-
2
-
-
67650601963
-
-
CELLB5 0092-8674 10.1016/j.cell.2009.07.002
-
J. C. Perez and E. A. Groisman, Cell 138, 233 (2009). CELLB5 0092-8674 10.1016/j.cell.2009.07.002
-
(2009)
Cell
, vol.138
, pp. 233
-
-
Perez, J.C.1
Groisman, E.A.2
-
3
-
-
28544451327
-
Foundations for engineering biology
-
DOI 10.1038/nature04342, PII N04342
-
D. Endy, Nature (London) 438, 449 (2005). NATUAS 0028-0836 10.1038/nature04342 (Pubitemid 41742010)
-
(2005)
Nature
, vol.438
, Issue.7067
, pp. 449-453
-
-
Endy, D.1
-
4
-
-
33748953866
-
Genetic parts to program bacteria
-
DOI 10.1016/j.copbio.2006.09.001, PII S0958166906001273, Systems Biology / Tissue and Cell Engineering
-
C. A. Voigt, Curr. Opin. Biotechnol. 17, 548 (2006). CUOBE3 0958-1669 10.1016/j.copbio.2006.09.001 (Pubitemid 44442933)
-
(2006)
Current Opinion in Biotechnology
, vol.17
, Issue.5
, pp. 548-557
-
-
Voigt, C.A.1
-
7
-
-
33847164986
-
-
BIPMAA 0006-3525 10.1002/bip.20627
-
H. G. Garcia, P. Grayson, L. Han, M. Inamdar, J. Kondev, P. C. Nelson, R. Phillips, J. Widom, and P. A. Wiggins, Biopolymers 85, 115 (2007). BIPMAA 0006-3525 10.1002/bip.20627
-
(2007)
Biopolymers
, vol.85
, pp. 115
-
-
Garcia, H.G.1
Grayson, P.2
Han, L.3
Inamdar, M.4
Kondev, J.5
Nelson, P.C.6
Phillips, R.7
Widom, J.8
Wiggins, P.A.9
-
8
-
-
0001422329
-
Quantitative model for gene regulation by λ phage repressor
-
DOI 10.1073/pnas.79.4.1129
-
G. K. Ackers, A. D. Johnson, and M. A. Shea, Proc. Natl. Acad. Sci. U.S.A. 79, 1129 (1982). PNASA6 0027-8424 10.1073/pnas.79.4.1129 (Pubitemid 12114078)
-
(1982)
Proceedings of the National Academy of Sciences of the United States of America
, vol.79
, Issue.4
, pp. 1129-1133
-
-
Ackers, G.K.1
Johnson, A.D.2
Shea, M.A.3
-
9
-
-
0037965981
-
On schemes of combinatorial transcription logic
-
DOI 10.1073/pnas.0930314100
-
N. E. Buchler, U. Gerland, and T. Hwa, Proc. Natl. Acad. Sci. U.S.A. 100, 5136 (2003). PNASA6 0027-8424 10.1073/pnas.0930314100 (Pubitemid 36542671)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.9
, pp. 5136-5141
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
10
-
-
15744387380
-
Transcriptional regulation by the numbers: Models
-
DOI 10.1016/j.gde.2005.02.007, Chromosomes and Expression Mechanisms
-
L. Bintu, N. E. Buchler, H. G. Garcia, U. Gerland, T. Hwa, J. Kondev, and R. Phillips, Curr. Opin. Genet. Dev. 15, 116 (2005). COGDET 0959-437X 10.1016/j.gde.2005.02.007 (Pubitemid 40410659)
-
(2005)
Current Opinion in Genetics and Development
, vol.15
, Issue.2
, 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
-
-
0027510369
-
In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo
-
DOI 10.1006/jmbi.1993.1133
-
S. M. Law, G. R. Bellomy, P. J. Schlax, and M. T. J. Record, J. Mol. Biol. 230, 161 (1993). JMOBAK 0022-2836 10.1006/jmbi.1993.1133 (Pubitemid 23093555)
-
(1993)
Journal of Molecular Biology
, vol.230
, Issue.1
, pp. 161-173
-
-
Law, S.M.1
Bellomy, G.R.2
Schlax, P.J.3
Record Jr., M.T.4
-
12
-
-
0042622638
-
DNA looping and physical constraints on transcription regulation
-
DOI 10.1016/S0022-2836(03)00764-2
-
J. M. Vilar and S. Leibler, J. Mol. Biol. 331, 981 (2003). JMOBAK 0022-2836 10.1016/S0022-2836(03)00764-2 (Pubitemid 36969959)
-
(2003)
Journal of Molecular Biology
, vol.331
, Issue.5
, pp. 981-989
-
-
Vilar, J.M.G.1
Leibler, S.2
-
13
-
-
15744387380
-
Transcriptional regulation by the numbers: Applications
-
DOI 10.1016/j.gde.2005.02.006, Chromosomes and Expression Mechanisms
-
L. Bintu, N. E. Buchler, H. G. Garcia, U. Gerland, T. Hwa, J. Kondev, T. Kuhlman, and R. Phillips, Curr. Opin. Genet. Dev. 15, 125 (2005). COGDET 0959-437X 10.1016/j.gde.2005.02.006 (Pubitemid 40410660)
-
(2005)
Current Opinion in Genetics and Development
, vol.15
, Issue.2
, pp. 125-135
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Kuhlman, T.7
Phillips, R.8
-
14
-
-
33645991551
-
-
BIOJAU 0006-3495 10.1529/biophysj.105.070490
-
Y. Zhang, A. E. McEwen, D. M. Crothers, and S. D. Levene, Biophys. J. 90, 1903 (2006). BIOJAU 0006-3495 10.1529/biophysj.105.070490
-
(2006)
Biophys. J.
, vol.90
, pp. 1903
-
-
Zhang, Y.1
McEwen, A.E.2
Crothers, D.M.3
Levene, S.D.4
-
15
-
-
34547642985
-
Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
-
DOI 10.1093/nar/gkm419
-
N. A. Becker, J. D. Kahn, and L. J. Maher, III, Nucleic Acids Res. 35, 3988 (2007). NARHAD 0305-1048 10.1093/nar/gkm419 (Pubitemid 47244620)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.12
, pp. 3988-4000
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
16
-
-
84871779747
-
-
See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevLett.110.018101 for detailed calculations, additional theoretical considerations and experimental controls.
-
-
-
-
17
-
-
79953661480
-
-
1553-7358 10.1371/journal.pcbi.1001100
-
A. Sanchez, H. G. Garcia, D. Jones, R. Phillips, and J. Kondev, PLoS Comput. Biol. 7, e1001100 (2011). 1553-7358 10.1371/journal.pcbi.1001100
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. 1001100
-
-
Sanchez, A.1
Garcia, H.G.2
Jones, D.3
Phillips, R.4
Kondev, J.5
-
18
-
-
84864318077
-
-
2211-1247 10.1016/j.celrep.2012.06.004
-
H. G. Garcia, A. Sanchez, J. Q. Boedicker, M. Osborne, J. Gelles, J. Kondev, and R. Phillips, Cell Reports 2, 150 (2012). 2211-1247 10.1016/j.celrep.2012.06.004
-
(2012)
Cell Reports
, vol.2
, pp. 150
-
-
Garcia, H.G.1
Sanchez, A.2
Boedicker, J.Q.3
Osborne, M.4
Gelles, J.5
Kondev, J.6
Phillips, R.7
-
19
-
-
80052000538
-
-
CELLB5 0092-8674 10.1016/j.cell.2011.07.006
-
T. C. Voss, R. L. Schiltz, M.-H. Sung, P. M. Yen, J. A. Stamatoyannopoulos, S. C. Biddie, T. A. Johnson, T. B. Miranda, S. John, and G. L. Hager, Cell 146, 544 (2011). CELLB5 0092-8674 10.1016/j.cell.2011.07.006
-
(2011)
Cell
, vol.146
, pp. 544
-
-
Voss, T.C.1
Schiltz, R.L.2
Sung, M.-H.3
Yen, P.M.4
Stamatoyannopoulos, J.A.5
Biddie, S.C.6
Johnson, T.A.7
Miranda, T.B.8
John, S.9
Hager, G.L.10
-
20
-
-
0032580207
-
Allosteric effects of DNA on transcriptional regulators
-
DOI 10.1038/31860
-
J. A. Lefstin and K. R. Yamamoto, Nature (London) 392, 885 (1998). NATUAS 0028-0836 10.1038/31860 (Pubitemid 28232051)
-
(1998)
Nature
, vol.392
, Issue.6679
, pp. 885-888
-
-
Lefstin, J.A.1
Yamamoto, K.R.2
-
21
-
-
34547604468
-
Noise in gene expression determines cell fate in Bacillus subtilis
-
DOI 10.1126/science.1140818
-
H. Maamar, A. Raj, and D. Dubnau, Science 317, 526 (2007). SCIEAS 0036-8075 10.1126/science.1140818 (Pubitemid 47196119)
-
(2007)
Science
, vol.317
, Issue.5837
, pp. 526-529
-
-
Maamar, H.1
Raj, A.2
Dubnau, D.3
-
23
-
-
34347232364
-
Combinatorial transcriptional control of the lactose operon of Escherichia coli
-
DOI 10.1073/pnas.0606717104
-
T. Kuhlman, Z. Zhang, M. H. Saier, Jr., and T. Hwa, Proc. Natl. Acad. Sci. U.S.A. 104, 6043 (2007). PNASA6 0027-8424 10.1073/pnas.0606717104 (Pubitemid 47175655)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.14
, pp. 6043-6048
-
-
Kuhlman, T.1
Zhang, Z.2
Saier Jr., M.H.3
Hwa, T.4
-
24
-
-
39449115716
-
Ab initio thermodynamic modeling of distal multisite transcription regulation
-
DOI 10.1093/nar/gkm1034
-
L. Saiz and J. M. Vilar, Nucleic Acids Res. 36, 726 (2008). NARHAD 0305-1048 10.1093/nar/gkm1034 (Pubitemid 351267230)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.3
, pp. 726-731
-
-
Saiz, L.1
Vilar, J.M.G.2
-
27
-
-
78650435917
-
-
NARHAD 0305-1048 10.1093/nar/gkq755
-
L. M. Bond, J. P. Peters, N. A. Becker, J. D. Kahn, and L. J. Maher, Nucleic Acids Res. 38, 8072 (2010). NARHAD 0305-1048 10.1093/nar/gkq755
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 8072
-
-
Bond, L.M.1
Peters, J.P.2
Becker, N.A.3
Kahn, J.D.4
Maher, L.J.5
-
29
-
-
33745595880
-
Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation
-
DOI 10.1073/pnas.0603557103
-
D. Swigon, B. D. Coleman, and W. K. Olson, Proc. Natl. Acad. Sci. U.S.A. 103, 9879 (2006). PNASA6 0027-8424 10.1073/pnas.0603557103 (Pubitemid 43993591)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.26
, pp. 9879-9884
-
-
Swigon, D.1
Coleman, B.D.2
Olson, W.K.3
-
30
-
-
34547852967
-
-
POLNCL 1932-6203 10.1371/journal.pone.0000136
-
Y. Zhang, A. E. McEwen, D. M. Crothers, and S. D. Levene, PLoS ONE 1, e136 (2006). POLNCL 1932-6203 10.1371/journal.pone.0000136
-
(2006)
PLoS ONE
, vol.1
, pp. 136
-
-
Zhang, Y.1
McEwen, A.E.2
Crothers, D.M.3
Levene, S.D.4
-
32
-
-
0029153579
-
-
EMJODG 0261-4189
-
H. E. Choy, S. W. Park, T. Aki, P. Parrack, N. Fujita, A. Ishihama, and S. Adhya, EMBO J. 14, 4523 (1995). EMJODG 0261-4189
-
(1995)
EMBO J.
, vol.14
, pp. 4523
-
-
Choy, H.E.1
Park, S.W.2
Aki, T.3
Parrack, P.4
Fujita, N.5
Ishihama, A.6
Adhya, S.7
-
33
-
-
0032569960
-
GalR-mediated repression and activation of hybrid lacUV5 promoter: Differential contacts with RNA polymerase
-
DOI 10.1016/S0378-1119(98)00237-6, PII S0378111998002376
-
S. Ryu, N. Fujita, A. Ishihama, and S. Adhya, Gene 223, 235 (1998). GENED6 0378-1119 10.1016/S0378-1119(98)00237-6 (Pubitemid 29015932)
-
(1998)
Gene
, vol.223
, Issue.1-2
, pp. 235-245
-
-
Ryu, S.1
Fujita, N.2
Ishihama, A.3
Adhya, S.4
-
34
-
-
7944220766
-
GalR represses galP1 by inhibiting the rate-determining open complex formation through RNA polymerase contact: A GalR negative control mutant
-
DOI 10.1016/j.jmb.2004.09.070, PII S0022283604012276
-
S. Roy, S. Semsey, M. Liu, G. N. Gussin, and S. Adhya, J. Mol. Biol. 344, 609 (2004). JMOBAK 0022-2836 10.1016/j.jmb.2004.09.070 (Pubitemid 39469207)
-
(2004)
Journal of Molecular Biology
, vol.344
, Issue.3
, pp. 609-618
-
-
Roy, S.1
Semsey, S.2
Liu, M.3
Gussin, G.N.4
Adhya, S.5
-
35
-
-
0024300816
-
-
BICHAW 0006-2960 10.1021/bi00411a002
-
G. R. Bellomy, M. C. Mossing, and M. T. Record, Jr., Biochemistry 27, 3900 (1988). BICHAW 0006-2960 10.1021/bi00411a002
-
(1988)
Biochemistry
, vol.27
, pp. 3900
-
-
Bellomy, G.R.1
Mossing, M.C.2
Record, Jr.M.T.3
|