-
1
-
-
0028220048
-
Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
-
Akashi H. 1994. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics. 136:927-935.
-
(1994)
Genetics
, vol.136
, pp. 927-935
-
-
Akashi, H.1
-
2
-
-
0028797897
-
Inferring weak selection from patterns of polymorphism and divergence at silent sites in Drosophila DNA
-
Akashi H. 1995. Inferring weak selection from patterns of polymorphism and divergence at silent sites in Drosophila DNA. Genetics. 139:1067-1076.
-
(1995)
Genetics
, vol.139
, pp. 1067-1076
-
-
Akashi, H.1
-
3
-
-
0035546157
-
Gene expression and molecular evolution
-
Akashi H. 2001. Gene expression and molecular evolution. Curr Opin Genet Dev. 11:660-666.
-
(2001)
Curr Opin Genet Dev
, vol.11
, pp. 660-666
-
-
Akashi, H.1
-
4
-
-
0041817645
-
Translational selection and yeast proteome evolution
-
Akashi H. 2003. Translational selection and yeast proteome evolution. Genetics. 164:1291-1303.
-
(2003)
Genetics
, vol.164
, pp. 1291-1303
-
-
Akashi, H.1
-
5
-
-
0031738130
-
Translational selection and molecular evolution
-
Akashi H, Eyre-Walker A. 1998. Translational selection and molecular evolution. Curr Opin Genet Dev. 8:688-693.
-
(1998)
Curr Opin Genet Dev
, vol.8
, pp. 688-693
-
-
Akashi, H.1
Eyre-Walker, A.2
-
6
-
-
0037388094
-
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
-
Arava Y, Wang YL, Storey JD, Liu CL, Brown PO, Herschlag D. 2003. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 100:3889-3894.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 3889-3894
-
-
Arava, Y.1
Wang, Y.L.2
Storey, J.D.3
Liu, C.L.4
Brown, P.O.5
Herschlag, D.6
-
7
-
-
33748925566
-
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the protein data bank
-
doi:10.1186/1471- 2148-6-43
-
Bastolla U, Porto M, Roman HE, Vendruscolo M. 2006. A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the protein data bank. BMC Evol Biol. 6. doi:10.1186/1471- 2148-6-43.
-
(2006)
BMC Evol Biol
, pp. 6
-
-
Bastolla, U.1
Porto, M.2
Roman, H.E.3
Vendruscolo, M.4
-
8
-
-
33846838995
-
Traffic of interacting ribosomes: Effects of single-machine mechanochemistry on protein synthesis
-
doi:10.1103/PhysRevE-75.021902
-
Basu A, Chowdhury D. 2007. Traffic of interacting ribosomes: effects of single-machine mechanochemistry on protein synthesis. Phys Rev E. 75. doi:10.1103/PhysRevE-75.021902.
-
(2007)
Phys Rev E
, pp. 75
-
-
Basu, A.1
Chowdhury, D.2
-
9
-
-
0020024572
-
Codon selection in yeast
-
Bennetzen JL, Hall BD. 1982. Codon selection in yeast. J Biol Chem. 257:3026-3031.
-
(1982)
J Biol Chem
, vol.257
, pp. 3026-3031
-
-
Bennetzen, J.L.1
Hall, B.D.2
-
10
-
-
26444497974
-
Stochastic evolution and transcription factor binding sites
-
Berg J, Lässig M. 2003. Stochastic evolution and transcription factor binding sites. Biophysics. 48:S36-S44.
-
(2003)
Biophysics
, vol.48
-
-
Berg, J.1
Lässig, M.2
-
11
-
-
33845503073
-
Adaptive evolution of transcription factor binding sites
-
Art. No. 021902 Part 1. doi:10.1186/1471-2148-4-42
-
Berg J, Willmann S, Lassig M. 2004. Adaptive evolution of transcription factor binding sites. BMC Evol Biol. 4. Art. No. 021902 Part 1. doi:10.1186/1471-2148-4-42.
-
(2004)
BMC Evol Biol
, vol.4
-
-
Berg, J.1
Willmann, S.2
Lassig, M.3
-
12
-
-
10944232800
-
Posttranscriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale
-
Beyer A, Hollunder J, Nasheuer HP, Wilhelm T. 2004. Posttranscriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale. Mol Cell Proteomics. 3:1083-1092.
-
(2004)
Mol Cell Proteomics
, vol.3
, pp. 1083-1092
-
-
Beyer, A.1
Hollunder, J.2
Nasheuer, H.P.3
Wilhelm, T.4
-
13
-
-
0346991738
-
The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: Implications for the correlation between the synonymous substitution rate and codon usage bias
-
Bierne N, Eyre-Walker A. 2003. The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias. Genetics. 165:1587-1597.
-
(2003)
Genetics
, vol.165
, pp. 1587-1597
-
-
Bierne, N.1
Eyre-Walker, A.2
-
14
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics. 129:897-907.
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.1
-
15
-
-
0036389689
-
Laplace approximations for hypergeometric functions with matrix argument
-
Butler RW, Wood ATA. 2002. Laplace approximations for hypergeometric functions with matrix argument. Ann Stat. 30:1155-1177.
-
(2002)
Ann Stat
, vol.30
, pp. 1155-1177
-
-
Butler, R.W.1
Wood, A.T.A.2
-
16
-
-
14544301585
-
Codon bias signatures, organization of microorganisms in codon space, and lifestyle
-
Carbone A, Kepes F, Zinovyev A. 2005. Codon bias signatures, organization of microorganisms in codon space, and lifestyle. Mol Biol Evol. 22:547-561.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 547-561
-
-
Carbone, A.1
Kepes, F.2
Zinovyev, A.3
-
17
-
-
0242391986
-
Codon adaptation index as a measure of dominating codon bias
-
Carbone A, Zinovyev A, Kepes F. 2003. Codon adaptation index as a measure of dominating codon bias. Bioinformatics. 19:2005-2015.
-
(2003)
Bioinformatics
, vol.19
, pp. 2005-2015
-
-
Carbone, A.1
Zinovyev, A.2
Kepes, F.3
-
18
-
-
0042845842
-
Ribosome recycling, diffusion, and mRNA loop formation in translational regulation
-
Chou T. 2003. Ribosome recycling, diffusion, and mRNA loop formation in translational regulation. Biophys J. 85:755-773.
-
(2003)
Biophys J
, vol.85
, pp. 755-773
-
-
Chou, T.1
-
19
-
-
0036263105
-
Population, evolutionary and genomic consequences of interference selection
-
Comeron JM, Kreitman M. 2002. Population, evolutionary and genomic consequences of interference selection. Genetics. 161:389-410.
-
(2002)
Genetics
, vol.161
, pp. 389-410
-
-
Comeron, J.M.1
Kreitman, M.2
-
20
-
-
0024962419
-
Rates of aminoacyl-trans-RNA selection at 29 sense codons invivo
-
Curran JF, Yarus M. 1989. Rates of aminoacyl-trans-RNA selection at 29 sense codons invivo. J Mol Biol. 209: 65-77.
-
(1989)
J Mol Biol
, vol.209
, pp. 65-77
-
-
Curran, J.F.1
Yarus, M.2
-
22
-
-
0038179369
-
Selective charging of tRNA isoacceptors explains patterns of codon usage
-
Elf J, Nilsson D, Tenson T, Ehrenberg M. 2003. Selective charging of tRNA isoacceptors explains patterns of codon usage. Science. 300:1718-1722.
-
(2003)
Science
, vol.300
, pp. 1718-1722
-
-
Elf, J.1
Nilsson, D.2
Tenson, T.3
Ehrenberg, M.4
-
23
-
-
0029931535
-
Synonymous codon bias is related to gene length in Escherichia coli: Selection for translational accuracy?
-
Eyre-Walker A. 1996. Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy? Mol Biol Evol. 13:864-872.
-
(1996)
Mol Biol Evol
, vol.13
, pp. 864-872
-
-
Eyre-Walker, A.1
-
25
-
-
33645399045
-
A model of protein translation including codon bias, nonsense errors, and ribosome recycling
-
Gilchrist MA, Wagner A. 2006. A model of protein translation including codon bias, nonsense errors, and ribosome recycling. J Theor Biol. 239:417-434.
-
(2006)
J Theor Biol
, vol.239
, pp. 417-434
-
-
Gilchrist, M.A.1
Wagner, A.2
-
26
-
-
0020491327
-
Codon usage in bacteria - correlation with gene expressivity
-
Gouy M, Gautier C. 1982. Codon usage in bacteria - correlation with gene expressivity. Nucleic Acids Res. 10:7055-7074.
-
(1982)
Nucleic Acids Res
, vol.10
, pp. 7055-7074
-
-
Gouy, M.1
Gautier, C.2
-
27
-
-
0141920354
-
Comparing protein abundance and mRNA expression levels on a genomic scale
-
Greenbaum D, Colangelo C, Williams K, Gerstein M. 2003. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4:117-124.
-
(2003)
Genome Biol
, vol.4
, pp. 117-124
-
-
Greenbaum, D.1
Colangelo, C.2
Williams, K.3
Gerstein, M.4
-
29
-
-
11044225797
-
CBS genome atlas database: A dynamic storage for bioinformatic results and sequence data
-
Hallin PF, Ussery DW. 2004. CBS genome atlas database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics. 20:3682-3686.
-
(2004)
Bioinformatics
, vol.20
, pp. 3682-3686
-
-
Hallin, P.F.1
Ussery, D.W.2
-
31
-
-
10344224528
-
Adjusting for selection on synonymous sites in estimates of evolutionary distance
-
Hirsh AE, Fraser HB, Wall DP. 2005. Adjusting for selection on synonymous sites in estimates of evolutionary distance. Mol Biol Evol. 22:174-177.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 174-177
-
-
Hirsh, A.E.1
Fraser, H.B.2
Wall, D.P.3
-
32
-
-
0034666387
-
Gradients in nucleotide and codon usage along Escherichia coli genes
-
Hooper SD, Berg OG. 2000. Gradients in nucleotide and codon usage along Escherichia coli genes. Nucleic Acids Res. 28:3517-3523.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 3517-3523
-
-
Hooper, S.D.1
Berg, O.G.2
-
33
-
-
0019824131
-
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 Escherichia-coli translational system
-
Ikemura T. 1981. 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 Escherichia-coli translational system. J Mol Biol. 151:389-409.
-
(1981)
J Mol Biol
, vol.151
, pp. 389-409
-
-
Ikemura, T.1
-
34
-
-
0021958933
-
Codon usage and transfer-RNA content in unicellular and multicellular organisms
-
Ikemura T. 1985. Codon usage and transfer-RNA content in unicellular and multicellular organisms. Mol Biol Evol. 2:13-34.
-
(1985)
Mol Biol Evol
, vol.2
, pp. 13-34
-
-
Ikemura, T.1
-
35
-
-
0025084414
-
Processivity errors of geneexpression in Escherichia coli
-
Jorgensen F, Kurland CG. 1990. Processivity errors of geneexpression in Escherichia coli. J Mol Biol. 215:511-521.
-
(1990)
J Mol Biol
, vol.215
, pp. 511-521
-
-
Jorgensen, F.1
Kurland, C.G.2
-
36
-
-
0028040734
-
The effects of mutation and natural-selection on codon bias in the genes of Drosophila
-
Kliman RM, Hey J. 1994. The effects of mutation and natural-selection on codon bias in the genes of Drosophila. Genetics. 137:1049-1056.
-
(1994)
Genetics
, vol.137
, pp. 1049-1056
-
-
Kliman, R.M.1
Hey, J.2
-
37
-
-
0041670890
-
Selection conflicts, gene expression, and codon usage trends in yeast
-
Kliman RM, Irving N, Santiago M. 2003. Selection conflicts, gene expression, and codon usage trends in yeast. J Mol Evol. 57:98-109.
-
(2003)
J Mol Evol
, vol.57
, pp. 98-109
-
-
Kliman, R.M.1
Irving, N.2
Santiago, M.3
-
38
-
-
0042492708
-
The modification of the wobble base of tRNA(glu) modulates the translation rate of glutamic acid codons in vivo
-
Kruger MK, Pedersen S, Hagervall TG, Sorensen MA. 1998. The modification of the wobble base of tRNA(glu) modulates the translation rate of glutamic acid codons in vivo. J Mol Biol. 284:621-631.
-
(1998)
J Mol Biol
, vol.284
, pp. 621-631
-
-
Kruger, M.K.1
Pedersen, S.2
Hagervall, T.G.3
Sorensen, M.A.4
-
39
-
-
0027104840
-
Translational accuracy and the fitness of bacteria
-
Kurland CG. 1992. Translational accuracy and the fitness of bacteria. Annu Rev Genet. 26:29-50.
-
(1992)
Annu Rev Genet
, vol.26
, pp. 29-50
-
-
Kurland, C.G.1
-
40
-
-
0030854739
-
tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
41
-
-
2642566765
-
-
MacKay VL, Li XH, Flory MR, et al. (12 co-authors). 2004. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics-response of yeast to mating pheromone. Mol Cell Proteomics. 3:478-489.
-
MacKay VL, Li XH, Flory MR, et al. (12 co-authors). 2004. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics-response of yeast to mating pheromone. Mol Cell Proteomics. 3:478-489.
-
-
-
-
42
-
-
0018250570
-
Synthesis and degradation of termination and premature-termination fragments of beta-galactosidase in vitro and in vivo
-
Manley JL. 1978. Synthesis and degradation of termination and premature-termination fragments of beta-galactosidase in vitro and in vivo. J Mol Biol. 125:407-432.
-
(1978)
J Mol Biol
, vol.125
, pp. 407-432
-
-
Manley, J.L.1
-
43
-
-
35848948019
-
-
Available from:, accessed on 2007 Sept 1
-
Peden J. 2005. Codonw. v.1.4.2. Available from: http://sourceforge.net/ projects/codonw/ (accessed on 2007 Sept 1).
-
(2005)
Codonw. v.1.4.2
-
-
Peden, J.1
-
44
-
-
17444449538
-
Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
-
Percudani R, Pavesi A, Ottonello S. 1997. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol. 268:322-330.
-
(1997)
J Mol Biol
, vol.268
, pp. 322-330
-
-
Percudani, R.1
Pavesi, A.2
Ottonello, S.3
-
46
-
-
11244324849
-
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes
-
Qin H, Wu WB, Comeron JM, Kreitman M, Li WH. 2004. Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes. Genetics. 168:2245-2260.
-
(2004)
Genetics
, vol.168
, pp. 2245-2260
-
-
Qin, H.1
Wu, W.B.2
Comeron, J.M.3
Kreitman, M.4
Li, W.H.5
-
47
-
-
22144437325
-
The application of statistical physics to evolutionary biology
-
Sella G, Hirsh AE. 2005. The application of statistical physics to evolutionary biology. Proc Natl Acad Sci USA. 102: 9541-9546.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 9541-9546
-
-
Sella, G.1
Hirsh, A.E.2
-
48
-
-
0023650543
-
The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp PM, Li WH. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
49
-
-
0023722029
-
Codon choice and gene-expression - synonymous codons differ in their ability to direct aminoacylated-transfer RNA-binding to ribosomes invitro
-
Thomas LK, Dix DB, Thompson RC. 1988. Codon choice and gene-expression - synonymous codons differ in their ability to direct aminoacylated-transfer RNA-binding to ribosomes invitro. Proc Natl Acad Sci USA. 85:4242-4246.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 4242-4246
-
-
Thomas, L.K.1
Dix, D.B.2
Thompson, R.C.3
-
50
-
-
0024516890
-
Factors affecting the efficiency of protein-synthesis in Escherichia coli - production of a polypeptide of more than 6000 amino-acid residues
-
Tsung K, Inouye S, Inouye M. 1989. Factors affecting the efficiency of protein-synthesis in Escherichia coli - production of a polypeptide of more than 6000 amino-acid residues. J Biol Chem. 264:4428-4433.
-
(1989)
J Biol Chem
, vol.264
, pp. 4428-4433
-
-
Tsung, K.1
Inouye, S.2
Inouye, M.3
-
51
-
-
19544389317
-
Energy constraints on the evolution of gene expression
-
Wagner A. 2005. Energy constraints on the evolution of gene expression. Mol Biol Evol. 22:1365-1374.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1365-1374
-
-
Wagner, A.1
-
52
-
-
35848969391
-
-
Wolfram Research Inc. 2005. Mathematica. version 5.2. Champaign, IL, Wolfram Research Inc
-
Wolfram Research Inc. 2005. Mathematica. version 5.2. Champaign, (IL): Wolfram Research Inc.
-
-
-
-
53
-
-
0025318864
-
The effective number of codons used in a gene
-
Wright F. 1990. The effective number of codons used in a gene. Gene. 87:23-29.
-
(1990)
Gene
, vol.87
, pp. 23-29
-
-
Wright, F.1
-
54
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang ZH, Nielsen R. 2000. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol. 17:32-43.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.H.1
Nielsen, R.2
-
55
-
-
33747835539
-
s with a consideration of unequal transitional substitutions
-
s with a consideration of unequal transitional substitutions. BMC Evol Biol Art. 6.
-
(2006)
BMC Evol Biol Art
, vol.6
-
-
Zhang, Z.1
Li, J.2
Yu, J.3
|