-
2
-
-
79955553550
-
Origin of bistability underlying mammalian cell cycle entry
-
Yao G, Tan C, West M, Nevins JR, You L (2011) Origin of bistability underlying mammalian cell cycle entry. Mol Syst Biol 7:485.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 485
-
-
Yao, G.1
Tan, C.2
West, M.3
Nevins, J.R.4
You, L.5
-
3
-
-
73049167504
-
Teleonomic mechanisms in cellular metabolism, growth, and differentiation
-
Monod J, Jacob F (1961) Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb Sym 26:389-401.
-
(1961)
Cold Spring Harb Sym
, vol.26
, pp. 389-401
-
-
Monod, J.1
Jacob, F.2
-
4
-
-
1442354192
-
Multistability in the lactose utilization network of Escherichia coli
-
Ozbudak EM, Thattai M, Lim HN, Shraiman BI, Van Oudenaarden A (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427(6976):737-740.
-
(2004)
Nature
, vol.427
, Issue.6976
, pp. 737-740
-
-
Ozbudak, E.M.1
Thattai, M.2
Lim, H.N.3
Shraiman, B.I.4
Van Oudenaarden, A.5
-
5
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
-
Arkin A, Ross J, McAdams HH (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149(4):1633-1648.
-
(1998)
Genetics
, vol.149
, Issue.4
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
6
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335-338.
-
(2000)
Nature
, vol.403
, Issue.6767
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
7
-
-
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(6767):339-342.
-
(2000)
Nature
, vol.403
, Issue.6767
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
8
-
-
0037079012
-
Engineered gene circuits
-
Hasty J, McMillen D, Collins JJ (2002) Engineered gene circuits. Nature 420(6912):224-230.
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 224-230
-
-
Hasty, J.1
McMillen, D.2
Collins, J.J.3
-
9
-
-
32844455250
-
A bottom-up approach to gene regulation
-
Guido NJ, et al. (2006) A bottom-up approach to gene regulation. Nature 439(7078):856-860.
-
(2006)
Nature
, vol.439
, Issue.7078
, pp. 856-860
-
-
Guido, N.J.1
-
10
-
-
80052493200
-
Synthetic biology: Integrated gene circuits
-
Nandagopal N, Elowitz MB (2011) Synthetic biology: Integrated gene circuits. Science 333(6047):1244-1248.
-
(2011)
Science
, vol.333
, Issue.6047
, pp. 1244-1248
-
-
Nandagopal, N.1
Elowitz, M.B.2
-
11
-
-
14844358192
-
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
-
Hooshangi S, Thiberge S, Weiss R (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc Natl Acad Sci USA 102(10):3581-3586.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.10
, pp. 3581-3586
-
-
Hooshangi, S.1
Thiberge, S.2
Weiss, R.3
-
12
-
-
66349125024
-
Synthetic gene networks that count
-
Friedland AE, et al. (2009) Synthetic gene networks that count. Science 324(5931):1199-1202.
-
(2009)
Science
, vol.324
, Issue.5931
, pp. 1199-1202
-
-
Friedland, A.E.1
-
13
-
-
3042822415
-
An engineered epigenetic transgene switch in mammalian cells
-
Kramer BP, et al. (2004) An engineered epigenetic transgene switch in mammalian cells. Nat Biotechnol 22(7):867-870.
-
(2004)
Nat Biotechnol
, vol.22
, Issue.7
, pp. 867-870
-
-
Kramer, B.P.1
-
14
-
-
0038241770
-
Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
-
Atkinson MR, Savageau MA, Myers JT, Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113(5):597-607.
-
(2003)
Cell
, vol.113
, Issue.5
, pp. 597-607
-
-
Atkinson, M.R.1
Savageau, M.A.2
Myers, J.T.3
Ninfa, A.J.4
-
15
-
-
77949405661
-
Synthesizing a novel genetic sequential logic circuit: A push-on push-off switch
-
Lou C, et al. (2010) Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Mol Syst Biol 6:350.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 350
-
-
Lou, C.1
-
16
-
-
71849110893
-
Next-generation synthetic gene networks
-
Lu TK, Khalil AS, Collins JJ (2009) Next-generation synthetic gene networks. Nat Biotechnol 27(12):1139-1150.
-
(2009)
Nat Biotechnol
, vol.27
, Issue.12
, pp. 1139-1150
-
-
Lu, T.K.1
Khalil, A.S.2
Collins, J.J.3
-
17
-
-
66249088017
-
The second wave of synthetic biology: From modules to systems
-
Purnick PEM, Weiss R (2009) The second wave of synthetic biology: From modules to systems. Nat Rev Mol Cell Biol 10(6):410-422.
-
(2009)
Nat Rev Mol Cell Biol
, vol.10
, Issue.6
, pp. 410-422
-
-
Purnick, P.E.M.1
Weiss, R.2
-
18
-
-
66149172363
-
Diversity-based, model-guided construction of synthetic gene networks with predicted functions
-
Ellis T, Wang X, Collins JJ (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol 27(5):465-471.
-
(2009)
Nat Biotechnol
, vol.27
, Issue.5
, pp. 465-471
-
-
Ellis, T.1
Wang, X.2
Collins, J.J.3
-
19
-
-
84855481443
-
Competition for catalytic resources alters biological network dynamics
-
Rondelez Y (2012) Competition for catalytic resources alters biological network dynamics. Phys Rev Lett 108(1):018102.
-
(2012)
Phys Rev Lett
, vol.108
, Issue.1
, pp. 018102
-
-
Rondelez, Y.1
-
20
-
-
61349161146
-
Delay-induced degrade-and-fire oscillations in small genetic circuits
-
Mather W, Bennett MR, Hasty J, Tsimring LS (2009) Delay-induced degrade-and-fire oscillations in small genetic circuits. Phys Rev Lett 102(6):068105.
-
(2009)
Phys Rev Lett
, vol.102
, Issue.6
, pp. 068105
-
-
Mather, W.1
Bennett, M.R.2
Hasty, J.3
Tsimring, L.S.4
-
21
-
-
70350324632
-
Emergent bistability by a growth-modulating positive feedback circuit
-
Tan C, Marguet P, You L (2009) Emergent bistability by a growth-modulating positive feedback circuit. Nat Chem Biol 5(11):842-848.
-
(2009)
Nat Chem Biol
, vol.5
, Issue.11
, pp. 842-848
-
-
Tan, C.1
Marguet, P.2
You, L.3
-
22
-
-
33846116559
-
Construction of an in vitro bistable circuit from synthetic transcriptional switches
-
Kim J, White KS, Winfree E (2006) Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol 2:68.
-
(2006)
Mol Syst Biol
, vol.2
, pp. 68
-
-
Kim, J.1
White, K.S.2
Winfree, E.3
-
23
-
-
79551586208
-
Programming an in vitro DNA oscillator using a molecular networking strategy
-
Montagne K, Plasson R, Sakai Y, Fujii T, Rondelez Y (2011) Programming an in vitro DNA oscillator using a molecular networking strategy. Mol Syst Biol 7:466.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 466
-
-
Montagne, K.1
Plasson, R.2
Sakai, Y.3
Fujii, T.4
Rondelez, Y.5
-
24
-
-
84863610029
-
An E. coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells
-
Shin J, Noireaux V (2012) An E. coli cell-free expression toolbox: Application to synthetic gene circuits and artificial cells. ACS Synth Biol 1(1):29-41.
-
(2012)
ACS Synth Biol
, vol.1
, Issue.1
, pp. 29-41
-
-
Shin, J.1
Noireaux, V.2
-
25
-
-
77950444491
-
DNA as a universal substrate for chemical kinetics
-
Soloveichik D, Seelig G, Winfree E (2010) DNA as a universal substrate for chemical kinetics. Proc Natl Acad Sci USA 107(12):5393-5398.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, Issue.12
, pp. 5393-5398
-
-
Soloveichik, D.1
Seelig, G.2
Winfree, E.3
-
26
-
-
33846108672
-
Cell-free synthetic biology: A bottom-up approach to discovery by design
-
Simpson ML (2006) Cell-free synthetic biology: A bottom-up approach to discovery by design. Mol Syst Biol 2:69.
-
(2006)
Mol Syst Biol
, vol.2
, pp. 69
-
-
Simpson, M.L.1
-
27
-
-
79551599731
-
Synthetic in vitro transcriptional oscillators
-
Kim J, Winfree E (2011) Synthetic in vitro transcriptional oscillators. Mol Syst Biol 7:465.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 465
-
-
Kim, J.1
Winfree, E.2
-
28
-
-
84868251212
-
Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch
-
Subsoontorn P, Kim J, Winfree E (2012) Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch. ACS Synth Biol 1(8):299-316.
-
(2012)
ACS Synth Biol
, vol.1
, Issue.8
, pp. 299-316
-
-
Subsoontorn, P.1
Kim, J.2
Winfree, E.3
-
29
-
-
56149111222
-
Experiments and simulation models of a basic computation element of an autonomous molecular computing system
-
Takinoue M, Kiga D, Shohda K-I, Suyama A (2008) Experiments and simulation models of a basic computation element of an autonomous molecular computing system. Phys Rev E Stat Nonlin Soft Matter Phys 78(4 Pt 1):041921.
-
(2008)
Phys Rev e Stat Nonlin Soft Matter Phys
, vol.78
, Issue.4 PART 1
, pp. 041921
-
-
Takinoue, M.1
Kiga, D.2
Shohda, K.-I.3
Suyama, A.4
-
30
-
-
33845411737
-
Enzyme-free nucleic acid logic circuits
-
Seelig G, Soloveichik D, Zhang DY, Winfree E (2006) Enzyme-free nucleic acid logic circuits. Science 314(5805):1585-1588.
-
(2006)
Science
, vol.314
, Issue.5805
, pp. 1585-1588
-
-
Seelig, G.1
Soloveichik, D.2
Zhang, D.Y.3
Winfree, E.4
-
31
-
-
79957946108
-
Scaling up digital circuit computation with DNA strand displacement cascades
-
Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332(6034):1196-1201.
-
(2011)
Science
, vol.332
, Issue.6034
, pp. 1196-1201
-
-
Qian, L.1
Winfree, E.2
-
32
-
-
67650666435
-
Modelling amorphous computations with transcription networks
-
Simpson ZB, Tsai TL, Nguyen N, Chen X, Ellington AD (2009) Modelling amorphous computations with transcription networks. J R Soc Interface 6(Suppl 4):S523-S533.
-
(2009)
J R Soc Interface
, vol.6
, Issue.SUPPL. 4
-
-
Simpson, Z.B.1
Tsai, T.L.2
Nguyen, N.3
Chen, X.4
Ellington, A.D.5
-
33
-
-
61349193830
-
Self-sustained replication of an RNA enzyme
-
Lincoln TA, Joyce GF (2009) Self-sustained replication of an RNA enzyme. Science 323(5918):1229-1232.
-
(2009)
Science
, vol.323
, Issue.5918
, pp. 1229-1232
-
-
Lincoln, T.A.1
Joyce, G.F.2
-
34
-
-
0345359924
-
A positive-feedback-based bistable 'memory module' that governs a cell fate decision
-
Xiong W, Ferrell JE, Jr. (2003) A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature 426(6965):460-465.
-
(2003)
Nature
, vol.426
, Issue.6965
, pp. 460-465
-
-
Xiong, W.1
Ferrell Jr., J.E.2
-
35
-
-
33845257870
-
Variability and memory of protein levels in human cells
-
Sigal A, et al. (2006) Variability and memory of protein levels in human cells. Nature 444(7119):643-646.
-
(2006)
Nature
, vol.444
, Issue.7119
, pp. 643-646
-
-
Sigal, A.1
-
36
-
-
84861865655
-
Rewritable digital data storage in live cells via engineered control of recombination directionality
-
Bonnet J, Subsoontorn P, Endy D (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci USA 109(23):8884-8889.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.23
, pp. 8884-8889
-
-
Bonnet, J.1
Subsoontorn, P.2
Endy, D.3
-
37
-
-
0035983262
-
Memory in bacteria and phage
-
Casadesús J, D'Ari R (2002) Memory in bacteria and phage. Bioessays 24(6):512-518.
-
(2002)
Bioessays
, vol.24
, Issue.6
, pp. 512-518
-
-
Casadesús, J.1
D'Ari, R.2
-
38
-
-
53849146767
-
Bistability, epigenetics, and bet-hedging in bacteria
-
Veening J-W, Smits WK, Kuipers OP (2008) Bistability, epigenetics, and bet-hedging in bacteria. Annu Rev Microbiol 62:193-210.
-
(2008)
Annu Rev Microbiol
, vol.62
, pp. 193-210
-
-
Veening, J.-W.1
Smits, W.K.2
Kuipers, O.P.3
-
39
-
-
77951129749
-
Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch
-
Robert L, et al. (2010) Pre-dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch. Mol Syst Biol 6:357.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 357
-
-
Robert, L.1
-
40
-
-
84864228102
-
Cell cycle commitment in budding yeast emerges from the cooperation of multiple bistable switches
-
Zhang T, Schmierer B, Novák B (2011) Cell cycle commitment in budding yeast emerges from the cooperation of multiple bistable switches. Open Biol 1(3):110009.
-
(2011)
Open Biol
, vol.1
, Issue.3
, pp. 110009
-
-
Zhang, T.1
Schmierer, B.2
Novák, B.3
-
41
-
-
18844448417
-
Developmental commitment in a bacterium
-
Dworkin J, Losick R (2005) Developmental commitment in a bacterium. Cell 121(3):401-409.
-
(2005)
Cell
, vol.121
, Issue.3
, pp. 401-409
-
-
Dworkin, J.1
Losick, R.2
-
42
-
-
0037047611
-
MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network
-
Bhalla US, Ram PT, Iyengar R (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297(5583):1018-1023.
-
(2002)
Science
, vol.297
, Issue.5583
, pp. 1018-1023
-
-
Bhalla, U.S.1
Ram, P.T.2
Iyengar, R.3
-
43
-
-
79951755320
-
Design and construction of a versatile synthetic network for bistable gene expression in mammalian systems
-
Polynikis A, et al. (2011) Design and construction of a versatile synthetic network for bistable gene expression in mammalian systems. J Comput Biol 18(2):195-203.
-
(2011)
J Comput Biol
, vol.18
, Issue.2
, pp. 195-203
-
-
Polynikis, A.1
-
44
-
-
69949088230
-
Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: The Schlögl model revisited
-
Vellela M, Qian H (2009) Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: The Schlögl model revisited. J R Soc Interface 6(39):925-940.
-
(2009)
J R Soc Interface
, vol.6
, Issue.39
, pp. 925-940
-
-
Vellela, M.1
Qian, H.2
-
45
-
-
77951231950
-
Structure of RecJ exonuclease defines its specificity for single-stranded DNA
-
Wakamatsu T, et al. (2010) Structure of RecJ exonuclease defines its specificity for single-stranded DNA. J Biol Chem 285(13):9762-9769.
-
(2010)
J Biol Chem
, vol.285
, Issue.13
, pp. 9762-9769
-
-
Wakamatsu, T.1
-
46
-
-
78951489764
-
Role of RecJ-like protein with 5′-3′ exonuclease activity in oligo(deoxy)nucleotide degradation
-
Wakamatsu T, et al. (2011) Role of RecJ-like protein with 5′-3′ exonuclease activity in oligo(deoxy)nucleotide degradation. J Biol Chem 286(4):2807-2816.
-
(2011)
J Biol Chem
, vol.286
, Issue.4
, pp. 2807-2816
-
-
Wakamatsu, T.1
-
47
-
-
84867284515
-
Quencher-free multiplexed monitoring of DNA reaction circuits
-
Padirac A, Fujii T, Rondelez Y (2012) Quencher-free multiplexed monitoring of DNA reaction circuits. Nucleic Acids Res 40(15):e118.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.15
-
-
Padirac, A.1
Fujii, T.2
Rondelez, Y.3
-
48
-
-
80053650824
-
Timing molecular motion and production with a synthetic transcriptional clock
-
Franco E, et al. (2011) Timing molecular motion and production with a synthetic transcriptional clock. Proc Natl Acad Sci USA 108(40):E784-E793.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.40
-
-
Franco, E.1
-
49
-
-
48249133689
-
Memory switches in chemical reaction space
-
Ramakrishnan N, Bhalla US (2008) Memory switches in chemical reaction space. PLOS Comput Biol 4(7):e1000122.
-
(2008)
PLOS Comput Biol
, vol.4
, Issue.7
-
-
Ramakrishnan, N.1
Bhalla, U.S.2
-
50
-
-
0347635508
-
Design of genetic networks with specified functions by evolution in silico
-
François P, Hakim V (2004) Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci USA 101(2):580-585.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.2
, pp. 580-585
-
-
François, P.1
Hakim, V.2
-
51
-
-
65549121563
-
Monomeric bistability and the role of autoloops in gene regulation
-
Widder S, Macía J, Solé R (2009) Monomeric bistability and the role of autoloops in gene regulation. PLoS ONE 4(4):e5399.
-
(2009)
PLoS ONE
, vol.4
, Issue.4
-
-
Widder, S.1
Macía, J.2
Solé, R.3
-
52
-
-
0003596284
-
-
Oxford University Press, London
-
Epstein IR, Pojman JA (2012) An introduction to nonlinear chemical dynamics: Oscillations, Waves, Patterns, and Chaos (Oxford University Press, London).
-
(2012)
An Introduction to Nonlinear Chemical Dynamics: Oscillations, Waves, Patterns, and Chaos
-
-
Epstein, I.R.1
Pojman, J.A.2
-
53
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
Tyson JJ, Chen KC, Novák B (2003) Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15(2):221-231.
-
(2003)
Curr Opin Cell Biol
, vol.15
, Issue.2
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novák, B.3
-
54
-
-
33745804402
-
Transitions from bistability to limit-cycle oscillations - Theoretical-analysis and experimental-evidence in an open chemicalsystem
-
Boissonade J, De Kepper P (1980) Transitions from bistability to limit-cycle oscillations - Theoretical-analysis and experimental-evidence in an open chemicalsystem. J Phys Chem 84:501-506.
-
(1980)
J Phys Chem
, vol.84
, pp. 501-506
-
-
Boissonade, J.1
De Kepper, P.2
-
56
-
-
0034696445
-
How to make a biological switch
-
Cherry JL, Adler FR (2000) How to make a biological switch. J Theor Biol 203(2):117-133.
-
(2000)
J Theor Biol
, vol.203
, Issue.2
, pp. 117-133
-
-
Cherry, J.L.1
Adler, F.R.2
-
57
-
-
0036532226
-
Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability
-
Ferrell JE, Jr. (2002) Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14(2):140-148.
-
(2002)
Curr Opin Cell Biol
, vol.14
, Issue.2
, pp. 140-148
-
-
Ferrell Jr., J.E.1
-
58
-
-
54249137797
-
Feedback loops shape cellular signals in space and time
-
Brandman O, Meyer T (2008) Feedback loops shape cellular signals in space and time. Science 322(5900):390-395.
-
(2008)
Science
, vol.322
, Issue.5900
, pp. 390-395
-
-
Brandman, O.1
Meyer, T.2
-
59
-
-
79251621970
-
Dynamic DNA nanotechnology using strand-displacement reactions
-
Zhang DY, Seelig G (2011) Dynamic DNA nanotechnology using strand-displacement reactions. Nat Chem 3(2):103-113.
-
(2011)
Nat Chem
, vol.3
, Issue.2
, pp. 103-113
-
-
Zhang, D.Y.1
Seelig, G.2
|