Codon Usage Bias and Determining Forces in Taenia solium Genome

목차 (Table of Contents)

• Abstract
• INTRODUCTION
• MATERIALS AND METHODS
• RESULTS
• DISCUSSION
• REFERENCES

참고문헌 (Reference)

1 Lowe TM, "tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence" 25 : 955-964, 1997

2 Naya H, "Translational selection shapes codon usage in the GC-rich genome of Chlamydomonas reinhardtii" 501 : 127-130, 2001

3 Greenacre MJ, "Theory and applications of correspondence analysis" Academic Press 1984

4 Wright F, "The ‘effective number of codons’ used in a gene" 87 : 23-29, 1990

5 Sharp PM, "The codon Adaptation index-a measure of directional synonymous codon usage bias, and its potential applications" 15 : 1281-1295, 1987

6 Lafay B, "Synonymous codon usage variation among Giardia lamblia genes and isolates" 16 : 1484-1495, 1999

7 Chen L, "Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes" 12 : 587-596, 2013

8 Castillo-Davis CI, "Selection for short introns in highly expressed genes" 31 : 415-418, 2002

9 Kliman RM, "Selection conflicts, gene expression, and codon usage trends in yeast" 57 : 98-109, 2003

10 McInerney JO, "Replicational and transcriptional selection on codon usage in Borrelia burgdorferi" 95 : 10698-10703, 1998

11 Jeffares DC, "Rapidly regulated genes are intron poor" 24 : 375-378, 2008

12 Kawabe A, "Patterns of codon usage bias in three dicot and four monocot plant species" 78 : 343-352, 2003

13 Flisser A, "Neurocysticercosis: regional status, epidemiology, impact and control measures in the Americas" 87 : 43-51, 2003

14 Comeron JM, "Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila" 151 : 239-249, 1999

15 Zhong J, "Mutation pressure shapes codon usage in the GC-rich genome of foot-and-mouth disease virus" 35 : 767-776, 2007

16 Rao Y, "Mutation bias is the driving force of codon usage in the Gallus gallus genome" 18 : 499-512, 2011

17 Coulombe-Huntington J, "Intron loss and gain in Drosophila" 24 : 2842-2850, 2007

18 Vinogradov AE, "Intron length and codon usage" 52 : 2-5, 2001

19 Sueoka N, "Intrastrand parity rules of DNA base composition and usage biases of synonymous codons" 40 : 318-325, 1995

20 Kliman RM, "Hill-Robertson interference in Drosophila melanogaster: reply to Marais, Mouchiroud and Duret" 81 : 89-90, 2003

21 Hershberg R, "General rules for optimal codon choice" 5 : e1000556-, 2009

22 Ingvarsson PK, "Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula" 24 : 836-844, 2007

23 Sau K, "Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ" 37 : 625-633, 2005

24 Duret L, "Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis" 96 : 4482-4487, 1999

25 Kane JF, "Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli" 6 : 494-500, 1995

26 Marais G, "Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes" 98 : 5688-5692, 2001

27 Sueoka N, "Directional mutation pressure and neutral molecular evolution" 85 : 2653-2657, 1988

28 Goetz RM, "Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli" 327 : 4-7, 2005

29 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" 151 : 389-409, 1981

30 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" 30 : 2599-2607, 2002

31 Nakamura Y, "Codon usage tabulated from the international DNA sequence databases" 25 : 244-245, 1997

32 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" 16 : 8207-8211, 1988

33 Waterkeyn JG, "Codon usage in Taenia species" 88 : 76-78, 1998

34 Romero H, "Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces" 28 : 2084-2090, 2000

35 Stenico M, "Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases" 22 : 2437-2446, 1994

36 Rocha EP, "Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization" 14 : 2279-2286, 2004

37 Moriyama EN, "Codon usage bias and tRNA abundance in Drosophila" 45 : 514-523, 1997

38 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" 53 : 290-298, 2001

39 Ikemura T, "Codon usage and tRNA content in unicellular and multicellular organisms" 2 : 13-34, 1985

40 Andersson S, "Codon preferences in free-living microorganisms" 54 : 198-210, 1990

41 Chen L, "Analysis of codon usage patterns in Taenia pisiformis through annotated transcriptome data" 430 : 1344-1348, 2013

42 Liu Q, "Analysis of codon usage pattern in the radioresistant bacterium Deinococcus radiodurans" 85 : 99-106, 2006

43 Sharp PM, "An evolutionary perspective on synonymous codon usage in unicellular organisms" 24 : 28-38, 1986

44 Salamov AA, "Ab initio gene finding in Drosophila genomic DNA" 10 : 516-522, 2000

45 Shields DC, "'Silent' sites in Drosophila genes are not neutral: evidence of selection among synonymous codons" 5 : 704-716, 1988