-
2
-
-
14844328879
-
SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks
-
Ander M., Beltrao P., Di Ventura B., et al. SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. Syst. Biol. 2004, 1:129-138.
-
(2004)
Syst. Biol.
, vol.1
, pp. 129-138
-
-
Ander, M.1
Beltrao, P.2
Di Ventura, B.3
-
3
-
-
78650624401
-
Stochastic reduction method for biological chemical kinetics using time-scale separation
-
Atzberger P.J., Pahlajani C.D., Khammash M. Stochastic reduction method for biological chemical kinetics using time-scale separation. J. Theor. Biol. 2011, 272:96-112.
-
(2011)
J. Theor. Biol.
, vol.272
, pp. 96-112
-
-
Atzberger, P.J.1
Pahlajani, C.D.2
Khammash, M.3
-
4
-
-
35448953506
-
Glutathione and Gts1p drive beneficial variability in the cadmium resistances of individual yeast cells
-
Avery S.V., Smith M.C.A., Sumner E.R. Glutathione and Gts1p drive beneficial variability in the cadmium resistances of individual yeast cells. Mol. Microbiol. 2007, 66:699-712.
-
(2007)
Mol. Microbiol.
, vol.66
, pp. 699-712
-
-
Avery, S.V.1
Smith, M.C.A.2
Sumner, E.R.3
-
5
-
-
72449204595
-
Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin
-
Bancaud A., Huet S., Daigle N., Mozziconacci J., Beaudouin J., Ellenberg J. Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J. 2009, 28(24):3785-3798.
-
(2009)
EMBO J.
, vol.28
, Issue.24
, pp. 3785-3798
-
-
Bancaud, A.1
Huet, S.2
Daigle, N.3
Mozziconacci, J.4
Beaudouin, J.5
Ellenberg, J.6
-
6
-
-
33745287724
-
Noise in protein expression scales with natural protein abundance
-
Bar-Even A., Paulsson J., Maheshri N., Carmi M., O'Shea E., Pilpel Y., Barkai N. Noise in protein expression scales with natural protein abundance. Nat. Genet. 2006, 38:636-643.
-
(2006)
Nat. Genet.
, vol.38
, pp. 636-643
-
-
Bar-Even, A.1
Paulsson, J.2
Maheshri, N.3
Carmi, M.4
O'Shea, E.5
Pilpel, Y.6
Barkai, N.7
-
7
-
-
0030381125
-
Reaction-diffusion master equation: a comparison with microscopic simulations
-
Baras F., Mansour M.M. Reaction-diffusion master equation: a comparison with microscopic simulations. Phys. Rev. E 1996, 54:6139-6148.
-
(1996)
Phys. Rev. E
, vol.54
, pp. 6139-6148
-
-
Baras, F.1
Mansour, M.M.2
-
9
-
-
50349141358
-
Treatment of staphylococcal infections with penicillin by intermittent sterilization
-
Bigger W.B. Treatment of staphylococcal infections with penicillin by intermittent sterilization. Lancet 1944, 2:497-500.
-
(1944)
Lancet
, vol.2
, pp. 497-500
-
-
Bigger, W.B.1
-
10
-
-
33845616177
-
Phenotypic consequences of promoter-mediated transcriptional noise
-
Blake W.J., Balazsi G., Kohanski M.A., Isaacs F.J., Murphy K.F., Kuang Y., Cantor C.R., Walt D.R., Collins J.J. Phenotypic consequences of promoter-mediated transcriptional noise. Mol. Cell 2006, 24:853-865.
-
(2006)
Mol. Cell
, vol.24
, pp. 853-865
-
-
Blake, W.J.1
Balazsi, G.2
Kohanski, M.A.3
Isaacs, F.J.4
Murphy, K.F.5
Kuang, Y.6
Cantor, C.R.7
Walt, D.R.8
Collins, J.J.9
-
11
-
-
33645027986
-
Stochastic protein expression in individual cells at the single molecule level
-
Cai L., Friedman N., Xie X.S. Stochastic protein expression in individual cells at the single molecule level. Nature 2006, 440:358-362.
-
(2006)
Nature
, vol.440
, pp. 358-362
-
-
Cai, L.1
Friedman, N.2
Xie, X.S.3
-
12
-
-
33847220720
-
K-leap method for accelerating stochastic simulation of coupled chemical reactions
-
Cai X.D., Xu Z.Y. K-leap method for accelerating stochastic simulation of coupled chemical reactions. J. Chem. Phys. 2007, 126.
-
(2007)
J. Chem. Phys.
, vol.126
-
-
Cai, X.D.1
Xu, Z.Y.2
-
13
-
-
22944480262
-
The slow-scale stochastic simulation algorithm
-
Cao Y., Gillespie D.T., Petzold L.R. The slow-scale stochastic simulation algorithm. J. Chem. Phys. 2005, 122:14116.
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 14116
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.R.3
-
14
-
-
22944469465
-
Binomial distribution based tau-leap accelerated stochastic simulation
-
Chatterjee A., Vlachos D.G., Katsoulakis M.A. Binomial distribution based tau-leap accelerated stochastic simulation. J. Chem. Phys. 2005, 122.
-
(2005)
J. Chem. Phys.
, vol.122
-
-
Chatterjee, A.1
Vlachos, D.G.2
Katsoulakis, M.A.3
-
15
-
-
54249083606
-
A stochastic single-molecule event triggers phenotype switching of a bacterial cell
-
Choi P.J., Cai L., Frieda K., Xie S. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 2008, 322:442-446.
-
(2008)
Science
, vol.322
, pp. 442-446
-
-
Choi, P.J.1
Cai, L.2
Frieda, K.3
Xie, S.4
-
16
-
-
33646591544
-
Transcriptional pulsing of a developmental gene
-
Chubb J.R., Trcek T., Shenoy S.M., Singer R.H. Transcriptional pulsing of a developmental gene. Curr. Biol. 2006, 16:1018-1025.
-
(2006)
Curr. Biol.
, vol.16
, pp. 1018-1025
-
-
Chubb, J.R.1
Trcek, T.2
Shenoy, S.M.3
Singer, R.H.4
-
17
-
-
21544473153
-
Real-time RNA profiling within a single bacterium
-
Cluzel P., Le T.T., Harlepp S., Guet C.C., Dittmar K., Emonet T., Pan T. Real-time RNA profiling within a single bacterium. Proc. Natl. Acad. Sci. U S A 2005, 102:9160-9164.
-
(2005)
Proc. Natl. Acad. Sci. U S A
, vol.102
, pp. 9160-9164
-
-
Cluzel, P.1
Le, T.T.2
Harlepp, S.3
Guet, C.C.4
Dittmar, K.5
Emonet, T.6
Pan, T.7
-
19
-
-
80054718671
-
A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks
-
Eissing T., Kuepfer L., Becker C., Block M., Coboeken K., Gaub T., Goerlitz L., Jaeger J., Loosen R., Ludewig B., et al. A computational systems biology software platform for multiscale modeling and simulation: integrating whole-body physiology, disease biology, and molecular reaction networks. Front. Physiol. 2011, 2:4.
-
(2011)
Front. Physiol.
, vol.2
, pp. 4
-
-
Eissing, T.1
Kuepfer, L.2
Becker, C.3
Block, M.4
Coboeken, K.5
Gaub, T.6
Goerlitz, L.7
Jaeger, J.8
Loosen, R.9
Ludewig, B.10
-
20
-
-
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
-
21
-
-
78650556702
-
Stochastic reaction-diffusion kinetics in the microscopic limit
-
Elf J., Fange D., Berg O.G., Sjoberg P. Stochastic reaction-diffusion kinetics in the microscopic limit. Proc. Natl. Acad. Sci. U S A 2010, 107:19820-19825.
-
(2010)
Proc. Natl. Acad. Sci. U S A
, vol.107
, pp. 19820-19825
-
-
Elf, J.1
Fange, D.2
Berg, O.G.3
Sjoberg, P.4
-
22
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie D.T. 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
-
23
-
-
44049109914
-
A rigorous derivation of the chemical master equation
-
Gillespie D.T. A rigorous derivation of the chemical master equation. Physica A 1992, 188:404-425.
-
(1992)
Physica A
, vol.188
, pp. 404-425
-
-
Gillespie, D.T.1
-
24
-
-
0035933994
-
Approximate accelerated stochastic simulation of chemically reacting systems
-
Gillespie D.T. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 2001, 115:1716-1733.
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 1716-1733
-
-
Gillespie, D.T.1
-
25
-
-
0242425970
-
Improved leap-size selection for accelerated stochastic simulation
-
Gillespie D.T., Petzold L.R. Improved leap-size selection for accelerated stochastic simulation. J. Chem. Phys. 2003, 119:8229-8234.
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 8229-8234
-
-
Gillespie, D.T.1
Petzold, L.R.2
-
26
-
-
28944434119
-
Real-time kinetics of gene activity in individual bacteria
-
Golding I., Paulsson J., Zawilski S.M., Cox E.C. Real-time kinetics of gene activity in individual bacteria. Cell 2005, 123:1025-1036.
-
(2005)
Cell
, vol.123
, pp. 1025-1036
-
-
Golding, I.1
Paulsson, J.2
Zawilski, S.M.3
Cox, E.C.4
-
27
-
-
33846250352
-
Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations
-
Gomez-Uribe C.A., Verghese G.C. Mass fluctuation kinetics: capturing stochastic effects in systems of chemical reactions through coupled mean-variance computations. J. Chem. Phys. 2007, 126.
-
(2007)
J. Chem. Phys.
, vol.126
-
-
Gomez-Uribe, C.A.1
Verghese, G.C.2
-
28
-
-
34447099234
-
Probing the limits to positional information
-
Gregor T., Tank D.W., Wieschaus E.F., Bialek W. Probing the limits to positional information. Cell 2007, 130:153-164.
-
(2007)
Cell
, vol.130
, pp. 153-164
-
-
Gregor, T.1
Tank, D.W.2
Wieschaus, E.F.3
Bialek, W.4
-
29
-
-
34447104600
-
Stability and nuclear dynamics of the bicoid morphogen gradient
-
Gregor T., Wieschaus E.F., McGregor A.P., Bialek W., Tank D.W. Stability and nuclear dynamics of the bicoid morphogen gradient. Cell 2007, 130:141-152.
-
(2007)
Cell
, vol.130
, pp. 141-152
-
-
Gregor, T.1
Wieschaus, E.F.2
McGregor, A.P.3
Bialek, W.4
Tank, D.W.5
-
30
-
-
22144498043
-
Sensitivity analysis of discrete stochastic systems
-
Gunawan R., Cao Y., Petzold L., Doyle F.J. Sensitivity analysis of discrete stochastic systems. Biophys. J. 2005, 88:2530-2540.
-
(2005)
Biophys. J.
, vol.88
, pp. 2530-2540
-
-
Gunawan, R.1
Cao, Y.2
Petzold, L.3
Doyle, F.J.4
-
31
-
-
0037109565
-
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
-
Haseltine E.L., Rawlings J.B. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J. Chem. Phys. 2002, 117:6959-6969.
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 6959-6969
-
-
Haseltine, E.L.1
Rawlings, J.B.2
-
33
-
-
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.
-
(2008)
PLOS Comput. Biol.
, vol.4
-
-
Hornung, G.1
Barkai, N.2
-
35
-
-
0346731136
-
Post-transcriptional regulation of the E/Daughterless ortholog HLH-2, negative feedback, and birth order bias during the AC/VU decision in C. elegans
-
Karp X., Greenwald I. Post-transcriptional regulation of the E/Daughterless ortholog HLH-2, negative feedback, and birth order bias during the AC/VU decision in C. elegans. Genes Dev. 2003, 17:3100-3111.
-
(2003)
Genes Dev.
, vol.17
, pp. 3100-3111
-
-
Karp, X.1
Greenwald, I.2
-
36
-
-
0034698011
-
Multiplicative moments and measures of persistence in ecology
-
Keeling M.J. Multiplicative moments and measures of persistence in ecology. J. Theor. Biol. 2000, 205:269-281.
-
(2000)
J. Theor. Biol.
, vol.205
, pp. 269-281
-
-
Keeling, M.J.1
-
37
-
-
33749018832
-
Crowding and confinement effects on protein diffusion in vivo
-
Konopka M.C., Shkel I.A., Cayley S., Record M.T., Weisshaar J.C. Crowding and confinement effects on protein diffusion in vivo. J Bacteriol. Sep 2006, 188(17):6115-6123.
-
(2006)
J Bacteriol.
, vol.188
, Issue.17
, pp. 6115-6123
-
-
Konopka, M.C.1
Shkel, I.A.2
Cayley, S.3
Record, M.T.4
Weisshaar, J.C.5
-
38
-
-
18844368812
-
Bacterial persistence: a model of survival in changing environments
-
Kussell E., Kishony R., Balaban N.Q., Leibler S. Bacterial persistence: a model of survival in changing environments. Genetics 2005, 169:1807-1814.
-
(2005)
Genetics
, vol.169
, pp. 1807-1814
-
-
Kussell, E.1
Kishony, R.2
Balaban, N.Q.3
Leibler, S.4
-
39
-
-
0033083733
-
It's a noisy business! Genetic regulation at the nanomolar scale
-
McAdams H.H., Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 1999, 15:65-69.
-
(1999)
Trends Genet.
, vol.15
, pp. 65-69
-
-
McAdams, H.H.1
Arkin, A.2
-
40
-
-
0031879114
-
Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
-
McAdams H.H., Arkin A., Ross J. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 1998, 149:1633-1648.
-
(1998)
Genetics
, vol.149
, pp. 1633-1648
-
-
McAdams, H.H.1
Arkin, A.2
Ross, J.3
-
41
-
-
0001601301
-
Stochastic approach to chemical kinetics
-
Mcquarri D.A. Stochastic approach to chemical kinetics. J. Appl. Probability 1967, 4:413-477.
-
(1967)
J. Appl. Probability
, vol.4
, pp. 413-477
-
-
Mcquarri, D.A.1
-
42
-
-
0032492834
-
Predicting temporal fluctuations in an intracellular signalling pathway
-
Morton-Firth C.J., Bray D. Predicting temporal fluctuations in an intracellular signalling pathway. J. Theor. Biol. 1998, 192:117-128.
-
(1998)
J. Theor. Biol.
, vol.192
, pp. 117-128
-
-
Morton-Firth, C.J.1
Bray, D.2
-
43
-
-
0022591020
-
Molecular-cloning and expression of HIPA, a gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis
-
Moyed H.S., Broderick S.H. Molecular-cloning and expression of HIPA, a gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis. J. Bacteriol. 1986, 166:399-403.
-
(1986)
J. Bacteriol.
, vol.166
, pp. 399-403
-
-
Moyed, H.S.1
Broderick, S.H.2
-
44
-
-
34547925618
-
Combinatorial promoter design for engineering noisy gene expression
-
Murphy K.F., Balazsi G., Collins J.J. Combinatorial promoter design for engineering noisy gene expression. Proc. Natl. Acad. Sci. U S A 2007, 104:12726-12731.
-
(2007)
Proc. Natl. Acad. Sci. U S A
, vol.104
, pp. 12726-12731
-
-
Murphy, K.F.1
Balazsi, G.2
Collins, J.J.3
-
45
-
-
0347506351
-
An extension of the moment closure method
-
Nasell I. An extension of the moment closure method. Theor. Popul. Biol. 2003, 64:233-239.
-
(2003)
Theor. Popul. Biol.
, vol.64
, pp. 233-239
-
-
Nasell, I.1
-
46
-
-
67649880601
-
Adiabatic coarse-graining and simulations of stochastic biochemical networks
-
Nemenman I., Sinitsyn N.A., Hengartner N. Adiabatic coarse-graining and simulations of stochastic biochemical networks. Proc. Natl. Acad. Sci. U S A 2009, 106:10546-10551.
-
(2009)
Proc. Natl. Acad. Sci. U S A
, vol.106
, pp. 10546-10551
-
-
Nemenman, I.1
Sinitsyn, N.A.2
Hengartner, N.3
-
47
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman J.R., Ghaemmaghami S., Ihmels J., Breslow D.K., Noble M., DeRisi J.L., Weissman J.S. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441:840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
Noble, M.5
DeRisi, J.L.6
Weissman, J.S.7
-
48
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman J.R.S., Ghaemmaghami S., Ihmels J., Breslow D.K., Noble M., DeRisi J.L., Weissman J.S. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 2006, 441:840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.S.1
Ghaemmaghami, S.2
Ihmels, J.3
Breslow, D.K.4
Noble, M.5
DeRisi, J.L.6
Weissman, J.S.7
-
49
-
-
0036578645
-
Regulation of noise in the expression of a single gene
-
Ozbudak E.M., Thattai M., Kurtser I., Grossman A.D., van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat. Genet. 2002, 31:69-73.
-
(2002)
Nat. Genet.
, vol.31
, pp. 69-73
-
-
Ozbudak, E.M.1
Thattai, M.2
Kurtser, I.3
Grossman, A.D.4
van Oudenaarden, A.5
-
50
-
-
20344389483
-
Models of stochastic gene expression
-
Paulsson J. Models of stochastic gene expression. Phys. Life Rev. 2005, 2:157-175.
-
(2005)
Phys. Life Rev.
, vol.2
, pp. 157-175
-
-
Paulsson, J.1
-
51
-
-
0034691214
-
Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation
-
Paulsson J., Berg O.G., 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
-
52
-
-
34250174164
-
Averaging methods for stochastic dynamics of complex reaction networks: description of multiscale couplings
-
Plyasunov S., Arkin A.P. Averaging methods for stochastic dynamics of complex reaction networks: description of multiscale couplings. Multiscale Modeling Simulation 2006, 5:497-513.
-
(2006)
Multiscale Modeling Simulation
, vol.5
, pp. 497-513
-
-
Plyasunov, S.1
Arkin, A.P.2
-
53
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
Raj A., Peskin C.S., Tranchina D., Vargas D.Y., Tyagi S. Stochastic mRNA synthesis in mammalian cells. PLOS Biol. 2006, 4:1707-1719.
-
(2006)
PLOS Biol.
, vol.4
, pp. 1707-1719
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
54
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm
-
Rao C.V., Arkin A.P. Stochastic chemical kinetics and the quasi-steady-state assumption: application to the Gillespie algorithm. J. Chem. Phys. 2003, 118:4999-5010.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 4999-5010
-
-
Rao, C.V.1
Arkin, A.P.2
-
55
-
-
0037078982
-
Control, exploitation and tolerance of intracellular noise
-
Rao C.V., Wolf D.M., Arkin A.P. 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
-
56
-
-
25444468618
-
Noise in gene expression: origins, consequences, and control
-
Raser J.M., O'Shea E.K. 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
-
57
-
-
34248583573
-
Reversible-equivalent-monomolecular tau: a leaping method for " small number and stiff" stochastic chemical systems
-
Rathinam M., El Samad H. Reversible-equivalent-monomolecular tau: a leaping method for " small number and stiff" stochastic chemical systems. J. Comput. Phys. 2007, 224:897-923.
-
(2007)
J. Comput. Phys.
, vol.224
, pp. 897-923
-
-
Rathinam, M.1
El Samad, H.2
-
58
-
-
77949884150
-
Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks
-
Rathinam M., Sheppard P.W., Khammash M. Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks. J. Chem. Phys. 2010, 132.
-
(2010)
J. Chem. Phys.
, vol.132
-
-
Rathinam, M.1
Sheppard, P.W.2
Khammash, M.3
-
59
-
-
68949178269
-
Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm
-
Ridgway D., Broderick G., Lopez-Campistrous A., Ru'aini M., Winter P., Hamilton M., Boulanger P., Kovalenko A., Ellison M.J. Coarse-grained molecular simulation of diffusion and reaction kinetics in a crowded virtual cytoplasm. Biophys. J. 2009, 96:2548.
-
(2009)
Biophys. J.
, vol.96
, pp. 2548
-
-
Ridgway, D.1
Broderick, G.2
Lopez-Campistrous, A.3
Ru'aini, M.4
Winter, P.5
Hamilton, M.6
Boulanger, P.7
Kovalenko, A.8
Ellison, M.J.9
-
60
-
-
3142577523
-
Stochastic approaches for modelling in vivo reactions
-
Schnell S., Turner T.E., 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
-
-
Schnell, S.1
Turner, T.E.2
Burrage, K.3
-
61
-
-
0346362447
-
Negative feedback regulation ensures the one receptor-one olfactory neuron rule in mouse
-
Serizawa S., Miyamichi K., Nakatani H., Suzuki M., Saito M., Yoshihara Y., Sakano H. Negative feedback regulation ensures the one receptor-one olfactory neuron rule in mouse. Science 2003, 302:2088-2094.
-
(2003)
Science
, vol.302
, pp. 2088-2094
-
-
Serizawa, S.1
Miyamichi, K.2
Nakatani, H.3
Suzuki, M.4
Saito, M.5
Yoshihara, Y.6
Sakano, H.7
-
62
-
-
34547683508
-
A derivative matching approach to moment closure for the stochastic logistic model
-
Singh A., Hespanha J.P. A derivative matching approach to moment closure for the stochastic logistic model. Bull. Math. Biol. 2007, 69:1909-1925.
-
(2007)
Bull. Math. Biol.
, vol.69
, pp. 1909-1925
-
-
Singh, A.1
Hespanha, J.P.2
-
63
-
-
78049436913
-
HIV promoter integration site primarily modulates transcriptional burst size rather than frequency
-
Skupsky R., Burnett J.C., Foley J.E., Schaffer D.V., Arkin A.P. HIV promoter integration site primarily modulates transcriptional burst size rather than frequency. PLOS Comput. Biol. 2010, 6.
-
(2010)
PLOS Comput. Biol.
, vol.6
-
-
Skupsky, R.1
Burnett, J.C.2
Foley, J.E.3
Schaffer, D.V.4
Arkin, A.P.5
-
65
-
-
0003490410
-
-
Addison-Wesley, Reading, MA
-
Strogatz S.H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering 1994, Addison-Wesley, Reading, MA.
-
(1994)
Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering
-
-
Strogatz, S.H.1
-
66
-
-
0030211187
-
Stochastic simulation of coupled reaction-diffusion processes
-
Stundzia A.B., Lumsden C.J. Stochastic simulation of coupled reaction-diffusion processes. J. Comput. Phys. 1996, 127:196-207.
-
(1996)
J. Comput. Phys.
, vol.127
, pp. 196-207
-
-
Stundzia, A.B.1
Lumsden, C.J.2
-
67
-
-
70350336588
-
Architecture-dependent noise discriminates functionally analogous differentiation circuits
-
Suel G.M., Cagatay T., Turcotte M., Elowitz M.B., Garcia-Ojalvo J. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 2009, 139:512-522.
-
(2009)
Cell
, vol.139
, pp. 512-522
-
-
Suel, G.M.1
Cagatay, T.2
Turcotte, M.3
Elowitz, M.B.4
Garcia-Ojalvo, J.5
-
68
-
-
33645293152
-
An excitable gene regulatory circuit induces transient cellular differentiation
-
Suel G.M., Garcia-Ojalvo J., Liberman L.M., Elowitz M.B. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 2006, 440:545-550.
-
(2006)
Nature
, vol.440
, pp. 545-550
-
-
Suel, G.M.1
Garcia-Ojalvo, J.2
Liberman, L.M.3
Elowitz, M.B.4
-
69
-
-
34047118521
-
Tunability and noise dependence in differentiation dynamics
-
Suel G.M., Kulkarni R.P., Dworkin J., Garcia-Ojalvo J., Elowitz M.B. Tunability and noise dependence in differentiation dynamics. Science 2007, 315:1716-1719.
-
(2007)
Science
, vol.315
, pp. 1716-1719
-
-
Suel, G.M.1
Kulkarni, R.P.2
Dworkin, J.3
Garcia-Ojalvo, J.4
Elowitz, M.B.5
-
70
-
-
77955102352
-
Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Taniguchi Y., Choi P.J., Li G.W., Chen H.Y., Babu M., Hearn J., Emili A., Xie X.S. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329:533-538.
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
Choi, P.J.2
Li, G.W.3
Chen, H.Y.4
Babu, M.5
Hearn, J.6
Emili, A.7
Xie, X.S.8
-
72
-
-
58249117722
-
A tunable synthetic mammalian oscillator
-
Tigges M., Marquez-Lago T.T., Stelling J., Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009, 457:309-312.
-
(2009)
Nature
, vol.457
, pp. 309-312
-
-
Tigges, M.1
Marquez-Lago, T.T.2
Stelling, J.3
Fussenegger, M.4
-
73
-
-
3042715501
-
Multivariate analysis of noise in genetic regulatory networks
-
Tomioka R., Kimura H., Kobayashi T.J., Aihara K. Multivariate analysis of noise in genetic regulatory networks. J. Theor. Biol. 2004, 229:501-521.
-
(2004)
J. Theor. Biol.
, vol.229
, pp. 501-521
-
-
Tomioka, R.1
Kimura, H.2
Kobayashi, T.J.3
Aihara, K.4
-
74
-
-
46849090495
-
Robust, tunable biological oscillations from interlinked positive and negative feedback loops
-
Tsai T.Y.C., Choi Y.S., Ma W.Z., Pomerening J.R., Tang C., Ferrell J.E. Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 2008, 321:126-129.
-
(2008)
Science
, vol.321
, pp. 126-129
-
-
Tsai, T.Y.C.1
Choi, Y.S.2
Ma, W.Z.3
Pomerening, J.R.4
Tang, C.5
Ferrell, J.E.6
-
75
-
-
41349119880
-
Stochastic switching as a survival strategy in fluctuating environments
-
van Oudenaarden A., Acar M., Mettetal J.T. Stochastic switching as a survival strategy in fluctuating environments. Nat. Genet. 2008, 40:471-475.
-
(2008)
Nat. Genet.
, vol.40
, pp. 471-475
-
-
van Oudenaarden, A.1
Acar, M.2
Mettetal, J.T.3
-
76
-
-
0003691678
-
-
Cambridge University Press, Cambridge, New York
-
Varma A., Morbidelli M., Wu H. Parametric Sensitivity in Chemical Systems 2005, Cambridge University Press, Cambridge, New York.
-
(2005)
Parametric Sensitivity in Chemical Systems
-
-
Varma, A.1
Morbidelli, M.2
Wu, H.3
-
77
-
-
84859297929
-
Uncorrelated diffusion of MHC class II proteins in the plasma membrane
-
523a
-
Vrljic M., Nishimura S.Y., Brasselet S., Moerner W.E., McConnell H.M. Uncorrelated diffusion of MHC class II proteins in the plasma membrane. Biophys. J. 2002, 82. 523a.
-
(2002)
Biophys. J.
, vol.82
-
-
Vrljic, M.1
Nishimura, S.Y.2
Brasselet, S.3
Moerner, W.E.4
McConnell, H.M.5
-
78
-
-
33749018832
-
Crowding and confinement effects on protein diffusion in vivo
-
Weisshaar J.C., Konopka M.C., Shkel I.A., Cayley S., Record M.T. Crowding and confinement effects on protein diffusion in vivo. J. Bacteriol. 2006, 188:6115-6123.
-
(2006)
J. Bacteriol.
, vol.188
, pp. 6115-6123
-
-
Weisshaar, J.C.1
Konopka, M.C.2
Shkel, I.A.3
Cayley, S.4
Record, M.T.5
-
79
-
-
0001637131
-
On the use of the normal approximation in the treatment of stochastic-processes
-
Whittle P. On the use of the normal approximation in the treatment of stochastic-processes. J. R. Stat. Soc. Ser. B-Stat. Methodol. 1957, 19:268-281.
-
(1957)
J. R. Stat. Soc. Ser. B-Stat. Methodol.
, vol.19
, pp. 268-281
-
-
Whittle, P.1
-
80
-
-
14744282987
-
Diversity in times of adversity: probabilistic strategies in microbial survival games
-
Wolf D.M., Vazirani V.V., Arkin A.P. Diversity in times of adversity: probabilistic strategies in microbial survival games. J. Theor. Biol. 2005, 234:227-253.
-
(2005)
J. Theor. Biol.
, vol.234
, pp. 227-253
-
-
Wolf, D.M.1
Vazirani, V.V.2
Arkin, A.P.3
-
81
-
-
33645033645
-
Probing gene expression in live cells, one protein molecule at a time
-
Yu J., Xiao J., Ren X.J., Lao K.Q., Xie X.S. Probing gene expression in live cells, one protein molecule at a time. Science 2006, 311:1600-1603.
-
(2006)
Science
, vol.311
, pp. 1600-1603
-
-
Yu, J.1
Xiao, J.2
Ren, X.J.3
Lao, K.Q.4
Xie, X.S.5
|