-
1
-
-
66249088017
-
The second wave of synthetic biology: From modules to systems
-
Purnick, P. E. and Weiss, R. (2009) The second wave of synthetic biology: From modules to systems Nat. Rev. Mol. Cell Biol. 10, 410 - 422
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 410-422
-
-
Purnick, P.E.1
Weiss, R.2
-
2
-
-
84869476328
-
Ribozyme-based insulator parts buffer synthetic circuits from genetic context
-
Lou, C., Stanton, B., Chen, Y. J., Munsky, B., and Voigt, C. A. (2012) Ribozyme-based insulator parts buffer synthetic circuits from genetic context Nat. Biotechnol. 30, 1137 - 1142
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 1137-1142
-
-
Lou, C.1
Stanton, B.2
Chen, Y.J.3
Munsky, B.4
Voigt, C.A.5
-
3
-
-
84869462746
-
Insulating gene circuits from context by RNA processing
-
Bashor, C. J. and Collins, J. J. (2012) Insulating gene circuits from context by RNA processing Nat. Biotechnol. 30, 1061 - 1062
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 1061-1062
-
-
Bashor, C.J.1
Collins, J.J.2
-
4
-
-
77749246295
-
Abduction and asylum in the lives of transcription factors
-
Burger, A., Walczak, A. M., and Wolynes, P. G. (2010) Abduction and asylum in the lives of transcription factors Proc. Natl. Acad. Sci. U.S.A. 107, 4016 - 4021
-
(2010)
Proc. Natl. Acad. Sci. U.S.A.
, vol.107
, pp. 4016-4021
-
-
Burger, A.1
Walczak, A.M.2
Wolynes, P.G.3
-
5
-
-
39149113411
-
Modular cell biology: Retroactivity and insulation
-
Del Vecchio, D., Ninfa, A. J., and Sontag, E. D. (2008) Modular cell biology: Retroactivity and insulation Mol. Syst. Biol. 4, 161
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 161
-
-
Del Vecchio, D.1
Ninfa, A.J.2
Sontag, E.D.3
-
6
-
-
84882676796
-
Retroactivity controls the temporal dynamics of gene transcription
-
Jayanthi, S., Nilgiriwala, K. S., and Del Vecchio, D. (2013) Retroactivity controls the temporal dynamics of gene transcription ACS Synth. Biol. 2, 431 - 441
-
(2013)
ACS Synth. Biol.
, vol.2
, pp. 431-441
-
-
Jayanthi, S.1
Nilgiriwala, K.S.2
Del Vecchio, D.3
-
7
-
-
84859206826
-
A regulatory role for repeated decoy transcription factor binding sites in target gene expression
-
Lee, T. H. and Maheshri, N. (2012) A regulatory role for repeated decoy transcription factor binding sites in target gene expression Mol. Syst. Biol. 8, 576
-
(2012)
Mol. Syst. Biol.
, vol.8
, pp. 576
-
-
Lee, T.H.1
Maheshri, N.2
-
8
-
-
56949098506
-
Molecular titration and ultrasensitivity in regulatory networks
-
Buchler, N. E. and Louis, M. (2008) Molecular titration and ultrasensitivity in regulatory networks J. Mol. Biol. 384, 1106 - 1119
-
(2008)
J. Mol. Biol.
, vol.384
, pp. 1106-1119
-
-
Buchler, N.E.1
Louis, M.2
-
9
-
-
84896392369
-
The transcription factor titration effect dictates level of gene expression
-
Brewster, R. C., Weinert, F. M., Garcia, H. G., Song, D., Rydenfelt, M., and Phillips, R. (2014) The transcription factor titration effect dictates level of gene expression Cell 156, 1312 - 1323
-
(2014)
Cell
, vol.156
, pp. 1312-1323
-
-
Brewster, R.C.1
Weinert, F.M.2
Garcia, H.G.3
Song, D.4
Rydenfelt, M.5
Phillips, R.6
-
10
-
-
15744394108
-
Dissecting the Puzzle of Life: Modularization of Signal Transduction Networks
-
Saez-Rodriguez, J., Kremling, A., and Gilles, E. D. (2005) Dissecting the Puzzle of Life: Modularization of Signal Transduction Networks Comput. Chem. Eng. 29, 619 - 629
-
(2005)
Comput. Chem. Eng.
, vol.29
, pp. 619-629
-
-
Saez-Rodriguez, J.1
Kremling, A.2
Gilles, E.D.3
-
11
-
-
84863322344
-
Contextualizing context for synthetic biology - Identifying causes of failure of synthetic biological systems
-
Cardinale, S. and Arkin, A. P. (2012) Contextualizing context for synthetic biology-Identifying causes of failure of synthetic biological systems Biotechnol. J. 7, 856 - 866
-
(2012)
Biotechnol. J.
, vol.7
, pp. 856-866
-
-
Cardinale, S.1
Arkin, A.P.2
-
12
-
-
79955662812
-
Two-component systems and their co-option for eukaryotic signal transduction
-
Schaller, G. E., Shiu, S. H., and Armitage, J. P. (2011) Two-component systems and their co-option for eukaryotic signal transduction Curr. Biol. 21, R320 - 330
-
(2011)
Curr. Biol.
, vol.21
, pp. R320-R330
-
-
Schaller, G.E.1
Shiu, S.H.2
Armitage, J.P.3
-
13
-
-
12544258487
-
Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli
-
Yamamoto, K., Hirao, K., Oshima, T., Aiba, H., Utsumi, R., and Ishihama, A. (2005) Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli J. Biol. Chem. 280, 1448 - 1456
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 1448-1456
-
-
Yamamoto, K.1
Hirao, K.2
Oshima, T.3
Aiba, H.4
Utsumi, R.5
Ishihama, A.6
-
14
-
-
0035026466
-
The molecular puzzle of two-component signaling cascades
-
Foussard, M., Cabantous, S., Pédelacq, J.-D., Guillet, V., Tranier, S., Mourey, L., Birck, C., and Samama, J.-P. (2001) The molecular puzzle of two-component signaling cascades Microbes Infect. 3, 417 - 424
-
(2001)
Microbes Infect
, vol.3
, pp. 417-424
-
-
Foussard, M.1
Cabantous, S.2
Pédelacq, J.-D.3
Guillet, V.4
Tranier, S.5
Mourey, L.6
Birck, C.7
Samama, J.-P.8
-
15
-
-
0003582512
-
A two-component regulatory system (phoP phoQ) controls Salmonella typhimurium virulence
-
Miller, S. I., Kukral, A. M., and Mekalanos, J. J. (1989) A two-component regulatory system (phoP phoQ) controls Salmonella typhimurium virulence Proc. Natl. Acad. Sci. U.S.A. 86, 5054 - 5058
-
(1989)
Proc. Natl. Acad. Sci. U.S.A.
, vol.86
, pp. 5054-5058
-
-
Miller, S.I.1
Kukral, A.M.2
Mekalanos, J.J.3
-
16
-
-
0011559747
-
Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC
-
Nixon, B. T., Ronson, C. W., and Ausubel, F. M. (1986) Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC Proc. Natl. Acad. Sci. U.S.A. 83, 7850 - 7854
-
(1986)
Proc. Natl. Acad. Sci. U.S.A.
, vol.83
, pp. 7850-7854
-
-
Nixon, B.T.1
Ronson, C.W.2
Ausubel, F.M.3
-
17
-
-
0025015462
-
The two-component regulatory system ompR-envZ controls the virulence of Shigella flexneri
-
Bernardini, M., Fontaine, A., and Sansonetti, P. (1990) The two-component regulatory system ompR-envZ controls the virulence of Shigella flexneri J. Bacteriol. 172, 6274 - 6281
-
(1990)
J. Bacteriol.
, vol.172
, pp. 6274-6281
-
-
Bernardini, M.1
Fontaine, A.2
Sansonetti, P.3
-
18
-
-
0035896019
-
The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system
-
Leonhartsberger, S., Huber, A., Lottspeich, F., and Bock, A. (2001) The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system J. Mol. Biol. 307, 93 - 105
-
(2001)
J. Mol. Biol.
, vol.307
, pp. 93-105
-
-
Leonhartsberger, S.1
Huber, A.2
Lottspeich, F.3
Bock, A.4
-
19
-
-
0032994344
-
Regulation of autophosphorylation of Escherichia coli nitrogen regulator II by the PII signal transduction protein
-
Jiang, P. and Ninfa, A. J. (1999) Regulation of autophosphorylation of Escherichia coli nitrogen regulator II by the PII signal transduction protein J. Bacteriol. 181, 1906 - 1911
-
(1999)
J. Bacteriol.
, vol.181
, pp. 1906-1911
-
-
Jiang, P.1
Ninfa, A.J.2
-
20
-
-
0034687819
-
Nitrogen regulatory protein C-controlled genes of Escherichia coli: Scavenging as a defense against nitrogen limitation
-
Zimmer, D. P., Soupene, E., Lee, H. L., Wendisch, V. F., Khodursky, A. B., Peter, B. J., Bender, R. A., and Kustu, S. (2000) Nitrogen regulatory protein C-controlled genes of Escherichia coli: Scavenging as a defense against nitrogen limitation Proc. Natl. Acad. Sci. U.S.A. 97, 14674 - 14679
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 14674-14679
-
-
Zimmer, D.P.1
Soupene, E.2
Lee, H.L.3
Wendisch, V.F.4
Khodursky, A.B.5
Peter, B.J.6
Bender, R.A.7
Kustu, S.8
-
21
-
-
84920104038
-
A synthetic biology approach to understanding biological oscillations: Developing a genetic oscillator for Escherichia coli
-
(Ditty, J., Mackey, S., and Johnson, C., Eds.), Springer, Berlin Heidelberg
-
Ninfa, A., Atkinson, M., Forger, D., Atkins, S., Arps, D., Selinsky, S., Court, D., Perry, N., and Mayo, A. (2009) A synthetic biology approach to understanding biological oscillations: Developing a genetic oscillator for Escherichia coli, In Bacterial Circadian Programs (Ditty, J., Mackey, S., and Johnson, C., Eds.), pp 301 - 329, Springer, Berlin Heidelberg.
-
(2009)
Bacterial Circadian Programs
, pp. 301-329
-
-
Ninfa, A.1
Atkinson, M.2
Forger, D.3
Atkins, S.4
Arps, D.5
Selinsky, S.6
Court, D.7
Perry, N.8
Mayo, A.9
-
22
-
-
0026773062
-
Phosphorylation of nitrogen regulator I of Escherichia coli induces strong cooperative binding to DNA essential for activation of transcription
-
Weiss, V., Claverie-Martin, F., and Magasanik, B. (1992) Phosphorylation of nitrogen regulator I of Escherichia coli induces strong cooperative binding to DNA essential for activation of transcription Proc. Natl. Acad. Sci. U.S.A. 89, 5088 - 5092
-
(1992)
Proc. Natl. Acad. Sci. U.S.A.
, vol.89
, pp. 5088-5092
-
-
Weiss, V.1
Claverie-Martin, F.2
Magasanik, B.3
-
23
-
-
0345353513
-
Phosphorylation of nitrogen regulator I (NRI) of Escherichia coli
-
Weiss, V. and Magasanik, B. (1988) Phosphorylation of nitrogen regulator I (NRI) of Escherichia coli Proc. Natl. Acad. Sci. U.S.A. 85, 8919 - 8923
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, pp. 8919-8923
-
-
Weiss, V.1
Magasanik, B.2
-
24
-
-
0037312799
-
Genetic and biochemical analysis of phosphatase activity of Escherichia coli NRII (NtrB) and its regulation by the PII signal transduction protein
-
Pioszak, A. A. and Ninfa, A. J. (2003) Genetic and biochemical analysis of phosphatase activity of Escherichia coli NRII (NtrB) and its regulation by the PII signal transduction protein J. Bacteriol. 185, 1299 - 1315
-
(2003)
J. Bacteriol.
, vol.185
, pp. 1299-1315
-
-
Pioszak, A.A.1
Ninfa, A.J.2
-
25
-
-
0027441194
-
Mutational analysis of the bacterial signal-transducing protein kinase/phosphatase nitrogen regulator II (NRII or NtrB)
-
Atkinson, M. R. and Ninfa, A. J. (1993) Mutational analysis of the bacterial signal-transducing protein kinase/phosphatase nitrogen regulator II (NRII or NtrB) J. Bacteriol. 175, 7016 - 7023
-
(1993)
J. Bacteriol.
, vol.175
, pp. 7016-7023
-
-
Atkinson, M.R.1
Ninfa, A.J.2
-
26
-
-
80054039227
-
Load-induced modulation of signal transduction networks
-
Jiang, P., Ventura, A. C., Sontag, E. D., Merajver, S. D., Ninfa, A. J., and Del Vecchio, D. (2011) Load-induced modulation of signal transduction networks Sci. Signal. 4, ra67
-
(2011)
Sci. Signal.
, vol.4
, pp. ra67
-
-
Jiang, P.1
Ventura, A.C.2
Sontag, E.D.3
Merajver, S.D.4
Ninfa, A.J.5
Del Vecchio, D.6
-
27
-
-
0034460872
-
The unphosphorylated receiver domain of PhoB silences the activity of its output domain
-
Ellison, D. W. and McCleary, W. R. (2000) The unphosphorylated receiver domain of PhoB silences the activity of its output domain J. Bacteriol. 182, 6592 - 6597
-
(2000)
J. Bacteriol.
, vol.182
, pp. 6592-6597
-
-
Ellison, D.W.1
McCleary, W.R.2
-
28
-
-
19944420855
-
The CovR response regulator of group A streptococcus (GAS) acts directly to repress its own promoter
-
Gusa, A. A. and Scott, J. R. (2005) The CovR response regulator of group A streptococcus (GAS) acts directly to repress its own promoter Mol. Microbiol. 56, 1195 - 1207
-
(2005)
Mol. Microbiol.
, vol.56
, pp. 1195-1207
-
-
Gusa, A.A.1
Scott, J.R.2
-
29
-
-
34548485562
-
Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon
-
Matta, M. K., Lioliou, E. E., Panagiotidis, C. H., Kyriakidis, D. A., and Panagiotidis, C. A. (2007) Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon J. Bacteriol. 189, 6324 - 6332
-
(2007)
J. Bacteriol.
, vol.189
, pp. 6324-6332
-
-
Matta, M.K.1
Lioliou, E.E.2
Panagiotidis, C.H.3
Kyriakidis, D.A.4
Panagiotidis, C.A.5
-
30
-
-
0026533766
-
Role of nitrogen regulator I (NtrC), the transcriptional activator of glnA in enteric bacteria, in reducing expression of glnA during nitrogen-limited growth
-
Shiau, S. P., Schneider, B. L., Gu, W., and Reitzer, L. J. (1992) Role of nitrogen regulator I (NtrC), the transcriptional activator of glnA in enteric bacteria, in reducing expression of glnA during nitrogen-limited growth J. Bacteriol. 174, 179 - 185
-
(1992)
J. Bacteriol.
, vol.174
, pp. 179-185
-
-
Shiau, S.P.1
Schneider, B.L.2
Gu, W.3
Reitzer, L.J.4
-
31
-
-
58149145777
-
The biphasic behavior of incoherent feed-forward loops in biomolecular regulatory networks
-
Kim, D., Kwon, Y. K., and Cho, K. H. (2008) The biphasic behavior of incoherent feed-forward loops in biomolecular regulatory networks BioEssays: News and Reviews in Molecular, Cellular, and Developmental Biology 30, 1204 - 1211
-
(2008)
BioEssays: News and Reviews in Molecular, Cellular, and Developmental Biology
, vol.30
, pp. 1204-1211
-
-
Kim, D.1
Kwon, Y.K.2
Cho, K.H.3
-
32
-
-
21644438022
-
Regulatory modules that generate biphasic signal response in biological systems
-
Levchenko, A., Bruck, J., and Sternberg, P. (2004) Regulatory modules that generate biphasic signal response in biological systems Syst. Biol. 1, 139 - 148
-
(2004)
Syst. Biol.
, vol.1
, pp. 139-148
-
-
Levchenko, A.1
Bruck, J.2
Sternberg, P.3
-
33
-
-
84883540561
-
Optimal design of phosphorylation-based insulation devices
-
IEEE
-
Rivera, P. M. and Del Vecchio, D. (2013) Optimal design of phosphorylation-based insulation devices Am. Control Conf. (ACC) 2013, 3783 - 3789 IEEE.
-
(2013)
Am. Control Conf. (ACC)
, vol.2013
, pp. 3783-3789
-
-
Rivera, P.M.1
Del Vecchio, D.2
-
34
-
-
84920260857
-
A load driver device for engineering modularity in biological networks
-
in press
-
Mishra, D., Rivera, P., Del Vecchio, D., and Weiss, R. (2014) A load driver device for engineering modularity in biological networks Nature Biotech., in press.
-
(2014)
Nature Biotech
-
-
Mishra, D.1
Rivera, P.2
Del Vecchio, D.3
Weiss, R.4
-
35
-
-
84871016428
-
Evolution of two-component signal transduction systems
-
Capra, E. J. and Laub, M. T. (2012) Evolution of two-component signal transduction systems Annu. Rev. Microbiol. 66, 325 - 347
-
(2012)
Annu. Rev. Microbiol.
, vol.66
, pp. 325-347
-
-
Capra, E.J.1
Laub, M.T.2
-
36
-
-
84868087234
-
Engineering robust control of two-component system phosphotransfer using modular scaffolds
-
Whitaker, W. R., Davis, S. A., Arkin, A. P., and Dueber, J. E. (2012) Engineering robust control of two-component system phosphotransfer using modular scaffolds Proc. Natl. Acad. Sci. U.S.A. 109, 18090 - 18095
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 18090-18095
-
-
Whitaker, W.R.1
Davis, S.A.2
Arkin, A.P.3
Dueber, J.E.4
-
37
-
-
34248205790
-
Bacterial response regulators: Versatile regulatory strategies from common domains
-
Gao, R., Mack, T. R., and Stock, A. M. (2007) Bacterial response regulators: Versatile regulatory strategies from common domains Trends Biochem. Sci. 32, 225 - 234
-
(2007)
Trends Biochem. Sci.
, vol.32
, pp. 225-234
-
-
Gao, R.1
MacK, T.R.2
Stock, A.M.3
-
39
-
-
84897463052
-
Modular composition of gene transcription networks
-
Gyorgy, A. and Del Vecchio, D. (2014) Modular composition of gene transcription networks PLoS Comput. Biol. 10, e1003486
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003486
-
-
Gyorgy, A.1
Del Vecchio, D.2
-
40
-
-
44449112421
-
Specificity in two-component signal transduction pathways
-
Laub, M. T. and Goulian, M. (2007) Specificity in two-component signal transduction pathways Annu. Rev. Genet. 41, 121 - 145
-
(2007)
Annu. Rev. Genet.
, vol.41
, pp. 121-145
-
-
Laub, M.T.1
Goulian, M.2
-
41
-
-
84858604873
-
Expanding the synthetic biology toolbox: Engineering orthogonal regulators of gene expression
-
Rao, C. V. (2012) Expanding the synthetic biology toolbox: Engineering orthogonal regulators of gene expression Curr. Opin. Biotechnol. 23, 689 - 694
-
(2012)
Curr. Opin. Biotechnol.
, vol.23
, pp. 689-694
-
-
Rao, C.V.1
-
42
-
-
66649105445
-
Synthesis of orthogonal transcription-translation networks
-
An, W. and Chin, J. W. (2009) Synthesis of orthogonal transcription-translation networks Proc. Natl. Acad. Sci. U.S.A. 106, 8477 - 8482
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 8477-8482
-
-
An, W.1
Chin, J.W.2
-
43
-
-
24044543111
-
A network of orthogonal ribosome·mRNA pairs
-
Rackham, O. and Chin, J. W. (2005) A network of orthogonal ribosome·mRNA pairs Nat. Chem. Biol. 1, 159 - 166
-
(2005)
Nat. Chem. Biol.
, vol.1
, pp. 159-166
-
-
Rackham, O.1
Chin, J.W.2
-
44
-
-
84905376865
-
A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase
-
Segall-Shapiro, T. H., Meyer, A. J., Ellington, A. D., Sontag, E. D., and Voigt, C. A. (2014) A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase Mol. Syst. Biol. 10, 742
-
(2014)
Mol. Syst. Biol.
, vol.10
, pp. 742
-
-
Segall-Shapiro, T.H.1
Meyer, A.J.2
Ellington, A.D.3
Sontag, E.D.4
Voigt, C.A.5
|