-
1
-
-
0014489272
-
Metabolic stability and epigenesis in randomly constructed genetic nets
-
S.A. Kauffman Metabolic stability and epigenesis in randomly constructed genetic nets J. Theor. Biol. 22 1969 437 467
-
(1969)
J. Theor. Biol.
, vol.22
, pp. 437-467
-
-
Kauffman, S.A.1
-
3
-
-
0028129315
-
Computational functions in biochemical reaction networks
-
A. Arkin, and J. Ross Computational functions in biochemical reaction networks Biophys. J. 67 1994 560 578
-
(1994)
Biophys. J.
, vol.67
, pp. 560-578
-
-
Arkin, A.1
Ross, J.2
-
4
-
-
0029267491
-
Dynamical behavior of biological regulatory networks. 1. biological role of feedback loops and practical use of the concept of the loop-characteristic state
-
R. Thomas, D. Thieffry, and M. Kaufman Dynamical behavior of biological regulatory networks. 1. biological role of feedback loops and practical use of the concept of the loop-characteristic state Bull. Math. Biol. 57 1995 247 276
-
(1995)
Bull. Math. Biol.
, vol.57
, pp. 247-276
-
-
Thomas, R.1
Thieffry, D.2
Kaufman, M.3
-
5
-
-
0032776303
-
Molecular interaction map of the mammalian cell cycle control and DNA repair systems
-
K.W. Kohn Molecular interaction map of the mammalian cell cycle control and DNA repair systems Mol. Biol. Cell 10 1999 2703 2734
-
(1999)
Mol. Biol. Cell
, vol.10
, pp. 2703-2734
-
-
Kohn, K.W.1
-
7
-
-
0036901602
-
Modeling transcriptional regulatory networks
-
H. Bolouri, and E.H. Davidson Modeling transcriptional regulatory networks BioEssays 24 2002 1118 1129
-
(2002)
BioEssays
, vol.24
, pp. 1118-1129
-
-
Bolouri, H.1
Davidson, E.H.2
-
8
-
-
0032077377
-
From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli
-
D. Thieffry, A.M. Huerta, E. Perez-Rueda, and J. Collado-Vides From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli BioEssays 20 1998 433 440
-
(1998)
BioEssays
, vol.20
, pp. 433-440
-
-
Thieffry, D.1
Huerta, A.M.2
Perez-Rueda, E.3
Collado-Vides, J.4
-
9
-
-
0029037739
-
Protein molecules as computational elements in living cells
-
D. Bray Protein molecules as computational elements in living cells Nature 376 1995 307 312
-
(1995)
Nature
, vol.376
, pp. 307-312
-
-
Bray, D.1
-
10
-
-
0036578795
-
Network motifs in the transcriptional regulation network of Escherichia coli
-
S.S. Shen-Orr, R. Milo, S. Mangan, and U. Alon Network motifs in the transcriptional regulation network of Escherichia coli Nature Genet. 31 2002 64 68
-
(2002)
Nature Genet.
, vol.31
, pp. 64-68
-
-
Shen-Orr, S.S.1
Milo, R.2
Mangan, S.3
Alon, U.4
-
11
-
-
0037174670
-
Network motifs: Simple building blocks of complex networks
-
R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon Network motifs: simple building blocks of complex networks Science 298 2002 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
-
12
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, and G.K. Gerber Transcriptional regulatory networks in Saccharomyces cerevisiae Science 298 2002 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
-
13
-
-
33847051248
-
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
-
L.V. Zhang, O.D. King, S.L. Wong, D.S. Goldberg, A.H. Tong, and G. Lesage Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network J. Biol. 4 2005 6
-
(2005)
J. Biol.
, vol.4
, pp. 6
-
-
Zhang, L.V.1
King, O.D.2
Wong, S.L.3
Goldberg, D.S.4
Tong, A.H.5
Lesage, G.6
-
14
-
-
1542287343
-
Superfamilies of evolved and designed networks
-
R. Milo, S. Itzkovitz, N. Kashtan, R. Levitt, S. Shen-Orr, and I. Ayzenshtat Superfamilies of evolved and designed networks Science 303 2004 1538 1542
-
(2004)
Science
, vol.303
, pp. 1538-1542
-
-
Milo, R.1
Itzkovitz, S.2
Kashtan, N.3
Levitt, R.4
Shen-Orr, S.5
Ayzenshtat, I.6
-
15
-
-
8844240734
-
The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis
-
P. Eichenberger, M. Fujita, S.T. Jensen, E.M. Conlon, D.Z. Rudner, and S.T. Wang The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis PLoS Biol. 2 2004 e328
-
(2004)
PLoS Biol.
, vol.2
, pp. 328
-
-
Eichenberger, P.1
Fujita, M.2
Jensen, S.T.3
Conlon, E.M.4
Rudner, D.Z.5
Wang, S.T.6
-
16
-
-
10744227070
-
Control of pancreas and liver gene expression by HNF transcription factors
-
D.T. Odom, N. Zizlsperger, D.B. Gordon, G.W. Bell, N.J. Rinaldi, and H.L. Murray Control of pancreas and liver gene expression by HNF transcription factors Science 303 2004 1378 1381
-
(2004)
Science
, vol.303
, pp. 1378-1381
-
-
Odom, D.T.1
Zizlsperger, N.2
Gordon, D.B.3
Bell, G.W.4
Rinaldi, N.J.5
Murray, H.L.6
-
17
-
-
25144525014
-
Core transcriptional regulatory circuitry in human embryonic stem cells
-
Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., et al. (2005). Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947-956.
-
(2005)
Cell
, vol.122
, pp. 947-956
-
-
Boyer, L.A.1
Lee, T.I.2
Cole, M.F.3
Johnstone, S.E.4
Levine, S.S.5
Zucker, J.P.6
-
18
-
-
0142027814
-
The structure and function of the feedforward loop network motif
-
S. Mangan, and U. Alon The structure and function of the feedforward loop network motif Proc. Natl Acad. Sci. USA 100 2003 11980 11985
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11980-11985
-
-
Mangan, S.1
Alon, U.2
-
19
-
-
27844551326
-
Dynamic properties of network motifs contribute to biological network organization
-
R.J. Prill, P.A. Iglesias, and A. Levchenko Dynamic properties of network motifs contribute to biological network organization PLoS Biol. 3 2005 e343
-
(2005)
PLoS Biol.
, vol.3
, pp. 343
-
-
Prill, R.J.1
Iglesias, P.A.2
Levchenko, A.3
-
20
-
-
0242364231
-
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks
-
S. Mangan, A. Zaslaver, and U. Alon The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks J. Mol. Biol. 334 2003 197 204
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 197-204
-
-
Mangan, S.1
Zaslaver, A.2
Alon, U.3
-
21
-
-
13544269611
-
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
-
H.W. Ma, B. Kumar, U. Ditges, F. Gunzer, J. Buer, and A.P. Zeng An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs Nucl. Acids Res. 32 2004 6643 6649
-
(2004)
Nucl. Acids Res.
, vol.32
, pp. 6643-6649
-
-
Ma, H.W.1
Kumar, B.2
Ditges, U.3
Gunzer, F.4
Buer, J.5
Zeng, A.P.6
-
22
-
-
27644443808
-
Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes
-
S. Ishihara, K. Fujimoto, and T. Shibata Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes Genes Cells 10 2005 1025 1038
-
(2005)
Genes Cells
, vol.10
, pp. 1025-1038
-
-
Ishihara, S.1
Fujimoto, K.2
Shibata, T.3
-
23
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
E. Dekel, and U. Alon Optimality and evolutionary tuning of the expression level of a protein Nature 436 2005 588 592
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
26
-
-
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
-
27
-
-
20444479428
-
C-Myc-regulated microRNAs modulate E2F1 expression
-
K.A. O'Donnell, E.A. Wentzel, K.I. Zeller, C.V. Dang, and J.T. Mendell c-Myc-regulated microRNAs modulate E2F1 expression Nature 435 2005 839 843
-
(2005)
Nature
, vol.435
, pp. 839-843
-
-
O'Donnell, K.A.1
Wentzel, E.A.2
Zeller, K.I.3
Dang, C.V.4
Mendell, J.T.5
-
28
-
-
0036428761
-
Negative autoregulation speeds the response times of transcription networks
-
N. Rosenfeld, M.B. Elowitz, and U. Alon Negative autoregulation speeds the response times of transcription networks J. Mol. Biol. 323 2002 785 793
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 785-793
-
-
Rosenfeld, N.1
Elowitz, M.B.2
Alon, U.3
-
29
-
-
0016419101
-
Quantitative aspects of protein induction
-
G. Yagil Quantitative aspects of protein induction Curr. Top. Cell. Regul. 9 1975 183 236
-
(1975)
Curr. Top. Cell. Regul.
, vol.9
, pp. 183-236
-
-
Yagil, G.1
-
30
-
-
2342578714
-
Spatiotemporal control of gene expression with pulse-generating networks
-
S. Basu, R. Mehreja, S. Thiberge, M.T. Chen, and R. Weiss Spatiotemporal control of gene expression with pulse-generating networks Proc. Natl Acad. Sci. USA 101 2004 6355 6360
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6355-6360
-
-
Basu, S.1
Mehreja, R.2
Thiberge, S.3
Chen, M.T.4
Weiss, R.5
-
31
-
-
0030940344
-
Interaction of Gal repressor with inducer and operator: Induction of gal transcription from repressor-bound DNA
-
S. Chatterjee, Y.N. Zhou, S. Roy, and S. Adhya Interaction of Gal repressor with inducer and operator: induction of gal transcription from repressor-bound DNA Proc. Natl Acad. Sci. USA 94 1997 2957 2962
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 2957-2962
-
-
Chatterjee, S.1
Zhou, Y.N.2
Roy, S.3
Adhya, S.4
-
32
-
-
0028298474
-
The allosteric interaction between d-galactose and the Escherichia coli galactose repressor protein
-
M.P. Brown, N. Shaikh, M. Brenowitz, and L. Brand The allosteric interaction between d-galactose and the Escherichia coli galactose repressor protein J. Biol. Chem. 269 1994 12600 12605
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 12600-12605
-
-
Brown, M.P.1
Shaikh, N.2
Brenowitz, M.3
Brand, L.4
-
33
-
-
0031026282
-
Functional characterization of roles of GalR and GalS as regulators of the gal regulon
-
M. Geanacopoulos, and S. Adhya Functional characterization of roles of GalR and GalS as regulators of the gal regulon J. Bacteriol. 179 1997 228 234
-
(1997)
J. Bacteriol.
, vol.179
, pp. 228-234
-
-
Geanacopoulos, M.1
Adhya, S.2
-
34
-
-
0026682712
-
Isorepressor of the gal regulon in Escherichia coli
-
M.J. Weickert, and S. Adhya Isorepressor of the gal regulon in Escherichia coli J. Mol. Biol. 226 1992 69 83
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 69-83
-
-
Weickert, M.J.1
Adhya, S.2
-
35
-
-
0027429065
-
The galactose regulon of Escherichia coli
-
M.J. Weickert, and S. Adhya The galactose regulon of Escherichia coli Mol. Microbiol. 10 1993 245 251
-
(1993)
Mol. Microbiol.
, vol.10
, pp. 245-251
-
-
Weickert, M.J.1
Adhya, S.2
-
36
-
-
0027471001
-
Control of transcription of gal repressor and isorepressor genes in Escherichia coli
-
M.J. Weickert, and S. Adhya Control of transcription of gal repressor and isorepressor genes in Escherichia coli J. Bacteriol. 175 1993 251 258
-
(1993)
J. Bacteriol.
, vol.175
, pp. 251-258
-
-
Weickert, M.J.1
Adhya, S.2
-
37
-
-
0016145568
-
Comparison of classical and autogenous systems of regulation in inducible operons
-
M.A. Savageau Comparison of classical and autogenous systems of regulation in inducible operons Nature 252 1974 546 549
-
(1974)
Nature
, vol.252
, pp. 546-549
-
-
Savageau, M.A.1
-
38
-
-
0034212551
-
Engineering stability in gene networks by autoregulation
-
A. Becskei, and L. Serrano Engineering stability in gene networks by autoregulation Nature 405 2000 590 593
-
(2000)
Nature
, vol.405
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
39
-
-
0036678794
-
Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
-
M. Ronen, R. Rosenberg, B.I. Shraiman, and U. Alon Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics Proc. Natl Acad. Sci. USA 99 2002 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
-
40
-
-
2442526837
-
Just-in-time transcription program in metabolic pathways
-
A. Zaslaver, A.E. Mayo, R. Rosenberg, P. Bashkin, H. Sberro, and M. Tsalyuk Just-in-time transcription program in metabolic pathways Nature. Genet. 36 2004 486 491
-
(2004)
Nature. Genet.
, vol.36
, pp. 486-491
-
-
Zaslaver, A.1
Mayo, A.E.2
Rosenberg, R.3
Bashkin, P.4
Sberro, H.5
Tsalyuk, M.6
-
41
-
-
0035875010
-
Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria
-
S. Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, and S. Leibler Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria Science 292 2001 2080 2083
-
(2001)
Science
, vol.292
, pp. 2080-2083
-
-
Kalir, S.1
McClure, J.2
Pabbaraju, K.3
Southward, C.4
Ronen, M.5
Leibler, S.6
-
42
-
-
0141484562
-
Biological networks: The tinkerer as an engineer
-
U. Alon Biological networks: the tinkerer as an engineer Science 301 2003 1866 1867
-
(2003)
Science
, vol.301
, pp. 1866-1867
-
-
Alon, U.1
-
43
-
-
0142215475
-
Global analysis of protein expression in yeast
-
S. Ghaemmaghami, W.K. Huh, K. Bower, R.W. Howson, A. Belle, and N. Dephoure Global analysis of protein expression in yeast Nature 425 2003 737 741
-
(2003)
Nature
, vol.425
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
-
44
-
-
0037168560
-
Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics
-
E.B. Goh, G. Yim, W. Tsui, J. McClure, M.G. Surette, and J. Davies Transcriptional modulation of bacterial gene expression by subinhibitory concentrations of antibiotics Proc. Natl Acad. Sci. USA 99 2002 17025 17030
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 17025-17030
-
-
Goh, E.B.1
Yim, G.2
Tsui, W.3
McClure, J.4
Surette, M.G.5
Davies, J.6
-
45
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
F.R. Blattner, G. Plunkett III, C.A. Bloch, N.T. Perna, V. Burland, and M. Riley The complete genome sequence of Escherichia coli K-12 Science 277 1997 1453 1474
-
(1997)
Science
, vol.277
, pp. 1453-1474
-
-
Blattner, F.R.1
Plunkett III, G.2
Bloch, C.A.3
Perna, N.T.4
Burland, V.5
Riley, M.6
-
46
-
-
0029973636
-
FACS-optimized mutants of the green fluorescent protein (GFP)
-
B.P. Cormack, R.H. Valdivia, and S. Falkow FACS-optimized mutants of the green fluorescent protein (GFP) Gene 173 1996 33 38
-
(1996)
Gene
, vol.173
, pp. 33-38
-
-
Cormack, B.P.1
Valdivia, R.H.2
Falkow, S.3
-
47
-
-
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 Nucl. Acids Res. 25 1997 1203 1210
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 1203-1210
-
-
Lutz, R.1
Bujard, H.2
-
49
-
-
13444262374
-
EcoCyc: A comprehensive database resource for Escherichia coli
-
I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, and I.T. Paulsen EcoCyc: a comprehensive database resource for Escherichia coli Nucl. Acids Res. 33 2005 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
Paulsen, I.T.6
-
50
-
-
0033964238
-
The EcoCyc and MetaCyc databases
-
P.D. Karp, M. Riley, M. Saier, I.T. Paulsen, S.M. Paley, and A. Pellegrini-Toole The EcoCyc and MetaCyc databases Nucl. Acids Res. 28 2000 56 59
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 56-59
-
-
Karp, P.D.1
Riley, M.2
Saier, M.3
Paulsen, I.T.4
Paley, S.M.5
Pellegrini-Toole, A.6
-
51
-
-
0036084127
-
The EcoCyc Database
-
P.D. Karp, M. Riley, M. Saier, I.T. Paulsen, J. Collado-Vides, and S.M. Paley The EcoCyc Database Nucl. Acids Res. 30 2002 56 58
-
(2002)
Nucl. Acids Res.
, vol.30
, pp. 56-58
-
-
Karp, P.D.1
Riley, M.2
Saier, M.3
Paulsen, I.T.4
Collado-Vides, J.5
Paley, S.M.6
-
52
-
-
0035860545
-
Pathway databases: A case study in computational symbolic theories
-
P.D. Karp Pathway databases: a case study in computational symbolic theories Science 293 2001 2040 2044
-
(2001)
Science
, vol.293
, pp. 2040-2044
-
-
Karp, P.D.1
-
53
-
-
19444376022
-
Multiple fnctions of a feed-forward-loopgene circuit
-
Wall, M.E., Dunlop, M.J. & Hlavacek, W.S. (2005). multiple fnctions of a feed-forward-loopgene circuit. J. Mol. Biol. 349, 501-514.
-
(2005)
J. Mol. Biol.
, vol.349
, pp. 501-514
-
-
Wall, M.E.1
Dunlop, M.J.2
Hlavacek, W.S.3
-
54
-
-
24144451839
-
Noise characteristics of feed forward loops
-
Ghosh, B., Karmakar, B. & Bose, J. (2005). Noise characteristics of feed forward loops. Phys. Biol. 2, 36-45.
-
(2005)
Phys. Biol.
, vol.2
, pp. 36-45
-
-
Ghosh, B.1
Karmakar, B.2
Bose, J.3
|