-
1
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
0035859953
-
Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid
-
Barnett M.J.et al. Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc. Natl. Acad. Sci. U. S. A. 98:2001;9883-9888.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 9883-9888
-
-
Barnett, M.J.1
-
3
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics. 129:1991;897-907.
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.1
-
4
-
-
0035859877
-
Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021
-
Capela D.et al. Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc. Natl. Acad. Sci. U. S. A. 98:2001;9877-9882.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 9877-9882
-
-
Capela, D.1
-
5
-
-
0033662116
-
Proteome analysis demonstrates complex replicon and luteolin interactions in pSyma-cured derivatives of Sinorhizobium meliloti strain 2011
-
Chen H., Higgins J., Oresnik I.J., Hynes M.F., Natera S., Djordjevic M.A., Weinman J.J., Rolfe B.G. Proteome analysis demonstrates complex replicon and luteolin interactions in pSyma-cured derivatives of Sinorhizobium meliloti strain 2011. Electrophoresis. 21:2000;3833-3842.
-
(2000)
Electrophoresis
, vol.21
, pp. 3833-3842
-
-
Chen, H.1
Higgins, J.2
Oresnik, I.J.3
Hynes, M.F.4
Natera, S.5
Djordjevic, M.A.6
Weinman, J.J.7
Rolfe, B.G.8
-
6
-
-
0033921447
-
Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae
-
de Miranda A.B., Alvarez-Valin F., Jabbari K., Degrave W.M., Bernardi G. Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae. J. Mol. Evol. 50:2000;45-55.
-
(2000)
J. Mol. Evol.
, vol.50
, pp. 45-55
-
-
De Miranda, A.B.1
Alvarez-Valin, F.2
Jabbari, K.3
Degrave, W.M.4
Bernardi, G.5
-
7
-
-
0035859832
-
The complete sequence of the 1683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti
-
Finan T.M., Weidner S., Wong K., Buhrmester J., Chain P., Vorholter F.J., Hernandez-Lucas I., Becker A., Cowie A., Gouzy J., Golding B., Puhler A. The complete sequence of the 1683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc. Natl. Acad. Sci. U. S. A. 98:2001;9889-9894.
-
(2001)
Proc. Natl. Acad. Sci. U. S. A.
, vol.98
, pp. 9889-9894
-
-
Finan, T.M.1
Weidner, S.2
Wong, K.3
Buhrmester, J.4
Chain, P.5
Vorholter, F.J.6
Hernandez-Lucas, I.7
Becker, A.8
Cowie, A.9
Gouzy, J.10
Golding, B.11
Puhler, A.12
-
8
-
-
0035958746
-
The composite genome of the legume symbiont Sinorhizobium meliloti
-
Galibert F.et al. The composite genome of the legume symbiont Sinorhizobium meliloti. Science. 293:2001;668-672.
-
(2001)
Science
, vol.293
, pp. 668-672
-
-
Galibert, F.1
-
10
-
-
0020491327
-
Codon usage in bacteria: Correlation with gene expressivity
-
Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10:1982;7055-7074.
-
(1982)
Nucleic Acids Res.
, vol.10
, pp. 7055-7074
-
-
Gouy, M.1
Gautier, C.2
-
11
-
-
0019519371
-
Codon catalog usage is a genome strategy modulated for gene expressivity
-
Grantham R., Gautier C., Gouy M., Jacobzone M., Mercier R. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 9:1981;r43-r74.
-
(1981)
Nucleic Acids Res.
, vol.9
-
-
Grantham, R.1
Gautier, C.2
Gouy, M.3
Jacobzone, M.4
Mercier, R.5
-
13
-
-
0036572274
-
Synonymous codon usage in Pseudomonas aeruginosa PA01
-
Grocock R.J., Sharp P.M. Synonymous codon usage in Pseudomonas aeruginosa PA01. Gene. 289:2002;131-139.
-
(2002)
Gene
, vol.289
, pp. 131-139
-
-
Grocock, R.J.1
Sharp, P.M.2
-
14
-
-
0031781977
-
Cloning and identification of conjugative transfer origins in the Rhizobium meliloti genome
-
Herrera-Cervera J.A., Sanjuan-Pinilla J.M., Olivares J., Sanjuan J. Cloning and identification of conjugative transfer origins in the Rhizobium meliloti genome. J. Bacteriol. 180:1998;4583-4590.
-
(1998)
J. Bacteriol.
, vol.180
, pp. 4583-4590
-
-
Herrera-Cervera, J.A.1
Sanjuan-Pinilla, J.M.2
Olivares, J.3
Sanjuan, J.4
-
15
-
-
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. 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. 238:1999;143-155.
-
(1999)
Gene
, vol.238
, pp. 143-155
-
-
Kanaya, S.1
Yamada, Y.2
Kudo, Y.3
Ikemura, T.4
-
16
-
-
0034739881
-
Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti
-
Kaneko T.et al. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7:2000;331-338.
-
(2000)
DNA Res.
, vol.7
, pp. 331-338
-
-
Kaneko, T.1
-
17
-
-
0033118273
-
Proteome composition and codon usage in spirochaetes: Species-specific and DNA strand-specific mutational biases
-
Lafay B., Lloyd A.T., McLean M.J., Devine K.M., Sharp P.M., Wolfe K.H. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res. 27:1999;1642-1649.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 1642-1649
-
-
Lafay, B.1
Lloyd, A.T.2
McLean, M.J.3
Devine, K.M.4
Sharp, P.M.5
Wolfe, K.H.6
-
18
-
-
0027403961
-
Unbiased estimation of the rates of synonymous and nonsynonymous substitution [letter]
-
Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution [letter]. J. Mol. Evol. 36:1993;96-99.
-
(1993)
J. Mol. Evol.
, vol.36
, pp. 96-99
-
-
Li, W.H.1
-
20
-
-
0032169578
-
Replicational and transcriptional selection on codon usage in Borrelia burgdorferi
-
McInerney J.O. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. U. S. A. 95:1998;10698-10703.
-
(1998)
Proc. Natl. Acad. Sci. U. S. A.
, vol.95
, pp. 10698-10703
-
-
McInerney, J.O.1
-
21
-
-
0033050538
-
Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: Compositional constraints and translational selection
-
Musto H., Romero H., Zavala A., Jabbari K., Bernardi G. Synonymous codon choices in the extremely GC-poor genome of Plasmodium falciparum: compositional constraints and translational selection. J. Mol. Evol. 49:1999;27-35.
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 27-35
-
-
Musto, H.1
Romero, H.2
Zavala, A.3
Jabbari, K.4
Bernardi, G.5
-
22
-
-
0034883460
-
Translational selection on codon usage in Xenopus laevis
-
Musto H., Cruveiller S., D'Onofrio G., Romero H., Bernardi G. Translational selection on codon usage in Xenopus laevis. Mol. Biol. Evol. 18:2001;1703-1707.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1703-1707
-
-
Musto, H.1
Cruveiller, S.2
D'Onofrio, G.3
Romero, H.4
Bernardi, G.5
-
23
-
-
0033846005
-
Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis
-
Natera S.H., Guerreiro N., Djordjevic M.A. Proteome analysis of differentially displayed proteins as a tool for the investigation of symbiosis. Mol. Plant-Microb. Interact. 13:2000;995-1009.
-
(2000)
Mol. Plant-Microb. Interact.
, vol.13
, pp. 995-1009
-
-
Natera, S.H.1
Guerreiro, N.2
Djordjevic, M.A.3
-
24
-
-
0034038755
-
Megaplasmid pRme2011a of Sinorhizobium meliloti is not required for viability
-
Oresnik I.J., Liu S.L., Yost C.K., Hynes M.F. Megaplasmid pRme2011a of Sinorhizobium meliloti is not required for viability. J. Bacteriol. 182:2000;3582-3586.
-
(2000)
J. Bacteriol.
, vol.182
, pp. 3582-3586
-
-
Oresnik, I.J.1
Liu, S.L.2
Yost, C.K.3
Hynes, M.F.4
-
25
-
-
0036285743
-
Key role of bacterial NH(4)(+) metabolism in Rhizobium-plant symbiosis
-
Patriarca E.J., Tate R., Iaccarino M. Key role of bacterial NH(4)(+) metabolism in Rhizobium-plant symbiosis. Microbiol. Mol. Biol. Rev. 66:2002;203-222.
-
(2002)
Microbiol. Mol. Biol. Rev.
, vol.66
, pp. 203-222
-
-
Patriarca, E.J.1
Tate, R.2
Iaccarino, M.3
-
26
-
-
0034657798
-
Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces
-
Romero H., Zavala A., Musto H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucleic Acids Res. 28:2000;2084-2090.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 2084-2090
-
-
Romero, H.1
Zavala, A.2
Musto, H.3
-
27
-
-
0024967181
-
Codon usage and gene expression level in Dictyostelium discoideum: Highly expressed genes do 'prefer' optimal codons
-
Sharp P.M., Devine K.M. Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons. Nucleic Acids Res. 17:1989;5029-5039.
-
(1989)
Nucleic Acids Res.
, vol.17
, pp. 5029-5039
-
-
Sharp, P.M.1
Devine, K.M.2
-
28
-
-
0022856787
-
An evolutionary perspective on synonymous codon usage in unicellular organisms
-
Sharp P.M., Li W.H. An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24:1986;28-38.
-
(1986)
J. Mol. Evol.
, vol.24
, pp. 28-38
-
-
Sharp, P.M.1
Li, W.H.2
-
29
-
-
0023650543
-
The codon adaptation index: A measure of directional synonymous codon usage bias, and its potential applications
-
Sharp P.M., Li W.H. The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1987;1281-1295.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
30
-
-
0023046874
-
Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes
-
Sharp P.M., Tuohy T.M., Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14:1986;5125-5143.
-
(1986)
Nucleic Acids Res.
, vol.14
, pp. 5125-5143
-
-
Sharp, P.M.1
Tuohy, T.M.2
Mosurski, K.R.3
-
31
-
-
0028359705
-
Codon usage in Caenorhabditis elegans: Delineation of translational selection and mutational biases
-
Stenico M., Lloyd A.T., Sharp P.M. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Res. 22:1994;2437-2446.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 2437-2446
-
-
Stenico, M.1
Lloyd, A.T.2
Sharp, P.M.3
-
32
-
-
0029049193
-
Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment
-
Sullivan J.T., Patrick H.N., Lowther W.L., Scott D.B., Ronson C.W. Nodulating strains of Rhizobium loti arise through chromosomal symbiotic gene transfer in the environment. Proc. Natl. Acad. Sci. U. S. A. 92:1995;8985-8989.
-
(1995)
Proc. Natl. Acad. Sci. U. S. A.
, vol.92
, pp. 8985-8989
-
-
Sullivan, J.T.1
Patrick, H.N.2
Lowther, W.L.3
Scott, D.B.4
Ronson, C.W.5
-
33
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
34
-
-
0033735359
-
Saprophytic intracellular rhizobia in alfalfa nodules
-
Timmers A.C., Soupene E., Auriac M.C., de Billy F., Vasse J., Boistard P., Truchet G. Saprophytic intracellular rhizobia in alfalfa nodules. Mol. Plant-Microb. Interact. 13:2000;1204-1213.
-
(2000)
Mol. Plant-Microb. Interact.
, vol.13
, pp. 1204-1213
-
-
Timmers, A.C.1
Soupene, E.2
Auriac, M.C.3
De Billy, F.4
Vasse, J.5
Boistard, P.6
Truchet, G.7
-
35
-
-
0032926125
-
Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: A case for the genetic coherence of rhizobial lineages
-
Wernegreen J.J., Riley M.A. Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages. Mol. Biol. Evol. 16:1999;98-113.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 98-113
-
-
Wernegreen, J.J.1
Riley, M.A.2
-
36
-
-
0030912101
-
Rhizobium gone native: Unexpected plasmid stability of indigenous Rhizobium leguminosarum
-
Wernegreen J.J., Harding E.E., Riley M.A. Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum. Proc. Natl. Acad. Sci. U. S. A. 94:1997;5483-5488.
-
(1997)
Proc. Natl. Acad. Sci. U. S. A.
, vol.94
, pp. 5483-5488
-
-
Wernegreen, J.J.1
Harding, E.E.2
Riley, M.A.3
-
37
-
-
0003109559
-
Diversity and phylogeny of rhizobia
-
Young J.P.W., Haukka K. Diversity and phylogeny of rhizobia. New Phytol. 133:1996;87-94.
-
(1996)
New Phytol.
, vol.133
, pp. 87-94
-
-
Young, J.P.W.1
Haukka, K.2
-
38
-
-
0036216144
-
Trends in codon and amino acid usage in Thermotoga maritima
-
Zavala A., Naya H., Romero H., Musto H. Trends in codon and amino acid usage in Thermotoga maritima. J. Mol. Evol. 54:2002;563-568.
-
(2002)
J. Mol. Evol.
, vol.54
, pp. 563-568
-
-
Zavala, A.1
Naya, H.2
Romero, H.3
Musto, H.4
|