-rich
Pseudomonas aeruginosa phage PhiKZ. Acta Biochim Biophys Sin (Shanghai) 2005;37:625-633.
27. Wright F. The ‘effective number of codons’ used in a gene. Gene 1990;87:23-29.
28. Sueoka N. Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol 1995;40:318-325.
29. Chen L, Yang DY, Liu TF, Nong X, Huang X, Xie Y, Fu Y, Zheng WP, Zhang RH, Wu XH, Gu XB, Wang SX, Peng XR, Yang GY. Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes. Genet Mol Res 2013;12:587-596.
30. Rao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X. Mutation bias is the driving force of codon usage in the
Gallus gallus genome. DNA Res 2011;18:499-512.
31. Goetz RM, Fuglsang A. Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from
Escherichia coli. Biochem Biophys Res Commun 2005;327:4-7.
33. Hershberg R, Petrov DA. General rules for optimal codon choice. PLoS Genet 2009;5:e1000556.
34. Kawabe A, Miyashita NT. Patterns of codon usage bias in three dicot and four monocot plant species. Genes Genet Syst 2003;78:343-352.
35. Waterkeyn JG, Gauci C, Cowman AF, Lightowlers MW. Codon usage in
Taenia species. Exp Parasitol 1998;88:76-78.
36. Ingvarsson PK. Gene expression and protein length influence codon usage and rates of sequence evolution in
Populus tremula. Mol Biol Evol 2007;24:836-844.
37. Comeron JM, Kreitman M, Aguadé M. Natural selection on synonymous sites is correlated with gene length and recombination in
Drosophila. Genetics 1999;151:239-249.
38. Moriyama EN, Powell JR. Codon usage bias and tRNA abundance in
Drosophila. J Mol Evol 1997;45:514-523.
39. Coulombe-Huntington J, Majewski J. Intron loss and gain in
Drosophila. Mol Biol Evol 2007;24:2842-2850.
40. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA. Selection for short introns in highly expressed genes. Nat Genet 2002;31:415-418.
41. Jeffares DC, Penkett CJ, Bähler J. Rapidly regulated genes are intron poor. Trends Genet 2008;24:375-378.
42. Andersson S, Kurland C. Codon preferences in free-living micro-organisms. Microbiol Rev 1990;54:198-210.
43. Shields DC, Sharp PM, Higgins DG, Wright F. " Silent" sites in
Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol 1988;5:704-716.
44. Stenico M, Lloyd AT, Sharp PM. Codon usage in
Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res 1994;22:2437-2446.
45. Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F. 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. Nucleic Acids Res 1988;16:8207-8211.