Published in J Mol Evol on September 01, 2004
The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet (2009) 3.11
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res (2007) 2.63
Decoding mechanisms by which silent codon changes influence protein biogenesis and function. Int J Biochem Cell Biol (2015) 1.04
Do universal codon-usage patterns minimize the effects of mutation and translation error? Genome Biol (2005) 1.02
Codon usage is associated with the evolutionary age of genes in metazoan genomes. BMC Evol Biol (2009) 0.98
Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation. Genome Biol (2007) 0.89
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage. Nucleic Acids Res (2009) 0.89
Differential selective constraints shaping codon usage pattern of housekeeping and tissue-specific homologous genes of rice and arabidopsis. DNA Res (2008) 0.89
Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies. Nucleic Acids Res (2011) 0.88
Modeling compositional dynamics based on GC and purine contents of protein-coding sequences. Biol Direct (2010) 0.88
Identification of conflicting selective effects on highly expressed genes. Evol Bioinform Online (2007) 0.84
The tri-frame model. J Theor Biol (2007) 0.81
High-density transcriptional initiation signals underline genomic islands in bacteria. PLoS One (2012) 0.79
Selection shapes the robustness of ligand-binding amino acids. J Mol Evol (2013) 0.78
Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint. Life (Basel) (2015) 0.76
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06
Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol (1985) 16.88
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol (2000) 13.01
Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . J Mol Biol (1971) 12.21
Codon catalog usage and the genome hypothesis. Nucleic Acids Res (1980) 11.97
Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng (1994) 9.42
Nucleotide sequence of the ribosomal protein gene cluster adjacent to the gene for RNA polymerase subunit beta in Escherichia coli. Proc Natl Acad Sci U S A (1979) 9.28
The 'effective number of codons' used in a gene. Gene (1990) 9.26
Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res (2000) 7.88
The mosaic genome of warm-blooded vertebrates. Science (1985) 7.54
Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics (1994) 6.83
Amino acid substitutions in structurally related proteins. A pattern recognition approach. Determination of a new and efficient scoring matrix. J Mol Biol (1988) 6.01
Complementary base pairing and the origin of substitution mutations. Nature (1976) 4.67
On the evolution of the genetic code. Proc Natl Acad Sci U S A (1965) 3.92
Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol (1998) 3.78
Mutation data matrix and its uses. Methods Enzymol (1990) 3.24
Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci U S A (1997) 3.05
Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev (2002) 2.95
Codon usage bias and tRNA abundance in Drosophila. J Mol Evol (1997) 2.77
A quantitative measure of error minimization in the genetic code. J Mol Evol (1991) 2.72
Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci (1992) 2.61
The genetic code is one in a million. J Mol Evol (1998) 2.57
Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci U S A (2001) 2.50
Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics (2001) 2.29
Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics (2002) 2.20
Selection, history and chemistry: the three faces of the genetic code. Trends Biochem Sci (1999) 2.15
The neutral theory is dead. Long live the neutral theory. Bioessays (1996) 1.50
Nonrandom patterns of codon usage and of nucleotide substitutions in human alpha- and beta-globin genes: an evolutionary strategy reducing the rate of mutations with drastic effects? Proc Natl Acad Sci U S A (1981) 1.45
Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions. Genetics (2000) 1.05
Role of the amino-acid "code" and of selection for conformation in the evolution of proteins. Nature (1966) 1.04
The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. Genetics (1999) 1.03
Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code. J Mol Evol (2004) 0.96
Evolutionary conservation of both the hydrophilic and hydrophobic nature of transmembrane residues. J Theor Biol (1995) 0.92
The origin of the genetic code. Trends Biochem Sci (2000) 0.90
Codon preference reflects mistranslational constraints: a proposal. Nucleic Acids Res (1988) 0.90
Measuring adaptation within the genetic code. Trends Biochem Sci (2000) 0.88
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. J Theor Biol (2001) 0.84
Genetic code origin and the strength of natural selection. J Theor Biol (2000) 0.83