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Nirenberg MW, Jones W, Leder P, Clark BFC, Sly WS, Pestka S: On the Coding of Genetic Information. Cold Spring Harb Symp Quant Biol 1963, 28: 549-558.

Crick FH: Codon--anticodon pairing: the wobble hypothesis. J Mol Biol 1966,19(2):548-555.

Crick FH: The origin of the genetic code. J Mol Biol 1968,38(3):367-379. 10.1016/0022-2836(68)90392-6

Woese C: The genetic code: the molecular basis for genetic expression. New York , Harper & Row; 1967.

Ambrogelly A, Palioura S, Soll D: Natural expansion of the genetic code. Nat Chem Biol 2007,3(1):29-35. 10.1038/nchembio847

Woese CR, Dugre DH, Saxinger WC, Dugre SA: The Molecular Basis for the Genetic Code. Proceedings of the National Academy of Sciences 1966,55(4):966-974. 10.1073/pnas.55.4.966

Ardell DH, Sella G: No accident: genetic codes freeze in error-correcting patterns of the standard genetic code. Philos Trans R Soc Lond B Biol Sci 2002,357(1427):1625-1642. 10.1098/rstb.2002.1071

Woese CR: On the evolution of the genetic code. Proc Natl Acad Sci U S A 1965,54(6):1546-1552. 10.1073/pnas.54.6.1546

Chechetkin VR: Block structure and stability of the genetic code. J Theor Biol 2003,222(2):177-188. 10.1016/S0022-5193(03)00025-0

Woese CR, Dugre DH, Dugre SA, Kondo M, Saxinger WC: On the fundamental nature and evolution of the genetic code. Cold Spring Harb Symp Quant Biol 1966, 31: 723-736.

Alff-Steinberger C: The Genetic Code and Error Transmission. Proceedings of the National Academy of Sciences 1969,64(2):584-591. 10.1073/pnas.64.2.584

Haig D, Hurst LD: A quantitative measure of error minimization in the genetic code. Journal of Molecular Evolution 1991,33(5):412-417. 10.1007/BF02103132

Goldman N: Further results on error minimization in the genetic code. Journal of Molecular Evolution 1993,37(6):662-664.

Freeland SJ, Wu T, Keulmann N: The case for an error minimizing standard genetic code. Orig Life Evol Biosph 2003,33(4-5):457-477. 10.1023/A:1025771327614

Sella G, Ardell DH: The coevolution of genes and genetic codes: Crick's frozen accident revisited. J Mol Evol 2006,63(3):297-313. 10.1007/s00239-004-0176-7

Davies J, Gilbert W, Gorini L: Streptomycin, Suppression, and the Code. Proceedings of the National Academy of Sciences 1964,51(5):883-890. 10.1073/pnas.51.5.883

Friedman SM, Weinstein IB: Lack of fidelity in the translation of ribopolynucleotides. Proc Natl Acad Sci USA 1964, 52: 988-996. 10.1073/pnas.52.4.988

Parker J: Errors and alternatives in reading the universal genetic code. Microbiology and Molecular Biology Reviews 1989,53(3):273-298.

Ardell DH, Sella G: On the evolution of redundancy in genetic codes. J Mol Evol 2001,53(4-5):269-281. 10.1007/s002390010217

Sella G, Ardell DH: The impact of message mutation on the fitness of a genetic code. J Mol Evol 2002,54(5):638-651. 10.1007/s00239-001-0060-7

Freeland SJ, Knight RD, Landweber LF, Hurst LD: Early Fixation of an Optimal Genetic Code. Molecular Biology and Evolution 2000, 17: 511-518.

Gilis D, Massar S, Cerf NJ, Rooman M: Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biol 2001,2(11):49.1–49.12. 10.1186/gb-2001-2-11-research0049

Goodarzi H, Nejad HA, Torabi N: On the optimality of the genetic code, with the consideration of termination codons. Biosystems 2004,77(1-3):163-173. 10.1016/j.biosystems.2004.05.031

Freeland SJ, Hurst LD: The Genetic Code Is One in a Million. Journal of Molecular Evolution 1998,47(3):238-248. 10.1007/PL00006381

Gamow G: Possible relation between deoxyribonucleic acid and protein structures. Nature 1954, 173: 318. 10.1038/173318a0

Pelc SR: Correlation between coding-triplets and amino acids. Nature 1965,207(4997):597-599. 10.1038/207597a0

Yarus M: Amino Acids as RNA Ligands: A Direct-RNA-Template Theory for the Code's Origin. Journal of Molecular Evolution 1998,47(1):109-117. 10.1007/PL00006357

Yarus M: A specific amino acid binding site composed of RNA. Science 1988,240(4860):1751. 10.1126/science.3381099

Di Giulio M: The origin of the genetic code: theories and their relationships, a review. Biosystems 2005,80(2):175-184. 10.1016/j.biosystems.2004.11.005

Knight RD, Freeland SJ, Landweber LF: Selection, history and chemistry: the three faces of the genetic code. J Biol Chem 1999, 273: 23019-23025.

Yarus M: RNA–ligand chemistry: A testable source for the genetic code. RNA 2000,6(04):475-484. 10.1017/S1355838200002569

Yarus M, Caporaso JG, Knight R: Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem 2005, 74: 179-198. 10.1146/annurev.biochem.74.082803.133119

Wolf YI, Koonin EV: On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol Direct 2007, 2: 14. 10.1186/1745-6150-2-14

Wong JTF: A Co-Evolution Theory of the Genetic Code. Proceedings of the National Academy of Sciences 1975,72(5):1909-1912. 10.1073/pnas.72.5.1909

Wong JTF: Role of Minimization of Chemical Distances between Amino Acids in the Evolution of the Genetic Code. Proceedings of the National Academy of Sciences 1980,77(2):1083-1086. 10.1073/pnas.77.2.1083

Di Giulio M: The coevolution theory of the origin of the genetic code. Physics of Life Reviews 2004,1(2):128-137. 10.1016/j.plrev.2004.05.001

Di Giulio M: The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code. Journal of Molecular Evolution 1998,46(6):615-621. 10.1007/PL00006341

Di Giulio M: Genetic Code Origin and the Strength of Natural Selection. Journal of Theoretical Biology 2000,205(4):659-661. 10.1006/jtbi.2000.2115

Freeland SJ, Hurst LD: Load minimization of the genetic code: history does not explain the pattern. Proceedings of the Royal Society B: Biological Sciences 1998,265(1410):2111-2119. 10.1098/rspb.1998.0547

Di Giulio M: The origin of the genetic code. Trends in Biochemical Sciences 2000,25(2):44. 10.1016/S0968-0004(99)01522-4

Freeland SJ, Knight RD, Landweber LF: Measuring adaptation within the genetic code. Trends Biochem Sci 2000,25(2):44-45. 10.1016/S0968-0004(99)01531-5

Di Giulio M, Capobianco MR, Medugno M: On the optimization of the physicochemical distances between amino acids in the evolution of the genetic code. J Theor Biol 1994,168(1):43-51. 10.1006/jtbi.1994.1086

Kramer EB, Farabaugh PJ: The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. Rna 2007,13(1):87-96. 10.1261/rna.294907

Archetti M: Codon Usage Bias and Mutation Constraints Reduce the Level of ErrorMinimization of the Genetic Code. Journal of Molecular Evolution 2004,59(2):258-266. 10.1007/s00239-004-2620-0

Zhu CT, Zeng XB, Huang WD: Codon Usage Decreases the Error Minimization Within the Genetic Code. Journal of Molecular Evolution 2003,57(5):533-537. 10.1007/s00239-003-2505-7

Ardell DH: On error minimization in a sequential origin of the standard genetic code. J Mol Evol 1998,47(1):1-13. 10.1007/PL00006356

Benner SA, Cohen MA, Gonnet GH: Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Engineering 1994, 7: 1323-1332. 10.1093/protein/7.11.1323

Di Giulio M: The Origin of the Genetic Code cannot be Studied using Measurements based on the PAM Matrix because this Matrix Reflects the Code Itself, Making any such Analyses Tautologous. Journal of Theoretical Biology 2001,208(2):141-144. 10.1006/jtbi.2000.2206

Ogle JM, Ramakrishnan V: Structural insights into translational fidelity. Annu Rev Biochem 2005, 74: 129-177. 10.1146/annurev.biochem.74.061903.155440

Ogle JM, Carter AP, Ramakrishnan V: Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 2003,28(5):259-266. 10.1016/S0968-0004(03)00066-5

Ogle JM, Brodersen DE, Clemons WM Jr., Tarry MJ, Carter AP, Ramakrishnan V: Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 2001,292(5518):897-902. 10.1126/science.1060612

Caporaso JG, Yarus M, Knight R: Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code. J Mol Evol 2005,61(5):597-607. 10.1007/s00239-004-0314-2

Goodarzi H, Shateri Najafabadi H, Torabi N: On the coevolution of genes and genetic code. Gene 2005, 362: 133-140. 10.1016/j.gene.2005.08.005

Hasegawa M, Miyata T: On the antisymmetry of the amino acid code table. Origins of Life and Evolution of Biospheres (Formerly Origins of Life and Evolution of the Biosphere) 1980,10(3):265-270.

King JL, Jukes TH: Non-Darwinian Evolution. Science 1969,164(3881):788-798. 10.1126/science.164.3881.788

Marquez R, Smit S, Knight R: Do universal codon-usage patterns minimize the effects of mutation and translation error? Genome Biol 2005,6(11):R91. 10.1186/gb-2005-6-11-r91

Goodarzi H, Najafabadi HS, Hassani K, Nejad HA, Torabi N: On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. J Theor Biol 2005,235(3):318-325. 10.1016/j.jtbi.2005.01.012

Jukes TH: Arginine as an evolutionary intruder into protein synthesis. Biochem Biophys Res Commun 1973,53(3):709-714. 10.1016/0006-291X(73)90151-4

Tolstrup N, Toftgard J, Engelbrecht J, Brunak S: Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies. J Mol Biol 1994,243(5):816-820. 10.1006/jmbi.1994.1683

Swanson R: A unifying concept for the amino acid code. Bulletin of Mathematical Biology 1984,46(2):187-203.

Jukes TH: Possibilities for the evolution of the genetic code from a preceding form. Nature 1973,246(5427):22-26. 10.1038/246022a0