Genetics Problem Spaces

Introduction Problem Spaces Codon Usage Overview Intro Exercise Research Questions Literature Resources Assignments Student Projects

Codon Usage Literature Annotated Bibliography Campbell WH (1990) Codon bias in maize nuclear genes. Maize Genetics Cooperation Newsletter 64: 64-65. Carlini DB, Wolfgang Stephan (2003) In vivo introduction of unpreferred synonymous codons into the Drosophila adh gene results in reduced levels of ADH protein. Genetics 163:239-243. Comeron JM, Aguade M (1998) An evaluation of measures of synonymous codon usage bias. J. Mol Evol 47:268-274. Conticello SG, Pilpel Y, Gulsuman G, Fainzilber M. (2000) Positional-specific codon conservation in hypervariable gene families. Trends in Genetics 16(2):57-59. Fedrov A, Saxonov S, Gilbert W (2002) Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res 30(5):1192-1197, Fennoy SL, Surti G, Bailey-Serres J (1993) Analysis of synonymous codon usage in maize. Maize Genetics Cooperation Newsletter 67:99-100. Hey J, Kliman RM (2002) Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160:595-608. Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNA’s and the Occurrence of the respective codons in its protein genes: a proposal for a synonomous codon choice that is optimal for the E. coli translational system. J Mol Biol 389-409. Ikemura T (1982) Correlation between the abundance of yeast transfer RNA’s and the occurance of the respective codons in protein genes. J Mol Biol 158:573-597. Lynn DJ, Singer GA, Hickey DA (2002) Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30:4272-4277. Morton BR, Levin JA (1997) The atypical codon usage of the plant psbA gene may beh the remnant of an ancestral bias. PNAS 94:11434-11438. Moriyama EN Powell JR (1998) Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces and Escherichia coli. Nucleic Acid Res 26(13):3188-93. Plotkin JB, Dushoff J (2003) Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. PNAS 100(12) 7152-7157. Powell JR, Moriyama, EN (1997) Evolution of codon usage bias in Drosophila. PNAS 94:7784-7790. Smith NGC, Eyre-Walker A (2001) Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans. Mol. Biol. Evol. 18(6):982-986. Susuki H, Arakawa K, Matsuzaki T, Saito R, Tomita M (2002) Correlation analysis between tRNA composition and codon usage using diversity and equitability index. Genome Informatics 13:406-407. Urrutia AO, Hurst LD (2001) Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159:1191-1199.