-
1
-
-
19544379881
-
Stochasticity in gene expression: from theories to phenotypes
-
Kaern M, Elston TC, Blake WJ, Collins JJ, (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451-464.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 451-464
-
-
Kaern, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
2
-
-
0037078982
-
Control, exploitation and tolerance of intracellular noise
-
Rao CV, Wolf DM, Arkin AP, (2002) Control, exploitation and tolerance of intracellular noise. Nature 420: 231-237.
-
(2002)
Nature
, vol.420
, pp. 231-237
-
-
Rao, C.V.1
Wolf, D.M.2
Arkin, A.P.3
-
3
-
-
77951101695
-
Transcript counting in single cells reveals dynamics of rDNA transcription
-
Tan RZ, van Oudenaarden A, (2010) Transcript counting in single cells reveals dynamics of rDNA transcription. Mol Syst Biol 6: 358.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 358
-
-
Tan, R.Z.1
van Oudenaarden, A.2
-
4
-
-
15544388848
-
Noise propagation in gene networks
-
Pedraza JM, van Oudenaarden A, (2005) Noise propagation in gene networks. Science 307: 1965-1969.
-
(2005)
Science
, vol.307
, pp. 1965-1969
-
-
Pedraza, J.M.1
van Oudenaarden, A.2
-
5
-
-
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 U S A 102: 3581-3586.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 3581-3586
-
-
Hooshangi, S.1
Thiberge, S.2
Weiss, R.3
-
6
-
-
41349119880
-
Stochastic switching as a survival strategy in fluctuating environments
-
Acar M, Mettetal JT, van Oudenaarden A, (2008) Stochastic switching as a survival strategy in fluctuating environments. Nat Genet 40: 471-475.
-
(2008)
Nat Genet
, vol.40
, pp. 471-475
-
-
Acar, M.1
Mettetal, J.T.2
van Oudenaarden, A.3
-
7
-
-
70350336588
-
Architecture-dependent noise discriminates functionally analogous differentiation circuits
-
Caǧatay T, Turcotte M, Elowitz M, Garcia-Ojalvo J, Süel G, (2009) Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139: 512-522.
-
(2009)
Cell
, vol.139
, pp. 512-522
-
-
Caǧatay, T.1
Turcotte, M.2
Elowitz, M.3
Garcia-Ojalvo, J.4
Süel, G.5
-
8
-
-
68049139696
-
Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells
-
Kalmar T, Lim C, Hayward P, Muñoz-Descalzo S, Nichols J, et al. (2009) Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol 7: e1000149.
-
(2009)
PLoS Biol
, vol.7
-
-
Kalmar, T.1
Lim, C.2
Hayward, P.3
Muñoz-Descalzo, S.4
Nichols, J.5
-
9
-
-
62449123034
-
A chance at survival: gene expression noise and phenotypic diversification strategies
-
Fraser D, Kærn M, (2009) A chance at survival: gene expression noise and phenotypic diversification strategies. Mol Microbiol 71: 1333-1340.
-
(2009)
Mol Microbiol
, vol.71
, pp. 1333-1340
-
-
Fraser, D.1
Kærn, M.2
-
10
-
-
33845616177
-
Phenotypic consequences of promoter-mediated transcriptional noise
-
Blake WJ, Balázsi G, Kohanski MA, Isaacs FJ, Murphy KF, et al. (2006) Phenotypic consequences of promoter-mediated transcriptional noise. Mol Cell 24: 853-865.
-
(2006)
Mol Cell
, vol.24
, pp. 853-865
-
-
Blake, W.J.1
Balázsi, G.2
Kohanski, M.A.3
Isaacs, F.J.4
Murphy, K.F.5
-
11
-
-
36749100036
-
Molecular level stochastic model for competence cycles in Bacillus subtilis
-
Schultz D, Ben-Jacob E, Onuchic JN, Wolynes PG, (2007) Molecular level stochastic model for competence cycles in Bacillus subtilis. Proc Natl Acad Sci U S A 104: 17582-17587.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 17582-17587
-
-
Schultz, D.1
Ben-Jacob, E.2
Onuchic, J.N.3
Wolynes, P.G.4
-
12
-
-
41749107942
-
Stochasticity and cell fate
-
Losick R, Desplan C, (2008) Stochasticity and cell fate. Science 320: 65-68.
-
(2008)
Science
, vol.320
, pp. 65-68
-
-
Losick, R.1
Desplan, C.2
-
13
-
-
75849116320
-
Deciding fate in adverse times: sporulation and competence in Bacillus subtilis
-
Schultz D, Wolynes PG, Ben-Jacob E, Onuchic JN, (2009) Deciding fate in adverse times: sporulation and competence in Bacillus subtilis. Proc Natl Acad Sci U S A 106: 21027-21034.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 21027-21034
-
-
Schultz, D.1
Wolynes, P.G.2
Ben-Jacob, E.3
Onuchic, J.N.4
-
14
-
-
77955830290
-
Biological role of noise encoded in a genetic network motif
-
Kittisopikul M, Süel GM, (2010) Biological role of noise encoded in a genetic network motif. Proc Natl Acad Sci U S A 107: 13300-13305.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 13300-13305
-
-
Kittisopikul, M.1
Süel, G.M.2
-
15
-
-
77955777543
-
Bacteria determine fate by playing dice with controlled odds
-
Ben-Jacob E, Schultz D, (2010) Bacteria determine fate by playing dice with controlled odds. Proc Natl Acad Sci U S A 107: 13197-13198.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 13197-13198
-
-
Ben-Jacob, E.1
Schultz, D.2
-
16
-
-
49449090300
-
Using noise to probe and characterize gene circuits
-
Cox CD, McCollum JM, Allen MS, Dar RD, Simpson ML, (2008) Using noise to probe and characterize gene circuits. Proc Natl Acad Sci U S A 105: 10809-10814.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 10809-10814
-
-
Cox, C.D.1
McCollum, J.M.2
Allen, M.S.3
Dar, R.D.4
Simpson, M.L.5
-
17
-
-
56749102636
-
Regulatory activity revealed by dynamic correlations in gene expression noise
-
Dunlop MJ, Cox RS, Levine JH, Murray RM, Elowitz MB, (2008) Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet 40: 1493-1498.
-
(2008)
Nat Genet
, vol.40
, pp. 1493-1498
-
-
Dunlop, M.J.1
Cox, R.S.2
Levine, J.H.3
Murray, R.M.4
Elowitz, M.B.5
-
18
-
-
56249093501
-
Signatures of combinatorial regulation in intrinsic biological noise
-
Warmflash A, Dinner AR, (2008) Signatures of combinatorial regulation in intrinsic biological noise. Proc Natl Acad Sci U S A 106: 17262-17267.
-
(2008)
Proc Natl Acad Sci U S A
, vol.106
, pp. 17262-17267
-
-
Warmflash, A.1
Dinner, A.R.2
-
19
-
-
73149105740
-
Listening to the noise: random fluctuations reveal gene network parameters
-
Munsky B, Trinh B, Khammash M, (2009) Listening to the noise: random fluctuations reveal gene network parameters. Mol Syst Biol 5: 318.
-
(2009)
Mol Syst Biol
, vol.5
, pp. 318
-
-
Munsky, B.1
Trinh, B.2
Khammash, M.3
-
20
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
-
(1977)
J Phys Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
21
-
-
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: 1633-1648.
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
Arkin, A.1
Ross, J.2
McAdams, H.H.3
-
22
-
-
3342965723
-
Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing
-
Garcia-Ojalvo J, Elowitz MB, Strogatz SH, (2004) Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc Natl Acad Sci U S A 101: 10955-10960.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 10955-10960
-
-
Garcia-Ojalvo, J.1
Elowitz, M.B.2
Strogatz, S.H.3
-
23
-
-
50949114239
-
Noise reduction by diffusional dissipation in a minimal quorum sensing motif
-
Tanouchi Y, Tu D, Kim J, You L, (2008) Noise reduction by diffusional dissipation in a minimal quorum sensing motif. PLoS Comput Biol 4: e1000167.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Tanouchi, Y.1
Tu, D.2
Kim, J.3
You, L.4
-
25
-
-
34447336982
-
Perfect sampling of the master equation for gene regulatory networks
-
Hemberg M, Barahona M, (2007) Perfect sampling of the master equation for gene regulatory networks. Biophys J 93: 401-410.
-
(2007)
Biophys J
, vol.93
, pp. 401-410
-
-
Hemberg, M.1
Barahona, M.2
-
26
-
-
0037119587
-
Stochastic gene expression in a single cell
-
Elowitz MB, Levine AJ, Siggia ED, Swain PS, (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
-
(2002)
Science
, vol.297
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
27
-
-
0036790975
-
Intrinsic and extrinsic contributions to stochasticity in gene expression
-
Swain PS, Elowitz MB, Siggia ED, (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A 99: 12795-12800.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 12795-12800
-
-
Swain, P.S.1
Elowitz, M.B.2
Siggia, E.D.3
-
28
-
-
33749842033
-
Deviant effects in molecular reaction pathways
-
Samoilov MS, Arkin AP, (2006) Deviant effects in molecular reaction pathways. Nature Biotech 24: 1235-1240.
-
(2006)
Nature Biotech
, vol.24
, pp. 1235-1240
-
-
Samoilov, M.S.1
Arkin, A.P.2
-
29
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
Raser JM, O'Shea EK, (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814.
-
(2004)
Science
, vol.304
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
30
-
-
33750247101
-
Linking stochastic dynamics to population distribution: an analytical framework of gene expression
-
Friedman N, Cai L, Xie XS, (2006) Linking stochastic dynamics to population distribution: an analytical framework of gene expression. Phys Rev Lett 97: 168302.
-
(2006)
Phys Rev Lett
, vol.97
, pp. 168302
-
-
Friedman, N.1
Cai, L.2
Xie, X.S.3
-
31
-
-
70349577937
-
Stochastic models and numerical algorithms for a class of regulatory gene networks
-
Fournier T, Gabriel J-P, Pasquier J, Mazza C, Galbete J, et al. (2009) Stochastic models and numerical algorithms for a class of regulatory gene networks. Bull Math Biol 71: 1394-1431.
-
(2009)
Bull Math Biol
, vol.71
, pp. 1394-1431
-
-
Fournier, T.1
Gabriel, J.-P.2
Pasquier, J.3
Mazza, C.4
Galbete, J.5
-
32
-
-
66149144779
-
A stochastic spectral analysis of transcriptional regulatory cascades
-
Walczak AM, Mugler A, Wiggins CH, (2009) A stochastic spectral analysis of transcriptional regulatory cascades. Proc Natl Acad Sci U S A 106: 6529-6534.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 6529-6534
-
-
Walczak, A.M.1
Mugler, A.2
Wiggins, C.H.3
-
33
-
-
34047225832
-
Potential energy landscape and robustness of a gene regulatory network: toggle switch
-
Kim KY, Wang J, (2007) Potential energy landscape and robustness of a gene regulatory network: toggle switch. PLoS Comput Biol 3: e60.
-
(2007)
PLoS Comput Biol
, vol.3
-
-
Kim, K.Y.1
Wang, J.2
-
34
-
-
43549125989
-
Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability
-
Cao Y, Liang J, (2008) Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability. BMC Syst Biol 2: 30.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 30
-
-
Cao, Y.1
Liang, J.2
-
35
-
-
78649871073
-
Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda
-
Cao Y, Lu H-M, Liang J, (2010) Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proc Natl Acad Sci U S A 107: 18445-18450.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 18445-18450
-
-
Cao, Y.1
Lu, H.-M.2
Liang, J.3
-
36
-
-
78149453584
-
Identification from stochastic cell-to-cell variation: a genetic switch case
-
Munsky B, Khammash M, (2010) Identification from stochastic cell-to-cell variation: a genetic switch case. IET Syst Biol 4: 356-66.
-
(2010)
IET Syst Biol
, vol.4
, pp. 356-366
-
-
Munsky, B.1
Khammash, M.2
-
37
-
-
0742288604
-
Potential in stochastic differential equations: novel construction
-
Ao P, (2004) Potential in stochastic differential equations: novel construction. J Phys A: Math Gen 37: L25-L30.
-
(2004)
J Phys A: Math Gen
, vol.37
-
-
Ao, P.1
-
38
-
-
50449104011
-
Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations
-
Wang J, Xu L, Wang E, (2008) Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations. Proc Natl Acad Sci U S A 105: 12271-12276.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 12271-12276
-
-
Wang, J.1
Xu, L.2
Wang, E.3
-
39
-
-
17244378347
-
Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
-
Qian H, Beard DA, (2005) Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. Biophys Chem 114: 213-220.
-
(2005)
Biophys Chem
, vol.114
, pp. 213-220
-
-
Qian, H.1
Beard, D.A.2
-
40
-
-
43249118966
-
Colored extrinsic fluctuations and stochastic gene expression
-
Shahrezaei V, Ollivier JF, Swain PS, (2008) Colored extrinsic fluctuations and stochastic gene expression. Mol Syst Biol 4: 196.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 196
-
-
Shahrezaei, V.1
Ollivier, J.F.2
Swain, P.S.3
-
41
-
-
77955102352
-
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
Choi, P.J.2
Li, G.-W.3
Chen, H.4
Babu, M.5
-
42
-
-
0021518209
-
Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images
-
Geman S, Geman D, (1984) Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans Pattern Anal and Mach Intell PAMI-6: 721-741.
-
(1984)
IEEE Trans Pattern Anal and Mach Intell PAMI
, vol.6
, pp. 721-741
-
-
Geman, S.1
Geman, D.2
-
43
-
-
84937730674
-
Explaining the Gibbs sampler
-
Casella G, George EI, (1992) Explaining the Gibbs sampler. Am Stat 46: 167-174.
-
(1992)
Am Stat
, vol.46
, pp. 167-174
-
-
Casella, G.1
George, E.I.2
-
44
-
-
21844490354
-
Gibbs sampler convergence criteria
-
Zellner A, Min C-K, (1995) Gibbs sampler convergence criteria. J Am Stat Assoc 90: 921-927.
-
(1995)
J Am Stat Assoc
, vol.90
, pp. 921-927
-
-
Zellner, A.1
Min, C.-K.2
-
45
-
-
0000207240
-
Convergence rates of the Gibbs sampler, the Metropolis algorithm and other single-site updating dynamics
-
Frigessi A, di Stefano P, Hwang C-R, Sheu S-J, (1993) Convergence rates of the Gibbs sampler, the Metropolis algorithm and other single-site updating dynamics. J R Stat Soc Series B Stat Methodol 55: 205-219.
-
(1993)
J R Stat Soc Series B Stat Methodol
, vol.55
, pp. 205-219
-
-
Frigessi, A.1
di Stefano, P.2
Hwang, C.-R.3
Sheu, S.-J.4
-
46
-
-
24344493048
-
Sufficient burn-in for Gibbs samplers for a hierarchical random effects model
-
Jones GL, Hobert JP, (2004) Sufficient burn-in for Gibbs samplers for a hierarchical random effects model. Ann Stat 32: 784-817.
-
(2004)
Ann Stat
, vol.32
, pp. 784-817
-
-
Jones, G.L.1
Hobert, J.P.2
-
47
-
-
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
-
48
-
-
2942614884
-
Programmable cells: interfacing natural and engineered gene networks
-
Kobayashi H, Kaern M, Araki M, Chung K, Gardner TS, et al. (2004) Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci U S A 101: 8414-8419.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 8414-8419
-
-
Kobayashi, H.1
Kaern, M.2
Araki, M.3
Chung, K.4
Gardner, T.S.5
-
49
-
-
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: 842-848.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 842-848
-
-
Tan, C.1
Marguet, P.2
You, L.3
-
50
-
-
43149108161
-
A bistable Rb-E2F switch underlies the restriction point
-
Yao G, Lee TJ, Mori S, Nevins JR, You L, (2008) A bistable Rb-E2F switch underlies the restriction point. Nat Cell Biol 10: 476-482.
-
(2008)
Nat Cell Biol
, vol.10
, pp. 476-482
-
-
Yao, G.1
Lee, T.J.2
Mori, S.3
Nevins, J.R.4
You, L.5
-
51
-
-
77957894780
-
Stochastic E2F activation and reconciliation of phenomenological cell-cycle models
-
Lee TJ, Yao G, Bennett DC, Nevins JR, You L, (2010) Stochastic E2F activation and reconciliation of phenomenological cell-cycle models. PLoS Biol 8: e1000488.
-
(2010)
PLoS Biol
, vol.8
-
-
Lee, T.J.1
Yao, G.2
Bennett, D.C.3
Nevins, J.R.4
You, L.5
-
52
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
Gillespie DT, (2007) Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 58: 35-55.
-
(2007)
Annu Rev Phys Chem
, vol.58
, pp. 35-55
-
-
Gillespie, D.T.1
|