Codon Usage Bias and Determining Forces in Taenia solium Genome

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참고문헌 (45)

1. Ikemura T, "Codon usage and tRNA content in unicellular and multicellular organisms", Mol Biol Evol, 2, pp.13~34 (1985)
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, 151, pp.389~409 (1981)
3. Nakamura Y, "Codon usage tabulated from the international DNA sequence databases", Nucleic Acids Res, 25, pp.244~245 (1997)
4. Sharp PM, "An evolutionary perspective on synonymous codon usage in unicellular organisms", J Mol Evol, 24, pp.28~38 (1986)
5. Duret L, "Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis", Proc Natl Acad Sci USA, 96, pp.4482~4487 (1999)
6. Marais G, "Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes", Proc Natl Acad Sci USA, 98, pp.5688~5692 (2001)
7. Kliman RM, "Hill-Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud and Duret", Genet Res, 81, pp.89~90 (2003)
8. Vinogradov AE, "Intron length and codon usage", J Mol Evol, 52, pp.2~5 (2001)
9. Romero H, "Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces", Nucleic Acids Res, 28, pp.2084~2090 (2000)
10. Kane JF, "Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli", Curr Opin Biotechnol, 6, pp.494~500 (1995)
11. Naya H, "Translational selection shapes codon usage in the GC-rich genome of Chlamydomonas reinhardtii", FEBS Lett, 501, pp.127~130 (2001)
12. Lin K, "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, 30, pp.2599~2607 (2002)
13. Salamov AA, "Ab initio gene finding in Drosophila genomic DNA", Genome Res, 10, pp.516~522 (2000)
14. Kliman RM, "Selection conflicts, gene expression, and codon usage trends in yeast", J Mol Evol, 57, pp.98~109 (2003)
15. Lafay B, "Synonymous codon usage variation among Giardia lamblia genes and isolates", Mol Biol Evol, 16, pp.1484~1495 (1999)
16. McInerney JO, "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi", Proc Natl Acad Sci USA, 95, pp.10698~10703 (1998)
17. Flisser A, "Neurocysticercosis: regional status, epidemiology, impact and control measures in the Americas", Acta Trop, 87, pp.43~51 (2003)
18. Kanaya S, "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, 53, pp.290~298 (2001)
19. Sharp PM, "The codon Adaptation index-a measure of directional synonymous codon usage bias, and its potential applications", Nucleic Acids Res, 15, pp.1281~1295 (1987)
20. Greenacre MJ, "Theory and applications of correspondence analysis" (1984), Academic Press
21. Lowe TM, "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence", Nucleic Acids Res, 25, pp.955~964 (1997)
22. Liu Q, "Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans", Biosystems, 85, pp.99~106 (2006)
23. Chen L, "Analysis of codon usage patterns in Taenia pisiformis through annotated transcriptome data", Biochem Biophys Res Commun, 430, pp.1344~1348 (2013)
24. Zhong J, "Mutation pressure shapes codon usage in the GC-rich genome of foot-and-mouth disease virus", Virus Genes, 35, pp.767~776 (2007)
25. Sau K, "Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ", Acta Biochim Biophys Sin (Shanghai), 37, pp.625~633 (2005)
26. Sueoka N, "Directional mutation pressure and neutral molecular evolution", Proc Natl Acad Sci USA, 85, pp.2653~2657 (1988)
27. Wright F, "The ‘effective number of codons’ used in a gene", Gene, 87, pp.23~29 (1990)
28. Sueoka N, "Intrastrand parity rules of DNA base composition and usage biases of synonymous codons", J Mol Evol, 40, pp.318~325 (1995)
29. Chen L, "Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes", Genet Mol Res, 12, pp.587~596 (2013)
30. Rao Y, "Mutation bias is the driving force of codon usage in the Gallus gallus genome", DNA Res, 18, pp.499~512 (2011)
31. Goetz RM, "Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli", Biochem Biophys Res Commun, 327, pp.4~7 (2005)
32. Rocha EP, "Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization", Genome Res, 14, pp.2279~2286 (2004)
33. Hershberg R, "General rules for optimal codon choice", PLoS Genet, 5, pp.e1000556~ (2009)
34. Kawabe A, "Patterns of codon usage bias in three dicot and four monocot plant species", Genes Genet Syst, 78, pp.343~352 (2003)
35. Waterkeyn JG, "Codon usage in Taenia species", Exp Parasitol, 88, pp.76~78 (1998)
36. Ingvarsson PK, "Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula", Mol Biol Evol, 24, pp.836~844 (2007)
37. Comeron JM, "Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila", Genetics, 151, pp.239~249 (1999)
38. Moriyama EN, "Codon usage bias and tRNA abundance in Drosophila", J Mol Evol, 45, pp.514~523 (1997)
39. Coulombe-Huntington J, "Intron loss and gain in Drosophila", Mol Biol Evol, 24, pp.2842~2850 (2007)
40. Castillo-Davis CI, "Selection for short introns in highly expressed genes", Nat Genet, 31, pp.415~418 (2002)
41. Jeffares DC, "Rapidly regulated genes are intron poor", Trends Genet, 24, pp.375~378 (2008)
42. Andersson S, "Codon preferences in free-living microorganisms", Microbiol Rev, 54, pp.198~210 (1990)
43. Shields DC, "'Silent' sites in Drosophila genes are not neutral: evidence of selection among synonymous codons", Mol Biol Evol, 5, pp.704~716 (1988)
44. Stenico M, "Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases", Nucleic Acids Res, 22, pp.2437~2446 (1994)
45. Sharp PM, "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, 16, pp.8207~8211 (1988)

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