-
1
-
-
0037686112
-
The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster
-
Albert, R., and Othmer, H.G. (2003) The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J Theor Biol 223: 1-18.
-
(2003)
J Theor Biol
, vol.223
, pp. 1-18
-
-
Albert, R.1
Othmer, H.G.2
-
2
-
-
34249079154
-
Network motifs: theory and experimental approaches
-
Alon, U. (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
3
-
-
0035910120
-
Transcription analysis of rpoH in Pseudomonas putida
-
Aramaki, H., Hirata, T., Hara, C., Fujita, M., and Sagara, Y. (2001) Transcription analysis of rpoH in Pseudomonas putida. FEMS Microbiol Lett 205: 165-169.
-
(2001)
FEMS Microbiol Lett
, vol.205
, pp. 165-169
-
-
Aramaki, H.1
Hirata, T.2
Hara, C.3
Fujita, M.4
Sagara, Y.5
-
4
-
-
23744431554
-
Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0
-
Aranda-Olmedo, I., Ramos, J.L., and Marques, S. (2005) Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0. Appl Environ Microbiol 71: 4191-4198.
-
(2005)
Appl Environ Microbiol
, vol.71
, pp. 4191-4198
-
-
Aranda-Olmedo, I.1
Ramos, J.L.2
Marques, S.3
-
5
-
-
33751007565
-
Role of the ptsN gene product in catabolite repression of the Pseudomonas putida TOL toluene degradation pathway in chemostat cultures
-
Aranda-Olmedo, I., Marin, P., Ramos, J.L., and Marques, 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
Marin, P.2
Ramos, J.L.3
Marques, S.4
-
6
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M., and Teichmann, S.A. (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14: 283-291.
-
(2004)
Curr Opin Struct Biol
, vol.14
, pp. 283-291
-
-
Babu, M.M.1
Luscombe, N.M.2
Aravind, L.3
Gerstein, M.4
Teichmann, S.A.5
-
7
-
-
0038483826
-
Emergence of scaling in random networks
-
Barabasi, A.L., and Albert, R. (1999) Emergence of scaling in random networks. Science 286: 509-512.
-
(1999)
Science
, vol.286
, pp. 509-512
-
-
Barabasi, A.L.1
Albert, R.2
-
9
-
-
46249112705
-
Boolean network models of cellular regulation: prospects and limitations
-
Bornholdt, S. (2008) Boolean network models of cellular regulation: prospects and limitations. J R Soc Interface 5 (Suppl. 1): S85-S94.
-
(2008)
J R Soc Interface
, vol.5
, Issue.SUPPL. 1
-
-
Bornholdt, S.1
-
10
-
-
13444302680
-
Promoters in the environment: transcriptional regulation in its natural context
-
Cases, I., and de Lorenzo, V. (2005) Promoters in the environment: transcriptional regulation in its natural context. Nat Rev Microbiol 3: 105-118.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 105-118
-
-
Cases, I.1
de Lorenzo, V.2
-
12
-
-
45849093636
-
Boolean network model predicts cell cycle sequence of fission yeast
-
Davidich, M.I., and Bornholdt, S. (2008) Boolean network model predicts cell cycle sequence of fission yeast. PLoS ONE 3: e1672.
-
(2008)
PLoS ONE
, vol.3
-
-
Davidich, M.I.1
Bornholdt, S.2
-
13
-
-
84855280819
-
Information routing driven by background chatter in a signaling network
-
Domedel-Puig, N., Rue, P., Pons, A.J., and Garcia-Ojalvo, J. (2011) Information routing driven by background chatter in a signaling network. PLoS Comput Biol 7: e1002297.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Domedel-Puig, N.1
Rue, P.2
Pons, A.J.3
Garcia-Ojalvo, J.4
-
15
-
-
79960906495
-
A SAT-based algorithm for finding attractors in synchronous Boolean networks
-
Dubrova, E., and Teslenko, M. (2011) A SAT-based algorithm for finding attractors in synchronous Boolean networks. IEEE/ACM Trans Comput Biol Bioinform 8: 1393-1399.
-
(2011)
IEEE/ACM Trans Comput Biol Bioinform
, vol.8
, pp. 1393-1399
-
-
Dubrova, E.1
Teslenko, M.2
-
16
-
-
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., Marques, 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
de Marques, S.2
Jong, C.3
van Ramos, J.L.4
Andel, J.G.5
-
17
-
-
0034821240
-
Monitoring intracellular levels of XylR in Pseudomonas putida with a single-chain antibody specific for aromatic-responsive enhancer-binding proteins
-
Fraile, S., Roncal, F., Fernandez, L.A., and de Lorenzo, V. (2001) Monitoring intracellular levels of XylR in Pseudomonas putida with a single-chain antibody specific for aromatic-responsive enhancer-binding proteins. J Bacteriol 183: 5571-5579.
-
(2001)
J Bacteriol
, vol.183
, pp. 5571-5579
-
-
Fraile, S.1
Roncal, F.2
de Fernandez, L.A.3
Lorenzo, V.4
-
18
-
-
79953314476
-
Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440
-
Frank, S., Schmidt, F., Klockgether, J., Davenport, C.F., Gesell Salazar, M., Volker, U., and Tummler, B. (2011) Functional genomics of the initial phase of cold adaptation of Pseudomonas putida KT2440. FEMS Microbiol Lett 318: 47-54.
-
(2011)
FEMS Microbiol Lett
, vol.318
, pp. 47-54
-
-
Frank, S.1
Schmidt, F.2
Klockgether, J.3
Davenport, C.F.4
Gesell Salazar, M.5
Volker, U.6
Tummler, B.7
-
19
-
-
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 Natl Acad Sci USA 78: 7458-7462.
-
(1981)
Proc Natl Acad Sci USA
, vol.78
, pp. 7458-7462
-
-
Franklin, F.C.1
Bagdasarian, M.2
Bagdasarian, M.M.3
Timmis, K.N.4
-
20
-
-
22744432208
-
Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria
-
Friedman, N., Vardi, S., Ronen, M., Alon, U., and Stavans, J. (2005) Precise temporal modulation in the response of the SOS DNA repair network in individual bacteria. PLoS Biol 3: e238.
-
(2005)
PLoS Biol
, vol.3
-
-
Friedman, N.1
Vardi, S.2
Ronen, M.3
Alon, U.4
Stavans, J.5
-
21
-
-
0029658258
-
S-dependent Pm promoter of the TOL plasmid is the minimum DNA segment required for transcription stimulation by XylS regulators
-
S-dependent Pm promoter of the TOL plasmid is the minimum DNA segment required for transcription stimulation by XylS regulators. J Bacteriol 178: 6427-6434.
-
(1996)
J Bacteriol
, vol.178
, pp. 6427-6434
-
-
Gallegos, M.T.1
Marques, S.2
Ramos, J.L.3
-
22
-
-
71149099313
-
The incoherent feedforward loop can provide fold-change detection in gene regulation
-
Goentoro, L., Shoval, O., Kirschner, M.W., and Alon, U. (2009) The incoherent feedforward loop can provide fold-change detection in gene regulation. Mol Cell 36: 894-899.
-
(2009)
Mol Cell
, vol.36
, pp. 894-899
-
-
Goentoro, L.1
Shoval, O.2
Kirschner, M.W.3
Alon, U.4
-
23
-
-
1542286907
-
Cellular XylS levels are a function of transcription of xylS from two independent promoters and the differential efficiency of translation of the two mRNAs
-
Gonzalez-Perez, M.M., Ramos, J.L., and Marques, S. (2004) Cellular XylS levels are a function of transcription of xylS from two independent promoters and the differential efficiency of translation of the two mRNAs. J Bacteriol 186: 1898-1901.
-
(2004)
J Bacteriol
, vol.186
, pp. 1898-1901
-
-
Gonzalez-Perez, M.M.1
Ramos, J.L.2
Marques, S.3
-
24
-
-
41149165188
-
Emergent decision-making in biological signal transduction networks
-
Helikar, T., Konvalina, J., Heidel, J., and Rogers, J.A. (2008) Emergent decision-making in biological signal transduction networks. Proc Natl Acad Sci USA 105: 1913-1918.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 1913-1918
-
-
Helikar, T.1
Konvalina, J.2
Heidel, J.3
Rogers, J.A.4
-
25
-
-
33846002036
-
Transcriptional regulation by competing transcription factor modules
-
Hermsen, R., Tans, S., and Wolde, P.R. (2006) Transcriptional regulation by competing transcription factor modules. PLoS Comput Biol 2: e164.
-
(2006)
PLoS Comput Biol
, vol.2
-
-
Hermsen, R.1
Tans, S.2
Wolde, P.R.3
-
26
-
-
0028204795
-
Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid
-
Holtel, A., Marques, S., Mohler, 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
Marques, S.2
Mohler, I.3
Jakubzik, U.4
Timmis, K.N.5
-
27
-
-
0020520053
-
Molecular cloning of regulatory gene xylR and operator-promoter regions of the xylABC and xylDEGF operons of the TOL plasmid
-
Inouye, S., Nakazawa, A., and Nakazawa, T. (1983) Molecular cloning of regulatory gene xylR and operator-promoter regions of the xylABC and xylDEGF operons of the TOL plasmid. J Bacteriol 155: 1192-1199.
-
(1983)
J Bacteriol
, vol.155
, pp. 1192-1199
-
-
Inouye, S.1
Nakazawa, A.2
Nakazawa, T.3
-
28
-
-
0023394536
-
Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product
-
Inouye, S., Nakazawa, A., and Nakazawa, T. (1987) Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product. Proc Natl Acad Sci USA 84: 5182-5186.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 5182-5186
-
-
Inouye, S.1
Nakazawa, A.2
Nakazawa, T.3
-
29
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: a literature review
-
de Jong, H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9: 67-103.
-
(2002)
J Comput Biol
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
30
-
-
33746428728
-
A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli
-
Kalir, S., Mangan, S., and Alon, U. (2005) A coherent feed-forward loop with a SUM input function prolongs flagella expression in Escherichia coli. Mol Syst Biol 1: 2005-0006.
-
(2005)
Mol Syst Biol
, vol.1
, pp. 2005-0006
-
-
Kalir, S.1
Mangan, S.2
Alon, U.3
-
31
-
-
47349095809
-
The incoherent feed-forward loop can generate non-monotonic input functions for genes
-
Kaplan, S., Bren, A., Dekel, E., and Alon, U. (2008) The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol 4: 203.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 203
-
-
Kaplan, S.1
Bren, A.2
Dekel, E.3
Alon, U.4
-
32
-
-
52649087274
-
Modelling and analysis of gene regulatory networks
-
Karlebach, G., and Shamir, R. (2008) Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol 9: 770-780.
-
(2008)
Nat Rev Mol Cell Biol
, vol.9
, pp. 770-780
-
-
Karlebach, G.1
Shamir, R.2
-
34
-
-
0028126485
-
The organization of the Pm promoter of the TOL plasmid reflects the structure of its cognate activator protein XylS
-
Kessler, B., Timmis, K.N., and de Lorenzo, V. (1994a) The organization of the Pm promoter of the TOL plasmid reflects the structure of its cognate activator protein XylS. Mol Gen Genet 244: 596-605.
-
(1994)
Mol Gen Genet
, vol.244
, pp. 596-605
-
-
Kessler, B.1
de Timmis, K.N.2
Lorenzo, V.3
-
35
-
-
0028238964
-
Genetic evidence that the XylS regulator of the Pseudomonas TOL meta operon controls the Pm promoter through weak DNA-protein interactions
-
Kessler, B., Herrero, M., Timmis, K.N., and de Lorenzo, V. (1994b) Genetic evidence that the XylS regulator of the Pseudomonas TOL meta operon controls the Pm promoter through weak DNA-protein interactions. J Bacteriol 176: 3171-3176.
-
(1994)
J Bacteriol
, vol.176
, pp. 3171-3176
-
-
Kessler, B.1
Herrero, M.2
de Timmis, K.N.3
Lorenzo, V.4
-
36
-
-
7644238181
-
Biological robustness
-
Kitano, H. (2004) Biological robustness. Nat Rev Genet 5: 826-837.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 826-837
-
-
Kitano, H.1
-
37
-
-
77957967615
-
The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid
-
Koutinas, M., Lam, M.C., Kiparissides, A., Silva-Rocha, R., Godinho, M., Livingston, A.G., etal. (2010) The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. Environ Microbiol 12: 1705-1718.
-
(2010)
Environ Microbiol
, vol.12
, pp. 1705-1718
-
-
Koutinas, M.1
Lam, M.C.2
Kiparissides, A.3
Silva-Rocha, R.4
Godinho, M.5
Livingston, A.G.6
-
38
-
-
79958723410
-
Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach
-
Koutinas, M., Kiparissides, A., Silva-Rocha, R., Lam, M.C., Martins dos Santos, V.A., de Lorenzo, V., etal. (2011) Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach. Metab Eng 13: 401-413.
-
(2011)
Metab Eng
, vol.13
, pp. 401-413
-
-
Koutinas, M.1
Kiparissides, A.2
Silva-Rocha, R.3
Lam, M.C.4
de Martins dos Santos, V.A.5
Lorenzo, V.6
-
39
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., etal. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
-
40
-
-
1842687878
-
The yeast cell-cycle network is robustly designed
-
Li, F., Long, T., Lu, Y., Ouyang, Q., and Tang, C. (2004) The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA 101: 4781-4786.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 4781-4786
-
-
Li, F.1
Long, T.2
Lu, Y.3
Ouyang, Q.4
Tang, C.5
-
42
-
-
33746207758
-
Bacterial regulatory networks are extremely flexible in evolution
-
Lozada-Chavez, I., Janga, S.C., and Collado-Vides, J. (2006) Bacterial regulatory networks are extremely flexible in evolution. Nucleic Acids Res 34: 3434-3445.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3434-3445
-
-
Lozada-Chavez, I.1
Janga, S.C.2
Collado-Vides, J.3
-
43
-
-
0142027814
-
Structure and function of the feed-forward loop network motif
-
Mangan, S., and Alon, U. (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 100: 11980-11985.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
44
-
-
0242364231
-
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks
-
Mangan, S., Zaslaver, A., and Alon, U. (2003) The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol 334: 197-204.
-
(2003)
J Mol Biol
, vol.334
, pp. 197-204
-
-
Mangan, S.1
Zaslaver, A.2
Alon, U.3
-
45
-
-
32044462728
-
The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli
-
Mangan, S., Itzkovitz, S., Zaslaver, A., and Alon, U. (2006) The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 356: 1073-1081.
-
(2006)
J Mol Biol
, vol.356
, pp. 1073-1081
-
-
Mangan, S.1
Itzkovitz, S.2
Zaslaver, A.3
Alon, U.4
-
46
-
-
0029174957
-
Role of sigma S in transcription from the positively controlled Pm promoter of the TOL plasmid of Pseudomonas putida
-
Marques, S., Gallegos, M.T., and Ramos, J.L. (1995) Role of sigma S in transcription from the positively controlled Pm promoter of the TOL plasmid of Pseudomonas putida. Mol Microbiol 18: 851-857.
-
(1995)
Mol Microbiol
, vol.18
, pp. 851-857
-
-
Marques, S.1
Gallegos, M.T.2
Ramos, J.L.3
-
47
-
-
0032469908
-
Activation and repression of transcription at the double tandem divergent promoters for the xylR and xylS genes of the TOL plasmid of Pseudomonas putida
-
Marques, S., Gallegos, M.T., Manzanera, M., Holtel, A., Timmis, K.N., and Ramos, J.L. (1998) Activation and repression of transcription at the double tandem divergent promoters for the xylR and xylS genes of the TOL plasmid of Pseudomonas putida. J Bacteriol 180: 2889-2894.
-
(1998)
J Bacteriol
, vol.180
, pp. 2889-2894
-
-
Marques, S.1
Gallegos, M.T.2
Manzanera, M.3
Holtel, A.4
Timmis, K.N.5
Ramos, J.L.6
-
49
-
-
0242386460
-
Identifying global regulators in transcriptional regulatory networks in bacteria
-
Martinez-Antonio, A., and Collado-Vides, J. (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 6: 482-489.
-
(2003)
Curr Opin Microbiol
, vol.6
, pp. 482-489
-
-
Martinez-Antonio, A.1
Collado-Vides, J.2
-
50
-
-
77958519731
-
High stability and fast recovery of expression of the TOL plasmid-carried toluene catabolism genes of Pseudomonas putida mt-2 under conditions of oxygen limitation and oscillation
-
Martinez-Lavanchy, P.M., Muller, C., Nijenhuis, I., Kappelmeyer, U., Buffing, M., McPherson, K., and Heipieper, H.J. (2010) High stability and fast recovery of expression of the TOL plasmid-carried toluene catabolism genes of Pseudomonas putida mt-2 under conditions of oxygen limitation and oscillation. Appl Environ Microbiol 76: 6715-6723.
-
(2010)
Appl Environ Microbiol
, vol.76
, pp. 6715-6723
-
-
Martinez-Lavanchy, P.M.1
Muller, C.2
Nijenhuis, I.3
Kappelmeyer, U.4
Buffing, M.5
McPherson, K.6
Heipieper, H.J.7
-
51
-
-
33646346114
-
A method for the generation of standardized qualitative dynamical systems of regulatory networks
-
Mendoza, L., and Xenarios, I. (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor Biol Med Model 3: 13.
-
(2006)
Theor Biol Med Model
, vol.3
, pp. 13
-
-
Mendoza, L.1
Xenarios, I.2
-
52
-
-
0023190414
-
The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon
-
Mermod, N., Ramos, J.L., Bairoch, A., and Timmis, K.N. (1987) The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon. Mol Gen Genet 207: 349-354.
-
(1987)
Mol Gen Genet
, vol.207
, pp. 349-354
-
-
Mermod, N.1
Ramos, J.L.2
Bairoch, A.3
Timmis, K.N.4
-
53
-
-
0037174670
-
Network motifs: simple building blocks of complex networks
-
Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D., and Alon, U. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chklovskii, D.5
Alon, U.6
-
54
-
-
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. (2009) 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
-
55
-
-
77955289214
-
The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes
-
Moreno, R., Fonseca, P., and Rojo, F. (2010) The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes. J Biol Chem 285: 24412-24419.
-
(2010)
J Biol Chem
, vol.285
, pp. 24412-24419
-
-
Moreno, R.1
Fonseca, P.2
Rojo, F.3
-
56
-
-
77952851181
-
BoolNet - an R package for generation, reconstruction and analysis of Boolean networks
-
Mussel, C., Hopfensitz, M., and Kestler, H.A. (2010) BoolNet - an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 26: 1378-1380.
-
(2010)
Bioinformatics
, vol.26
, pp. 1378-1380
-
-
Mussel, C.1
Hopfensitz, M.2
Kestler, H.A.3
-
57
-
-
0028980296
-
54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR
-
54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR. J Bacteriol 177: 3758-3763.
-
(1995)
J Bacteriol
, vol.177
, pp. 3758-3763
-
-
Perez-Martin, J.1
de Lorenzo, V.2
-
58
-
-
34547117885
-
Growth-dependent phosphorylation of the PtsN (EIINtr) protein of Pseudomonas putida
-
Pfluger, K., and de Lorenzo, V. (2007) Growth-dependent phosphorylation of the PtsN (EIINtr) protein of Pseudomonas putida. J Biol Chem 282: 18206-18211.
-
(2007)
J Biol Chem
, vol.282
, pp. 18206-18211
-
-
Pfluger, K.1
de Lorenzo, V.2
-
59
-
-
0030860391
-
Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators
-
Ramos, J.L., Marques, S., and Timmis, K.N. (1997) Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 51: 341-373.
-
(1997)
Annu Rev Microbiol
, vol.51
, pp. 341-373
-
-
Ramos, J.L.1
Marques, S.2
Timmis, K.N.3
-
60
-
-
0031780471
-
Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440
-
Ramos-Gonzalez, M.I., and Molin, S. (1998) Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440. J Bacteriol 180: 3421-3431.
-
(1998)
J Bacteriol
, vol.180
, pp. 3421-3431
-
-
Ramos-Gonzalez, M.I.1
Molin, S.2
-
61
-
-
1542319979
-
Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures
-
Rescalli, E., Saini, S., Bartocci, C., Rychlewski, L., de Lorenzo, V., and Bertoni, G. (2004) Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures. J Biol Chem 279: 7777-7784.
-
(2004)
J Biol Chem
, vol.279
, pp. 7777-7784
-
-
Rescalli, E.1
Saini, S.2
Bartocci, C.3
de Rychlewski, L.4
Lorenzo, V.5
Bertoni, G.6
-
62
-
-
0036678794
-
Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics
-
Ronen, M., Rosenberg, R., Shraiman, B.I., and Alon, U. (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA 99: 10555-10560.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 10555-10560
-
-
Ronen, M.1
Rosenberg, R.2
Shraiman, B.I.3
Alon, U.4
-
63
-
-
18944369815
-
Levels and activity of the Pseudomonas putida global regulatory protein Crc vary according to growth conditions
-
Ruiz-Manzano, A., Yuste, L., and Rojo, F. (2005) Levels and activity of the Pseudomonas putida global regulatory protein Crc vary according to growth conditions. J Bacteriol 187: 3678-3686.
-
(2005)
J Bacteriol
, vol.187
, pp. 3678-3686
-
-
Ruiz-Manzano, A.1
Yuste, L.2
Rojo, F.3
-
64
-
-
74549172058
-
ON/OFF and beyond - a boolean model of apoptosis
-
Schlatter, R., Schmich, K., Avalos Vizcarra, I., Scheurich, P., Sauter, T., Borner, C., etal. (2009) ON/OFF and beyond - a boolean model of apoptosis. PLoS Comput Biol 5: e1000595.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Schlatter, R.1
Schmich, K.2
Avalos Vizcarra, I.3
Scheurich, P.4
Sauter, T.5
Borner, C.6
-
65
-
-
77957766590
-
SnapShot: network motifs
-
Shoval, O., and Alon, U. (2010) SnapShot: network motifs. Cell 143: 326-e321.
-
(2010)
Cell
, vol.143
-
-
Shoval, O.1
Alon, U.2
-
66
-
-
41149090591
-
Mining logic gates in prokaryotic transcriptional regulation networks
-
Silva-Rocha, R., and de Lorenzo, V. (2008) Mining logic gates in prokaryotic transcriptional regulation networks. FEBS Lett 582: 1237-1244.
-
(2008)
FEBS Lett
, vol.582
, pp. 1237-1244
-
-
Silva-Rocha, R.1
de Lorenzo, V.2
-
67
-
-
80054033830
-
A composite feed-forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations
-
Silva-Rocha, R., and de Lorenzo, V. (2011) A composite feed-forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations. Mol Biosyst 7: 2982-2990.
-
(2011)
Mol Biosyst
, vol.7
, pp. 2982-2990
-
-
Silva-Rocha, R.1
de Lorenzo, V.2
-
68
-
-
84867080098
-
Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene
-
Silva-Rocha, R., and de Lorenzo, V. (2012a) Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene. Mol Microbiol 86: 199-211.
-
(2012)
Mol Microbiol
, vol.86
, pp. 199-211
-
-
Silva-Rocha, R.1
de Lorenzo, V.2
-
69
-
-
84859517094
-
A GFP-lacZ bicistronic reporter system for promoter analysis inenvironmental gram-negative bacteria
-
Silva-Rocha, R., and de Lorenzo, V. (2012b) A GFP-lacZ bicistronic reporter system for promoter analysis inenvironmental gram-negative bacteria. PLoS ONE 7: e34675.
-
(2012)
PLoS ONE
, vol.7
-
-
Silva-Rocha, R.1
de Lorenzo, V.2
-
70
-
-
80052612366
-
The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms
-
Silva-Rocha, R., Tamames, J., dos Santos, V.M., and de Lorenzo, V. (2011a) The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol 13: 2389-2402.
-
(2011)
Environ Microbiol
, vol.13
, pp. 2389-2402
-
-
Silva-Rocha, R.1
Tamames, J.2
de dos Santos, V.M.3
Lorenzo, V.4
-
71
-
-
81055148316
-
The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene
-
Silva-Rocha, R., de Jong, H., Tamames, J., and de Lorenzo, V. (2011b) The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC Syst Biol 5: 191.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 191
-
-
Silva-Rocha, R.1
de Jong, H.2
de Tamames, J.3
Lorenzo, V.4
-
72
-
-
84871938834
-
The IHF regulon of exponentially growing Pseudomonas putida cells
-
doi:10.1111/j.1462-2920.2012.02750.x.
-
Silva-Rocha, R., Chavarria, M., Kleijn, R.J., Sauer, U., and de Lorenzo, V. (2012) The IHF regulon of exponentially growing Pseudomonas putida cells. Environ Microbiol. doi:10.1111/j.1462-2920.2012.02750.x.
-
(2012)
Environ Microbiol
-
-
Silva-Rocha, R.1
Chavarria, M.2
Kleijn, R.J.3
de Sauer, U.4
Lorenzo, V.5
-
73
-
-
0035902599
-
Intrinsic noise in gene regulatory networks
-
Thattai, M., and van Oudenaarden, A. (2001) Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci USA 98: 8614-8619.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 8614-8619
-
-
Thattai, M.1
van Oudenaarden, A.2
-
74
-
-
0037127286
-
54 Pu promoter reveals that integration host factor couples transcriptional activity to growth phase
-
54 Pu promoter reveals that integration host factor couples transcriptional activity to growth phase. J Biol Chem 277: 2169-2175.
-
(2002)
J Biol Chem
, vol.277
, pp. 2169-2175
-
-
Valls, M.1
de Buckle, M.2
Lorenzo, V.3
-
75
-
-
33644837639
-
The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes
-
Velazquez, F., de Lorenzo, V., and Valls, M. (2006) The m-xylene biodegradation capacity of Pseudomonas putida mt-2 is submitted to adaptation to abiotic stresses: evidence from expression profiling of xyl genes. Environ Microbiol 8: 591-602.
-
(2006)
Environ Microbiol
, vol.8
, pp. 591-602
-
-
Velazquez, F.1
de Lorenzo, V.2
Valls, M.3
-
77
-
-
0016197816
-
Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid
-
Williams, P.A., and Murray, K. (1974) Metabolism of benzoate and the methylbenzoates by Pseudomonas putida (arvilla) mt-2: evidence for the existence of a TOL plasmid. J Bacteriol 120: 416-423.
-
(1974)
J Bacteriol
, vol.120
, pp. 416-423
-
-
Williams, P.A.1
Murray, K.2
-
78
-
-
33749514099
-
Genomic analysis of the hierarchical structure of regulatory networks
-
Yu, H., and Gerstein, M. (2006) Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci USA 103: 14724-14731.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 14724-14731
-
-
Yu, H.1
Gerstein, M.2
|