-
1
-
-
33751007565
-
Role of the ptsN gene product in catabolite repression of the Pseudomonas putida TOL toluene degradation pathway in chemostat cultures
-
Aranda-Olmedo, I., Marín, P., Ramos, J.L., and Marqués, S. (2006) Role of the ptsN gene product in catabolite repression of the Pseudomonas putida TOL toluene degradation pathway in chemostat cultures. Appl Environ Microbiol 72: 7418-7421.
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 7418-7421
-
-
Aranda-Olmedo, I.1
Marín, P.2
Ramos, J.L.3
Marqués, S.4
-
2
-
-
0030681260
-
The significance of digital gene expression profiles
-
Audic, S., and Claverie, J.M. (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995.
-
(1997)
Genome Res
, vol.7
, pp. 986-995
-
-
Audic, S.1
Claverie, J.M.2
-
3
-
-
0000404096
-
The growth of microorganisms in relation to their energy supply
-
Bauchop, T., and Eldsen, S.R. (1960) The growth of microorganisms in relation to their energy supply. J Gen Microbiol 23: 457-569.
-
(1960)
J Gen Microbiol
, vol.23
, pp. 457-569
-
-
Bauchop, T.1
Eldsen, S.R.2
-
4
-
-
44949225040
-
Context-specific metabolic networks are consistent with experiments
-
Becker, S.A., and Palsson, B.O. (2008) Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 4: e1000082.
-
(2008)
PLoS Comput Biol
, vol.4
, pp. e1000082
-
-
Becker, S.A.1
Palsson, B.O.2
-
5
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B 57: 289-300.
-
(1995)
J Roy Stat Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
6
-
-
77955968811
-
Catabolite repression of the TodS/TodT two-component system and effector-dependent transphosphorylation of TodT as the basis for toluene dioxygenase catabolic pathway control
-
Busch, A., Lacal, J., Silva-Jimenez, H., Krell, T., and Ramos, J.L. (2010) Catabolite repression of the TodS/TodT two-component system and effector-dependent transphosphorylation of TodT as the basis for toluene dioxygenase catabolic pathway control. J Bacteriol 192: 4246-4250.
-
(2010)
J Bacteriol
, vol.192
, pp. 4246-4250
-
-
Busch, A.1
Lacal, J.2
Silva-Jimenez, H.3
Krell, T.4
Ramos, J.L.5
-
7
-
-
0032589264
-
The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma 54-dependent Pu promoter of the TOL plasmid
-
Cases, I., Pérez-Martín, J., and de Lorenzo, V. (1999) The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma 54-dependent Pu promoter of the TOL plasmid. J Biol Chem 274: 15562-15568.
-
(1999)
J Biol Chem
, vol.274
, pp. 15562-15568
-
-
Cases, I.1
Pérez-Martín, J.2
de Lorenzo, V.3
-
8
-
-
34548548565
-
Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways
-
del Castillo, T., and Ramos, J.L. (2007) Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. J Bacteriol 189: 6602-6610.
-
(2007)
J Bacteriol
, vol.189
, pp. 6602-6610
-
-
del Castillo, T.1
Ramos, J.L.2
-
9
-
-
34447522100
-
Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
-
del Castillo, T., Ramos, J.L., Rodríguez-Hervá, 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-Hervá, J.J.3
Fuhrer, T.4
Sauer, U.5
Duque, E.6
-
10
-
-
41549126717
-
A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate
-
del Castillo, T., Duque, E., and Ramos, J.L. (2008) A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate. J Bacteriol 190: 2331-2339.
-
(2008)
J Bacteriol
, vol.190
, pp. 2331-2339
-
-
del Castillo, T.1
Duque, E.2
Ramos, J.L.3
-
11
-
-
84860532358
-
Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism
-
Chavarría, M., Kleijn, R.J., Sauer, U., Pflüger-Grau, K., and de Lorenzo, V. (2012) Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism. mBio 3: e00028-12.
-
(2012)
mBio
, vol.3
, pp. e00012-e00028
-
-
Chavarría, M.1
Kleijn, R.J.2
Sauer, U.3
Pflüger-Grau, K.4
de Lorenzo, V.5
-
12
-
-
84899047521
-
Coordination of microbial metabolism
-
Chubukov, V., Gerosa, L., Kochanowski, K., and Sauer, U. (2014) Coordination of microbial metabolism. Nat Rev Microbiol 12: 327-340.
-
(2014)
Nat Rev Microbiol
, vol.12
, pp. 327-340
-
-
Chubukov, V.1
Gerosa, L.2
Kochanowski, K.3
Sauer, U.4
-
13
-
-
42049092081
-
The mechanisms of carbon catabolite repression in bacteria
-
Deutscher, J. (2008) The mechanisms of carbon catabolite repression in bacteria. Curr Opin Microbiol 11: 87-93.
-
(2008)
Curr Opin Microbiol
, vol.11
, pp. 87-93
-
-
Deutscher, J.1
-
14
-
-
0028226744
-
Inducibility of the TOL catabolic pathway in Pseudomonas putida (pWW0) growing on succinate in continuous culture: evidence of carbon catabolite repression control
-
Duetz, W.A., Marqués, S., de Jong, C., Ramos, J.L., and van Andel, J.G. (1994) Inducibility of the TOL catabolic pathway in Pseudomonas putida (pWW0) growing on succinate in continuous culture: evidence of carbon catabolite repression control. J Bacteriol 176: 2354-2361.
-
(1994)
J Bacteriol
, vol.176
, pp. 2354-2361
-
-
Duetz, W.A.1
Marqués, S.2
de Jong, C.3
Ramos, J.L.4
van Andel, J.G.5
-
15
-
-
0030052826
-
Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation in chemostat culture
-
Duetz, W.A., Marqués, S., Wind, B., Ramos, J.L., and van Andel, J.G. (1996) Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation in chemostat culture. Appl Environ Microbiol 62: 601-606.
-
(1996)
Appl Environ Microbiol
, vol.62
, pp. 601-606
-
-
Duetz, W.A.1
Marqués, S.2
Wind, B.3
Ramos, J.L.4
van Andel, J.G.5
-
16
-
-
34347332311
-
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
-
Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., etal. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3: 121.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 121
-
-
Feist, A.M.1
Henry, C.S.2
Reed, J.L.3
Krummenacker, M.4
Joyce, A.R.5
Karp, P.D.6
-
17
-
-
58549108388
-
Reconstruction of biochemical networks in microorganisms
-
Feist, A.M., Herrgard, M.J., Thiele, I., Reed, J.L., and Palsson, B.O. (2009) Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7: 129-143.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 129-143
-
-
Feist, A.M.1
Herrgard, M.J.2
Thiele, I.3
Reed, J.L.4
Palsson, B.O.5
-
18
-
-
0005536404
-
Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway
-
Franklin, F.C., Bagdasarian, M., Bagdasarian, M.M., and Timmis, K.N. (1981) Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway. Proc Nat Acad Sci USA 78: 7458-7462.
-
(1981)
Proc Nat Acad Sci USA
, vol.78
, pp. 7458-7462
-
-
Franklin, F.C.1
Bagdasarian, M.2
Bagdasarian, M.M.3
Timmis, K.N.4
-
19
-
-
64049099490
-
Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism
-
Fuhrer, T., and Sauer, U. (2009) Different biochemical mechanisms ensure network-wide balancing of reducing equivalents in microbial metabolism. J Bacteriol 191: 2112-2121.
-
(2009)
J Bacteriol
, vol.191
, pp. 2112-2121
-
-
Fuhrer, T.1
Sauer, U.2
-
20
-
-
84879506930
-
Transcriptional activation of the CrcZ and CrcY regulatory RNAs by the CbrB response regulator in Pseudomonas putida
-
García-Mauriño, S.M., Pérez-Martínez, I., Amador, C.I., Canosa, I., and Santero, E. (2013) Transcriptional activation of the CrcZ and CrcY regulatory RNAs by the CbrB response regulator in Pseudomonas putida. Mol Microbiol 89: 189-205.
-
(2013)
Mol Microbiol
, vol.89
, pp. 189-205
-
-
García-Mauriño, S.M.1
Pérez-Martínez, I.2
Amador, C.I.3
Canosa, I.4
Santero, E.5
-
21
-
-
47549110972
-
Carbon catabolite repression in bacteria: many ways to make the most out of nutrients
-
Görke, B., and Stülke, J. (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6: 613-624.
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 613-624
-
-
Görke, B.1
Stülke, J.2
-
22
-
-
84871936356
-
The translational repressor Crc controls the Pseudomonas putida benzoate and alkane catabolic pathways using a multi-tier regulation strategy
-
Hernández-Arranz, S., Moreno, R., and Rojo, F. (2013) The translational repressor Crc controls the Pseudomonas putida benzoate and alkane catabolic pathways using a multi-tier regulation strategy. Environ Microbiol 15: 227-241.
-
(2013)
Environ Microbiol
, vol.15
, pp. 227-241
-
-
Hernández-Arranz, S.1
Moreno, R.2
Rojo, F.3
-
23
-
-
0033967977
-
Crc is involved in catabolite repression control of the bkd operons of Pseudomonas putida and Pseudomonas aeruginosa
-
Hester, K.L., Lehman, J., Najar, F., Song, L., Roe, B.A., MacGregor, C.H., etal. (2000) Crc is involved in catabolite repression control of the bkd operons of Pseudomonas putida and Pseudomonas aeruginosa. J Bacteriol 182: 1144-1149.
-
(2000)
J Bacteriol
, vol.182
, pp. 1144-1149
-
-
Hester, K.L.1
Lehman, J.2
Najar, F.3
Song, L.4
Roe, B.A.5
MacGregor, C.H.6
-
24
-
-
0028204795
-
Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid
-
Holtel, A., Marqués, S., Möhler, I., Jakubzik, U., and Timmis, K.N. (1994) Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid. J Bacteriol 176: 1773-1776.
-
(1994)
J Bacteriol
, vol.176
, pp. 1773-1776
-
-
Holtel, A.1
Marqués, S.2
Möhler, I.3
Jakubzik, U.4
Timmis, K.N.5
-
25
-
-
84872093417
-
Analysis of omics data with genome-scale models of metabolism
-
Hyduke, D.R., Lewis, N.E., and Palsson, B.O. (2013) Analysis of omics data with genome-scale models of metabolism. Mol Biosyst 9: 167-174.
-
(2013)
Mol Biosyst
, vol.9
, pp. 167-174
-
-
Hyduke, D.R.1
Lewis, N.E.2
Palsson, B.O.3
-
26
-
-
84891631269
-
The Crc protein inhibits the production of polyhydroxyalkanoates in Pseudomonas putida under balanced carbon/nitrogen growth conditions
-
La Rosa, R., de la Peña, F., Prieto, M.A., and Rojo, F. (2014) The Crc protein inhibits the production of polyhydroxyalkanoates in Pseudomonas putida under balanced carbon/nitrogen growth conditions. Environ Microbiol 16: 278-290.
-
(2014)
Environ Microbiol
, vol.16
, pp. 278-290
-
-
La Rosa, R.1
de la Peña, F.2
Prieto, M.A.3
Rojo, F.4
-
27
-
-
77955141026
-
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
-
Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., etal. (2010) Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 6: 390.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 390
-
-
Lewis, N.E.1
Hixson, K.K.2
Conrad, T.M.3
Lerman, J.A.4
Charusanti, P.5
Polpitiya, A.D.6
-
28
-
-
84858439602
-
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
-
Lewis, N.E., Nagarajan, H., and Palsson, B.O. (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 10: 291-305.
-
(2012)
Nat Rev Microbiol
, vol.10
, pp. 291-305
-
-
Lewis, N.E.1
Nagarajan, H.2
Palsson, B.O.3
-
29
-
-
67650711615
-
SOAP2: an improved ultrafast tool for short read alignment
-
Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K., and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.W.4
Yiu, S.M.5
Kristiansen, K.6
Wang, J.7
-
30
-
-
78650070851
-
The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa
-
Linares, J.F., Moreno, R., Fajardo, A., Martínez-Solano, L., Escalante, R., Rojo, F., and Martínez, J.L. (2010) The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa. Environ Microbiol 12: 3196-3212.
-
(2010)
Environ Microbiol
, vol.12
, pp. 3196-3212
-
-
Linares, J.F.1
Moreno, R.2
Fajardo, A.3
Martínez-Solano, L.4
Escalante, R.5
Rojo, F.6
Martínez, J.L.7
-
31
-
-
33947503169
-
Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry
-
Luo, B., Groenke, K., Takors, R., Wandrey, C., and Oldiges, M. (2007) Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J Chromatogr A 1147: 153-164.
-
(2007)
J Chromatogr A
, vol.1147
, pp. 153-164
-
-
Luo, B.1
Groenke, K.2
Takors, R.3
Wandrey, C.4
Oldiges, M.5
-
32
-
-
0002862672
-
Catabolite repression control in Pseudomonas aeruginosa
-
In Galli, E., Silver, S., and Witholt, B. (eds). Washington, DC, USA: American Society for Microbiology.
-
MacGregor, C.H., Wolff, J.A., Arora, S.K., Hylemon, P.B., and Phibbs, P.V., Jr (1992) Catabolite repression control in Pseudomonas aeruginosa. In Pseudomonas, Molecular Biology and Biotechnology. Galli, E., Silver, S., and Witholt, B. (eds). Washington, DC, USA: American Society for Microbiology, pp. 198-206.
-
(1992)
Pseudomonas, Molecular Biology and Biotechnology
, pp. 198-206
-
-
MacGregor, C.H.1
Wolff, J.A.2
Arora, S.K.3
Hylemon, P.B.4
Phibbs Jr, P.V.5
-
33
-
-
84921890921
-
Transcriptional and translational control through the 5′-leader region of the dmpR master regulatory gene of phenol metabolism
-
Madhushani, A., Del Peso-Santos, T., Moreno, R., Rojo, F., and Shingler, V. (2015) Transcriptional and translational control through the 5′-leader region of the dmpR master regulatory gene of phenol metabolism. Environ Microbiol 17: 119-133.
-
(2015)
Environ Microbiol
, vol.17
, pp. 119-133
-
-
Madhushani, A.1
Del Peso-Santos, T.2
Moreno, R.3
Rojo, F.4
Shingler, V.5
-
34
-
-
33748313067
-
Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases
-
Morales, G., Ugidos, A., and Rojo, F. (2006) Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases. Environ Microbiol 8: 1764-1774.
-
(2006)
Environ Microbiol
, vol.8
, pp. 1764-1774
-
-
Morales, G.1
Ugidos, A.2
Rojo, F.3
-
35
-
-
39749101662
-
The target for the Pseudomonas putida Crc global regulator in the benzoate degradation pathway is the BenR transcriptional regulator
-
Moreno, R., and Rojo, F. (2008) The target for the Pseudomonas putida Crc global regulator in the benzoate degradation pathway is the BenR transcriptional regulator. J Bacteriol 190: 1539-1545.
-
(2008)
J Bacteriol
, vol.190
, pp. 1539-1545
-
-
Moreno, R.1
Rojo, F.2
-
36
-
-
34247509259
-
The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator
-
Moreno, R., Ruiz-Manzano, A., Yuste, L., and Rojo, F. (2007) The Pseudomonas putida Crc global regulator is an RNA binding protein that inhibits translation of the AlkS transcriptional regulator. Mol Microbiol 64: 665-675.
-
(2007)
Mol Microbiol
, vol.64
, pp. 665-675
-
-
Moreno, R.1
Ruiz-Manzano, A.2
Yuste, L.3
Rojo, F.4
-
37
-
-
67649201763
-
The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: evidence from proteomic and genomic analyses
-
Moreno, R., Martínez-Gomariz, M., Yuste, L., Gil, C., and Rojo, F. (2009a) The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: evidence from proteomic and genomic analyses. Proteomics 9: 2910-2928.
-
(2009)
Proteomics
, vol.9
, pp. 2910-2928
-
-
Moreno, R.1
Martínez-Gomariz, M.2
Yuste, L.3
Gil, C.4
Rojo, F.5
-
38
-
-
75649099354
-
The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation
-
Moreno, R., Marzi, S., Romby, P., and Rojo, F. (2009b) The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation. Nucleic Acids Res 37: 7678-7690.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 7678-7690
-
-
Moreno, R.1
Marzi, S.2
Romby, P.3
Rojo, F.4
-
39
-
-
84155165433
-
Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression
-
Moreno, R., Fonseca, P., and Rojo, F. (2012) Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression. Mol Microbiol 83: 24-40.
-
(2012)
Mol Microbiol
, vol.83
, pp. 24-40
-
-
Moreno, R.1
Fonseca, P.2
Rojo, F.3
-
40
-
-
84921841177
-
The Crc and Hfq proteins of Pseudomonas putida cooperate in catabolite repression and formation of ribonucleic acid complexes with specific target motifs
-
Moreno, R., Hernández-Arranz, S., La Rosa, R., Yuste, L., Madhushani, A., Shingler, V., and Rojo, F. (2015) The Crc and Hfq proteins of Pseudomonas putida cooperate in catabolite repression and formation of ribonucleic acid complexes with specific target motifs. Environ Microbiol 17: 105-118.
-
(2015)
Environ Microbiol
, vol.17
, pp. 105-118
-
-
Moreno, R.1
Hernández-Arranz, S.2
La Rosa, R.3
Yuste, L.4
Madhushani, A.5
Shingler, V.6
Rojo, F.7
-
41
-
-
0029874406
-
Carbon catabolite repression of phenol degradation in Pseudomonas putida is mediated by the inhibition of the activator protein PhlR
-
Müller, C., Petruschka, L., Cuypers, H., Burchhardt, G., and Herrmann, H. (1996) Carbon catabolite repression of phenol degradation in Pseudomonas putida is mediated by the inhibition of the activator protein PhlR. J Bacteriol 178: 2030-2036.
-
(1996)
J Bacteriol
, vol.178
, pp. 2030-2036
-
-
Müller, C.1
Petruschka, L.2
Cuypers, H.3
Burchhardt, G.4
Herrmann, H.5
-
42
-
-
84907584722
-
A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks
-
Nam, H., Campodonico, M., Bordbar, A., Hyduke, D.R., Kim, S., Zielinski, D.C., and Palsson, B.O. (2014) A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks. PLoS Comput Biol 10: e1003837.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003837
-
-
Nam, H.1
Campodonico, M.2
Bordbar, A.3
Hyduke, D.R.4
Kim, S.5
Zielinski, D.C.6
Palsson, B.O.7
-
43
-
-
54449092307
-
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
-
Nogales, J., Palsson, B.O., and Thiele, I. (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2: 79.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 79
-
-
Nogales, J.1
Palsson, B.O.2
Thiele, I.3
-
44
-
-
84880509445
-
An interactive server for analysing DNA microarrays experiments with replicates
-
FIESTA@BioinfoGP. [WWW document].
-
Oliveros, J.C. (2007). FIESTA@BioinfoGP. An interactive server for analysing DNA microarrays experiments with replicates. [WWW document]. URL http://www.bioinfogp.cnb.csic.es/tools/FIESTA.
-
(2007)
-
-
Oliveros, J.C.1
-
45
-
-
77749320898
-
What is flux balance analysis?
-
Orth, J.D., Thiele, I., and Palsson, B.O. (2010) What is flux balance analysis? Nat Biotechnol 28: 245-248.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 245-248
-
-
Orth, J.D.1
Thiele, I.2
Palsson, B.O.3
-
46
-
-
1242283921
-
Use of genome-scale microbial models for metabolic engineering
-
Patil, K.R., Akesson, M., and Nielsen, J. (2004) Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol 15: 64-69.
-
(2004)
Curr Opin Biotechnol
, vol.15
, pp. 64-69
-
-
Patil, K.R.1
Akesson, M.2
Nielsen, J.3
-
47
-
-
77955132055
-
Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment
-
Rojo, F. (2010) Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 34: 658-684.
-
(2010)
FEMS Microbiol Rev
, vol.34
, pp. 658-684
-
-
Rojo, F.1
-
48
-
-
84895986259
-
Recent advances in the reconstruction of metabolic models and integration of omics data
-
Saha, R., Chowdhury, A., and Maranas, C.D. (2014) Recent advances in the reconstruction of metabolic models and integration of omics data. Curr Opin Biotechnol 29C: 39-45.
-
(2014)
Curr Opin Biotechnol
, vol.29C
, pp. 39-45
-
-
Saha, R.1
Chowdhury, A.2
Maranas, C.D.3
-
50
-
-
65549092780
-
Use of randomized sampling for analysis of metabolic networks
-
Schellenberger, J., and Palsson, B.O. (2009) Use of randomized sampling for analysis of metabolic networks. J Biol Chem 284: 5457-5461.
-
(2009)
J Biol Chem
, vol.284
, pp. 5457-5461
-
-
Schellenberger, J.1
Palsson, B.O.2
-
51
-
-
79551662521
-
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
-
Schellenberger, J., Que, R., Fleming, R.M., Thiele, I., Orth, J.D., Feist, A.M., etal. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6: 1290-1307.
-
(2011)
Nat Protoc
, vol.6
, pp. 1290-1307
-
-
Schellenberger, J.1
Que, R.2
Fleming, R.M.3
Thiele, I.4
Orth, J.D.5
Feist, A.M.6
-
52
-
-
0028102772
-
Aerobic catabolism of phenylacetic acid in Pseudomonas putida U: biochemical characterization of a specific phenylacetic acid transport system and formal demonstration that phenylacetyl-coenzyme A is a catabolic intermediate
-
Schleissner, C., Olivera, E.R., Fernandez-Valverde, M., and Luengo, J.M. (1994) Aerobic catabolism of phenylacetic acid in Pseudomonas putida U: biochemical characterization of a specific phenylacetic acid transport system and formal demonstration that phenylacetyl-coenzyme A is a catabolic intermediate. J Bacteriol 176: 7667-7676.
-
(1994)
J Bacteriol
, vol.176
, pp. 7667-7676
-
-
Schleissner, C.1
Olivera, E.R.2
Fernandez-Valverde, M.3
Luengo, J.M.4
-
53
-
-
84887773125
-
The Pseudomonas putida HskA hybrid sensor kinase responds to redox signals and contributes to the adaptation of the electron transport chain composition in response to oxygen availability
-
Sevilla, E., Alvarez-Ortega, C., Krell, T., and Rojo, F. (2013) The Pseudomonas putida HskA hybrid sensor kinase responds to redox signals and contributes to the adaptation of the electron transport chain composition in response to oxygen availability. Environ Microbiol Rep 5: 825-834.
-
(2013)
Environ Microbiol Rep
, vol.5
, pp. 825-834
-
-
Sevilla, E.1
Alvarez-Ortega, C.2
Krell, T.3
Rojo, F.4
-
54
-
-
84903465076
-
Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression
-
Sonnleitner, E., and Blasi, U. (2014) Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression. PLoS Genet 10: e1004440.
-
(2014)
PLoS Genet
, vol.10
, pp. e1004440
-
-
Sonnleitner, E.1
Blasi, U.2
-
55
-
-
76049120271
-
Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa
-
Sonnleitner, E., Abdou, L., and Haas, D. (2009) Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa. Proc Natl Acad Sci USA 106: 21866-21871.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 21866-21871
-
-
Sonnleitner, E.1
Abdou, L.2
Haas, D.3
-
56
-
-
84868107469
-
Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa
-
Sonnleitner, E., Valentini, M., Wenner, N., Haichar, F.Z., Haas, D., and Lapouge, K. (2012) Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa. PLoS ONE 7: e44637.
-
(2012)
PLoS ONE
, vol.7
, pp. e44637
-
-
Sonnleitner, E.1
Valentini, M.2
Wenner, N.3
Haichar, F.Z.4
Haas, D.5
Lapouge, K.6
-
57
-
-
84905913777
-
The functional structure of central carbon metabolism in Pseudomonas putida KT2440
-
Sudarsan, S., Dethlefsen, S., Blank, L.M., Siemann-Herzberg, M., and Schmid, A. (2014) The functional structure of central carbon metabolism in Pseudomonas putida KT2440. Appl Environ Microbiol 80: 5292-5303.
-
(2014)
Appl Environ Microbiol
, vol.80
, pp. 5292-5303
-
-
Sudarsan, S.1
Dethlefsen, S.2
Blank, L.M.3
Siemann-Herzberg, M.4
Schmid, A.5
-
58
-
-
84875634162
-
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
-
Thorvaldsdottir, H., Robinson, J.T., and Mesirov, J.P. (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178-192.
-
(2013)
Brief Bioinform
, vol.14
, pp. 178-192
-
-
Thorvaldsdottir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
59
-
-
84878635781
-
Catabolite repression in Pseudomonas aeruginosa PAO1 regulates the uptake of C4 -dicarboxylates depending on succinate concentration
-
Valentini, M., and Lapouge, K. (2013) Catabolite repression in Pseudomonas aeruginosa PAO1 regulates the uptake of C4 -dicarboxylates depending on succinate concentration. Environ Microbiol 15: 1707-1716.
-
(2013)
Environ Microbiol
, vol.15
, pp. 1707-1716
-
-
Valentini, M.1
Lapouge, K.2
-
60
-
-
80052337933
-
Identification of C(4)-dicarboxylate transport systems in Pseudomonas aeruginosa PAO1
-
Valentini, M., Storelli, N., and Lapouge, K. (2011) Identification of C(4)-dicarboxylate transport systems in Pseudomonas aeruginosa PAO1. J Bacteriol 193: 4307-4316.
-
(2011)
J Bacteriol
, vol.193
, pp. 4307-4316
-
-
Valentini, M.1
Storelli, N.2
Lapouge, K.3
-
61
-
-
84930335225
-
Hierarchical management of carbon sources is regulated similarly by the CbrA/B systems in Pseudomonas aeruginosa and Pseudomonas putida
-
Valentini, M., García-Mauriño, S.M., Pérez-Martínez, I., Santero, E., Canosa, I., and Lapouge, K. (2014) Hierarchical management of carbon sources is regulated similarly by the CbrA/B systems in Pseudomonas aeruginosa and Pseudomonas putida. Microbiology 160: 2243-2252.
-
(2014)
Microbiology
, vol.160
, pp. 2243-2252
-
-
Valentini, M.1
García-Mauriño, S.M.2
Pérez-Martínez, I.3
Santero, E.4
Canosa, I.5
Lapouge, K.6
-
62
-
-
0029635981
-
Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism
-
Varma, A., and Palsson, B.O. (1995) Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism. Biotechnol Bioeng 45: 69-79.
-
(1995)
Biotechnol Bioeng
, vol.45
, pp. 69-79
-
-
Varma, A.1
Palsson, B.O.2
-
63
-
-
10044274277
-
Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma54 Pu promoter of Pseudomonas putida
-
Velázquez, F., di Bartolo, I., and de Lorenzo, V. (2004) Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma54 Pu promoter of Pseudomonas putida. J Bacteriol 186: 8267-8275.
-
(2004)
J Bacteriol
, vol.186
, pp. 8267-8275
-
-
Velázquez, F.1
di Bartolo, I.2
de Lorenzo, V.3
-
64
-
-
84863246260
-
Rewiring carbon catabolite repression for microbial cell factory
-
Vinuselvi, P., Kim, M.K., Lee, S.K., and Ghim, C.M. (2012) Rewiring carbon catabolite repression for microbial cell factory. BMB reports 45: 59-70.
-
(2012)
BMB reports
, vol.45
, pp. 59-70
-
-
Vinuselvi, P.1
Kim, M.K.2
Lee, S.K.3
Ghim, C.M.4
-
65
-
-
78651267246
-
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
-
Winsor, G.L., Lam, D.K., Fleming, L., Lo, R., Whiteside, M.D., Yu, N.Y., etal. (2011) Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 39: D596-D600.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D596-D600
-
-
Winsor, G.L.1
Lam, D.K.2
Fleming, L.3
Lo, R.4
Whiteside, M.D.5
Yu, N.Y.6
-
66
-
-
0035682220
-
Role of the crc gene in catabolic repression of the Pseudomonas putida GPo1 alkane degradation pathway
-
Yuste, L., and Rojo, F. (2001) Role of the crc gene in catabolic repression of the Pseudomonas putida GPo1 alkane degradation pathway. J Bacteriol 183: 6197-6206.
-
(2001)
J Bacteriol
, vol.183
, pp. 6197-6206
-
-
Yuste, L.1
Rojo, F.2
-
67
-
-
0031691310
-
Carbon-source-dependent expression of the PalkB promoter from the Pseudomonas oleovorans alkane degradation pathway
-
Yuste, L., Canosa, I., and Rojo, F. (1998) Carbon-source-dependent expression of the PalkB promoter from the Pseudomonas oleovorans alkane degradation pathway. J Bacteriol 180: 5218-5226.
-
(1998)
J Bacteriol
, vol.180
, pp. 5218-5226
-
-
Yuste, L.1
Canosa, I.2
Rojo, F.3
|