-
1
-
-
4444293086
-
-
Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York
-
M. Ptashne Genetic Switch: Phage Lambda Revisited 2004 Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York The latest (third) edition of this classic book on gene regulation summarizes much recent progress towards a more quantitative understanding of the genetic control mechanisms that determine the life-style of phage λ.
-
(2004)
Genetic Switch: Phage Lambda Revisited
-
-
Ptashne, M.1
-
3
-
-
0035319006
-
Computational studies of gene regulation networks: In numero molecular biology
-
J. Hasty, D. McMillen, F. Isaacs, and J.J. Collins Computational studies of gene regulation networks: in numero molecular biology Nat Rev Genet 2 2002 268 279
-
(2002)
Nat Rev Genet
, vol.2
, pp. 268-279
-
-
Hasty, J.1
McMillen, D.2
Isaacs, F.3
Collins, J.J.4
-
4
-
-
1542380403
-
The evolution of genetic regulatory systems in bacteria
-
H.H. McAdams, B. Srinivasan, and A.P. Arkin The evolution of genetic regulatory systems in bacteria Nat Rev Genet 5 2004 169 178
-
(2004)
Nat Rev Genet
, vol.5
, pp. 169-178
-
-
McAdams, H.H.1
Srinivasan, B.2
Arkin, A.P.3
-
5
-
-
0036500609
-
A genomic regulatory network for development
-
E.H. Davidson, J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.H. Yuh, T. Minokawa, G. Amore, V. Hinman, and C. Arenas-Mena A genomic regulatory network for development Science 295 2002 1669 1678
-
(2002)
Science
, vol.295
, pp. 1669-1678
-
-
Davidson, E.H.1
Rast, J.P.2
Oliveri, P.3
Ransick, A.4
Calestani, C.5
Yuh, C.H.6
Minokawa, T.7
Amore, G.8
Hinman, V.9
Arenas-Mena, C.10
-
7
-
-
0032556443
-
On the relationship between genomic regulatory element organization and gene regulatory dynamics
-
D.M. Wolf, and F.H. Eeckman On the relationship between genomic regulatory element organization and gene regulatory dynamics J Theor Biol 195 1998 167 186
-
(1998)
J Theor Biol
, vol.195
, pp. 167-186
-
-
Wolf, D.M.1
Eeckman, F.H.2
-
8
-
-
1842591130
-
The regulation of bacterial transcription initiation
-
D.F. Browning, and S.J.W. Busby The regulation of bacterial transcription initiation Nat Rev Microbiol 2 2004 1 9 An excellent review of transcriptional regulation in bacteria, with special emphasis on the different mechanisms and cis-regulatory architectures involved in transcriptional activation, repression and co-dependence between two activators.
-
(2004)
Nat Rev Microbiol
, vol.2
, pp. 1-9
-
-
Browning, D.F.1
Busby, S.J.W.2
-
9
-
-
15744394192
-
Transcriptional regulation by the numbers: Models
-
Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R: Transcriptional regulation by the numbers: models. Curr Opin Genetics Dev 2005, 15:116-124. In the companion paper to this article we review thermodynamic models of gene regulation. These models provide an explicit framework to relate molecular information (e.g. protein-DNA binding energies, number of binding sites, cis-regulatory architechtures) to the effective thermodynamic description used in this paper.
-
(2005)
Curr Opin Genetics Dev
, vol.15
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Phillips, R.7
-
11
-
-
2942612846
-
Using a quantitative blueprint to reprogram the dynamics of the flagella gene network
-
S. Kalir, and U. Alon Using a quantitative blueprint to reprogram the dynamics of the flagella gene network Cell 117 2004 713 720
-
(2004)
Cell
, vol.117
, pp. 713-720
-
-
Kalir, S.1
Alon, U.2
-
12
-
-
0035150199
-
High-density microarray-mediated gene expression profiling of Escherichia coli
-
Y. Wei, J.M. Lee, C. Richmond, F.R. Blattner, J.A. Rafalski, and R.A. LaRossa High-density microarray-mediated gene expression profiling of Escherichia coli J Bacteriol 183 2001 545 556
-
(2001)
J Bacteriol
, vol.183
, pp. 545-556
-
-
Wei, Y.1
Lee, J.M.2
Richmond, C.3
Blattner, F.R.4
Rafalski, J.A.5
Larossa, R.A.6
-
13
-
-
0027225271
-
Transcription activation at class I CAP-dependent promoters
-
R.H. Ebright Transcription activation at class I CAP-dependent promoters Mol Microbiol 8 1992 797 802
-
(1992)
Mol Microbiol
, vol.8
, pp. 797-802
-
-
Ebright, R.H.1
-
15
-
-
0346728474
-
Design of gene circuits: Lessons from bacteria
-
M.E. Wall, W.S. Hlavacek, and M.A. Savageau Design of gene circuits: lessons from bacteria Nat Rev Genet 5 2004 34 42 A review of possible design principles of genetic circuits, including a summary of the pioneering work of Savageau [49] and Burns et al. [50].
-
(2004)
Nat Rev Genet
, vol.5
, pp. 34-42
-
-
Wall, M.E.1
Hlavacek, W.S.2
Savageau, M.A.3
-
16
-
-
0037126615
-
A simple mechanism for co-dependence on two activators at an Escherichia coli promoter
-
J.T. Wade, T.A. Belyaeva, E.I. Hyde, and S.J. Busby A simple mechanism for co-dependence on two activators at an Escherichia coli promoter EMBO J 20 2001 7160 7167
-
(2001)
EMBO J
, vol.20
, pp. 7160-7167
-
-
Wade, J.T.1
Belyaeva, T.A.2
Hyde, E.I.3
Busby, S.J.4
-
17
-
-
0037965981
-
On schemes of combinatorial transcription control
-
N.E. Buchler, U. Gerland, and T. Hwa On schemes of combinatorial transcription control Proc Natl Acad Sci USA 100 2003 5136 5141 A theoretical paper on transcriptional control that explores how far 'regulated recruitment' between regulatory factors in the cis-regulatory region can go towards integrating signals and generating complex combinatorial logic.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 5136-5141
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
18
-
-
0032488056
-
Imposing specificity by localization: Mechanism and evolvability
-
M. Ptashne, and A. Gann Imposing specificity by localization: mechanism and evolvability Curr Biol 8 1998 R897
-
(1998)
Curr Biol
, vol.8
, pp. 897
-
-
Ptashne, M.1
Gann, A.2
-
19
-
-
0027476456
-
Synergistic activation of transcription by E. coli cAMP receptor protein
-
J.K. Joung, L.U. Le, and A. Hochschild Synergistic activation of transcription by E. coli cAMP receptor protein Proc Natl Acad Sci USA 90 1993 3083 3087
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 3083-3087
-
-
Joung, J.K.1
Le L., U.2
Hochschild, A.3
-
20
-
-
0028094718
-
Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically
-
S. Busby, D. West, M. Lawes, C. Webster, A. Ishihama, and A. Kolb Transcription activation by the Escherichia coli cyclic AMP receptor protein. Receptors bound in tandem at promoters can interact synergistically J Mol Biol 241 1994 341 352
-
(1994)
J Mol Biol
, vol.241
, pp. 341-352
-
-
Busby, S.1
West, D.2
Lawes, M.3
Webster, C.4
Ishihama, A.5
Kolb, A.6
-
21
-
-
0028051844
-
Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein
-
J.K. Joung, D.M. Koepp, and A. Hochschild Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein Science 265 1994 1863 1866
-
(1994)
Science
, vol.265
, pp. 1863-1866
-
-
Joung, J.K.1
Koepp, D.M.2
Hochschild, A.3
-
22
-
-
0029609262
-
Transcriptional co-activation at the ansB promoters: Involvement of the activating regions of CRP and FNR when bound in tandem
-
S. Scott, S. Busby, and I. Beacham Transcriptional co-activation at the ansB promoters: involvement of the activating regions of CRP and FNR when bound in tandem Mol Microbiol 18 1995 521 531
-
(1995)
Mol Microbiol
, vol.18
, pp. 521-531
-
-
Scott, S.1
Busby, S.2
Beacham, I.3
-
23
-
-
0032502838
-
Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: Organisation of the RNA polymerase alpha subunits
-
T.A. Belyaeva, V.A. Rhodius, C.L. Webster, and S.J. Busby Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: organisation of the RNA polymerase alpha subunits J Mol Biol 277 1998 789 804
-
(1998)
J Mol Biol
, vol.277
, pp. 789-804
-
-
Belyaeva, T.A.1
Rhodius, V.A.2
Webster, C.L.3
Busby, S.J.4
-
24
-
-
0037161194
-
Architectural requirements for optimal activation by tandem CRP molecules at a Class I CRP-dependent promoter
-
J. Tebbutt, V. Rhodius, C. Webster, and S. Busby Architectural requirements for optimal activation by tandem CRP molecules at a Class I CRP-dependent promoter FEMS Microbiol Lett 210 2002 55 60
-
(2002)
FEMS Microbiol Lett
, vol.210
, pp. 55-60
-
-
Tebbutt, J.1
Rhodius, V.2
Webster, C.3
Busby, S.4
-
25
-
-
0042890424
-
CRP-dependent activation of the E. coli acsP2 promoter by a synergistic Class III mechanism
-
C. Beatty, D. Browning, S. Busby, and A. Wolfe CRP-dependent activation of the E. coli acsP2 promoter by a synergistic Class III mechanism J Bacteriol 185 2003 5148 5157
-
(2003)
J Bacteriol
, vol.185
, pp. 5148-5157
-
-
Beatty, C.1
Browning, D.2
Busby, S.3
Wolfe, A.4
-
26
-
-
0032698634
-
Transcription activation by catabolite activator protein (CAP)
-
S. Busby, and R.H. Ebright Transcription activation by catabolite activator protein (CAP) J Mol Biol 293 1999 199 213
-
(1999)
J Mol Biol
, vol.293
, pp. 199-213
-
-
Busby, S.1
Ebright, R.H.2
-
27
-
-
0028365289
-
Quality and position of the three lac operators of E. coli define efficiency of repression
-
S. Oehler, M. Amouyal, P. Kolkhof, B. von Wilcken-Bergmann, and B. Müller-Hill Quality and position of the three lac operators of E. coli define efficiency of repression EMBO J 13 1994 3348 3355
-
(1994)
EMBO J
, vol.13
, pp. 3348-3355
-
-
Oehler, S.1
Amouyal, M.2
Kolkhof, P.3
Von Wilcken-Bergmann, B.4
Müller-Hill, B.5
-
28
-
-
0042622638
-
DNA looping and physical constraints on transcription regulation
-
J.M. Vilar, and S. Leibler DNA looping and physical constraints on transcription regulation J Mol Biol 331 2003 981 989 An example of using thermodynamic models to interpret in vivo looping data in the lac operon, which was studied by Oehler et al. [27]. The authors explore the possible role of DNA looping and auxiliary operators to help suppress stochastic fluctuations in lac gene expression.
-
(2003)
J Mol Biol
, vol.331
, pp. 981-989
-
-
Vilar, J.M.1
Leibler, S.2
-
29
-
-
0016640172
-
The general affinity of lac repressor for E. coli DNA: Implications for gene regulation in procaryotes and eucaryotes
-
S. Lin, and A. Riggs The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes Cell 4 1975 107 111
-
(1975)
Cell
, vol.4
, pp. 107-111
-
-
Lin, S.1
Riggs, A.2
-
30
-
-
0018800287
-
"Second" and "third operator" of the lac operon: An investigation of their role in the regulatory mechanism
-
M. Pfahl, V. Gulde, and S. Bourgeois "Second" and "third operator" of the lac operon: an investigation of their role in the regulatory mechanism J Mol Biol 127 1979 339 344
-
(1979)
J Mol Biol
, vol.127
, pp. 339-344
-
-
Pfahl, M.1
Gulde, V.2
Bourgeois, S.3
-
31
-
-
0019816896
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor-operator interaction: Equilibrium measurements
-
R.B. Winter, and P.H. von Hippel Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor-operator interaction: equilibrium measurements Biochemistry 20 1981 6948 6960
-
(1981)
Biochemistry
, vol.20
, pp. 6948-6960
-
-
Winter, R.B.1
Von Hippel, P.H.2
-
32
-
-
0037126028
-
Physical constraints and functional characteristics of transcription factor-DNA interaction
-
U. Gerland, J.D. Moroz, and T. Hwa Physical constraints and functional characteristics of transcription factor-DNA interaction Proc Natl Acad Sci USA 99 2002 12015 12020
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 12015-12020
-
-
Gerland, U.1
Moroz, J.D.2
Hwa, T.3
-
33
-
-
0025622722
-
Stable DNA loops in vivo and in vitro: Roles in gene regulation at a distance and in biophysical characterization of DNA
-
G.R. Bellomy, and M.T. Record Jr. Stable DNA loops in vivo and in vitro: roles in gene regulation at a distance and in biophysical characterization of DNA Prog Nucleic Acid Res Mol Biol 39 1990 81 128
-
(1990)
Prog Nucleic Acid Res Mol Biol
, vol.39
, pp. 81-128
-
-
Bellomy, G.R.1
Record Jr., M.T.2
-
34
-
-
0029975889
-
Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
-
J. Müller, S. Oehler, and B. Müller-Hill Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator J Mol Biol 257 1996 21 29
-
(1996)
J Mol Biol
, vol.257
, pp. 21-29
-
-
Müller, J.1
Oehler, S.2
Müller-Hill, B.3
-
35
-
-
0031908629
-
A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli
-
M. Dmitrova, G. Younes-Cauet, P. Oertel-Buchheit, D. Porte, M. Schnarr, and M. Granger-Schnarr A new LexA-based genetic system for monitoring and analyzing protein heterodimerization in Escherichia coli Mol Gen Genet 257 1998 205 212
-
(1998)
Mol Gen Genet
, vol.257
, pp. 205-212
-
-
Dmitrova, M.1
Younes-Cauet, G.2
Oertel-Buchheit, P.3
Porte, D.4
Schnarr, M.5
Granger-Schnarr, M.6
-
36
-
-
0034049099
-
E. coli one- and two-hybrid systems for the analysis and identification of protein-protein interactions
-
J.C. Hu, M.G. Kornacker, and A. Hochschild E. coli one- and two-hybrid systems for the analysis and identification of protein-protein interactions Methods 20 2000 80 94
-
(2000)
Methods
, vol.20
, pp. 80-94
-
-
Hu, J.C.1
Kornacker, M.G.2
Hochschild, A.3
-
37
-
-
0033847495
-
Two-hybrid system for characterization of protein-protein interactions in E. coli
-
L.B. Hays, Y.S. Chen, and J.C. Hu Two-hybrid system for characterization of protein-protein interactions in E. coli BioTechniques 29 2000 288 294
-
(2000)
BioTechniques
, vol.29
, pp. 288-294
-
-
Hays, L.B.1
Chen, Y.S.2
Hu, J.C.3
-
38
-
-
0030861452
-
Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements
-
R. Lutz, and H. Bujard Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements Nucleic Acids Res 25 1997 1203 1210
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 1203-1210
-
-
Lutz, R.1
Bujard, H.2
-
39
-
-
0037369952
-
Collaborative competition mechanism for gene activation in vivo
-
J.A. Miller, and J. Widom Collaborative competition mechanism for gene activation in vivo Mol Cell Biol 23 2003 1623 1632
-
(2003)
Mol Cell Biol
, vol.23
, pp. 1623-1632
-
-
Miller, J.A.1
Widom, J.2
-
40
-
-
0004211673
-
-
Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York
-
M. Ptashne, and A. Gann Genes and Signals 2002 Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York
-
(2002)
Genes and Signals
-
-
Ptashne, M.1
Gann, A.2
-
41
-
-
0015506054
-
Evidence for two sites in the lac promoter region
-
J. Beckwith, T. Grodzicker, and R. Arditti Evidence for two sites in the lac promoter region J Mol Biol 69 1972 155 160
-
(1972)
J Mol Biol
, vol.69
, pp. 155-160
-
-
Beckwith, J.1
Grodzicker, T.2
Arditti, R.3
-
42
-
-
0020444656
-
Stoichiometry of catabolite activator protein/adenosine cyclic 3′ 5′-monophosphate interactions at the lac promoter of Escherichia coli
-
M.M. Garner, and A. Revzin Stoichiometry of catabolite activator protein/adenosine cyclic 3′ 5′-monophosphate interactions at the lac promoter of Escherichia coli Biochemistry 21 1982 6032 6036
-
(1982)
Biochemistry
, vol.21
, pp. 6032-6036
-
-
Garner, M.M.1
Revzin, A.2
-
43
-
-
0021327730
-
Equilibrium studies of the cyclic AMP receptor protein-DNA interaction
-
M.G. Fried, and D.M. Crothers Equilibrium studies of the cyclic AMP receptor protein-DNA interaction J Mol Biol 172 1984 241 262
-
(1984)
J Mol Biol
, vol.172
, pp. 241-262
-
-
Fried, M.G.1
Crothers, D.M.2
-
44
-
-
0024381106
-
Ligand-modulated binding of a gene regulatory protein to DNA: Quantitative analysis of cyclic-AMP induced binding of CRP from Escherichia coli to non-specific and specific DNA targets
-
M. Takahashi, B. Blazy, and A. Baudras Ligand-modulated binding of a gene regulatory protein to DNA: quantitative analysis of cyclic-AMP induced binding of CRP from Escherichia coli to non-specific and specific DNA targets J Mol Biol 207 1989 783 796
-
(1989)
J Mol Biol
, vol.207
, pp. 783-796
-
-
Takahashi, M.1
Blazy, B.2
Baudras, A.3
-
45
-
-
1042278041
-
Cooperativity in long-range gene regulation by the lambda cI repressor
-
I.B. Dodd, K.E. Shearwin, A.J. Perkins, T. Burr, A. Hochschild, and J.B. Egan Cooperativity in long-range gene regulation by the lambda cI repressor Genes Dev 18 2004 344 354
-
(2004)
Genes Dev
, vol.18
, pp. 344-354
-
-
Dodd, I.B.1
Shearwin, K.E.2
Perkins, A.J.3
Burr, T.4
Hochschild, A.5
Egan, J.B.6
-
47
-
-
0026567857
-
Site-specific enthalpic regulation of DNA transcription at bacteriophage lambda or
-
K.S. Koblan, and G.K. Ackers Site-specific enthalpic regulation of DNA transcription at bacteriophage lambda OR Biochemistry 31 1992 57 65
-
(1992)
Biochemistry
, vol.31
, pp. 57-65
-
-
Koblan, K.S.1
Ackers, G.K.2
-
50
-
-
0002352498
-
Control analysis of metabolic systems
-
J.A. Burns, A. Cornish-Bowden, A.K. Groen, R. Heinrich, H. Kacser, J.W. Porteous, S.M. Rapoport, T.A. Rapoport, J.W. Stucki, J.M. Tager, R.J.A. Wanders, and H.V. Westerhoff Control analysis of metabolic systems Trends Biochem Sci 10 1985 16
-
(1985)
Trends Biochem Sci
, vol.10
, pp. 16
-
-
Burns, J.A.1
Cornish-Bowden, A.2
Groen, A.K.3
Heinrich, R.4
Kacser, H.5
Porteous, J.W.6
Rapoport, S.M.7
Rapoport, T.A.8
Stucki, J.W.9
Tager, J.M.10
Wanders, R.J.A.11
Westerhoff, H.V.12
|