-
1
-
-
53249118703
-
Stochastic modeling of intracellular kinetics
-
Cambridge, MA: The MIT Press
-
Paulsson J, Elf J. Stochastic modeling of intracellular kinetics. System Modeling in Cellular Biology. Cambridge, MA: The MIT Press; 2006, 149-176.
-
(2006)
System Modeling in Cellular Biology
, pp. 149-176
-
-
Paulsson, J.1
Elf, J.2
-
2
-
-
0037078982
-
Control, exploitation and tolerance of intracellular noise
-
Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature 2002, 420:231-237.
-
(2002)
Nature
, vol.420
, pp. 231-237
-
-
Rao, C.V.1
Wolf, D.M.2
Arkin, A.P.3
-
3
-
-
0842285841
-
Summing up the noise
-
Paulsson J. Summing up the noise. Nature 2004, 427:415-418.
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
4
-
-
19544379881
-
Stochasticity in gene expression: from theories to phenotypes
-
1471-0056
-
Kaern M, Elston TC, BlakeWJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 2005, 6:451-464. ISSN 1471-0056.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 451464
-
-
Kaern, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
5
-
-
25444468618
-
Noise in gene expression: origins, consequences, and control
-
Raser JM, O'Shea EK. Noise in gene expression: origins, consequences, and control. Science 2005, 309:2010-2013.
-
(2005)
Science
, vol.309
, pp. 2010-2013
-
-
Raser, J.M.1
O'Shea, E.K.2
-
6
-
-
0033855774
-
Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated
-
Berg OG, Paulsson J, Ehrenberg M. Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys J 2000, 79:1228-1236.
-
(2000)
Biophys J
, vol.79
, pp. 1228-1236
-
-
Berg, O.G.1
Paulsson, J.2
Ehrenberg, M.3
-
7
-
-
34250334326
-
Intrinsic fluctuations, robustness, and tunability in signaling cycles
-
Levine J, Kueh HY, Mirny L. Intrinsic fluctuations, robustness, and tunability in signaling cycles. Biophys J 2007, 92:4473-4481.
-
(2007)
Biophys J
, vol.92
, pp. 4473-4481
-
-
Levine, J.1
Kueh, H.Y.2
Mirny, L.3
-
8
-
-
20344389483
-
Models of stochastic gene expression
-
Paulsson J. Models of stochastic gene expression. Phys Life Rev 2005, 2:157-75.
-
(2005)
Phys Life Rev
, vol.2
, pp. 157-175
-
-
Paulsson, J.1
-
9
-
-
0242490781
-
Fast evaluation of fluctuations in biochemical networks with the linear noise approximation
-
Elf J, Ehrenberg M. Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome Res 2003, 13:2475-2484.
-
(2003)
Genome Res
, vol.13
, pp. 2475-2484
-
-
Elf, J.1
Ehrenberg, M.2
-
10
-
-
33646975343
-
Stochastic fluctuations in gene expression far from equilibrium: omega expansion and linear noise approximation
-
Tao Yi, Jia Y, Dewey TG. Stochastic fluctuations in gene expression far from equilibrium: omega expansion and linear noise approximation. J Chem Phys 2005, 122:124108.
-
(2005)
J Chem Phys
, vol.122
, pp. 124108
-
-
Tao, Y.1
Jia, Y.2
Dewey, T.G.3
-
12
-
-
0000315224
-
Physical aspects of the growth and regulation of microtubule structures
-
Dogterom M, Leibler S. Physical aspects of the growth and regulation of microtubule structures. Phys Rev Lett 1993, 70:1347.
-
(1993)
Phys Rev Lett
, vol.70
, pp. 1347
-
-
Dogterom, M.1
Leibler, S.2
-
13
-
-
0034981558
-
Noise in a minimal regulatory network: plasmid copy number control
-
Paulsson J, Ehrenberg M. Noise in a minimal regulatory network: plasmid copy number control. Q Rev Biophys 2001, 34:1-59.
-
(2001)
Q Rev Biophys
, vol.34
, pp. 1-59
-
-
Paulsson, J.1
Ehrenberg, M.2
-
14
-
-
0036135425
-
From discrete protein kinetics to continuous Brownian dynamics: a new perspective
-
Qian H. From discrete protein kinetics to continuous Brownian dynamics: a new perspective. Protein Sci 2002, 11:1-5.
-
(2002)
Protein Sci
, vol.11
, pp. 1-5
-
-
Qian, H.1
-
15
-
-
0037197850
-
Mechanisms of noise-resistance in genetic oscillators
-
Vilar JMG, Kueh HY, Barkai N, Leibler S.Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci U S A 2002, 99:5988-5992.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 5988-5992
-
-
Vilar, J.M.G.1
Kueh, H.Y.2
Barkai, N.3
Leibler, S.4
-
16
-
-
12244269687
-
Near-critical phenomena in intracellular metabolite pools
-
Elf J, Paulsson J, Berg OG, Ehrenberg M. Near-critical phenomena in intracellular metabolite pools. Biophys J 2003, 84:154-170.
-
(2003)
Biophys J
, vol.84
, pp. 154-170
-
-
Elf, J.1
Paulsson, J.2
Berg, O.G.3
Ehrenberg, M.4
-
17
-
-
3042522538
-
-
First International Symposium on Control, Communications and Signal Processing, Hammamet, Tunisia
-
El Samad H, Khammash M. Intrinsic noise rejection in gene networks by regulation of stability. First International Symposium on Control, Communications and Signal Processing, Hammamet, Tunisia, 2004, 187-190.
-
(2004)
Intrinsic noise rejection in gene networks by regulation of stability
, pp. 187-190
-
-
El Samad, H.1
Khammash, M.2
-
18
-
-
0036111831
-
Attenuation of noise in ultrasensitive signaling cascades
-
Thattai M, van Oudenaarden A. Attenuation of noise in ultrasensitive signaling cascades. Biophys J 2002, 82:2943-2950.
-
(2002)
Biophys J
, vol.82
, pp. 2943-2950
-
-
Thattai, M.1
van Oudenaarden, A.2
-
19
-
-
16644373292
-
Noise minimization in eukaryotic gene expression
-
Fraser HB, Hirsh AE, Giaever G, Kumm J, Eisen MB. Noise minimization in eukaryotic gene expression. PLoS Biol 2004, 2:e137.
-
(2004)
PLoS Biol
, vol.2
-
-
Fraser, H.B.1
Hirsh, A.E.2
Giaever, G.3
Kumm, J.4
Eisen, M.B.5
-
20
-
-
2342470688
-
Noise-reduction through interaction in gene expression and biochemical reaction processes
-
Morishita Y, Aihara K. Noise-reduction through interaction in gene expression and biochemical reaction processes. J Theor Biol 2004, 228:315-325.
-
(2004)
J Theor Biol
, vol.228
, pp. 315-325
-
-
Morishita, Y.1
Aihara, K.2
-
21
-
-
0034608143
-
Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks
-
Paulsson J, Ehrenberg M. Random signal fluctuations can reduce random fluctuations in regulated components of chemical regulatory networks. Phys Rev Lett 2000, 84:5447-5450.
-
(2000)
Phys Rev Lett
, vol.84
, pp. 5447-5450
-
-
Paulsson, J.1
Ehrenberg, M.2
-
22
-
-
38949194331
-
Noise propagation and signaling sensitivity in biological networks: a role for positive feedback
-
Hornung G, Barkai N. Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol 2008, 4:e8.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Hornung, G.1
Barkai, N.2
-
23
-
-
33750147302
-
The interplay between discrete noise and nonlinear chemical kinetics in a signal amplification cascade
-
Lan Y, Papoian GA. The interplay between discrete noise and nonlinear chemical kinetics in a signal amplification cascade. J Chem Phys 2006, 125:154901.
-
(2006)
J Chem Phys
, vol.125
, pp. 154901
-
-
Lan, Y.1
Papoian, G.A.2
-
24
-
-
15544388848
-
Noise propagation in gene networks
-
Pedraza JM, van Oudenaarden A. Noise propagation in gene networks. Science 2005, 307:1965-1969.
-
(2005)
Science
, vol.307
, pp. 1965-1969
-
-
Pedraza, J.M.1
van Oudenaarden, A.2
-
25
-
-
25144450143
-
Contributions of low molecule number and chromosomal positioning to stochastic gene expression
-
ISSN 1061-4036
-
Becskei A, Kaufmann BB, van Oudenaarden A. Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet 2005, 37:937-944. ISSN 1061-4036.
-
(2005)
Nat Genet
, vol.37
, pp. 9370-944
-
-
Becskei, A.1
Kaufmann, B.B.2
van Oudenaarden, A.3
-
26
-
-
46849105469
-
Noise generation, amplification and propagation in chemotactic signaling systems of living cells
-
Shibata T, Ueda M. Noise generation, amplification and propagation in chemotactic signaling systems of living cells. Biosystems 2008, 93:126-132.
-
(2008)
Biosystems
, vol.93
, pp. 126-132
-
-
Shibata, T.1
Ueda, M.2
-
27
-
-
33749644563
-
Fluctuations for good and bad: the role of noise in living systems
-
Blomberg C. Fluctuations for good and bad: the role of noise in living systems. Phys Life Rev 2006, 3:133-161.
-
(2006)
Phys Life Rev
, vol.3
, pp. 133-161
-
-
Blomberg, C.1
-
28
-
-
33645813418
-
On the attenuation and amplification of molecular noise in genetic regulatory networks
-
Chen BS, Wang YC. On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics 2006, 7:52.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 52
-
-
Chen, B.S.1
Wang, Y.C.2
-
29
-
-
0034050722
-
Noise-based switches and amplifiers for gene expression
-
Hasty J, Pradines J, Dolnik M, Collins JJ. Noise-based switches and amplifiers for gene expression. Proc Natl Acad Sci U S A 2000, 97:2075-2080.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 2075-2080
-
-
Hasty, J.1
Pradines, J.2
Dolnik, M.3
Collins, J.J.4
-
30
-
-
34047130839
-
Roles of noise in single and coupled multiple genetic oscillators
-
Yoda M, Ushikubo T, Inoue W, Sasai M. Roles of noise in single and coupled multiple genetic oscillators. J Chem Phys 2007, 126:115101.
-
(2007)
J Chem Phys
, vol.126
, pp. 115101
-
-
Yoda, M.1
Ushikubo, T.2
Inoue, W.3
Sasai, M.4
-
31
-
-
14044265753
-
Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations
-
Samoilov M, Plyasunov S, Arkin AP. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc Natl Acad Sci U S A 2005, 102:2310-2315.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 2310-2315
-
-
Samoilov, M.1
Plyasunov, S.2
Arkin, A.P.3
-
32
-
-
0034691214
-
Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation
-
Paulsson J, BergOG, Ehrenberg M. Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc Natl Acad Sci U S A 2000, 97:7148-7153.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 7148-7153
-
-
Paulsson, J.1
Berg, O.G.2
Ehrenberg, M.3
-
33
-
-
0037605637
-
Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible
-
ISSN 1054-1500
-
Ferrell JE, Xiong W. Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible. Chaos 2001, 11:227-236. ISSN 1054-1500.
-
(2001)
Chaos
, vol.11
, pp. 227-236
-
-
Ferrell, J.E.1
Xiong, W.2
-
35
-
-
1442354192
-
Multistability in the lactose utilization network of Escherichia coli
-
Ozbudak EM, Thattai M, Lim HN, Shraiman BI, van Oudenaarden A. Multistability in the lactose utilization network of Escherichia coli. Nature 2004, 427:737-740.
-
(2004)
Nature
, vol.427
, pp. 737-740
-
-
Ozbudak, E.M.1
Thattai, M.2
Lim, H.N.3
Shraiman, B.I.4
van Oudenaarden, A.5
-
36
-
-
37649018636
-
Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities
-
Artyomov MN, Das J, Kardar M, Chakraborty AK. Purely stochastic binary decisions in cell signaling models without underlying deterministic bistabilities. Proc Natl Acad Sci U S A 2007, 104:18958-18963.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 18958-18963
-
-
Artyomov, M.N.1
Das, J.2
Kardar, M.3
Chakraborty, A.K.4
-
37
-
-
44049103351
-
Internal noise-sustained circadian rhythms in a Drosophila model
-
Li Q, Lang X. Internal noise-sustained circadian rhythms in a Drosophila model. Biophys J 2008, 94:1983-1994.
-
(2008)
Biophys J
, vol.94
, pp. 1983-1994
-
-
Li, Q.1
Lang, X.2
-
38
-
-
57349131603
-
A genetic timer through noise-induced stabilization of an unstable state
-
TurcotteM, Garcia-Ojalvo J, Sü el GM. A genetic timer through noise-induced stabilization of an unstable state. Proc Nat Acad Sci 2008, 105:15732-15737.
-
(2008)
Proc Nat Acad Sci
, vol.105
, pp. 15732-15737
-
-
Turcotte, M.1
Garcia-Ojalvo, J.2
Sü el, G.M.3
-
39
-
-
33947575324
-
Switching dynamics in reaction networks induced by molecular discreteness
-
Togashi Y, Kaneko K. Switching dynamics in reaction networks induced by molecular discreteness. J Phy: Condens Matter 2007, 19:065150.
-
(2007)
J Phy: Condens Matter
, vol.19
, pp. 065150
-
-
Togashi, Y.1
Kaneko, K.2
-
41
-
-
58549110252
-
Stochastic modelling for quantitative description of heterogeneous biological systems
-
ISSN 1471-0056
-
Wilkinson DJ. Stochastic modelling for quantitative description of heterogeneous biological systems. Nat Rev Genet 2009, 10:122-133. ISSN 1471-0056.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 122-133
-
-
Wilkinson, D.J.1
-
42
-
-
33749043018
-
Testing the transition state theory in stochastic dynamics of a genetic switch
-
Ushikubo T, Inoue W, Yoda M, Sasai M. Testing the transition state theory in stochastic dynamics of a genetic switch. Chem Phys Lett 2006, 430:139-143.
-
(2006)
Chem Phys Lett
, vol.430
, pp. 139-143
-
-
Ushikubo, T.1
Inoue, W.2
Yoda, M.3
Sasai, M.4
-
43
-
-
33846250352
-
Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations
-
Gó mez-Uribe CA, Verghese GC. Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations. J Chem Phys 2007, 126:024109.
-
(2007)
J Chem Phys
, vol.126
, pp. 024109
-
-
Gó mez-Uribe, C.A.1
Verghese, G.C.2
-
44
-
-
33846108256
-
Noise in transcription negative feedback loops: simulation and experimental analysis
-
Dublanche Y, Michalodimitrakis K, Kümmerer N, Foglierini M, Serrano L. Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol 2006, 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
-
45
-
-
3142577523
-
Stochastic approaches for modelling in vivo reactions
-
Turner TE, Schnell S, Burrage K. Stochastic approaches for modelling in vivo reactions. Comput Biol Chem 2004, 28:165-178.
-
(2004)
Comput Biol Chem
, vol.28
, pp. 165-178
-
-
Turner, T.E.1
Schnell, S.2
Burrage, K.3
-
46
-
-
79956111270
-
Stochastic Simulation, Analysis of Biochemical Networks
-
PhD thesis, Humboldt-Universiẗ at zu Berlin
-
Pahle J. Stochastic Simulation and Analysis of Biochemical Networks. PhD thesis, Humboldt-Universiẗ at zu Berlin, 2008.
-
(2008)
-
-
Pahle, J.1
-
47
-
-
53549123008
-
Nature, nurture, or chance: stochastic gene expression and its consequences
-
ISSN 0092-8674
-
Raj A, van Oudenaarden A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 2008, 135:216-226. ISSN 0092-8674.
-
(2008)
Cell
, vol.135
, pp. 216-226
-
-
Raj, A.1
van Oudenaarden, A.2
-
48
-
-
34250450481
-
Chemical reaction models for nonequilibrium phase transitions
-
Schlö gl F. Chemical reaction models for nonequilibrium phase transitions. Z Physik A Hadrons d Nucl 1972, 253:147-161.
-
(1972)
Z Physik A Hadrons d Nucl
, vol.253
, pp. 147-161
-
-
Schlö gl, F.1
-
55
-
-
0000374975
-
On the theory of order statistics
-
Ŕenyi A. On the theory of order statistics. Acta Math Hungarica 1953, 4:191-231.
-
(1953)
Acta Math Hungarica
, vol.4
, pp. 191-231
-
-
Ŕenyi, A.1
-
56
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
-
(1977)
J Phys Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
57
-
-
0030516386
-
The multivariate Langevin and Fokker-Planck equations
-
Gillespie DT. The multivariate Langevin and Fokker-Planck equations. Am J Phys 1996, 64:1246-1257.
-
(1996)
Am J Phys
, vol.64
, pp. 1246-1257
-
-
Gillespie, D.T.1
-
58
-
-
27244445075
-
The linear noise approximation for molecular fluctuations within cells
-
ISSN 1478-3975
-
Hayot F, Jayaprakash C. The linear noise approximation for molecular fluctuations within cells. Phys Biol 2004, 1:205-210. ISSN 1478-3975.
-
(2004)
Phys Biol
, vol.1
, pp. 205-210
-
-
Hayot, F.1
Jayaprakash, C.2
-
59
-
-
33751566347
-
Reduction and solution of the chemical master equation using time scale separation and finite state projection
-
Peles S, Munsky B, Khammash M. Reduction and solution of the chemical master equation using time scale separation and finite state projection. J Chem Phys 2006, 125:204104.
-
(2006)
J Chem Phys
, vol.125
, pp. 204104
-
-
Peles, S.1
Munsky, B.2
Khammash, M.3
-
60
-
-
39649109479
-
A reduced model solution for the chemical master equation arising in stochastic analyses of biological networks
-
Munsky B, Khammash M. A reduced model solution for the chemical master equation arising in stochastic analyses of biological networks. Decision and Control, 2006 45th IEEE Conference, 2006, 25-30.
-
(2006)
Decision and Control, 2006 45th IEEE Conference
, pp. 25-30
-
-
Munsky, B.1
Khammash, M.2
-
62
-
-
0034225547
-
The chemical Langevin equation
-
Gillespie DT. The chemical Langevin equation. J Chem Phys 2000, 113:297-306.
-
(2000)
J Chem Phys
, vol.113
, pp. 297-306
-
-
Gillespie, D.T.1
-
63
-
-
0035439412
-
An algorithmic introduction to numerical simulation of stochastic differential equations
-
Higham DJ. An algorithmic introduction to numerical simulation of stochastic differential equations. SIAM Rev 2001, 43:525-546.
-
(2001)
SIAM Rev
, vol.43
, pp. 525-546
-
-
Higham, D.J.1
-
64
-
-
33144465372
-
A hiddenMarkov model for transcriptional regulation in single cells
-
Goutsias J. A hiddenMarkov model for transcriptional regulation in single cells. IEEE/ACM Trans Comput Biol Bioinform 2006, 3:57-71.
-
(2006)
IEEE/ACM Trans Comput Biol Bioinform
, vol.3
, pp. 57-71
-
-
Goutsias, J.1
-
65
-
-
69249209842
-
Investigating the twomoment characterisation of subcellular biochemical networks
-
ISSN 0022-5193
-
Ullah M, Wolkenhauer O. Investigating the twomoment characterisation of subcellular biochemical networks. J Theor Biol 2009, 260:340-352. ISSN 0022-5193.
-
(2009)
J Theor Biol
, vol.260
, pp. 340-352
-
-
Ullah, M.1
Wolkenhauer, O.2
|