-
2
-
-
17044396348
-
Gene regulatory networks special feature: Logic functions of the genomic cis-regulatory code
-
doi:10.1073/pnas.0409624102
-
Istrail S, Davidson EH (2005) Gene regulatory networks special feature: Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci U S A 102: 4954-4959. doi:10.1073/pnas.0409624102
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 4954-4959
-
-
Istrail, S.1
Davidson, E.H.2
-
3
-
-
0032549745
-
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
-
doi:10.1126/science.279.5358.1896
-
Yuh CH, Bolouri H, Davidson EH (1998) Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science 279: 1896-1902. doi:10.1126/science.279.5358.1896
-
(1998)
Science
, vol.279
, pp. 1896-1902
-
-
Yuh, C.H.1
Bolouri, H.2
Davidson, E.H.3
-
4
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318-356.
-
(1961)
J Mol Biol
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
6
-
-
0004211673
-
-
New York: Cold Spring Harbor Laboratory Press. 208 p
-
Ptashne M, Gann A (2002) Genes and signals. New York: Cold Spring Harbor Laboratory Press. 208 p.
-
(2002)
Genes and signals
-
-
Ptashne, M.1
Gann, A.2
-
8
-
-
13444262374
-
EcoCyc:A comprehensive database resource for Escherichia coli
-
Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, et al. (2005) EcoCyc:A comprehensive database resource for Escherichia coli. Nucl Acids Res 33: D334-D337.
-
(2005)
Nucl Acids Res
, vol.33
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
-
9
-
-
0032034820
-
Some repressors of bacterial transcription
-
Müller-Hill B (1998) Some repressors of bacterial transcription. Curr Opin Micobiol 1: 145-151.
-
(1998)
Curr Opin Micobiol
, vol.1
, pp. 145-151
-
-
Müller-Hill, B.1
-
10
-
-
0347635508
-
Design of genetic networks with specified functions by evolution in silico
-
Francois P, Hakim Y (2004) Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci U S A 101: 580-585.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 580-585
-
-
Francois, P.1
Hakim, Y.2
-
12
-
-
0022429106
-
The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation
-
Shea MA, Ackers GK (1985) The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation. J Mol Biol 181: 211-230.
-
(1985)
J Mol Biol
, vol.181
, pp. 211-230
-
-
Shea, M.A.1
Ackers, G.K.2
-
13
-
-
15744394192
-
Transcription regulation by the numbers 1: Models
-
Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, et al. (2005) Transcription regulation by the numbers 1: Models. Curr Opin Gen Dev 15: 116-124.
-
(2005)
Curr Opin Gen Dev
, vol.15
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
-
14
-
-
15744387380
-
Transcription regulation by the numbers 2: Applications
-
Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, et al. (2005) Transcription regulation by the numbers 2: Applications. Curr Opin Gen Dev 15: 125-135.
-
(2005)
Curr Opin Gen Dev
, vol.15
, pp. 125-135
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
-
15
-
-
0027230594
-
-
Lisser S, Margalit H (1993) Compilation of E. coli mRNA promoter sequences. NAR 21: 1507-1516.
-
Lisser S, Margalit H (1993) Compilation of E. coli mRNA promoter sequences. NAR 21: 1507-1516.
-
-
-
-
16
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
-
Berg OG, von Hippel PH (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 193: 723-750.
-
(1987)
J Mol Biol
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
von Hippel, P.H.2
-
17
-
-
0023774773
-
Selection of DNA binding sites by regulatory proteins. Functional specificity and pseudosite competition
-
Berg OG (1988) Selection of DNA binding sites by regulatory proteins. Functional specificity and pseudosite competition. J Biomol Struc Dynam 6: 275-297.
-
(1988)
J Biomol Struc Dynam
, vol.6
, pp. 275-297
-
-
Berg, O.G.1
-
18
-
-
0023147228
-
Selection of DNA binding sites by regulatory proteins ii. The binding specificity of Cyclic AMP receptor protein to recognition sites
-
Berg OG, von Hippel PH (1987) Selection of DNA binding sites by regulatory proteins ii. The binding specificity of Cyclic AMP receptor protein to recognition sites. J Mol Biol 193: 723-750.
-
(1987)
J Mol Biol
, vol.193
, pp. 723-750
-
-
Berg, O.G.1
von Hippel, P.H.2
-
19
-
-
0242574990
-
A biophysical approach to transcription factor binding site discovery
-
Djordjevic M, Sengupta AM, Shraiman BI (2003) A biophysical approach to transcription factor binding site discovery. Genome Res 13: 2381-2390.
-
(2003)
Genome Res
, vol.13
, pp. 2381-2390
-
-
Djordjevic, M.1
Sengupta, A.M.2
Shraiman, B.I.3
-
21
-
-
0032032780
-
Specificity, free energy and information content in protein-DNA interactions
-
Stormo GD, Fields DS (1998) Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 23: 109-113.
-
(1998)
Trends Biochem Sci
, vol.23
, pp. 109-113
-
-
Stormo, G.D.1
Fields, D.S.2
-
22
-
-
0036787402
-
On the selection and evolution of regulatory DNA motifs
-
Gerland U, Hwa T (2002) On the selection and evolution of regulatory DNA motifs. J Mol Evol 55: 386-400.
-
(2002)
J Mol Evol
, vol.55
, pp. 386-400
-
-
Gerland, U.1
Hwa, T.2
-
23
-
-
0037126028
-
Physical constraints and functional characteristics of transcription factor-DNA interaction
-
Gerland U, Moroz DJ, Hwa T (2002) Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A 99: 12015-12020.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 12015-12020
-
-
Gerland, U.1
Moroz, D.J.2
Hwa, T.3
-
24
-
-
0028061282
-
Promoter structure, promoter recognition, and transcription activation in prokaryotes
-
Busby S, Ebright RH (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79: 743-746.
-
(1994)
Cell
, vol.79
, pp. 743-746
-
-
Busby, S.1
Ebright, R.H.2
-
25
-
-
0034597003
-
Synergistic transcription activation: A dual role for CRP in the activation of an Escherichia coli promoter depending on MalT and CRP
-
Richet E (2000) Synergistic transcription activation: A dual role for CRP in the activation of an Escherichia coli promoter depending on MalT and CRP. EMBO J 19: 5222-5232.
-
(2000)
EMBO J
, vol.19
, pp. 5222-5232
-
-
Richet, E.1
-
26
-
-
0037126615
-
A simple mechanism for co-dependence on two activators at an Escherichia coli promoter
-
Wade J, Belyaeva T, Hyde E, Busby S (2001) A simple mechanism for co-dependence on two activators at an Escherichia coli promoter. EMBO J 20: 7160-7167.
-
(2001)
EMBO J
, vol.20
, pp. 7160-7167
-
-
Wade, J.1
Belyaeva, T.2
Hyde, E.3
Busby, S.4
-
27
-
-
33744821614
-
Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor
-
Marincs F, Manfield IW, Stead JA, McDowall KJ, Stockley PG (2006) Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the Escherichia coli methionine repressor. Biochem J 396: 227-234.
-
(2006)
Biochem J
, vol.396
, pp. 227-234
-
-
Marincs, F.1
Manfield, I.W.2
Stead, J.A.3
McDowall, K.J.4
Stockley, P.G.5
-
28
-
-
0027461910
-
Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvih
-
Wang Q, Calvo JM (1993) Lrp, a global regulatory protein of Escherichia coli, binds co-operatively to multiple sites and activates transcription of ilvih. J Mol Biol 229: 306-318.
-
(1993)
J Mol Biol
, vol.229
, pp. 306-318
-
-
Wang, Q.1
Calvo, J.M.2
-
29
-
-
0034637480
-
Evidence of an unusually long operator for the Fur repressor in the aerobactin promoter of Escherichia coli
-
Escolar L, Perez-Martin J, de Lorenzo V (2000) Evidence of an unusually long operator for the Fur repressor in the aerobactin promoter of Escherichia coli. J Biol Chem 275: 24709-24714.
-
(2000)
J Biol Chem
, vol.275
, pp. 24709-24714
-
-
Escolar, L.1
Perez-Martin, J.2
de Lorenzo, V.3
-
30
-
-
0029858049
-
Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: Characterization of DNA binding at target promoters
-
Lynch A, Lin E (1996) Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: Characterization of DNA binding at target promoters. J Bacteriol 178: 6238-6249.
-
(1996)
J Bacteriol
, vol.178
, pp. 6238-6249
-
-
Lynch, A.1
Lin, E.2
-
31
-
-
0030609130
-
Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli
-
Shen J, Gunsalus R (1997) Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli. Mol Microbiol 26: 223-236.
-
(1997)
Mol Microbiol
, vol.26
, pp. 223-236
-
-
Shen, J.1
Gunsalus, R.2
-
32
-
-
13444283630
-
Interaction network containing conserved and essential protein complexes in Escherichia coli
-
Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537.
-
(2005)
Nature
, vol.433
, pp. 531-537
-
-
Butland, G.1
Peregrin-Alvarez, J.M.2
Li, J.3
Yang, W.4
Yang, X.5
-
33
-
-
33845503073
-
Adaptive evolution of transcription factor binding sites. BCM
-
Berg J, Willmann S, Lässig M (2004) Adaptive evolution of transcription factor binding sites. BCM Evol Biol 4: 42.
-
(2004)
Evol Biol
, vol.4
, pp. 42
-
-
Berg, J.1
Willmann, S.2
Lässig, M.3
-
34
-
-
0003880161
-
-
3rd edition. New York: Garland. 1408 p
-
Alberts B, Bray D, Lewis J, Raff M, Roberts K, et al. (1994) Molecular biology of the cell. 3rd edition. New York: Garland. 1408 p.
-
(1994)
Molecular biology of the cell
-
-
Alberts, B.1
Bray, D.2
Lewis, J.3
Raff, M.4
Roberts, K.5
-
36
-
-
0027446708
-
Molecular biology of the LysR family of transcriptional regulators
-
Schell MA (1993) Molecular biology of the LysR family of transcriptional regulators. Ann Rev Microbiol 47: 597-626.
-
(1993)
Ann Rev Microbiol
, vol.47
, pp. 597-626
-
-
Schell, M.A.1
-
37
-
-
0029080491
-
DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli
-
Wilson R, Urbanowski M, Stauffer G (1995) DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli. J Bacteriol 177: 4940-4946.
-
(1995)
J Bacteriol
, vol.177
, pp. 4940-4946
-
-
Wilson, R.1
Urbanowski, M.2
Stauffer, G.3
-
38
-
-
0028109899
-
Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation
-
Lamblin A, Fuchs J (1994) Functional analysis of the Escherichia coli K-12 cyn operon transcriptional regulation. J Bacteriol 176: 6613-6622.
-
(1994)
J Bacteriol
, vol.176
, pp. 6613-6622
-
-
Lamblin, A.1
Fuchs, J.2
-
39
-
-
0035072749
-
Mechanisms of transcriptional repression
-
Rojo F (2001) Mechanisms of transcriptional repression. Curr Opin Micobiol 4: 145-151.
-
(2001)
Curr Opin Micobiol
, vol.4
, pp. 145-151
-
-
Rojo, F.1
-
40
-
-
0040075183
-
Occlusion of RNA polymerase by oligomerization of DnaA protein over the dnaA promoter of Escherichia coli
-
Lee YS, Hwang DS (1997) Occlusion of RNA polymerase by oligomerization of DnaA protein over the dnaA promoter of Escherichia coli. J Biol Chem 272: 83-88.
-
(1997)
J Biol Chem
, vol.272
, pp. 83-88
-
-
Lee, Y.S.1
Hwang, D.S.2
-
41
-
-
0012099926
-
Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences
-
Jeeves M, Evans PD, Parslow RA, Jaseja M, Hyde EI (1999) Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences. Eur J Biochem 265: 919-928.
-
(1999)
Eur J Biochem
, vol.265
, pp. 919-928
-
-
Jeeves, M.1
Evans, P.D.2
Parslow, R.A.3
Jaseja, M.4
Hyde, E.I.5
-
42
-
-
0029010741
-
aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp
-
Xu J, Johnson R (1995) aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp. J Bacteriol 177: 3166-3175.
-
(1995)
J Bacteriol
, vol.177
, pp. 3166-3175
-
-
Xu, J.1
Johnson, R.2
-
43
-
-
0027983641
-
CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending
-
Richet E, Sogaard-Andersen L (1994) CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending. EMBO J 13: 4558-4567.
-
(1994)
EMBO J
, vol.13
, pp. 4558-4567
-
-
Richet, E.1
Sogaard-Andersen, L.2
-
44
-
-
0029865234
-
Analysis of CRP-CytR interactions at the Escherichia coli udp promoter
-
Brikun I, Suziedelis K, Stemmann O, Zhong R, Alikhanian L, et al. (1996) Analysis of CRP-CytR interactions at the Escherichia coli udp promoter. J Bacteriol 178: 1614-1622.
-
(1996)
J Bacteriol
, vol.178
, pp. 1614-1622
-
-
Brikun, I.1
Suziedelis, K.2
Stemmann, O.3
Zhong, R.4
Alikhanian, L.5
-
45
-
-
0028828823
-
Gene-regulatory modules in Escherichia coli: Nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter
-
Pedersen H, Dall J, Dandanell G, Valentin-Hansen P (1995) Gene-regulatory modules in Escherichia coli: Nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter. Mol Microbiol 17: 843-853.
-
(1995)
Mol Microbiol
, vol.17
, pp. 843-853
-
-
Pedersen, H.1
Dall, J.2
Dandanell, G.3
Valentin-Hansen, P.4
-
46
-
-
0026000281
-
The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli k-12
-
Gerlach P, Sogaard-Andersen L, Pedersen H, Martinussen J, Valentin-Hansen P, et al. (1991) The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli k-12. J Bacteriol 173: 5419-5430.
-
(1991)
J Bacteriol
, vol.173
, pp. 5419-5430
-
-
Gerlach, P.1
Sogaard-Andersen, L.2
Pedersen, H.3
Martinussen, J.4
Valentin-Hansen, P.5
-
47
-
-
0035476678
-
Repression of deoP2 in Escherichia coli by CytR: Conversion of a transcription activator into a repressor
-
Shin M, Kang S, Hyun S, Fujita N, Ishihama A, et al. (2001) Repression of deoP2 in Escherichia coli by CytR: Conversion of a transcription activator into a repressor. EMBO J 20: 5392-5399.
-
(2001)
EMBO J
, vol.20
, pp. 5392-5399
-
-
Shin, M.1
Kang, S.2
Hyun, S.3
Fujita, N.4
Ishihama, A.5
-
48
-
-
0036300938
-
Thermodynamics of E. coli cytidine repressor interactions with DNA: Distinct modes of binding to different operators suggests a role in differential gene regulation
-
Tretyachenko-Ladokhina V, Ross J, Senear D (2002) Thermodynamics of E. coli cytidine repressor interactions with DNA: Distinct modes of binding to different operators suggests a role in differential gene regulation. J Mol Biol 316: 531-546.
-
(2002)
J Mol Biol
, vol.316
, pp. 531-546
-
-
Tretyachenko-Ladokhina, V.1
Ross, J.2
Senear, D.3
-
49
-
-
0032956969
-
Dissection of a surface-exposed portion of the cAMP-CRP complex that mediates transcription activation and repression
-
Meibom K, Sogaard-Andersen L, Mironov A, Valentin-Hansen P (1999) Dissection of a surface-exposed portion of the cAMP-CRP complex that mediates transcription activation and repression. Mol Microbiol 32: 497-504.
-
(1999)
Mol Microbiol
, vol.32
, pp. 497-504
-
-
Meibom, K.1
Sogaard-Andersen, L.2
Mironov, A.3
Valentin-Hansen, P.4
-
50
-
-
27444437323
-
LRP and H-NS - Cooperative partners for transcription regulation at Escherichia coli rrna promoters
-
Pul U, Wurm R, Lux B, Meltzer M, Menzel A, et al. (2005) LRP and H-NS - Cooperative partners for transcription regulation at Escherichia coli rrna promoters. Mol Microbiol 58: 864-876.
-
(2005)
Mol Microbiol
, vol.58
, pp. 864-876
-
-
Pul, U.1
Wurm, R.2
Lux, B.3
Meltzer, M.4
Menzel, A.5
-
51
-
-
0004210529
-
-
7th edition. Sunderland Massachusetts, Sinauer
-
Gilbert SF (2003) Developmental biology. 7th edition. Sunderland (Massachusetts): Sinauer.
-
(2003)
Developmental biology
-
-
Gilbert, S.F.1
-
52
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.
-
(2002)
Nat Genet
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
54
-
-
0037303198
-
Functional determinants of transcription factors in Escherichia coli: Protein families and binding sites
-
Madan Babu M, Teichmann SA (2003) Functional determinants of transcription factors in Escherichia coli: Protein families and binding sites. Trends Genet 19: 75-79.
-
(2003)
Trends Genet
, vol.19
, pp. 75-79
-
-
Madan Babu, M.1
Teichmann, S.A.2
-
55
-
-
0343963178
-
The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12
-
Pérez-Rueda E, Collado-Vides J (2003) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucl Acids Res 28: 1838-1847.
-
(2003)
Nucl Acids Res
, vol.28
, pp. 1838-1847
-
-
Pérez-Rueda, E.1
Collado-Vides, J.2
|