-
1
-
-
34249079154
-
Network motifs: Theory and experimental approaches
-
Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8 : 450 461.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
3
-
-
34547916832
-
Environmental signal integration by a modular and gate
-
Anderson JC, Voigt CA Arkin AP (2007) Environmental signal integration by a modular AND gate. Mol Syst Biol 3 : 133.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 133
-
-
Anderson, J.C.1
Voigt, C.A.2
Arkin, A.P.3
-
4
-
-
0038241770
-
Development of genetic circuitry exhibiting toggle switch or oscillatory behaviour in Escherichia coli
-
Atkinson MR, Savageau MA, Myers JT Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behaviour in Escherichia coli. Cell 113 : 597 607.
-
(2003)
Cell
, vol.113
, pp. 597-607
-
-
Atkinson, M.R.1
Savageau, M.A.2
Myers, J.T.3
Ninfa, A.J.4
-
5
-
-
4444256116
-
Regulatory circuit design and evolution using phage λ
-
Atsumi S Little JW (2004) Regulatory circuit design and evolution using phage λ. Genes Dev 18 : 2086 2094.
-
(2004)
Genes Dev
, vol.18
, pp. 2086-2094
-
-
Atsumi, S.1
Little, J.W.2
-
6
-
-
35548990232
-
A synthetic phage λ regulatory circuit
-
Atsumi S Little JW (2006) A synthetic phage λ regulatory circuit. P Natl Acad Sci USA 103 : 19045 19050.
-
(2006)
P Natl Acad Sci USA
, vol.103
, pp. 19045-19050
-
-
Atsumi, S.1
Little, J.W.2
-
8
-
-
42149089190
-
A synthetic Escherichia coli predator-prey ecosystem
-
Balagaddé FK, Song H, Ozaki J, Collins CH, Barnet M, Arnold FH, Quake SR You L (2008) A synthetic Escherichia coli predator-prey ecosystem. Mol Syst Biol 4 : 187.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 187
-
-
Balagaddé, F.K.1
Song, H.2
Ozaki, J.3
Collins, C.H.4
Barnet, M.5
Arnold, F.H.6
Quake, S.R.7
You, L.8
-
9
-
-
17844374314
-
A synthetic multicellular system for programmed pattern formation
-
Basu S, Gerchman Y, Collins CH, Arnold FH Weiss R (2005) A synthetic multicellular system for programmed pattern formation. Nature 434 : 1130 1134.
-
(2005)
Nature
, vol.434
, pp. 1130-1134
-
-
Basu, S.1
Gerchman, Y.2
Collins, C.H.3
Arnold, F.H.4
Weiss, R.5
-
10
-
-
0034212551
-
Engineering stability in gene networks by autoregulation
-
Becskei A Serrano L (2000) Engineering stability in gene networks by autoregulation. Nature 405 : 590 593.
-
(2000)
Nature
, vol.405
, pp. 590-593
-
-
Becskei, A.1
Serrano, L.2
-
11
-
-
5644304158
-
Bacterial gene regulation: From transcription attenuation to riboswitches and ribozymes
-
Brantl S (2004) Bacterial gene regulation: from transcription attenuation to riboswitches and ribozymes. Trends Microbiol 12 : 473 475.
-
(2004)
Trends Microbiol
, vol.12
, pp. 473-475
-
-
Brantl, S.1
-
12
-
-
22144443131
-
Nonlinear protein degradation and the function of genetic circuits
-
Buchler NE, Gerland U Hwa T (2005) Nonlinear protein degradation and the function of genetic circuits. P Natl Acad Sci USA 102 : 9559 9564.
-
(2005)
P Natl Acad Sci USA
, vol.102
, pp. 9559-9564
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
13
-
-
1442306167
-
Design of artificial cell-cell communication using gene and metabolic networks
-
Bulter T, Lee SG, Wong WW, Fung E, Connor MR Liao JC (2004) Design of artificial cell-cell communication using gene and metabolic networks. P Natl Acad Sci USA 101 : 2299 2304.
-
(2004)
P Natl Acad Sci USA
, vol.101
, pp. 2299-2304
-
-
Bulter, T.1
Lee, S.G.2
Wong, W.W.3
Fung, E.4
Connor, M.R.5
Liao, J.C.6
-
14
-
-
33645813418
-
On the attenuation and amplification of molecular noise in genetic regulatory networks
-
Chen BS Wang YC (2006) On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics 7 : 52.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 52
-
-
Chen, B.S.1
Wang, Y.C.2
-
15
-
-
39749104182
-
Engineering Escherichia coli heat-resistance by synthetic gene amplification
-
Christ D Chin JW (2007) Engineering Escherichia coli heat-resistance by synthetic gene amplification. Protein Eng Des Sel 21 : 121 125.
-
(2007)
Protein Eng des Sel
, vol.21
, pp. 121-125
-
-
Christ, D.1
Chin, J.W.2
-
16
-
-
42549159572
-
OptCircuit: An optimization based method for computational design of genetic circuits
-
Dasika MS Maranas CD (2008) OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst Biol 3 : 24.
-
(2008)
BMC Syst Biol
, vol.3
, pp. 24
-
-
Dasika, M.S.1
Maranas, C.D.2
-
17
-
-
23144432213
-
Optimality and evolutionary tuning of the expression level of a protein
-
Dekel E Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436 : 588 592.
-
(2005)
Nature
, vol.436
, pp. 588-592
-
-
Dekel, E.1
Alon, U.2
-
18
-
-
6044261460
-
Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation
-
Desai SK Gallivan JP (2004) Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J Am Chem Soc 126 : 13247 13254.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 13247-13254
-
-
Desai, S.K.1
Gallivan, J.P.2
-
20
-
-
33846108256
-
Noise in transcription negative feedback loops: Simulation and experimental analysis
-
Dublanche Y, Michalodimitrakis K, Kümmerer N, Foglierini M Serrano L (2006) Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol 2 : 41.
-
(2006)
Mol Syst Biol
, vol.2
, pp. 41
-
-
Dublanche, Y.1
Michalodimitrakis, K.2
Kümmerer, N.3
Foglierini, M.4
Serrano, L.5
-
21
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz MB Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403 : 335 338.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
22
-
-
0034024497
-
Improving lycopene production in Escherichia coli by engineering metabolic control
-
Farmer WR Liao JC (2000) Improving lycopene production in Escherichia coli by engineering metabolic control. Nature 18 : 533 537.
-
(2000)
Nature
, vol.18
, pp. 533-537
-
-
Farmer, W.R.1
Liao, J.C.2
-
23
-
-
14844364430
-
Optimizing genetic circuits by global sensitivity analysis
-
Feng XJ, Hooshangi S, Chen D, Li G, Weiss R Rabitz H (2004) Optimizing genetic circuits by global sensitivity analysis. Biophys J 87 : 2195 2202.
-
(2004)
Biophys J
, vol.87
, pp. 2195-2202
-
-
Feng, X.J.1
Hooshangi, S.2
Chen, D.3
Li, G.4
Weiss, R.5
Rabitz, H.6
-
24
-
-
18344381476
-
A synthetic gene-metabolice oscillator
-
Fung E, Wong WW, Suen JK, Bulter T, Lee SG Liao JC (2005) A synthetic gene-metabolice oscillator. Nature 435 : 118 122.
-
(2005)
Nature
, vol.435
, pp. 118-122
-
-
Fung, E.1
Wong, W.W.2
Suen, J.K.3
Bulter, T.4
Lee, S.G.5
Liao, J.C.6
-
25
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner TS, Cantor CR Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403 : 339 342.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
26
-
-
33750874085
-
From ribosome to riboswitch: Control of gene expression in Bacteria by RNA structural rearrangements
-
Grundy FJ Henkin TM (2006) From ribosome to riboswitch: control of gene expression in Bacteria by RNA structural rearrangements. Crit Rev Biochem Mol Biol 41 : 329 338.
-
(2006)
Crit Rev Biochem Mol Biol
, vol.41
, pp. 329-338
-
-
Grundy, F.J.1
Henkin, T.M.2
-
28
-
-
32844455250
-
A bottom-up approach to gene regulation
-
Guido NJ, Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC Collins JJ (2006) A bottom-up approach to gene regulation. Nature 439 : 856 860.
-
(2006)
Nature
, vol.439
, pp. 856-860
-
-
Guido, N.J.1
Wang, X.2
Adalsteinsson, D.3
McMillen, D.4
Hasty, J.5
Cantor, C.R.6
Elston, T.C.7
Collins, J.J.8
-
30
-
-
38349096406
-
Implications of rewiring bacterial quorum sensing
-
Haseltine EL Arnold FH (2008) Implications of rewiring bacterial quorum sensing. Appl Environ Microbiol 74 : 437 445.
-
(2008)
Appl Environ Microbiol
, vol.74
, pp. 437-445
-
-
Haseltine, E.L.1
Arnold, F.H.2
-
32
-
-
14844358192
-
Ultrasensitivity and noise propagation in synthetic transcriptional cascade
-
Hooshangi S, Thiberge S Weiss R (2005) Ultrasensitivity and noise propagation in synthetic transcriptional cascade. P Natl Acad Sci USA 102 : 3581 3586.
-
(2005)
P Natl Acad Sci USA
, vol.102
, pp. 3581-3586
-
-
Hooshangi, S.1
Thiberge, S.2
Weiss, R.3
-
33
-
-
51349119090
-
Dark proteins: Effect of inclusion body formation on quantification of protein expression
-
Iafolla MA, Mazumder M, Sardana V, Velauthapillai T, Pannu K McMillen DR (2008) Dark proteins: effect of inclusion body formation on quantification of protein expression. Proteins 72 : 1233 1242.
-
(2008)
Proteins
, vol.72
, pp. 1233-1242
-
-
Iafolla, M.A.1
Mazumder, M.2
Sardana, V.3
Velauthapillai, T.4
Pannu, K.5
McMillen, D.R.6
-
34
-
-
3042741121
-
Engineered riboregulators enable post-transcriptional control of gene expression
-
Isaacs FJ, Dwyer DJ, Ding C, Pervouchine DD, Cantor CR Collins JJ (2004) Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotech 22 : 841 847.
-
(2004)
Nat Biotech
, vol.22
, pp. 841-847
-
-
Isaacs, F.J.1
Dwyer, D.J.2
Ding, C.3
Pervouchine, D.D.4
Cantor, C.R.5
Collins, J.J.6
-
36
-
-
0034930363
-
A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter
-
Isalan M, Klug A Choo Y (2001) A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter. Nat Biotech 19 : 656 660.
-
(2001)
Nat Biotech
, vol.19
, pp. 656-660
-
-
Isalan, M.1
Klug, A.2
Choo, Y.3
-
37
-
-
18144363600
-
Engineering gene networks to emulate Drosophila embryonic pattern formation
-
Isalan M, Lemerle C Serrano L (2005) Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol 3 : e64.
-
(2005)
PLoS Biol
, vol.3
-
-
Isalan, M.1
Lemerle, C.2
Serrano, L.3
-
38
-
-
42249098422
-
Evolvability and hierarchy in rewired bacterial gene networks
-
Isalan M, Lemerle C, Michalodimitrakis K, Horn C, Beltrao P, Raineri E, Garriga-Canut M Serrano L (2008) Evolvability and hierarchy in rewired bacterial gene networks. Nature 452 : 840 845.
-
(2008)
Nature
, vol.452
, pp. 840-845
-
-
Isalan, M.1
Lemerle, C.2
Michalodimitrakis, K.3
Horn, C.4
Beltrao, P.5
Raineri, E.6
Garriga-Canut, M.7
Serrano, L.8
-
39
-
-
35848958822
-
Autonomous synchronization of the circardian KaiC phosphorylation rhythm
-
Ito H, Kageyama H, Mutsuda M, Nakajima M, Oyama T Kondo T (2007) Autonomous synchronization of the circardian KaiC phosphorylation rhythm. Nat Struct Mol Biol 14 : 1084 1088.
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 1084-1088
-
-
Ito, H.1
Kageyama, H.2
Mutsuda, M.3
Nakajima, M.4
Oyama, T.5
Kondo, T.6
-
41
-
-
16344364226
-
Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system
-
Karig D Weiss R (2005) Signal-amplifying genetic circuit enables in vivo observation of weak promoter activation in the Rhl quorum sensing system. Biotechnol Bioeng 89 : 709 718.
-
(2005)
Biotechnol Bioeng
, vol.89
, pp. 709-718
-
-
Karig, D.1
Weiss, R.2
-
42
-
-
38349013623
-
Coupled feedback loops form dynamic motifs of cellular networks
-
Kim JR, Yoon Y Cho KH (2008) Coupled feedback loops form dynamic motifs of cellular networks. Biophys J 94 : 359 365.
-
(2008)
Biophys J
, vol.94
, pp. 359-365
-
-
Kim, J.R.1
Yoon, Y.2
Cho, K.H.3
-
43
-
-
33744794380
-
Regulatory dynamics of synthetic gene networks with positive feedback
-
Maeda YT Sano M (2006) Regulatory dynamics of synthetic gene networks with positive feedback. J Mol Biol 359 : 1107 1124.
-
(2006)
J Mol Biol
, vol.359
, pp. 1107-1124
-
-
Maeda, Y.T.1
Sano, M.2
-
44
-
-
0038391517
-
Engineering a mevalonate pathway in Escherichia coli for production of terpenoids
-
Martin VJJ, Pitera DJ, Withers ST, Newman JD Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21 : 1558 1561.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 1558-1561
-
-
Martin, V.J.J.1
Pitera, D.J.2
Withers, S.T.3
Newman, J.D.4
Keasling, J.D.5
-
46
-
-
34547925618
-
Combinatorial promoter design for engineering noisy gene expression
-
Murphy KF, Balázsi G Collins JJ (2007) Combinatorial promoter design for engineering noisy gene expression. P Natl Acad Sci USA 104 : 12727 12731.
-
(2007)
P Natl Acad Sci USA
, vol.104
, pp. 12727-12731
-
-
Murphy, K.F.1
Balázsi, G.2
Collins, J.J.3
-
48
-
-
17244373578
-
Reconstitution of circadian oscillatio of cyanobacterial KaiC phosphorylation in vitro
-
Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T Kondo T (2005) Reconstitution of circadian oscillatio of cyanobacterial KaiC phosphorylation in vitro. Science 308 : 414 415.
-
(2005)
Science
, vol.308
, pp. 414-415
-
-
Nakajima, M.1
Imai, K.2
Ito, H.3
Nishiwaki, T.4
Murayama, Y.5
Iwasaki, H.6
Oyama, T.7
Kondo, T.8
-
50
-
-
36148970816
-
Reengineering a natural riboswitch by dual genetic selection
-
Nomura Y Yokobayashi Y (2007) Reengineering a natural riboswitch by dual genetic selection. J Am Chem Soc 129 : 13814 13815.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 13814-13815
-
-
Nomura, Y.1
Yokobayashi, Y.2
-
51
-
-
42949166288
-
Development of a new-type riboswitch using an aptazyme and an anti-RBS sequence
-
Ogawa A Maeda M (2007) Development of a new-type riboswitch using an aptazyme and an anti-RBS sequence. Nucleic Acids Symp Ser (Oxford) 51 : 389 390.
-
(2007)
Nucleic Acids Symp Ser (Oxford)
, vol.51
, pp. 389-390
-
-
Ogawa, A.1
Maeda, M.2
-
52
-
-
50549090249
-
Targeted development of registries of biological parts
-
Peccoud J, Blauvelt MF, Cai Y et al 2008) Targeted development of registries of biological parts. PLoS ONE 3 : e2671.
-
(2008)
PLoS ONE
, vol.3
-
-
Peccoud, J.1
Blauvelt, M.F.2
Cai, Y.3
Al, E.4
-
53
-
-
33747078696
-
Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes
-
Pfleger BF, Pitera DJ, Smolke CD Keasling JD (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24 : 1027 1032.
-
(2006)
Nat Biotechnol
, vol.24
, pp. 1027-1032
-
-
Pfleger, B.F.1
Pitera, D.J.2
Smolke, C.D.3
Keasling, J.D.4
-
54
-
-
0004211673
-
-
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
-
Ptashne M Gann A (2002) Genes and Signals. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
-
(2002)
Genes and Signals.
-
-
Ptashne, M.1
Gann, A.2
-
55
-
-
24044543111
-
A network of orthogonal ribosome-mRNA pairs
-
Rackham O Chin JW (2005a) 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
-
56
-
-
29344453148
-
Cellular logic with orthogonal ribosomes
-
Rackham O Chin JW (2005b) Cellular logic with orthogonal ribosomes. J Am Chem Soc 127 : 17584 17585.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 17584-17585
-
-
Rackham, O.1
Chin, J.W.2
-
57
-
-
34547861255
-
Genetdes: Automatic design of transcriptional networks
-
Rodrigo G, Carrera J Jaramillo A (2007) Genetdes: automatic design of transcriptional networks. Bioinformatics 23 : 1857 1858.
-
(2007)
Bioinformatics
, vol.23
, pp. 1857-1858
-
-
Rodrigo, G.1
Carrera, J.2
Jaramillo, A.3
-
58
-
-
36248980394
-
Accurate prediction of gene feedback circuit behavior from component properties
-
Rosenfeld N, Young JW, Alon U, Swain PS Elowitz MB (2007) Accurate prediction of gene feedback circuit behavior from component properties. Mol Syst Biol 3 : 143.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 143
-
-
Rosenfeld, N.1
Young, J.W.2
Alon, U.3
Swain, P.S.4
Elowitz, M.B.5
-
59
-
-
34848885875
-
Construction and engineering of positive feedback loops
-
Sayut DJ, Niu Y Sun L (2006) Construction and engineering of positive feedback loops. Chem Biol 1 : 692 696.
-
(2006)
Chem Biol
, vol.1
, pp. 692-696
-
-
Sayut, D.J.1
Niu, Y.2
Sun, L.3
-
60
-
-
36248967767
-
Engineering and applications of genetic circuits
-
Sayut DJ, Kambam PK Sun L (2007) Engineering and applications of genetic circuits. Mol Biosyst 3 : 835 840.
-
(2007)
Mol Biosyst
, vol.3
, pp. 835-840
-
-
Sayut, D.J.1
Kambam, P.K.2
Sun, L.3
-
61
-
-
45149118469
-
Engineering BioBrick vectors from biobrick parts
-
Shetty RP, Endy D Knight Jr. TF (2008) Engineering BioBrick vectors from biobrick parts. J Biol Eng 2 : 5.
-
(2008)
J Biol Eng
, vol.2
, pp. 5
-
-
Shetty, R.P.1
Endy, D.2
Knightjr., T.F.3
-
62
-
-
34447518290
-
Synthetic tetracycline-inducible regulatory networks: Computer-aided design of dynamic phenotypes
-
Sotiropoulos V Kaznessis YN (2007) Synthetic tetracycline-inducible regulatory networks: computer-aided design of dynamic phenotypes. BMC Syst Biol 1 : 7.
-
(2007)
BMC Syst Biol
, vol.1
, pp. 7
-
-
Sotiropoulos, V.1
Kaznessis, Y.N.2
-
63
-
-
2542601538
-
A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo
-
Suess B, Fink B, Berens C, Stenz R Hillen W (2004) A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. Nucleic Acids Res 32 : 1610 1614.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1610-1614
-
-
Suess, B.1
Fink, B.2
Berens, C.3
Stenz, R.4
Hillen, W.5
-
64
-
-
34249806305
-
Guiding bacteria with small molecules and RNA
-
Topp S Gallivan JP (2007) Guiding bacteria with small molecules and RNA. J Am Chem Soc 129 : 6807 6811.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 6807-6811
-
-
Topp, S.1
Gallivan, J.P.2
-
66
-
-
0032500736
-
Controlling gene expression in living cells through small molecule-RNA interactions
-
Werstuck G Green MR (1998) Controlling gene expression in living cells through small molecule-RNA interactions. Science 282 : 296 298.
-
(1998)
Science
, vol.282
, pp. 296-298
-
-
Werstuck, G.1
Green, M.R.2
-
67
-
-
1642586299
-
Control of gene expression by a natural metabolite-responsive ribozyme
-
Winkler WC, Nahvi A, Roth A, Collins JA Breaker RR (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428 : 281 286.
-
(2004)
Nature
, vol.428
, pp. 281-286
-
-
Winkler, W.C.1
Nahvi, A.2
Roth, A.3
Collins, J.A.4
Breaker, R.R.5
|