-
1
-
-
0019474499
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
-
Ikemura,T. (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol., 146, 1-21.
-
(1981)
J. Mol. Biol
, vol.146
, pp. 1-21
-
-
Ikemura, T.1
-
2
-
-
0019824131
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its p rotein 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 p rotein 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
-
3
-
-
0020024572
-
Codon selection in yeast
-
Bennetzen,J.L. and Hall,B.D. (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
-
4
-
-
0019949369
-
Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in its protein genes: Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
-
Ikemura,T. (1982) Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in its protein genes: differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol., 158, 573-597.
-
(1982)
J. Mol. Biol
, vol.158
, pp. 573-597
-
-
Ikemura, T.1
-
5
-
-
0021710537
-
The relationship between base composition and codon usage in bacterial genes and its use for simple and reliable identification of protein-coding sequences
-
Bibb,M.J., Findlay,P.R. and Johnson,M.W. (1984) The relationship between base composition and codon usage in bacterial genes and its use for simple and reliable identification of protein-coding sequences. Gene 30, 157-166.
-
(1984)
Gene
, vol.30
, pp. 157-166
-
-
Bibb, M.J.1
Findlay, P.R.2
Johnson, M.W.3
-
6
-
-
0032931770
-
6 + C content variation along and among Saccharomyces cerevisiae chromosomes
-
Bradnam,K.R., Seoighe,C., Sharp,P.M. and Wolfe,K.H. (1999) 6 + C content variation along and among Saccharomyces cerevisiae chromosomes. Mol. Mot Evol., 16, 666-675.
-
(1999)
Mol. Mot Evol
, vol.16
, pp. 666-675
-
-
Bradnam, K.R.1
Seoighe, C.2
Sharp, P.M.3
Wolfe, K.H.4
-
7
-
-
0029985398
-
Asymmetric substitution patterns in the two DNA strands of bacteria
-
Lobry,JR. (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol. Biol. Evol., 13, 660-665.
-
(1996)
Mol. Biol. Evol
, vol.13
, pp. 660-665
-
-
Lobry, J.R.1
-
8
-
-
0032169578
-
Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
-
McInerney,J.O. (1998) Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl Acad. Sci., 95 10698-10703.
-
(1998)
Proc. Natl Acad. Sci
, vol.95
, pp. 10698-10703
-
-
McInerney, J.O.1
-
9
-
-
0032910674
-
Universal replication biases in bacteria
-
Rocha,E.P.C., Danchin,A. and Viari,A. (1999) Universal replication biases in bacteria. Mol. Microbiol., 32, 11-16.
-
(1999)
Mol. Microbiol
, vol.32
, pp. 11-16
-
-
Rocha, E.P.C.1
Danchin, A.2
Viari, A.3
-
10
-
-
0023650543
-
The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp,P.M. and Li,W.-H. (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
-
11
-
-
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
-
12
-
-
0034666040
-
Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae
-
Coghlan,A. and Wolfe,K.H. (2000) Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae. Yeast 16, 1131-1145.
-
(2000)
Yeast
, vol.16
, pp. 1131-1145
-
-
Coghlan, A.1
Wolfe, K.H.2
-
13
-
-
0025286203
-
The effect of context on synonymous codon usage in genes with low codon usage bias
-
Buhner,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
-
-
Buhner, M.1
-
14
-
-
4043074964
-
Bioinformatic analysis of the link between gene composition and expressivity in Saccharomyces cerevisiae and Schizosaccharomyces pombe
-
Fuglsang,A. (2004) Bioinformatic analysis of the link between gene composition and expressivity in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Antonie van Leeuwenhoek, 86, 135-147.
-
(2004)
Antonie van Leeuwenhoek
, vol.86
, pp. 135-147
-
-
Fuglsang, A.1
-
15
-
-
34247882805
-
The factors shaping synonymous codon usage in the genome of Burkholderia mallei
-
Zhao,S., Zhang,Q., Chen,Z., Zhao,Y. and Zhong,J. (2007) The factors shaping synonymous codon usage in the genome of Burkholderia mallei. J. Gen. Gen., 34, 362-372.
-
(2007)
J. Gen. Gen
, vol.34
, pp. 362-372
-
-
Zhao, S.1
Zhang, Q.2
Chen, Z.3
Zhao, Y.4
Zhong, J.5
-
16
-
-
0037109119
-
Use and misuse of correspondence analysis in codon usage studies
-
Perrière,G. and 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
-
17
-
-
33646228611
-
Codon usage domains over bacterial chromosomes
-
Bailly-Bechet,M., Danchin,A., Iqbal,M., Marsili,M. and Vergassola,M. (2006) Codon usage domains over bacterial chromosomes. PLoS Comput. Biol., 2, e37.
-
(2006)
PLoS Comput. Biol
, vol.2
-
-
Bailly-Bechet, M.1
Danchin, A.2
Iqbal, M.3
Marsili, M.4
Vergassola, M.5
-
18
-
-
0011083028
-
Analyse de l'inertie intra-classe par l'analyse d'un tableau des correspondances
-
Analyse de l'inertie intra-classe par l'analyse d'un tableau des correspondances. Les Cahiers de l'analyse des Données, 8, 351-358.
-
(1983)
Les Cahiers de l'analyse des Données
, vol.8
, pp. 351-358
-
-
Benzrecri, J.-P.1
-
19
-
-
14644391463
-
Online synonymous codon usage analyses with the ade4 and sequinR packages
-
Charif,D., Thioulouse,J., Lobry,J.R. and Perrière,G. (2004) Online synonymous codon usage analyses with the ade4 and sequinR packages. Bioinformatics, 21, 545-547.
-
(2004)
Bioinformatics
, vol.21
, pp. 545-547
-
-
Charif, D.1
Thioulouse, J.2
Lobry, J.R.3
Perrière, G.4
-
20
-
-
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
-
21
-
-
0001735517
-
On the mathematical foundations of theoretical statistics
-
Fisher,R.A. (1922) On the mathematical foundations of theoretical statistics. Philos. Trans. Roy. Soc. London Ser. A, 222, 309-368.
-
(1922)
Philos. Trans. Roy. Soc. London Ser. A
, vol.222
, pp. 309-368
-
-
Fisher, R.A.1
-
22
-
-
0022856787
-
An evolutionary perspective on synonymous codon usage in unicellular organisms
-
Sharp,P.M. and 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
-
23
-
-
33846165487
-
Absolute protein expression pro.ling estimates the relative contributions of transcriptional and translational regulation
-
Lu,P., Vogel,C., Wang,R., Yao,X. and Marcotte,E.M. (2007) Absolute protein expression pro.ling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol., 25, 117-124.
-
(2007)
Nat. Biotechnol
, vol.25
, pp. 117-124
-
-
Lu, P.1
Vogel, C.2
Wang, R.3
Yao, X.4
Marcotte, E.M.5
-
24
-
-
0142215475
-
Global analysis of protein expression in yeast
-
Ghaemmaghami,S., Huh,W.-K., Bower,K., Howson,R.W., Belle,A., Dephoure,N., O'Shea,E.K. and Weissman,J.S. (2003) Global analysis of protein expression in yeast. Nature, 425, 737-741.
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.-K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
25
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman,J.R.S., Ghaemmaghami,S., Ihmels,J., Breslow,D.K., Noble,M., DeRisi,J.L. and Weissman,J.S. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441, 840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.S.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
Noble, M.5
DeRisi, J.L.6
Weissman, J.S.7
-
26
-
-
0032694167
-
A sampling of the yeast proteome
-
Futcher,B., Latter,G.I., Monardo,P., McLaughlin,C.S. and Garrels,J.I. (1999) A sampling of the yeast proteome. Mol. Cell. Biol., 19 7357-7368.
-
(1999)
Mol. Cell. Biol
, vol.19
, pp. 7357-7368
-
-
Futcher, B.1
Latter, G.I.2
Monardo, P.3
McLaughlin, C.S.4
Garrels, J.I.5
-
27
-
-
0032567081
-
Dissecting the regulatory circuitry of a eukaryotic genome
-
Holstege,F.C.P., Jennings,E.G., Wyrick,J.J., Lee,T.I., Hengartner,C.J., Green,M.R., Golub,T.R., Lander,E.S. and Young,R.A. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell, 95, 717-728.
-
(1998)
Cell
, vol.95
, pp. 717-728
-
-
Holstege, F.C.P.1
Jennings, E.G.2
Wyrick, J.J.3
Lee, T.I.4
Hengartner, C.J.5
Green, M.R.6
Golub, T.R.7
Lander, E.S.8
Young, R.A.9
-
28
-
-
0031442518
-
-
Velculescu,V.E., Zhang,L., Zhou,W., Vogelstein,J., Basrai,M.A., Basset.D.E., Jr, Hieter,P., Vogelstein,B. and Kinzler,K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
-
Velculescu,V.E., Zhang,L., Zhou,W., Vogelstein,J., Basrai,M.A., Basset.D.E., Jr, Hieter,P., Vogelstein,B. and Kinzler,K.W. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
-
-
-
-
29
-
-
0037197892
-
Precision and functional specificity in mRNA decay
-
Wang,Y., Liu,C.L., Storey,J.D., Tibshirani,R.J., Herschlag,D. and Brown,P.O. (2002) Precision and functional specificity in mRNA decay. Proc. Natl Acad. Sci., 99, 5860-5865.
-
(2002)
Proc. Natl Acad. Sci
, vol.99
, pp. 5860-5865
-
-
Wang, Y.1
Liu, C.L.2
Storey, J.D.3
Tibshirani, R.J.4
Herschlag, D.5
Brown, P.O.6
-
30
-
-
33846921299
-
The correlation between recombination rate and codon bias in yeast mainly results from mutational bias associated with recombination rather than Hill-Robertson interference
-
doi: 10.1109/IEMBS.2005.1615542 [Epub ahead of print
-
Zhou,T., Lu,Z.H. and Sun,X. (2006) The correlation between recombination rate and codon bias in yeast mainly results from mutational bias associated with recombination rather than Hill-Robertson interference. EMBS 2005, doi: 10.1109/IEMBS.2005.1615542 [Epub ahead of print].
-
(2006)
EMBS 2005
-
-
Zhou, T.1
Lu, Z.H.2
Sun, X.3
-
31
-
-
0034086295
-
Absence of translationally selected synonymous codon usage bias in Helicobacter pylori
-
Lafay,B., Atherton,J.C. and Sharp,P.M. (2000) Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiol., 146, 851-860.
-
(2000)
Microbiol
, vol.146
, pp. 851-860
-
-
Lafay, B.1
Atherton, J.C.2
Sharp, P.M.3
-
32
-
-
17044389822
-
Subproteomes of soluble and structure-bound Helicobacter pylori proteins analyzed by two-dimensional gel electrophoresis and mass spectrometry
-
Backert,S., Kwok,T., Schmid,M., Selbach,M., Moese,S., Peek,R.M. Jr., König,W., Meyer,T.F. and Jungblut,P.R. (2005) Subproteomes of soluble and structure-bound Helicobacter pylori proteins analyzed by two-dimensional gel electrophoresis and mass spectrometry. Proteomics 5, 1331-1345.
-
(2005)
Proteomics
, vol.5
, pp. 1331-1345
-
-
Backert, S.1
Kwok, T.2
Schmid, M.3
Selbach, M.4
Moese, S.5
Peek Jr., R.M.6
König, W.7
Meyer, T.F.8
Jungblut, P.R.9
-
33
-
-
0027161465
-
Regional base composition variation along yeast chromosome III: Evolution of chromosome primary structure
-
Sharp,P.M. and Lloyd,A.T. (1993) Regional base composition variation along yeast chromosome III: Evolution of chromosome primary structure. Nucleic Acids Res., 21, 179-183.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 179-183
-
-
Sharp, P.M.1
Lloyd, A.T.2
-
34
-
-
0032482924
-
Molecular archaeology of the Escherichia coli genome
-
Lawrence,J.G. and Ochman,H. (1998) Molecular archaeology of the Escherichia coli genome. Proc. Natl Acad. Sci., 95, 9413-9417.
-
(1998)
Proc. Natl Acad. Sci
, vol.95
, pp. 9413-9417
-
-
Lawrence, J.G.1
Ochman, H.2
-
35
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman,H., Lawrence,J.G. and Groisman,E.A. (2000) Lateral gene transfer and the nature of bacterial innovation. Nature, 405, 299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
36
-
-
0035948585
-
Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa
-
Gupta,S.K. and Ghosh,T.C. (2001) Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gene, 273, 63-70.
-
(2001)
Gene
, vol.273
, pp. 63-70
-
-
Gupta, S.K.1
Ghosh, T.C.2
-
37
-
-
27744507140
-
A problem in multivariate analysis of codon usage data and a possible solution
-
Suzuki,H., Saito,R. and Tomita,M. (2005) A problem in multivariate analysis of codon usage data and a possible solution. FEBS Lett., 579, 6499-6504.
-
(2005)
FEBS Lett
, vol.579
, pp. 6499-6504
-
-
Suzuki, H.1
Saito, R.2
Tomita, M.3
-
38
-
-
0034937294
-
Codon-usage based regulation of colicin K synthesis by the stress alarmone ppGpp
-
Kuhar,I., van Putten,J.P.M., Žgur-Bertok,D., Gaastra,W. and Jordi,B.J.A.M. (2001) Codon-usage based regulation of colicin K synthesis by the stress alarmone ppGpp. Mol. Microbiol., 41, 207-216.
-
(2001)
Mol. Microbiol
, vol.41
, pp. 207-216
-
-
Kuhar, I.1
van Putten, J.P.M.2
Žgur-Bertok, D.3
Gaastra, W.4
Jordi, B.J.A.M.5
-
39
-
-
0034666387
-
Gradients in nucleotide and codon usage along Escherichia coli genes
-
Hooper,S.D. and Berg,O.G. (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
-
40
-
-
11244324849
-
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes
-
Qin,H., Wu,W.B., Comeron,J.M., Kreitman,M. and Li,W.-H. (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
-
41
-
-
35848952077
-
Combining models of protein translation and population genetics to predict protein production rates from codon usage patterns
-
doi:10.1093/molbev/msm169 [Epub ahead of print
-
Gilchrist,M.A. (2007) Combining models of protein translation and population genetics to predict protein production rates from codon usage patterns. Mol. Biol. Evol., doi:10.1093/molbev/msm169 [Epub ahead of print].
-
(2007)
Mol. Biol. Evol
-
-
Gilchrist, M.A.1
|