-
1
-
-
33846269602
-
TRNA's wobble decoding of the genome: 40 years of modification
-
Agris P, Vendeix F, Graham W. 2007. tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol. 366:1-13.
-
(2007)
J Mol Biol
, vol.366
, pp. 1-13
-
-
Agris, P.1
Vendeix, F.2
Graham, W.3
-
2
-
-
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
-
3
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
4
-
-
48249093081
-
Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host
-
Angov E, Hillier CJ, Kincaid RL, Lyon JA. 2008. Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host. PLoS One 3: e2189.
-
(2008)
PLoS One
, vol.3
-
-
Angov, E.1
Hillier, C.J.2
Kincaid, R.L.3
Lyon, J.A.4
-
5
-
-
0029587471
-
The human genome: Organization and evolutionary history
-
Bernardi G. 1995. The human genome: organization and evolutionary history. Annu Rev Genet. 29:445-476.
-
(1995)
Annu Rev Genet
, vol.29
, pp. 445-476
-
-
Bernardi, G.1
-
6
-
-
0022914759
-
Compositional constraints and genome evolution
-
Bernardi G, Bernardi G. 1986. Compositional constraints and genome evolution. J Mol Evol. 24:1-11.
-
(1986)
J Mol Evol
, vol.24
, pp. 1-11
-
-
Bernardi, G.1
Bernardi, G.2
-
7
-
-
84993842127
-
Are codon usage patterns in unicellular organisms determined by selection-mutation balance?
-
Bulmer M. 1988. Are codon usage patterns in unicellular organisms determined by selection-mutation balance? J Evol Biol. 1:15-26.
-
(1988)
J Evol Biol
, vol.1
, pp. 15-26
-
-
Bulmer, M.1
-
8
-
-
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
-
9
-
-
58149189877
-
Gtrnadb: A database of transfer RNA genes detected in genomic sequence
-
Chan PP, Lowe TM. 2009. Gtrnadb: A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37: D93-D97.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Chan, P.P.1
Lowe, T.M.2
-
10
-
-
60349093708
-
Effective population size and patterns of molecular evolution and variation
-
Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nat Rev Genet. 10:195-205.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 195-205
-
-
Charlesworth, B.1
-
11
-
-
47549097539
-
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
-
Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352.
-
(2008)
Cell
, vol.134
, pp. 341-352
-
-
Drummond, D.A.1
Wilke, C.O.2
-
12
-
-
0034237669
-
TRNA gene number and codon usage in the C. Elegans genome are co-adapted for optimal translation of highly expressed genes
-
Duret L. 2000. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 16:287-289.
-
(2000)
Trends Genet
, vol.16
, pp. 287-289
-
-
Duret, L.1
-
13
-
-
0033551151
-
Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
-
Duret L, Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci U S A. 96:4482.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 4482
-
-
Duret, L.1
Mouchiroud, D.2
-
14
-
-
84858221706
-
Ensembl 2012
-
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S. 2012. Ensembl 2012. Nucleic Acids Res. 40:D84-D90.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
15
-
-
11144241326
-
Correlation of codon bias measures with mRNA levels: Analysis of transcriptome data from Escherichia coli
-
Goetz RM, Fuglsang A. 2005. Correlation of codon bias measures with mRNA levels: Analysis of transcriptome data from Escherichia coli. Biochem Biophys Res Commun. 327:4-7.
-
(2005)
Biochem Biophys Res Commun
, vol.327
, pp. 4-7
-
-
Goetz, R.M.1
Fuglsang, A.2
-
16
-
-
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
-
18
-
-
42149137980
-
TRNA's modification brings order to gene expression
-
Gustilo E, Vendeix F, Agris P. 2008. tRNA's modification brings order to gene expression. Curr Opin Microbiol. 11:134-140.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 134-140
-
-
Gustilo, E.1
Vendeix, F.2
Agris, P.3
-
19
-
-
80053121999
-
Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins
-
Hudson NJ, Gu Q, Nagaraj SH, Ding YS, Dalrymple BP, Reverter A. 2011. Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins. PLoS One 6: e25457.
-
(2011)
PLoS One
, vol.6
-
-
Hudson, N.J.1
Gu, Q.2
Nagaraj, S.H.3
Ding, Y.S.4
Dalrymple, B.P.5
Reverter, A.6
-
20
-
-
67349173173
-
More radical amino acid replacements in primates than in rodents: Support for the evolutionary role of effective population size
-
Hughes AL, Friedman R. 2009. More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene 440:50-56.
-
(2009)
Gene, 440
, pp. 50-56
-
-
Hughes, A.L.1
Friedman, R.2
-
21
-
-
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.
-
(1981)
J Mol Biol
, vol.151
, pp. 389
-
-
Ikemura, T.1
-
22
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 2:13-34.
-
(1985)
Mol Biol Evol
, vol.2
, pp. 13-34
-
-
Ikemura, T.1
-
23
-
-
0032882170
-
Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAS: Gene expression level and species-specific diversity of codon usage based on multivariate analysis
-
Kanaya S, Yamada Y, Kudo Y, Ikemura T. 1999. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAS: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238: 143-155.
-
(1999)
Gene
, vol.238
, pp. 143-155
-
-
Kanaya, S.1
Yamada, Y.2
Kudo, Y.3
Ikemura, T.4
-
24
-
-
33846504706
-
A "silent" polymorphism in the MDR1 gene changes substrate specificity
-
Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM. 2007. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 315:525-528.
-
(2007)
Science
, vol.315
, pp. 525-528
-
-
Kimchi-Sarfaty, C.1
Oh, J.M.2
Kim, I.W.3
Sauna, Z.E.4
Calcagno, A.M.5
Ambudkar, S.V.6
Gottesman, M.M.7
-
25
-
-
0034086295
-
Absence of translationally selected synonymous codon usage bias in Helicobacter pylori
-
Lafay B, Atherton JC, Sharp PM. 2000. Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiology 146:851-860.
-
(2000)
Microbiology
, vol.146
, pp. 851-860
-
-
Lafay, B.1
Atherton, J.C.2
Sharp, P.M.3
-
26
-
-
17444449846
-
Codon usage and the origin of P elements
-
Lerat E, Biémont C, Capy P. 2000. Codon usage and the origin of P elements. Mol Biol Evol. 17:467-468.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 467-468
-
-
Lerat, E.1
Biémont, C.2
Capy, P.3
-
27
-
-
0030731696
-
Codon usage bias and tRNA abundance in Drosophila
-
Moriyama EN, Powell JR. 1997. Codon usage bias and tRNA abundance in Drosophila. J Mol Evol. 45:514-523.
-
(1997)
J Mol Evol
, vol.45
, pp. 514-523
-
-
Moriyama, E.N.1
Powell, J.R.2
-
28
-
-
0034883460
-
Translational selection on codon usage in Xenopus laevis
-
Musto H, Cruveiller S, D'Onofrio G, Romero H, Bernardi G. 2001. Translational selection on codon usage in Xenopus laevis. Mol Biol Evol. 18:1703.
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1703
-
-
Musto, H.1
Cruveiller, S.2
D'Onofrio, G.3
Romero, H.4
Bernardi, G.5
-
29
-
-
34547709593
-
Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals
-
Parmley JL, Hurst LD. 2007. Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol. 24:1600-1603.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1600-1603
-
-
Parmley, J.L.1
Hurst, L.D.2
-
30
-
-
84888611315
-
-
Dublin: Trinity College
-
Peden J. 1997. Codon W. Dublin: Trinity College.
-
(1997)
Codon W
-
-
Peden, J.1
-
31
-
-
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
-
32
-
-
0037109119
-
Use and misuse of correspondence - Analysis in codon usage studies
-
Perrière G, Thioulouse J. 2002. Use and misuse of correspondence - Analysis in codon usage studies. Nucleic Acids Res. 30: 4548-4555.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4548-4555
-
-
Perrière, G.1
Thioulouse, J.2
-
33
-
-
82255194216
-
Mutation bias is the driving force of codon usage in the Gallus gallus genome
-
Rao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X. 2011. Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Res. 18:499-512.
-
(2011)
DNA Res
, vol.18
, pp. 499-512
-
-
Rao, Y.1
Wu, G.2
Wang, Z.3
Chai, X.4
Nie, Q.5
Zhang, X.6
-
34
-
-
0242290126
-
The influence of translational selection on codon usage in fishes from the family cyprinidae
-
Romero H, Zavala A, Musto H, Bernardi G. 2003. The influence of translational selection on codon usage in fishes from the family cyprinidae. Gene 317:141-147.
-
(2003)
Gene
, vol.317
, pp. 141-147
-
-
Romero, H.1
Zavala, A.2
Musto, H.3
Bernardi, G.4
-
35
-
-
80052964856
-
Understanding the contribution of synonymous mutations to human disease
-
Sauna ZE, Kimchi-Sarfaty C. 2011. Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet. 12: 683-691.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 683-691
-
-
Sauna, Z.E.1
Kimchi-Sarfaty, C.2
-
36
-
-
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
-
37
-
-
0024116811
-
Silent" sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons
-
Shields DC, Sharp PM, Higgins DG, Wright F. 1988. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol. 5:704-716.
-
(1988)
Mol Biol Evol
, vol.5
, pp. 704-716
-
-
Shields, D.C.1
Sharp, P.M.2
Higgins, D.G.3
Wright, F.4
-
38
-
-
33846786904
-
Synonymous codon usage in Escherichia coli: Selection for translational accuracy
-
Stoletzki N, Eyre-Walker A. 2007. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol. 24:374-381.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 374-381
-
-
Stoletzki, N.1
Eyre-Walker, A.2
-
39
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su AI, Wiltshire T, Batalov S, Lapp H, Ching K, Block D, Zhang J, Soden R, Hayakawa M, Kreimen G. 2004. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 101:6062-6067.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
Wiltshire, T.2
Batalov, S.3
Lapp, H.4
Ching, K.5
Block, D.6
Zhang, J.7
Soden, R.8
Hayakawa, M.9
Kreimen, G.10
-
40
-
-
0035671698
-
Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection
-
Urrutia AO, Hurst LD. 2001. Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159:1191-1199.
-
(2001)
Genetics
, vol.159
, pp. 1191-1199
-
-
Urrutia, A.O.1
Hurst, L.D.2
-
41
-
-
0142092546
-
The signature of selection mediated by expression on human genes
-
Urrutia AO, Hurst LD. 2003. The signature of selection mediated by expression on human genes. Genome Res. 13:2260-2264.
-
(2003)
Genome Res
, vol.13
, pp. 2260-2264
-
-
Urrutia, A.O.1
Hurst, L.D.2
-
42
-
-
39749161509
-
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
-
Yang Z, Nielsen R. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol. 25:568-579.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 568-579
-
-
Yang, Z.1
Nielsen, R.2
-
43
-
-
84862827380
-
Codon Deviation Coefficient: A novel measure for estimating codon usage bias and its statistical significance
-
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. 2012. Codon Deviation Coefficient: A novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 13:43.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 43
-
-
Zhang, Z.1
Li, J.2
Cui, P.3
Ding, F.4
Li, A.5
Townsend, J.P.6
Yu, J.7
-
44
-
-
67649356943
-
Translationally optimal codons associate with structurally sensitive sites in proteins
-
Zhou T, Weems M, Wilke CO. 2009. Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol. 26:1571-1580.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1571-1580
-
-
Zhou, T.1
Weems, M.2
Wilke, C.O.3
|