-
1
-
-
33747892409
-
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
-
Alexeyenko, A., Tamas, I., Liu, G., and Sonnhammer, E.L.L. (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: e9–e15.
-
(2006)
Bioinformatics
, vol.22
, pp. e9-e15
-
-
Alexeyenko, A.1
Tamas, I.2
Liu, G.3
Sonnhammer, E.L.L.4
-
2
-
-
40549120596
-
The RAST Server: Rapid annotations using subsystems technology
-
Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., et al. (2008) The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 9: 75.
-
(2008)
BMC Genomics
, vol.9
, pp. 75
-
-
Aziz, R.K.1
Bartels, D.2
Best, A.A.3
DeJongh, M.4
Disz, T.5
Edwards, R.A.6
-
3
-
-
33947210693
-
Transcriptome analysis of phosphate starvation response in Escherichia coli
-
Baek, J.H., and Lee, S.Y. (2007) Transcriptome analysis of phosphate starvation response in Escherichia coli. J Microbiol Biotechnol 17: 244–252.
-
(2007)
J Microbiol Biotechnol
, vol.17
, pp. 244-252
-
-
Baek, J.H.1
Lee, S.Y.2
-
4
-
-
0019805971
-
Specific-purpose plasmid cloning vectors II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas
-
Bagdasarian, M., Lurz, R., Rückert, B., Franklin, F.C., Bagdasarian, M.M., Frey, J., and Timmis, K.N. (1981) Specific-purpose plasmid cloning vectors II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene 16: 237–247.
-
(1981)
Gene
, vol.16
, pp. 237-247
-
-
Bagdasarian, M.1
Lurz, R.2
Rückert, B.3
Franklin, F.C.4
Bagdasarian, M.M.5
Frey, J.6
Timmis, K.N.7
-
5
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner, F.R., Plunkett, G., Bloch, C.A., Perna, N.T., Burland, V., Riley, M., 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
Plunkett, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
-
6
-
-
59649114597
-
Analysis of dibenzothiophene desulfurization in a recombinant Pseudomonas putida strain
-
Calzada, J., Zamarro, M.T., Alcón, A., Santos, E., Díaz, E., García, J.L., et al. (2009) Analysis of dibenzothiophene desulfurization in a recombinant Pseudomonas putida strain. Appl Environ Microbiol 75: 875–877.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 875-877
-
-
Calzada, J.1
Zamarro, M.T.2
Alcón, A.3
Santos, E.4
Díaz, E.5
García, J.L.6
-
7
-
-
58049208278
-
DNAPlotter: circular and linear interactive genome visualization
-
Carver, T., Thomson, N., Bleasby, A., Berriman, M., and Parkhill, J. (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119–120.
-
(2009)
Bioinformatics
, vol.25
, pp. 119-120
-
-
Carver, T.1
Thomson, N.2
Bleasby, A.3
Berriman, M.4
Parkhill, J.5
-
8
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540–552.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
9
-
-
84878639396
-
The Entner–Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress
-
Chavarría, M., Nikel, P.I., Pérez-Pantoja, D., and de Lorenzo, V. (2013) The Entner–Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol 15: 1772–1785.
-
(2013)
Environ Microbiol
, vol.15
, pp. 1772-1785
-
-
Chavarría, M.1
Nikel, P.I.2
Pérez-Pantoja, D.3
de Lorenzo, V.4
-
10
-
-
34447522100
-
Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
-
del Castillo, T., Ramos, J.L., Rodríguez-Herva, J.J., Fuhrer, T., Sauer, U., and Duque, E. (2007) Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis. J Bacteriol 189: 5142–5152.
-
(2007)
J Bacteriol
, vol.189
, pp. 5142-5152
-
-
del Castillo, T.1
Ramos, J.L.2
Rodríguez-Herva, J.J.3
Fuhrer, T.4
Sauer, U.5
Duque, E.6
-
11
-
-
77956193448
-
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement
-
Darling, A.E., Mau, B., and Perna, N.T. (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5: e11147.
-
(2010)
PLoS ONE
, vol.5
-
-
Darling, A.E.1
Mau, B.2
Perna, N.T.3
-
12
-
-
84864453108
-
jModelTest 2: more models, new heuristics and parallel computing CircadiOmics: integrating circadian genomics, transcriptomics, proteomics
-
Darriba, D., Taboada, G.L., Doallo, R., and Posada, D. (2012) jModelTest 2: more models, new heuristics and parallel computing CircadiOmics: integrating circadian genomics, transcriptomics, proteomics. Nat Methods 9: 772.
-
(2012)
Nat Methods
, vol.9
, pp. 772
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
13
-
-
57049138931
-
Towards a genome-wide mutant library of Pseudomonas putida strain KT2440
-
In, Ramos, J.L., Filloux, A., (eds)., Dordrecht, the Netherlands, Springer
-
Duque, E., Molina-Henares, A.J., de la Torre, J., Molina-Henares, M.A., del Castillo, T., Lam, J., and Ramos, J.L. (2007) Towards a genome-wide mutant library of Pseudomonas putida strain KT2440. In Pseudomonas: A Model System in Biology. Ramos, J.L., and Filloux, A. (eds). Dordrecht, the Netherlands: Springer, pp. 227–251.
-
(2007)
Pseudomonas: A Model System in Biology
, pp. 227-251
-
-
Duque, E.1
Molina-Henares, A.J.2
de la Torre, J.3
Molina-Henares, M.A.4
del Castillo, T.5
Lam, J.6
Ramos, J.L.7
-
14
-
-
84871929682
-
Identification of reciprocal adhesion genes in pathogenic and non-pathogenic Pseudomonas
-
Duque, E., de la Torre, J., Bernal, P., Molina-Henares, M.A., Alaminos, M., Espinosa-Urgel, M., et al. (2013) Identification of reciprocal adhesion genes in pathogenic and non-pathogenic Pseudomonas. Environ Microbiol 15: 36–48.
-
(2013)
Environ Microbiol
, vol.15
, pp. 36-48
-
-
Duque, E.1
de la Torre, J.2
Bernal, P.3
Molina-Henares, M.A.4
Alaminos, M.5
Espinosa-Urgel, M.6
-
15
-
-
13244255415
-
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
-
Edgar, R. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5: 113.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 113
-
-
Edgar, R.1
-
16
-
-
84866172978
-
Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid
-
Fernández, M., Niqui-Arroyo, J.L., Conde, S., Ramos, J.L., and Duque, E. (2012) Enhanced tolerance to naphthalene and enhanced rhizoremediation performance for Pseudomonas putida KT2440 via the NAH7 catabolic plasmid. Appl Environ Microbiol 78: 5104–5110.
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 5104-5110
-
-
Fernández, M.1
Niqui-Arroyo, J.L.2
Conde, S.3
Ramos, J.L.4
Duque, E.5
-
17
-
-
79955017837
-
Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics
-
Frank, S., Klockgether, J., Hagendorf, P., Geffers, R., Schöck, U., Pohl, T., et al. (2011) Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics. Environ Microbiol 13: 1309–1326.
-
(2011)
Environ Microbiol
, vol.13
, pp. 1309-1326
-
-
Frank, S.1
Klockgether, J.2
Hagendorf, P.3
Geffers, R.4
Schöck, U.5
Pohl, T.6
-
18
-
-
0024342933
-
Flagellation of Pseudomonas putida and analysis of its motile behavior
-
Harwood, C.S., Fosnaugh, K., and Dispensa, M. (1989) Flagellation of Pseudomonas putida and analysis of its motile behavior. J Bacteriol 171: 4063–4066.
-
(1989)
J Bacteriol
, vol.171
, pp. 4063-4066
-
-
Harwood, C.S.1
Fosnaugh, K.2
Dispensa, M.3
-
19
-
-
77949903823
-
Bacterial phosphate metabolism and its application to phosphorus recovery and industrial bioprocesses
-
Hirota, R., Kuroda, A., Kato, J., and Ohtake, H. (2010) Bacterial phosphate metabolism and its application to phosphorus recovery and industrial bioprocesses. J Biosci Bioeng 109: 423–432.
-
(2010)
J Biosci Bioeng
, vol.109
, pp. 423-432
-
-
Hirota, R.1
Kuroda, A.2
Kato, J.3
Ohtake, H.4
-
20
-
-
70549083899
-
Modulation of cellular function by polyamines
-
Igarashi, K., and Kashiwagi, K. (2010) Modulation of cellular function by polyamines. Int J Biochem Cell Biol 42: 39–51.
-
(2010)
Int J Biochem Cell Biol
, vol.42
, pp. 39-51
-
-
Igarashi, K.1
Kashiwagi, K.2
-
21
-
-
33644748770
-
Arginine and polyamine metabolism
-
In, Ramos, J.L., (ed.)., New York, NY, USA, Kluwer Academic
-
Itoh, Y., and Nakada, Y. (2004) Arginine and polyamine metabolism. In Pseudomonas Volume 3: Biosynthesis of Macromolecules and Molecular Metabolism. Ramos, J.L. (ed.). New York, NY, USA: Kluwer Academic, pp. 243–272.
-
(2004)
Pseudomonas Volume 3: Biosynthesis of Macromolecules and Molecular Metabolism
, pp. 243-272
-
-
Itoh, Y.1
Nakada, Y.2
-
22
-
-
84055224165
-
Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome
-
Karberg, K.A., Olsen, G.J., and Davis, J.J. (2011) Similarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome. PNAS 108: 20154–20159.
-
(2011)
PNAS
, vol.108
, pp. 20154-20159
-
-
Karberg, K.A.1
Olsen, G.J.2
Davis, J.J.3
-
23
-
-
33645816587
-
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
-
Keane, T.M., Creevey, C.J., Pentony, M.M., Naughton, T.J., and Mclnerney, J.O. (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6: 29.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 29
-
-
Keane, T.M.1
Creevey, C.J.2
Pentony, M.M.3
Naughton, T.J.4
Mclnerney, J.O.5
-
24
-
-
58949096129
-
Dual regulation of zwf-1 by both 2-keto-3-deoxy-6-phosphogluconate and oxidative stress in Pseudomonas putida
-
Kim, J., Jeon, C.O., and Park, W. (2008) Dual regulation of zwf-1 by both 2-keto-3-deoxy-6-phosphogluconate and oxidative stress in Pseudomonas putida. Microbiology 154: 3905–3916.
-
(2008)
Microbiology
, vol.154
, pp. 3905-3916
-
-
Kim, J.1
Jeon, C.O.2
Park, W.3
-
25
-
-
0042208192
-
Bacteria that express lateral flagella enable dissection of the multifunctional roles of flagella in pathogenesis
-
Kirov, S.M. (2003) Bacteria that express lateral flagella enable dissection of the multifunctional roles of flagella in pathogenesis. FEMS Microbiol Lett 224: 151–159.
-
(2003)
FEMS Microbiol Lett
, vol.224
, pp. 151-159
-
-
Kirov, S.M.1
-
26
-
-
84877085438
-
Identification of plant growth-promoting bacteria-responsive proteins in cucumber roots under hypoxic stress using a proteomic approach
-
Li, J., McConkey, B.J., Cheng, Z., Guo, S., and Glick, B.R. (2013) Identification of plant growth-promoting bacteria-responsive proteins in cucumber roots under hypoxic stress using a proteomic approach. J Proteom 84: 119–131.
-
(2013)
J Proteom
, vol.84
, pp. 119-131
-
-
Li, J.1
McConkey, B.J.2
Cheng, Z.3
Guo, S.4
Glick, B.R.5
-
27
-
-
34249856320
-
Stepwise formation of the bacterial flagellar system
-
Liu, R., and Ochman, H. (2007) Stepwise formation of the bacterial flagellar system. PNAS 104: 7116–7121.
-
(2007)
PNAS
, vol.104
, pp. 7116-7121
-
-
Liu, R.1
Ochman, H.2
-
28
-
-
33644771430
-
Pathways and regulation of bacterial arginine metabolism and perspectives for obtaining arginine overproducing strains
-
Lu, C. (2006) Pathways and regulation of bacterial arginine metabolism and perspectives for obtaining arginine overproducing strains. Appl Microbiol Biotechnol 70: 261–272.
-
(2006)
Appl Microbiol Biotechnol
, vol.70
, pp. 261-272
-
-
Lu, C.1
-
29
-
-
84891631101
-
The metabolic cost of flagellar motion in Pseudomonas putida KT2440
-
Martinez-García, E., Nikel, P.I., Chavarría, M., and de Lorenzo, V. (2014) The metabolic cost of flagellar motion in Pseudomonas putida KT2440. Environ Microbiol 16: 291–303.
-
(2014)
Environ Microbiol
, vol.16
, pp. 291-303
-
-
Martinez-García, E.1
Nikel, P.I.2
Chavarría, M.3
de Lorenzo, V.4
-
30
-
-
79951604920
-
Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1
-
Matilla, M.A., Pizarro-Tobias, P., Roca, A., Fernández, M., Duque, E., Molina, L., et al. (2011) Complete genome of the plant growth-promoting rhizobacterium Pseudomonas putida BIRD-1. J Bacteriol 193: 1290.
-
(2011)
J Bacteriol
, vol.193
, pp. 1290
-
-
Matilla, M.A.1
Pizarro-Tobias, P.2
Roca, A.3
Fernández, M.4
Duque, E.5
Molina, L.6
-
31
-
-
0034089814
-
Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions
-
Molina, L., Ramos, C., Duque, E., Ronchel, M.C., Garcia, J.M., Wyke, L., and Ramos, J.L. (2000) Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions. Soil Biol Biochem 32: 315–321.
-
(2000)
Soil Biol Biochem
, vol.32
, pp. 315-321
-
-
Molina, L.1
Ramos, C.2
Duque, E.3
Ronchel, M.C.4
Garcia, J.M.5
Wyke, L.6
Ramos, J.L.7
-
32
-
-
84898451715
-
Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital
-
Molina, L., Udaondo, Z., Duque, E., Fernández, M., Molina-Santiago, C., Roca, A., et al. (2014) Antibiotic resistance determinants in a Pseudomonas putida strain isolated from a hospital. PLoS ONE 9: e81604.
-
(2014)
PLoS ONE
, vol.9
-
-
Molina, L.1
Udaondo, Z.2
Duque, E.3
Fernández, M.4
Molina-Santiago, C.5
Roca, A.6
-
33
-
-
77957963526
-
Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library
-
Molina-Henares, M.A., de la Torre, J., García-Salamanca, A., Molina-Henares, J.A., Herrera, M.C., Ramos, J.L., and Duque, E. (2010) Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library. Environ Microbiol 12: 1468–1485.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1468-1485
-
-
Molina-Henares, M.A.1
de la Torre, J.2
García-Salamanca, A.3
Molina-Henares, J.A.4
Herrera, M.C.5
Ramos, J.L.6
Duque, E.7
-
34
-
-
34547588704
-
KAAS: an automatic genome annotation and pathway reconstruction server
-
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., and Kanehisa, M. (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35: W182–W185.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. W182-W185
-
-
Moriya, Y.1
Itoh, M.2
Okuda, S.3
Yoshizawa, A.C.4
Kanehisa, M.5
-
35
-
-
77955516907
-
DNA sequence-based analysis of the Pseudomonas species
-
Mulet, M., Lalucat, J., and García-Valdés, E. (2010) DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 12: 1513–1530.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1513-1530
-
-
Mulet, M.1
Lalucat, J.2
García-Valdés, E.3
-
36
-
-
0036933705
-
Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
-
Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Fouts, D.E., et al. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4: 799–808.
-
(2002)
Environ Microbiol
, vol.4
, pp. 799-808
-
-
Nelson, K.E.1
Weinel, C.2
Paulsen, I.T.3
Dodson, R.J.4
Hilbert, H.5
Fouts, D.E.6
-
37
-
-
0030734657
-
Partial purification and characterization of manganese-oxidizing factors of Pseudomonas fluorescens GB-1
-
Okazaki, M., Sugita, T., Shimizu, M., Ohode, Y., Iwamoto, K., de Vrind-de Jong, E.W., et al. (1997) Partial purification and characterization of manganese-oxidizing factors of Pseudomonas fluorescens GB-1. Appl Environ Microbiol 63: 4793–4799.
-
(1997)
Appl Environ Microbiol
, vol.63
, pp. 4793-4799
-
-
Okazaki, M.1
Sugita, T.2
Shimizu, M.3
Ohode, Y.4
Iwamoto, K.5
de Vrind-de Jong, E.W.6
-
38
-
-
0000803252
-
Gram negative aerobic rods and cocci, family I: Pseudomonadaceae
-
In, Williams, A., Krieg, N.R., Holt, J.G., (eds)., Baltimore, MD, USA, Williams and Wilkins Co
-
Palleroni, N.J. (1984) Gram negative aerobic rods and cocci, family I: Pseudomonadaceae. In Bergey's Manual of Systematic Bacteriology. Williams, A., Krieg, N.R., and Holt, J.G. (eds). Baltimore, MD, USA: Williams and Wilkins Co, pp. 141–199.
-
(1984)
Bergey's Manual of Systematic Bacteriology
, pp. 141-199
-
-
Palleroni, N.J.1
-
39
-
-
84977800416
-
Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: resolving the taxonomic affiliation of the Cicer canariense rhizobia
-
Pérez-Yépez, J., Armas-Capote, N., Velázquez, E., Pérez-Galdona, R., Rivas, R., and León-Barrios, M. (2014) Evaluation of seven housekeeping genes for multilocus sequence analysis of the genus Mesorhizobium: resolving the taxonomic affiliation of the Cicer canariense rhizobia. Syst Appl Microbiol 37: 553–559.
-
(2014)
Syst Appl Microbiol
, vol.37
, pp. 553-559
-
-
Pérez-Yépez, J.1
Armas-Capote, N.2
Velázquez, E.3
Pérez-Galdona, R.4
Rivas, R.5
León-Barrios, M.6
-
40
-
-
0347567135
-
Characterization of a new solvent-responsive gene locus in Pseudomonas putida F1 and its functionalization as a versatile biosensor
-
Phoenix, P., Keane, A., Patel, A., Bergeron, H., Ghoshal, S., and Lau, P.C.K. (2003) Characterization of a new solvent-responsive gene locus in Pseudomonas putida F1 and its functionalization as a versatile biosensor. Environ Microbiol 5: 1309–1327.
-
(2003)
Environ Microbiol
, vol.5
, pp. 1309-1327
-
-
Phoenix, P.1
Keane, A.2
Patel, A.3
Bergeron, H.4
Ghoshal, S.5
Lau, P.C.K.6
-
41
-
-
84922645130
-
Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial
-
Pizarro-Tobías, P., Fernández, M., Niqui, J.L., Solano, J., Duque, E., Ramos, J.L., and Roca, A. (2014) Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial. Microb Biotechnol 8: 77–92.
-
(2014)
Microb Biotechnol
, vol.8
, pp. 77-92
-
-
Pizarro-Tobías, P.1
Fernández, M.2
Niqui, J.L.3
Solano, J.4
Duque, E.5
Ramos, J.L.6
Roca, A.7
-
42
-
-
77954080071
-
A process optimization for bio-catalytic production of substituted catechols (3-nitrocatechol and 3-methylcatechol)
-
Prakash, D., Pandey, J., Tiwary, B.N., and Jain, R.K. (2010) A process optimization for bio-catalytic production of substituted catechols (3-nitrocatechol and 3-methylcatechol). BMC Biotechnol 10: 49.
-
(2010)
BMC Biotechnol
, vol.10
, pp. 49
-
-
Prakash, D.1
Pandey, J.2
Tiwary, B.N.3
Jain, R.K.4
-
43
-
-
0343419040
-
Altered effector specificities in regulators of gene expression: TOL plasmid xylS mutants and their use to engineer expansion of the range of aromatics degraded by bacteria
-
Ramos, J.L., Stolz, A., Reineke, W., and Timmis, K.N. (1986) Altered effector specificities in regulators of gene expression: TOL plasmid xylS mutants and their use to engineer expansion of the range of aromatics degraded by bacteria. PNAS 83: 8467–8471.
-
(1986)
PNAS
, vol.83
, pp. 8467-8471
-
-
Ramos, J.L.1
Stolz, A.2
Reineke, W.3
Timmis, K.N.4
-
44
-
-
0023443646
-
Regulatory circuits controlling transcription of TOL plasmid operon encoding meta-cleavage pathway for degradation of alkylbenzoates by Pseudomonas
-
Ramos, J.L., Mermod, N., and Timmis, K.N. (1987) Regulatory circuits controlling transcription of TOL plasmid operon encoding meta-cleavage pathway for degradation of alkylbenzoates by Pseudomonas. Mol Microbiol 1: 293–300.
-
(1987)
Mol Microbiol
, vol.1
, pp. 293-300
-
-
Ramos, J.L.1
Mermod, N.2
Timmis, K.N.3
-
45
-
-
0031786573
-
Combined physical and genetic map of the Pseudomonas putida KT2440 chromosome
-
Ramos-Díaz, M.A., and Ramos, J.L. (1998) Combined physical and genetic map of the Pseudomonas putida KT2440 chromosome. J Bacteriol 180: 6352–6363.
-
(1998)
J Bacteriol
, vol.180
, pp. 6352-6363
-
-
Ramos-Díaz, M.A.1
Ramos, J.L.2
-
46
-
-
84899738542
-
Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea
-
Ran, W., Kristensen, D.M., and Koonin, E.V. (2014) Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea. MBio 5: 1–11.
-
(2014)
MBio
, vol.5
, pp. 1-11
-
-
Ran, W.1
Kristensen, D.M.2
Koonin, E.V.3
-
47
-
-
0020003601
-
TOL plasmid pWWO in constructed halobenzoate-degrading Pseudomonas strains: prevention of meta pathway
-
Reineke, W., Jeenes, D.J., Williams, P.A., and Knackmuss, H.-J. (1982) TOL plasmid pWWO in constructed halobenzoate-degrading Pseudomonas strains: prevention of meta pathway. J Bacteriol 150: 196–201.
-
(1982)
J Bacteriol
, vol.150
, pp. 196-201
-
-
Reineke, W.1
Jeenes, D.J.2
Williams, P.A.3
Knackmuss, H.-J.4
-
48
-
-
0035861990
-
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons
-
Remm, M., Storm, C.E.V., and Sonnhammer, E.L.L. (2001) Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol 314: 1041–1052.
-
(2001)
J Mol Biol
, vol.314
, pp. 1041-1052
-
-
Remm, M.1
Storm, C.E.V.2
Sonnhammer, E.L.L.3
-
49
-
-
0034201441
-
EMBOSS: the European molecular biology open software suite
-
Rice, P., Longden, I., and Bleasby, A. (2000) EMBOSS: the European molecular biology open software suite. Trends Genet 16: 276–277.
-
(2000)
Trends Genet
, vol.16
, pp. 276-277
-
-
Rice, P.1
Longden, I.2
Bleasby, A.3
-
50
-
-
84874729370
-
Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1
-
Roca, A., Pizarro-Tobías, P., Udaondo, Z., Fernández, M., Matilla, M.A., Molina-Henares, M.A., et al. (2013) Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacterium Pseudomonas putida BIRD-1. Environ Microbiol 15: 780–794.
-
(2013)
Environ Microbiol
, vol.15
, pp. 780-794
-
-
Roca, A.1
Pizarro-Tobías, P.2
Udaondo, Z.3
Fernández, M.4
Matilla, M.A.5
Molina-Henares, M.A.6
-
51
-
-
65249112754
-
Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome
-
Roymondal, U., Das, S., and Sahoo, S. (2009) Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome. DNA Res 16: 13–30.
-
(2009)
DNA Res
, vol.16
, pp. 13-30
-
-
Roymondal, U.1
Das, S.2
Sahoo, S.3
-
52
-
-
84927645733
-
Pseudomonas chemotaxis
-
Sampedro, I., Parales, R.E., Krell, T., and Hill, J.E. (2015) Pseudomonas chemotaxis. FEMS Microbiol Rev 39: 17–46.
-
(2015)
FEMS Microbiol Rev
, vol.39
, pp. 17-46
-
-
Sampedro, I.1
Parales, R.E.2
Krell, T.3
Hill, J.E.4
-
53
-
-
4444316792
-
Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics
-
Santos, P.M., Benndorf, D., and Sá-Correia, I. (2004) Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4: 2640–2652.
-
(2004)
Proteomics
, vol.4
, pp. 2640-2652
-
-
Santos, P.M.1
Benndorf, D.2
Sá-Correia, I.3
-
54
-
-
77950661324
-
Transgenic expression of glucose dehydrogenase in Azotobacter vinelandii enhances mineral phosphate solubilization and growth of sorghum seedlings
-
Sashidhar, B., and Podile, A.R. (2009) Transgenic expression of glucose dehydrogenase in Azotobacter vinelandii enhances mineral phosphate solubilization and growth of sorghum seedlings. Microbial biotechnology 2: 521–529.
-
(2009)
Microbial biotechnology
, vol.2
, pp. 521-529
-
-
Sashidhar, B.1
Podile, A.R.2
-
55
-
-
84878656630
-
Plant–bacteria interactions in the removal of pollutants
-
Segura, A., and Ramos, J.L. (2013) Plant–bacteria interactions in the removal of pollutants. Curr Opin Biotechnol 24: 467–473.
-
(2013)
Curr Opin Biotechnol
, vol.24
, pp. 467-473
-
-
Segura, A.1
Ramos, J.L.2
-
56
-
-
84899553363
-
RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis, A. (2014) RAxML Version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
57
-
-
79960610118
-
REVIGO summarizes and visualizes long lists of gene ontology terms
-
Supek, F., Bošnjak, M., Škunca, N., and Šmuc, T. (2011) REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6: e21800.
-
(2011)
PLoS ONE
, vol.6
-
-
Supek, F.1
Bošnjak, M.2
Škunca, N.3
Šmuc, T.4
-
58
-
-
29144469077
-
Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene
-
Taghavi, S., Barac, T., Greenberg, B., Borremans, B., Vangronsveld, J., and van der Lelie, D. (2005) Horizontal gene transfer to endogenous endophytic bacteria from poplar improves phytoremediation of toluene. Appl Environ Microbiol 71: 8500–8505.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 8500-8505
-
-
Taghavi, S.1
Barac, T.2
Greenberg, B.3
Borremans, B.4
Vangronsveld, J.5
van der Lelie, D.6
-
59
-
-
79957613599
-
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
-
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2731-2739
-
-
Tamura, K.1
Peterson, D.2
Peterson, N.3
Stecher, G.4
Nei, M.5
Kumar, S.6
-
60
-
-
84862909265
-
Genome sequence of Pseudomonas putida Idaho, a unique organic-solvent-tolerant bacterium
-
Tao, F., Tang, H., Gai, Z., Su, F., Wang, X., He, X., and Xu, P. (2011) Genome sequence of Pseudomonas putida Idaho, a unique organic-solvent-tolerant bacterium. J Bacteriol 193: 7011–7012.
-
(2011)
J Bacteriol
, vol.193
, pp. 7011-7012
-
-
Tao, F.1
Tang, H.2
Gai, Z.3
Su, F.4
Wang, X.5
He, X.6
Xu, P.7
-
61
-
-
25444524604
-
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ‘pan-genome
-
Tettelin, H., Masignani, V., Cieslewicz, M.J., Donati, C., Medini, D., Ward, N.L., et al. (2005) Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ‘pan-genome. PNAS 102: 13950–13955.
-
(2005)
PNAS
, vol.102
, pp. 13950-13955
-
-
Tettelin, H.1
Masignani, V.2
Cieslewicz, M.J.3
Donati, C.4
Medini, D.5
Ward, N.L.6
-
62
-
-
84885970388
-
A bacterial swimmer with two alternating speeds of propagation
-
Theves, M., Taktikos, J., Zaburdaev, V., Stark, H., and Beta, C. (2013) A bacterial swimmer with two alternating speeds of propagation. Biophys J 105: 1915–1924.
-
(2013)
Biophys J
, vol.105
, pp. 1915-1924
-
-
Theves, M.1
Taktikos, J.2
Zaburdaev, V.3
Stark, H.4
Beta, C.5
-
63
-
-
0036937672
-
Pseudomonas putida: a cosmopolitan opportunist par excellence
-
Timmis, K.N. (2002) Pseudomonas putida: a cosmopolitan opportunist par excellence. Environ Microbiol 4: 779–781.
-
(2002)
Environ Microbiol
, vol.4
, pp. 779-781
-
-
Timmis, K.N.1
-
64
-
-
84882253298
-
Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome
-
Udaondo, Z., Molina, L., Daniels, C., Gómez, M.J., Molina-Henares, M.A., Matilla, M.A., et al. (2013) Metabolic potential of the organic-solvent tolerant Pseudomonas putida DOT-T1E deduced from its annotated genome. Microbial biotechnology 6: 598–611.
-
(2013)
Microbial biotechnology
, vol.6
, pp. 598-611
-
-
Udaondo, Z.1
Molina, L.2
Daniels, C.3
Gómez, M.J.4
Molina-Henares, M.A.5
Matilla, M.A.6
-
65
-
-
77953606371
-
Bioremediation, a broad perspective
-
van Dillewijn, P., Nojiri, H., Van der Meer, J.R., and Wood, T.K. (2009) Bioremediation, a broad perspective. Microb Biotechnol 2: 125–127.
-
(2009)
Microb Biotechnol
, vol.2
, pp. 125-127
-
-
van Dillewijn, P.1
Nojiri, H.2
Van der Meer, J.R.3
Wood, T.K.4
-
66
-
-
0036937356
-
Global features of the Pseudomonas putida KT2440 genome sequence
-
Weinel, C., Nelson, K.E., and Tümmler, B. (2002) Global features of the Pseudomonas putida KT2440 genome sequence. Environ Microbiol 4: 809–818.
-
(2002)
Environ Microbiol
, vol.4
, pp. 809-818
-
-
Weinel, C.1
Nelson, K.E.2
Tümmler, B.3
-
67
-
-
77958184628
-
Potential of the TCE-degrading endophyte Pseudomonas putida W619-TCE to improve plant growth and reduce TCE phytotoxicity and evapotranspiration in poplar cuttings
-
Weyens, N., Truyens, S., Dupae, J., Newman, L., Taghavi, S., van der Lelie, D., et al. (2010) Potential of the TCE-degrading endophyte Pseudomonas putida W619-TCE to improve plant growth and reduce TCE phytotoxicity and evapotranspiration in poplar cuttings. Environ Pollut 158: 2915–2919.
-
(2010)
Environ Pollut
, vol.158
, pp. 2915-2919
-
-
Weyens, N.1
Truyens, S.2
Dupae, J.3
Newman, L.4
Taghavi, S.5
van der Lelie, D.6
-
68
-
-
77950211271
-
Discovery of an operon that participates in agmatine metabolism and regulates biofilm formation in Pseudomonas aeruginosa
-
Williams, B.J., Du, R.-H., Calcutt, M.W., Abdolrasulnia, R., Christman, B.W., and Blackwell, T.S. (2010) Discovery of an operon that participates in agmatine metabolism and regulates biofilm formation in Pseudomonas aeruginosa. Mol Microbiol 76: 104–119.
-
(2010)
Mol Microbiol
, vol.76
, pp. 104-119
-
-
Williams, B.J.1
Du, R.-H.2
Calcutt, M.W.3
Abdolrasulnia, R.4
Christman, B.W.5
Blackwell, T.S.6
-
69
-
-
0031827993
-
Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes
-
Yamamoto, S., and Harayama, S. (1998) Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 48: 813–819.
-
(1998)
Int J Syst Bacteriol
, vol.48
, pp. 813-819
-
-
Yamamoto, S.1
Harayama, S.2
-
70
-
-
0033764790
-
Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes
-
Yamamoto, S., Kasai, H., Arnold, D.L., Jackson, R.W., Vivian, A., and Harayama, S. (2000) Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146: 2385–2394.
-
(2000)
Microbiology
, vol.146
, pp. 2385-2394
-
-
Yamamoto, S.1
Kasai, H.2
Arnold, D.L.3
Jackson, R.W.4
Vivian, A.5
Harayama, S.6
-
71
-
-
80053604142
-
Complete genome sequence of the nicotine-degrading Pseudomonas putida strain S16
-
Yu, H., Tang, H., Wang, L., Yao, Y., Wu, G., and Xu, P. (2011) Complete genome sequence of the nicotine-degrading Pseudomonas putida strain S16. J Bacteriol 193: 5541–5542.
-
(2011)
J Bacteriol
, vol.193
, pp. 5541-5542
-
-
Yu, H.1
Tang, H.2
Wang, L.3
Yao, Y.4
Wu, G.5
Xu, P.6
-
72
-
-
0036952282
-
The product of arcR, the sixth gene of the arc operon of Lactobacillus sakei, is essential for expression of the arginine deiminase pathway
-
Zúñiga, M., Miralles, M.D.M.C., and Pérez-Martínez, G. (2002) The product of arcR, the sixth gene of the arc operon of Lactobacillus sakei, is essential for expression of the arginine deiminase pathway. Appl Environ Microbiol 68: 6051–6058.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 6051-6058
-
-
Zúñiga, M.1
Miralles, M.D.M.C.2
Pérez-Martínez, G.3
|