-
1
-
-
0025297285
-
Codon preferences in free living microorganisms
-
Andersson S.G.E., and Kurland C.G. Codon preferences in free living microorganisms. Microbiol. Rev. 54 (1990) 198-210
-
(1990)
Microbiol. Rev.
, vol.54
, pp. 198-210
-
-
Andersson, S.G.E.1
Kurland, C.G.2
-
2
-
-
0030806245
-
Codon bias in Escherichia coli: the influence of codon context on mutation and selection
-
Berg O.G., and Silva P.J. Codon bias in Escherichia coli: the influence of codon context on mutation and selection. Nucleic Acids Res. 25 (1977) 397-404
-
(1977)
Nucleic Acids Res.
, vol.25
, pp. 397-404
-
-
Berg, O.G.1
Silva, P.J.2
-
3
-
-
0011051225
-
Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage
-
Beutler E., Gelbart T., Han J.H., Koziol J.A., and Beutler B. Evolution of the genome and the genetic code: selection at the dinucleotide level by methylation and polyribonucleotide cleavage. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 192-196
-
(1989)
Proc. Natl. Acad. Sci. U. S. A.
, vol.86
, pp. 192-196
-
-
Beutler, E.1
Gelbart, T.2
Han, J.H.3
Koziol, J.A.4
Beutler, B.5
-
5
-
-
33644862478
-
tRNA properties help shape codon pair preferences in open reading frames
-
Buchan J.R., Aucott L.S., and Stansfield I. tRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Res. 34 (2006) 1015-1027
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 1015-1027
-
-
Buchan, J.R.1
Aucott, L.S.2
Stansfield, I.3
-
6
-
-
0028804862
-
Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 39 nucleotide to the codon has a context effect
-
Curran J.F., Poole E.S., Tate W.P., and Gross B.L. Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 39 nucleotide to the codon has a context effect. Nucleic Acids Res. 23 (1995) 4104-4108
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 4104-4108
-
-
Curran, J.F.1
Poole, E.S.2
Tate, W.P.3
Gross, B.L.4
-
7
-
-
0035918578
-
Absence of effect of varying Thr-Leu codon pairs on protein synthesis in a T7 system
-
Cheng L., and Goldman E. Absence of effect of varying Thr-Leu codon pairs on protein synthesis in a T7 system. Biochemistry 40 (2001) 6102-6106
-
(2001)
Biochemistry
, vol.40
, pp. 6102-6106
-
-
Cheng, L.1
Goldman, E.2
-
8
-
-
17744364327
-
Gardening the genome: DNA methylation in Arabidopsis thaliana
-
Chan S.W., Henderson I.R., and Jacobsen S.E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat. Rev. Genet. 6 (2005) 351-360
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 351-360
-
-
Chan, S.W.1
Henderson, I.R.2
Jacobsen, S.E.3
-
10
-
-
0034237669
-
tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
-
Duret L. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 16 (2000) 287-289
-
(2000)
Trends Genet.
, vol.16
, pp. 287-289
-
-
Duret, L.1
-
11
-
-
0346104825
-
Mammalian mutation pressure, synonymous codon choice, and mRNA degradation
-
Duan J., and Antezana M.A. Mammalian mutation pressure, synonymous codon choice, and mRNA degradation. J. Mol. Evol. 57 (2003) 694-701
-
(2003)
J. Mol. Evol.
, vol.57
, pp. 694-701
-
-
Duan, J.1
Antezana, M.A.2
-
13
-
-
0024427630
-
Codon contexts from weakly expressed genes reduce expression in vivo
-
Folley L.S., and Yarus M. Codon contexts from weakly expressed genes reduce expression in vivo. J. Mol. Biol. 209 (1989) 359-378
-
(1989)
J. Mol. Biol.
, vol.209
, pp. 359-378
-
-
Folley, L.S.1
Yarus, M.2
-
14
-
-
0036493203
-
Regularities of context-dependent codon bias in eukaryotic genes
-
Fedorov A., Saxonov S., and Gilbert W. Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res. 30 (2002) 1192-1197
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1192-1197
-
-
Fedorov, A.1
Saxonov, S.2
Gilbert, W.3
-
15
-
-
59649112459
-
The distribution mode of open reading frame length in different genomes and the genome evolution
-
Feng L.Q., and Li H. The distribution mode of open reading frame length in different genomes and the genome evolution. Acta Biophysica Sinca 20 (2004) 375-381
-
(2004)
Acta Biophysica Sinca
, vol.20
, pp. 375-381
-
-
Feng, L.Q.1
Li, H.2
-
16
-
-
0024673103
-
Non-random utilization of codon pairs in Escherichia coli
-
Gutman G.A., and Hatfield G.W. Non-random utilization of codon pairs in Escherichia coli. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 3699-3703
-
(1989)
Proc. Natl. Acad. Sci. U. S. A.
, vol.86
, pp. 3699-3703
-
-
Gutman, G.A.1
Hatfield, G.W.2
-
17
-
-
0028168856
-
Codon based model of nucleotide substitution for protein coding DNA sequences
-
Goldman N., and Yang Z.H. Codon based model of nucleotide substitution for protein coding DNA sequences. Mol. Biol. Evol. 11 (1994) 725-736
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.H.2
-
18
-
-
0037428483
-
Minimal model for genome evolution and growth
-
Hsieh L.C., Luo L.F., and Ji F.M. Minimal model for genome evolution and growth. Phys. Rev. Lett. 90 (2003) 1-4
-
(2003)
Phys. Rev. Lett.
, vol.90
, pp. 1-4
-
-
Hsieh, L.C.1
Luo, L.F.2
Ji, F.M.3
-
19
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2 (1985) 12-34
-
(1985)
Mol. Biol. Evol.
, vol.2
, pp. 12-34
-
-
Ikemura, T.1
-
20
-
-
0025744599
-
Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data
-
Ikemura T., and Wada K.N. Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. Nucleic Acids Res. 19 (1991) 4333-4339
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 4333-4339
-
-
Ikemura, T.1
Wada, K.N.2
-
21
-
-
0029162727
-
Codon pair utilization biases influence translational elongation step times
-
Irwin B., Heck J.D., and Hatfield G.W. Codon pair utilization biases influence translational elongation step times. J. Biol. Chem. 270 (1995) 22801-22806
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 22801-22806
-
-
Irwin, B.1
Heck, J.D.2
Hatfield, G.W.3
-
22
-
-
0022881350
-
Silent nucleotide substitutions and G + C content of some mitochondrial and Bacterial genes
-
Jukes T.-H., and Bhushan V. Silent nucleotide substitutions and G + C content of some mitochondrial and Bacterial genes. J. Mol. Evol. 24 (1986) 864-875
-
(1986)
J. Mol. Evol.
, vol.24
, pp. 864-875
-
-
Jukes, T.-H.1
Bhushan, V.2
-
23
-
-
0016842629
-
Amino acid compositions of proteins: selection against the genetic code
-
Jukes T.-H., Holmquist R., and Moise H. Amino acid compositions of proteins: selection against the genetic code. Science 189 (1975) 50-51
-
(1975)
Science
, vol.189
, pp. 50-51
-
-
Jukes, T.-H.1
Holmquist, R.2
Moise, H.3
-
24
-
-
0014680905
-
Non-Darwinian evolution
-
King J.-L., and Jukes T.-H. Non-Darwinian evolution. Science 164 (1969) 788-798
-
(1969)
Science
, vol.164
, pp. 788-798
-
-
King, J.-L.1
Jukes, T.-H.2
-
25
-
-
0027762486
-
Major codon preference: theme and variations
-
Kurland C.G. Major codon preference: theme and variations. Biochem. Soc. Trans. 21 (1993) 841-845
-
(1993)
Biochem. Soc. Trans.
, vol.21
, pp. 841-845
-
-
Kurland, C.G.1
-
26
-
-
0021633530
-
Codon context effects in missense suppression
-
Murgola E.J., Pagel F.T., and Hijazi K.A. Codon context effects in missense suppression. J. Mol. Biol. 175 (1984) 19-27
-
(1984)
J. Mol. Biol.
, vol.175
, pp. 19-27
-
-
Murgola, E.J.1
Pagel, F.T.2
Hijazi, K.A.3
-
27
-
-
0030731696
-
Codon usage bias and tRNA abundance in Drosophila
-
Moriyama E.N., and Powell J.R. Codon usage bias and tRNA abundance in Drosophila. J. Mol. Evol. 45 (1997) 514-523
-
(1997)
J. Mol. Evol.
, vol.45
, pp. 514-523
-
-
Moriyama, E.N.1
Powell, J.R.2
-
28
-
-
0033917194
-
Evolutionary lability of context-dependent codon bias in bacteria
-
Mcvean G.A.T., and Hurst G.D.D. Evolutionary lability of context-dependent codon bias in bacteria. J. Mol. Evol. 50 (2000) 264-275
-
(2000)
J. Mol. Evol.
, vol.50
, pp. 264-275
-
-
Mcvean, G.A.T.1
Hurst, G.D.D.2
-
29
-
-
33644889434
-
Comparative context analysis of codon pairs on an ORFeome scale
-
Moura G., Pinheiro M., Silva R., et al. Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol. 6 (2005) R28
-
(2005)
Genome Biol.
, vol.6
-
-
Moura, G.1
Pinheiro, M.2
Silva, R.3
-
30
-
-
39449087192
-
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure
-
Moura G., Pinheiro M., Arrais J., Gomes A.C., Carreto L., Freitas A., et al. Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. Plos one 2 (2007) e847
-
(2007)
Plos one
, vol.2
-
-
Moura, G.1
Pinheiro, M.2
Arrais, J.3
Gomes, A.C.4
Carreto, L.5
Freitas, A.6
-
31
-
-
0029022870
-
Phylogeny inferred from codon usage pattern in 31 organisms
-
Nesti C., Poli G., Chicca M., Ambrosino P., and Scapoli C. Phylogeny inferred from codon usage pattern in 31 organisms. Comput. Appl. Biosci. 2 (1995) 167-171
-
(1995)
Comput. Appl. Biosci.
, vol.2
, pp. 167-171
-
-
Nesti, C.1
Poli, G.2
Chicca, M.3
Ambrosino, P.4
Scapoli, C.5
-
32
-
-
0028272132
-
Divergence in codon usage of Lactobacillus species
-
Pouwels P.H., and Leunissen J.A.M. Divergence in codon usage of Lactobacillus species. Nucleic Acids Res. 22 (1994) 929-936
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 929-936
-
-
Pouwels, P.H.1
Leunissen, J.A.M.2
-
33
-
-
17444449538
-
Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
-
Percudani R., Pavesi A., and Ottonello S. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol. 268 (1997) 322-330
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 322-330
-
-
Percudani, R.1
Pavesi, A.2
Ottonello, S.3
-
34
-
-
0032519296
-
Translational termination in Escherichia coli: three bases following the stop codon crosslink to release factor 2 and affect the decoding efficiency of UGA-containing signals
-
Poole E.S., Major L.L., and Mannering S.A. Translational termination in Escherichia coli: three bases following the stop codon crosslink to release factor 2 and affect the decoding efficiency of UGA-containing signals. Nucleic Acid Res. 26 (1998) 954-960
-
(1998)
Nucleic Acid Res.
, vol.26
, pp. 954-960
-
-
Poole, E.S.1
Major, L.L.2
Mannering, S.A.3
-
35
-
-
0021760637
-
Codon usage can affect efficiency of translation of genes in Escherichia coli
-
Robinson M., Lilley R., Little S., et al. Codon usage can affect efficiency of translation of genes in Escherichia coli. Nucleic Acids Res. 12 (1984) 6663-6671
-
(1984)
Nucleic Acids Res.
, vol.12
, pp. 6663-6671
-
-
Robinson, M.1
Lilley, R.2
Little, S.3
-
36
-
-
0036567071
-
Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?
-
Rocha E.P., Matic I., and Taddei F. Over-representation of repeats in stress response genes: a strategy to increase versatility under stressful conditions?. Nucleic Acids Res. 30 (2002) 1886-1894
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1886-1894
-
-
Rocha, E.P.1
Matic, I.2
Taddei, F.3
-
37
-
-
0040298763
-
tRNA-tRNA interactions within cellular ribosomes
-
Smith D., and Yarus M. tRNA-tRNA interactions within cellular ribosomes. Proc. Natl. Acad. Sci. U. S. A. 86 (1989) 4397-4401
-
(1989)
Proc. Natl. Acad. Sci. U. S. A.
, vol.86
, pp. 4397-4401
-
-
Smith, D.1
Yarus, M.2
-
38
-
-
0026691099
-
Directional mutation pressure, selective constraints, and genetic equilibria
-
Sueoka N. Directional mutation pressure, selective constraints, and genetic equilibria. J. Mol. Evol. 34 (1992) 95-114
-
(1992)
J. Mol. Evol.
, vol.34
, pp. 95-114
-
-
Sueoka, N.1
-
40
-
-
0032881563
-
Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and bacterial mechanisms in translation initiation
-
Saito R., and Tomita M. Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and bacterial mechanisms in translation initiation. Gene 238 (1999) 79-83
-
(1999)
Gene
, vol.238
, pp. 79-83
-
-
Saito, R.1
Tomita, M.2
-
41
-
-
0036677820
-
Computational identification of putative programmed translational frameshift sites
-
Shah A.A., Giddings M.C., Gesteland R.F., Atkins J.F., and Ivanov I.P. Computational identification of putative programmed translational frameshift sites. Bioinformatics 18 (2002) 1046-1053
-
(2002)
Bioinformatics
, vol.18
, pp. 1046-1053
-
-
Shah, A.A.1
Giddings, M.C.2
Gesteland, R.F.3
Atkins, J.F.4
Ivanov, I.P.5
-
43
-
-
1342286071
-
The major 59 determinant in stop codon read-through involves two adjacent adenines
-
Tork S., Hatin I., Rousset J.P., and Fabret C. The major 59 determinant in stop codon read-through involves two adjacent adenines. Nucleic Acids Res. 32 (2004) 415-421
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 415-421
-
-
Tork, S.1
Hatin, I.2
Rousset, J.P.3
Fabret, C.4
-
44
-
-
59649083571
-
Codon pairs usage and genome evolution
-
Wang F.P., and Li H. Codon pairs usage and genome evolution. Acta Biophysica Sinca 23 (2007) 176-184
-
(2007)
Acta Biophysica Sinca
, vol.23
, pp. 176-184
-
-
Wang, F.P.1
Li, H.2
-
45
-
-
59649087264
-
The research of the occurrence frequency distribution of k-mer in whole DNA sequence
-
Wang S.L., Wang J., Chen H.W., and Zhang D.X. The research of the occurrence frequency distribution of k-mer in whole DNA sequence. Acta Biophysica Sinca 22 (2006) 178-195
-
(2006)
Acta Biophysica Sinca
, vol.22
, pp. 178-195
-
-
Wang, S.L.1
Wang, J.2
Chen, H.W.3
Zhang, D.X.4
-
46
-
-
0022405085
-
Sense codons are found in specific contexts
-
Yarus M., and Folley L.S. Sense codons are found in specific contexts. J. Mol. Biol. 182 (1985) 529-540
-
(1985)
J. Mol. Biol.
, vol.182
, pp. 529-540
-
-
Yarus, M.1
Folley, L.S.2
|