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Below is a growing list of references concerning the evolution of the genetic code. References are listed alphabetically by author, but you can search the references by author, title, keyword, or categoy by using the Search References form on the left. If you have a publication that you would like to add or remove from the list, please use our Request to Add or Remove a Reference form. To view publications from the Freeland Lab, please visit our Publications page.

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    A
  1. Akashi H., "Codon bias evolution in Drosophila. Population genetics of mutation-selection drift," Gene, vol. 205, pp. 269-78, 1997. [Link] [Edit]
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  4. ALesbians, "DLesbians," Bioinformatics, vol. 0, pp. http://lesbian.2hp.e, 2005. [Link] [Edit]
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    15. Back to Top

    B
  15. Bada, J.L., Glavin, D.P., McDonald, G.D. and Becker, L., "A search for endogenous amino acids in martian meteorite ALH84001.," Science, vol. 279, pp. 362-365, 1998. [Link] [Edit]
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  25. Bulmer, M., "Coevolution of codon usage and transfer RNA abundance," Nature, vol. 325, pp. 728-30, 1987. [Link] [Edit]
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    C
  27. Chang MS, Benner SA, "Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments," J Mol Biol, vol. 341, pp. 617-631, 2004. [Link] [Edit]
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    34. Back to Top

    D
  34. Dayhoff MO, Schwartz RM, Orcutt BC: A model of evolutionary change in proteins. In Atlas of Protein Science and Structure. Edited by Dayhoff MO. National Biomedical Research Foundation; 1978. [Link] [Edit]
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  40. Duret, L., "tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes," Trends Genet, vol. 16, pp. 287-9, 2000. [Link] [Edit]

    41. Back to Top

    E
  41. Edgar RC, "MUSCLE: a multiple sequence alignment method with reduced time and space complexity," BMC Bioinformatics, vol. 5, pp. 113, 2004. [Link] [Edit]
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    46. Back to Top

    F
  46. Fox, S.W., "Thermal synthesis of amino acids and the origin of life.," Geochim Cosmochim Acta, vol. 59, pp. 1213-1214, 1995. [Link] [Edit]
  47. Fuglsang, A., "Codon optimizer: a freeware tool for codon optimization," Protein Expr Purif, vol. 31, pp. 247-9, 2003. [Link] [Edit]

    48. Back to Top

    G
  48. Gamow, G., "Possible relation between deoxyribonucleic acid and protein structure.," Nature, vol. 173, pp. 318, 1954. [Link] [Edit]
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  50. Gilbert, W., "Origin of life: The RNA world.," Nature, vol. 319, pp. 618, 1986. [Link] [Edit]
  51. Gouy, M., and C. Gautier, "Codon usage in bacteria: correlation with gene expressivity," Nucleic Acids Res, vol. 10, pp. 7055-74, 1982. [Link] [Edit]
  52. Grantham, R., C. Gautier, M. Gouy, M. Jacobzone, and R. Mercier, "Codon catalog usage is a genome strategy modulated for gene expressivity," Nucleic Acids Res, vol. 9, pp. r43-74, 1981. [Link] [Edit]
  53. Grosjean, H., and W. Fiers, "Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes," Gene, vol. 18, pp. 199-209, 1982. [Link] [Edit]
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    H
  56. Hartman, H., "Speculations on the origin of the genetic code.," J Mol Evol, vol. 40, pp. 541-544, 1995. [Link] [Edit]
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    I
  62. 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, vol. 151, pp. 389-409, 1981. [Link] [Edit]
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  66. Jansen, R., H. J. Bussemaker, and M. Gerstein, "Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models," Nucleic Acids Res, vol. 31, pp. 2242-51, 2003. [Link] [Edit]
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