-
1
-
-
0034888743
-
Characterizations of highly expressed genes of four fast-growing bacteria
-
Karlin, S., Mrázek, J., Campbell, A. and Kaiser, D. (2001). Characterizations of highly expressed genes of four fast-growing bacteria. J Bacteriol. 183, 5025-5040.
-
(2001)
J Bacteriol
, vol.183
, pp. 5025-5040
-
-
Karlin, S.1
Mrázek, J.2
Campbell, A.3
Kaiser, D.4
-
2
-
-
14544277543
-
Variation in the strength of selected codon usage bias among bacteria
-
Sharp, P. M., Bailes, E., Grocock, R. J., Peden, J. F. and Sockett, R. E. (2005). Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33, 1141-1153.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 1141-1153
-
-
Sharp, P.M.1
Bailes, E.2
Grocock, R.J.3
Peden, J.F.4
Sockett, R.E.5
-
3
-
-
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 optmal for the E. coli translational system
-
Ikernura, T. (1982). 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 optmal for the E. coli translational system. J. Mol. Biol. 151, 389-409.
-
(1982)
J. Mol. Biol
, vol.151
, pp. 389-409
-
-
Ikernura, T.1
-
4
-
-
8744310123
-
Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization
-
Rocha, E. P. (2004). Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Genome Res. 14, 2279-2286.
-
(2004)
Genome Res
, vol.14
, pp. 2279-2286
-
-
Rocha, E.P.1
-
5
-
-
33845648054
-
Error minimization explains the codon usage of highly expressed genes in Escherichia coli
-
Najafabadi, H. S., Lehmann, J. and Omidi, M. (2006). Error minimization explains the codon usage of highly expressed genes in Escherichia coli. Gene 387, 150-155.
-
(2006)
Gene
, vol.387
, pp. 150-155
-
-
Najafabadi, H.S.1
Lehmann, J.2
Omidi, M.3
-
6
-
-
33846039881
-
Energetics of codon-anticodon recognition on the small ribosomal subunit
-
Almlöf, M., Andér, M. and Aqvist, J. (2007). Energetics of codon-anticodon recognition on the small ribosomal subunit Biochemistry 46, 200-209.
-
(2007)
Biochemistry
, vol.46
, pp. 200-209
-
-
Almlöf, M.1
Andér, M.2
Aqvist, J.3
-
7
-
-
14544296732
-
Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type- 1
-
Meintjes, P. L. and Rodrigo, A. G. (2005). Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type- 1. J. Bioinform. Comput. Biol. 3, 157-168.
-
(2005)
J. Bioinform. Comput. Biol
, vol.3
, pp. 157-168
-
-
Meintjes, P.L.1
Rodrigo, A.G.2
-
8
-
-
0033016717
-
Correlation between protein and mRNA abundance in yeast
-
Gygi, S. R, Rochon, Y., Franza, B. R. and Aebersold, R. (1999). Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19, 1720-1730.
-
(1999)
Mol. Cell. Biol
, vol.19
, pp. 1720-1730
-
-
Gygi, S.R.1
Rochon, Y.2
Franza, B.R.3
Aebersold, R.4
-
9
-
-
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
-
10
-
-
0028359705
-
Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases
-
Stenico, M., Lloyd, A. T. and Sharp, P. M. (1994). Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases. Nucleic Acids Res. 22, 2437-2446.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 2437-2446
-
-
Stenico, M.1
Lloyd, A.T.2
Sharp, P.M.3
-
11
-
-
0034193767
-
Studies on codon usage in Entamoeba histolytica
-
Ghosh, T. C., Gupta, S. K. and Majumdar, S. (2000). Studies on codon usage in Entamoeba histolytica. Int J. Parasitol. 30, 715-722.
-
(2000)
Int J. Parasitol
, vol.30
, pp. 715-722
-
-
Ghosh, T.C.1
Gupta, S.K.2
Majumdar, S.3
-
12
-
-
0034658427
-
Optimizirig heterologous expression in Dictyostelium: Importance of 5' codon adaptation
-
Vervoort, E. B., van Ravestein, A., van Peij, N. N. M. E., Heikoop, J. C., van Haastert, P. J. M., Verheijden, G. F. and Linskens, M. H. K. (2000). Optimizirig heterologous expression in Dictyostelium: importance of 5' codon adaptation. Nucleic Acids Res. 28, 2069-2074.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 2069-2074
-
-
Vervoort, E.B.1
van Ravestein, A.2
van Peij, N.N.M.E.3
Heikoop, J.C.4
van Haastert, P.J.M.5
Verheijden, G.F.6
Linskens, M.H.K.7
-
13
-
-
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
-
14
-
-
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
-
15
-
-
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
-
16
-
-
11144241326
-
Correlation of codon bias measures with mRNA levels: Analysis of transcriptome data from Escherichia coli
-
Goetz, R. M.and Fugisang, 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
Fugisang, A.2
-
17
-
-
33646859041
-
A calibration method for estimating absolute expression levels from microarray data
-
Engelen, K, Naudts, B., De Moor, B. and Marchal, K. (2006). A calibration method for estimating absolute expression levels from microarray data. Bioinformatics 22, 1251-1258.
-
(2006)
Bioinformatics
, vol.22
, pp. 1251-1258
-
-
Engelen, K.1
Naudts, B.2
De Moor, B.3
Marchal, K.4
-
18
-
-
0942287071
-
Comparing expression level-dependent features in codon usage with protein abundance: An analysis of predictive proteomics
-
McHardy, A. C., Pühler, A., Kalinowski, J. and Meyer, F. (2004). Comparing expression level-dependent features in codon usage with protein abundance: An analysis of predictive proteomics'. Proteomics 4, 46-58.
-
(2004)
Proteomics
, vol.4
, pp. 46-58
-
-
McHardy, A.C.1
Pühler, A.2
Kalinowski, J.3
Meyer, F.4
-
19
-
-
0242391986
-
Codon adaptation index as a measure of dominating codon bias
-
Carbone, A., Zinovyev, A. and Képes, R (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
Képes, R.3
-
20
-
-
33646063776
-
Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence
-
Wu, G.; Nie, L. and Zhang, W. (2006). Predicted highly expressed genes in Nocardia farcinica and the implication for its primary metabolism and nocardial virulence. Antonie Van Leeuwenhoek 89, 135-146.
-
(2006)
Antonie Van Leeuwenhoek
, vol.89
, pp. 135-146
-
-
Wu, G.1
Nie, L.2
Zhang, W.3
-
21
-
-
22144453213
-
Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermutilis and the implications for their metabolism
-
Wu, G., Culley, D. E. and Zhang, W. (2005). Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermutilis and the implications for their metabolism. Microbiology 151, 2175-2187.
-
(2005)
Microbiology
, vol.151
, pp. 2175-2187
-
-
Wu, G.1
Culley, D.E.2
Zhang, W.3
-
22
-
-
1542618322
-
Codon usage between genomes is constrained by genome-wide mutational processes
-
Chen, S. L., Lee, W., Hottes, A. K., Shapiro, L. and McAdams, H. H. (2004). Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. USA 101, 3480-3485.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3480-3485
-
-
Chen, S.L.1
Lee, W.2
Hottes, A.K.3
Shapiro, L.4
McAdams, H.H.5
-
23
-
-
0026597059
-
Codon usage in the G+C-rich Streptomyces genome
-
Wright, F. and Bibb, M. J. (1992). Codon usage in the G+C-rich Streptomyces genome. Gene 113, 55-65.
-
(1992)
Gene
, vol.113
, pp. 55-65
-
-
Wright, F.1
Bibb, M.J.2
-
24
-
-
0025283965
-
Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content
-
Ohama, T., Muto, A, and Osawa, S. (1990). Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content Nucleic Acids Res. 18, 1565-1569.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 1565-1569
-
-
Ohama, T.1
Muto, A.2
Osawa, S.3
-
25
-
-
0025181355
-
Switches in species-specific codon preferences: The influence of mutation biases
-
Shields, D. C. (1990). Switches in species-specific codon preferences: the influence of mutation biases. J. Mol. Evol. 31, 71-80.
-
(1990)
J. Mol. Evol
, vol.31
, pp. 71-80
-
-
Shields, D.C.1
-
26
-
-
34047223024
-
Posttranscriptional expression regulation: What determines translation rates?
-
Brockmann, R., Beyer, A., Heinisch, J. J. and Wilhelm T. (2007). Posttranscriptional expression regulation: What determines translation rates? PLoS Comput. Biol. 3, e57.
-
(2007)
PLoS Comput. Biol
, vol.3
-
-
Brockmann, R.1
Beyer, A.2
Heinisch, J.J.3
Wilhelm, T.4
-
27
-
-
23144444226
-
JCat: A novel tool to adapt codon usage of a target gene to its potential expression host
-
Grote, A., Hiller, K., Scheer, M., Münch, R., Nörtemann, B., Hempel, D. C. and Jahn, D. (2005). JCat: A novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 33, W526-531.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Grote, A.1
Hiller, K.2
Scheer, M.3
Münch, R.4
Nörtemann, B.5
Hempel, D.C.6
Jahn, D.7
-
28
-
-
0342614926
-
Codon usage tabulated from international DNA sequence databases: Status for the year 2000
-
Nakamura, Y., Gojobori, T. and Ikemura, T. (2000). Codon usage tabulated from international DNA sequence databases: Status for the year 2000. Nucleic Acids Res. 28, 292.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 292
-
-
Nakamura, Y.1
Gojobori, T.2
Ikemura, T.3
-
29
-
-
34547579086
-
OPTIMIZER: A web server for optimizing the codon-usage of DNA sequences
-
Puigbò, P., Guzmán, E., Romeu, A. and Garcia-Vallvé, S. (2007). OPTIMIZER: A web server for optimizing the codon-usage of DNA sequences. Nucleic Acids Res. 35, W126-131.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Puigbò, P.1
Guzmán, E.2
Romeu, A.3
Garcia-Vallvé, S.4
-
30
-
-
0344668838
-
Gene essentiality determines chromosome organisation in bacteria
-
Rocha, E. P. and Danchin, A. (2003). Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res. 31, 6570-6577.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 6570-6577
-
-
Rocha, E.P.1
Danchin, A.2
-
31
-
-
0032910674
-
Universal replication biases in bacteria
-
Rocha, E. P., 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.1
Danchin, A.2
Viari, A.3
-
32
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., Rao, B. S., Smirnov, S., Sverdlov, A. V., Vasudevan, S., Wolf, Y I., Yin, J. J. and Natale, D. A. (2003). The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4, 41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
Jacobs, A.R.4
Kiryutin, B.5
Koonin, E.V.6
Krylov, D.M.7
Mazumder, R.8
Mekhedov, S.L.9
Nikolskaya, A.N.10
Rao, B.S.11
Smirnov, S.12
Sverdlov, A.V.13
Vasudevan, S.14
Wolf, Y.I.15
Yin, J.J.16
Natale, D.A.17
-
33
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
34
-
-
32344441400
-
Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states
-
VerBerkmoes, N. C., Shah, M. B., Lankford, P. K., Pelletier, D. A., Strader, M. B., Tabb D. L., McDonald, W. H., Barton, J. W., Hurst, G. B., Hauser, L., Davison, B. H., Beatty, J. T., Harwood, C. S., Tabita, F. R., Hettich, R. L. and Larimer, F. W. (2006). Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states. J. Proteome Res. 5, 287-298.
-
(2006)
J. Proteome Res
, vol.5
, pp. 287-298
-
-
VerBerkmoes, N.C.1
Shah, M.B.2
Lankford, P.K.3
Pelletier, D.A.4
Strader, M.B.5
Tabb, D.L.6
McDonald, W.H.7
Barton, J.W.8
Hurst, G.B.9
Hauser, L.10
Davison, B.H.11
Beatty, J.T.12
Harwood, C.S.13
Tabita, F.R.14
Hettich, R.L.15
Larimer, F.W.16
-
35
-
-
33845874641
-
Predicting gene expression level from codon usage bias
-
Henry, I. and Sharp, P. M. (2006). Predicting gene expression level from codon usage bias. Mol. Biol. Evol. 24, 10-12.
-
(2006)
Mol. Biol. Evol
, vol.24
, pp. 10-12
-
-
Henry, I.1
Sharp, P.M.2
-
36
-
-
0034086295
-
Absence of translationatly selected synonymous codon usage bias in Helicobacter pylori
-
Lafay, B., Atherton, J. C. and Sharp, P. M. (2000). Absence of translationatly 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
|