-
1
-
-
0030806245
-
Codon bias in Escherichia coli: The influence of codon context on mutation and selection
-
Berg OG, Silva PJN (1997) Codon bias in Escherichia coli: The influence of codon context on mutation and selection. Nucleic Acids Res 25:1397-1404
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 1397-1404
-
-
Berg, O.G.1
Silva, P.J.N.2
-
2
-
-
0026552754
-
DNA mismatch correction by very short patch repair may have altered the abundance of oligonucleotides in the E. coli genome
-
Bhagwat AS, McClelland M (1992) DNA mismatch correction by Very Short Patch repair may have altered the abundance of oligonucleotides in the E. coli genome. Nucleic Acids Res 20:1663-1668
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 1663-1668
-
-
Bhagwat, A.S.1
McClelland, M.2
-
3
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner FR, Plunket GI, Bloch CA, et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462
-
(1997)
Science
, vol.277
, pp. 1453-1462
-
-
Blattner, F.R.1
Plunket, G.I.2
Bloch, C.A.3
-
4
-
-
0021103423
-
Context effects: Translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message
-
Bossi L (1983) Context effects: Translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message. J Mol Biol 164:73-87
-
(1983)
J Mol Biol
, vol.164
, pp. 73-87
-
-
Bossi, L.1
-
5
-
-
0015806892
-
-
Boyer HW, Chow LT, Dugaiczyk A, Hedgpeth J, Goodman HM (1973) Nature New Biol 244:40-43
-
(1973)
Nature New Biol
, vol.244
, pp. 40-43
-
-
Boyer, H.W.1
Chow, L.T.2
Dugaiczyk, A.3
Hedgpeth, J.4
Goodman, H.M.5
-
6
-
-
0025286203
-
The effect of context on synonymous codon usage in genes with low codon usage bias
-
Bulmer M ( 1990) The effect of context on synonymous codon usage in genes with low codon usage bias. Nucleic Acids Res 18:2869-2873
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 2869-2873
-
-
Bulmer, M.1
-
7
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
Bulmer MG (1991) The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.G.1
-
8
-
-
16044367245
-
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
-
Bull CJ, White O, Olsen GJ, et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073
-
(1996)
Science
, vol.273
, pp. 1058-1073
-
-
Bult, C.J.1
White, O.2
Olsen, G.J.3
-
9
-
-
0026502711
-
Over- and underrepresentation of short oligonucleotides in DNA sequences
-
Burge C, Campbell AM, Karlin S (1992) Over-and underrepresentation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci USA 89:1368-1362
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 1368-11362
-
-
Burge, C.1
Campbell, A.M.2
Karlin, S.3
-
10
-
-
0018185292
-
Molecular basis of base substitution hotspots in Escherichia coli
-
Coulondre C, Miller JH, Farabaugh PJ, Gilbert W (1978) Molecular basis of base substitution hotspots in Escherichia coli. Nature 274: 775-780
-
(1978)
Nature
, vol.274
, pp. 775-780
-
-
Coulondre, C.1
Miller, J.H.2
Farabaugh, P.J.3
Gilbert, W.4
-
11
-
-
0029320785
-
Does Very Short Patch (VSP) repair efficiency vary in relation to gene expression levels?
-
Eyre-Walker A (1995) Does Very Short Patch (VSP) repair efficiency vary in relation to gene expression levels? J Mol Evol 40:705-706
-
(1995)
J Mol Evol
, vol.40
, pp. 705-706
-
-
Eyre-Walker, A.1
-
12
-
-
0030457112
-
Programmed translational frameshifting
-
Farabaugh PJ (1996) Programmed translational frameshifting. Annu Rev Genet 30:507-528
-
(1996)
Annu Rev Genet
, vol.30
, pp. 507-528
-
-
Farabaugh, P.J.1
-
13
-
-
0029653518
-
Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
-
Fleischmann RD, Adams MD, White O, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
-
(1995)
Science
, vol.269
, pp. 496-512
-
-
Fleischmann, R.D.1
Adams, M.D.2
White, O.3
-
14
-
-
0030976320
-
Strand asymmetries in DNA evolution
-
Francino MP, Ochman H (1997) Strand asymmetries in DNA evolution. Trends Genet 13:240-245
-
(1997)
Trends Genet
, vol.13
, pp. 240-245
-
-
Francino, M.P.1
Ochman, H.2
-
15
-
-
0028829125
-
The minimal gene complement of Mycoplasma genitalium
-
Fraser CM, Gocayne JD, White O, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397-4-03
-
(1995)
Science
, vol.270
, pp. 397-403
-
-
Fraser, C.M.1
Gocayne, J.D.2
White, O.3
-
16
-
-
0031470826
-
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
-
Fraser CM, Casjens S, Huang WM, et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390:580-586
-
(1997)
Nature
, vol.390
, pp. 580-586
-
-
Fraser, C.M.1
Casjens, S.2
Huang, W.M.3
-
17
-
-
0032540874
-
Complete genome sequence of Treponema pallidum, the syphilis spirochete
-
Fraser CM, Norris SJ, Weinstock CM, et al. (1998) Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281:375-388
-
(1998)
Science
, vol.281
, pp. 375-388
-
-
Fraser, C.M.1
Norris, S.J.2
Weinstock, C.M.3
-
18
-
-
0028854033
-
Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome
-
Gläsner W, Merkl R, Schellenberger V, Fritz H (1995) Substrate preferences of Vsr DNA mismatch endonuclease and their consequences for the evolution of the Escherichia coli K-12 genome. J Mol Biol 245:1-7
-
(1995)
J Mol Biol
, vol.245
, pp. 1-7
-
-
Gläsner, W.1
Merkl, R.2
Schellenberger, V.3
Fritz, H.4
-
19
-
-
0023372221
-
Codon contexts in enterobacterial and coliphage genes
-
Gouy M (1987) Codon contexts in enterobacterial and coliphage genes. Mol Biol Evol 4:426-444
-
(1987)
Mol Biol Evol
, vol.4
, pp. 426-444
-
-
Gouy, M.1
-
20
-
-
0019519371
-
Codon catalog usage is a genome strategy modulated for gene expressivity
-
Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981) Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 8:r49-r62
-
(1981)
Nucleic Acids Res
, vol.8
-
-
Grantham, R.1
Gautier, C.2
Gouy, M.3
Jacobzone, M.4
Mercier, R.5
-
21
-
-
0028106987
-
Compositional heterogeneity of the Escherichia coli genome: A role for VSP repair?
-
Gutiérrez G, Casadesús J, Oliver J, Marín A (1994) Compositional heterogeneity of the Escherichia coli genome: A role for VSP repair? J Mol Evol 39:340-346
-
(1994)
J Mol Evol
, vol.39
, pp. 340-346
-
-
Gutiérrez, G.1
Casadesús, J.2
Oliver, J.3
Marín, A.4
-
22
-
-
0024673103
-
Nonrandom utilization of codon pairs in Escherichia coli
-
Gutman GA, Hatfield GW (1989) Nonrandom utilization of codon pairs in Escherichia coli. Proc Natl Acad Sci USA 86:3699-3703
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, pp. 3699-3703
-
-
Gutman, G.A.1
Hatfield, G.W.2
-
23
-
-
0024398960
-
Novel third-letter bias in Escherichia coli codons revealed by rigorous treatment of coding constraints
-
Hanai R, Wada A (1989) Novel third-letter bias in Escherichia coli codons revealed by rigorous treatment of coding constraints. J Mol Biol 207:655-660
-
(1989)
J Mol Biol
, vol.207
, pp. 655-660
-
-
Hanai, R.1
Wada, A.2
-
24
-
-
10544255079
-
Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae
-
Himmelreich R, Hubert H, Plagens H, et al. (1996) Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res 24:4420-4449
-
(1996)
Nucleic Acids Res
, vol.24
, pp. 4420-4449
-
-
Himmelreich, R.1
Hubert, H.2
Plagens, H.3
-
25
-
-
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 E. 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 E. coli translational system. J Mol Biol 151:389-409
-
(1981)
J Mol Biol
, vol.151
, pp. 389-409
-
-
Ikemura, T.1
-
26
-
-
1842332701
-
Compositional biases of bacterial genomes and evolutionary implications
-
Karlin S, Mrázek J, Campbell AM (1997) Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 179: 3899-3913
-
(1997)
J Bacteriol
, vol.179
, pp. 3899-3913
-
-
Karlin, S.1
Mrázek, J.2
Campbell, A.M.3
-
27
-
-
0030886877
-
Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae
-
Kerr ARW, Peden JF, Sharp PM (1997) Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae. Mol Microbiol 25:1177-1179
-
(1997)
Mol Microbiol
, vol.25
, pp. 1177-1179
-
-
Kerr, A.R.W.1
Peden, J.F.2
Sharp, P.M.3
-
28
-
-
0031458333
-
The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus
-
Klenk HP, Clayton RA, Tomb JF, et al. (1998) The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-379
-
(1998)
Nature
, vol.390
, pp. 364-379
-
-
Klenk, H.P.1
Clayton, R.A.2
Tomb, J.F.3
-
30
-
-
0025754787
-
Spontaneous mutation at a 5-methylcytosine is prevented by Very Short Patch (VSP) mismatch repair
-
Lieb M (1991) Spontaneous mutation at a 5-methylcytosine is prevented by Very Short Patch (VSP) mismatch repair. Genetics 128: 23-27
-
(1991)
Genetics
, vol.128
, pp. 23-27
-
-
Lieb, M.1
-
31
-
-
0026860173
-
CODONS: A microcomputer program for codon usage analysis
-
Lloyd AT, Sharp PM (1992) CODONS: A microcomputer program for codon usage analysis. J Hered 83:239-240
-
(1992)
J Hered
, vol.83
, pp. 239-240
-
-
Lloyd, A.T.1
Sharp, P.M.2
-
32
-
-
15844423271
-
Site-specific codon bias in bacteria
-
Maynard Smith J, Smith NH (1996) Site-specific codon bias in bacteria. Genetics 142:1037-1043
-
(1996)
Genetics
, vol.142
, pp. 1037-1043
-
-
Maynard Smith, J.1
Smith, N.H.2
-
33
-
-
0026046977
-
Escherichia coli molecular genetic map (1500 kbp): Update II
-
Médigue C, Viari A, Hénaut A, Danchi A (1991) Escherichia coli molecular genetic map (1500 kbp): Update II. Mol Microbiol 5: 2629-2640
-
(1991)
Mol Microbiol
, vol.5
, pp. 2629-2640
-
-
Médigue, C.1
Viari, A.2
Hénaut, A.3
Danchi, A.4
-
34
-
-
0026538522
-
Statistical evaluation and biological interpretation of non-random abundance in the E. coli K-12 genome of tetra-and pentanucleotide sequences related to VSP DNA mismatch repair
-
Merkl R, Kröger M, Rice P, Fritz H (1992) Statistical evaluation and biological interpretation of non-random abundance in the E. coli K-12 genome of tetra-and pentanucleotide sequences related to VSP DNA mismatch repair. Nucleic Acids Res 20:1657-1662
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 1657-1662
-
-
Merkl, R.1
Kröger, M.2
Rice, P.3
Fritz, H.4
-
35
-
-
0033609333
-
Evidence for lateral gene transfer between archaea and bacteria from genome sequences of Thermotoga maritima
-
Nelson KE, Clayton RA, Gill SR, et al. (1999) Evidence for lateral gene transfer between Archaea and Bacteria from genome sequences of Thermotoga maritima. Nature 399:323-329
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
-
36
-
-
0023664154
-
Mono-through hexanucleotide composition of the Escherichia coli genome: A Markov chain analysis
-
Phillips GJ, Arnold J, Ivarie R (1987) Mono-through hexanucleotide composition of the Escherichia coli genome: A Markov chain analysis, Nucleic Acids Res 15:2611-2626
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 2611-2626
-
-
Phillips, G.J.1
Arnold, J.2
Ivarie, R.3
-
37
-
-
0023655732
-
Missense misreading of asparagine codons as a function of codon identity and context
-
Precup J, Parker J (1987) Missense misreading of asparagine codons as a function of codon identity and context. J Biol Chem 262:11351-11355
-
(1987)
J Biol Chem
, vol.262
, pp. 11351-11355
-
-
Precup, J.1
Parker, J.2
-
39
-
-
0022856787
-
An evolutionary perspective on synonymous codon usage in unicellular organisms
-
Sharp PM, Li W-H (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24:28-38
-
(1986)
J Mol Evol
, vol.24
, pp. 28-38
-
-
Sharp, P.M.1
Li, W.-H.2
-
40
-
-
0023650543
-
The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential application
-
Sharp PM, Li W-H (1987) The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential application. Nucleic Acids Res 15:1281-1295
-
(1987)
Nucleic Acids Res
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.-H.2
-
41
-
-
0022616874
-
Constraints on codon context in Escherichia coli genes - Their possible role in modulating the efficiency of translation
-
Shpaer EG (1986) Constraints on codon context in Escherichia coli genes-Their possible role in modulating the efficiency of translation. J Mol Biol 188:555-564
-
(1986)
J Mol Biol
, vol.188
, pp. 555-564
-
-
Shpaer, E.G.1
-
43
-
-
0031804156
-
Compilation of tRNA sequences and sequences of tRNA genes
-
Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26:148-153
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 148-153
-
-
Sprinzl, M.1
Horn, C.2
Brown, M.3
Ioudovitch, A.4
Steinberg, S.5
-
44
-
-
0030835739
-
The complete genome sequence of the gastric pathogen Helicobacter pylori
-
Tomb JF, White O, Kerlavage AR, et al. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547
-
(1997)
Nature
, vol.388
, pp. 539-547
-
-
Tomb, J.F.1
White, O.2
Kerlavage, A.R.3
-
45
-
-
0021861277
-
UGA is read as tryptophan in Mycoplasma capricolum
-
Yamao F, Muto A, Kawauchi Y, et al. (1985) UGA is read as tryptophan in Mycoplasma capricolum. Proc Natl Acad Sci USA 82: 2306-2309
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 2306-2309
-
-
Yamao, F.1
Muto, A.2
Kawauchi, Y.3
-
46
-
-
0022405085
-
Sense codons are found in specific contexts
-
Yarus M, Folley LS (1985) Sense codons are found in specific contexts. J Mol Biol 182:529-540
-
(1985)
J Mol Biol
, vol.182
, pp. 529-540
-
-
Yarus, M.1
Folley, L.S.2
|