-
1
-
-
35748931160
-
Data-based identifiability analysis of non-linear dynamical models
-
DOI 10.1093/bioinformatics/btm382
-
Hengl S, Kreutz C, Timmer J, Maiwald T (2007) Data-based identifiability analysis of non-linear dynamical models. Bioinformatics 23:2612-2618. (Pubitemid 350048365)
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2612-2618
-
-
Hengl, S.1
Kreutz, C.2
Timmer, J.3
Maiwald, T.4
-
2
-
-
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
-
3
-
-
41549140160
-
Bayesian inference for a discretely observed stochastic kinetic model
-
Boys RJ, Wilkinson DJ, Kirkwood TBL (2007) Bayesian inference for a discretely observed stochastic kinetic model. Stat Comput 18:125-135.
-
(2007)
Stat Comput
, vol.18
, pp. 125-135
-
-
Boys, R.J.1
Wilkinson, D.J.2
Kirkwood, T.B.L.3
-
4
-
-
0037119587
-
Stochastic gene expression in a single cell
-
DOI 10.1126/science.1070919
-
Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297:1183-1186. (Pubitemid 36193353)
-
(2002)
Science
, vol.297
, Issue.5584
, pp. 1183-1186
-
-
Elowitz, M.B.1
Levine, A.J.2
Siggia, E.D.3
Swain, P.S.4
-
5
-
-
26944476331
-
Regulated cell-to-cell variation in a cell-fate decision system
-
DOI 10.1038/nature03998, PII N03998
-
Colman-Lerner A, et al. (2005) Regulated cell-to-cell variation in a cell-fate decision system. Nature 437:699-706. (Pubitemid 41486534)
-
(2005)
Nature
, vol.437
, Issue.7059
, pp. 699-706
-
-
Colman-Lerner, A.1
Gordon, A.2
Serra, E.3
Chin, T.4
Resnekov, O.5
Endy, D.6
Pesce, C.G.7
Brent, R.8
-
6
-
-
78951470515
-
Origins of regulated cell-to-cell variability
-
Snijder B, Pelkmans L (2011) Origins of regulated cell-to-cell variability. Nat Rev Mol Cell Biol 12:119-125.
-
(2011)
Nat Rev Mol Cell Biol
, vol.12
, pp. 119-125
-
-
Snijder, B.1
Pelkmans, L.2
-
7
-
-
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
-
8
-
-
79961051673
-
Separating intrinsic from extrinsic fluctuations in dynamic biological systems
-
Hilfinger A, Paulsson J (2011) Separating intrinsic from extrinsic fluctuations in dynamic biological systems. Proc Natl Acad Sci USA 108:12167-12172.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 12167-12172
-
-
Hilfinger, A.1
Paulsson, J.2
-
9
-
-
79955135865
-
Identification of models of heterogeneous cell populations from population snapshot data
-
Hasenauer J, et al. (2011) Identification of models of heterogeneous cell populations from population snapshot data. BMC Bioinformatics 12:125.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 125
-
-
Hasenauer, J.1
-
10
-
-
84861650075
-
Accounting for extrinsic variability in the estimation of stochastic rate constants
-
10.1002/ rnc.2804
-
Koeppl H, Zechner C, Ganguly A, Pelet S, Peter M (2012) Accounting for extrinsic variability in the estimation of stochastic rate constants. Int J Robust Nonlin, 10.1002/ rnc.2804.
-
(2012)
Int J Robust Nonlin
-
-
Koeppl, H.1
Zechner, C.2
Ganguly, A.3
Pelet, S.4
Peter, M.5
-
11
-
-
27744503232
-
Bayesian inference for stochastic kinetic models using a diffusion approximation
-
Golightly A, Wilkinson DJ (2005) Bayesian inference for stochastic kinetic models using a diffusion approximation. Biometrics 61:781-788.
-
(2005)
Biometrics
, vol.61
, pp. 781-788
-
-
Golightly, A.1
Wilkinson, D.J.2
-
12
-
-
33646540711
-
Predicting stochastic gene expression dynamics in single cells
-
DOI 10.1073/pnas.0509874103
-
Mettetal JT, Muzzey D, Pedraza JM, Ozbudak EM, van Oudenaarden A (2006) Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci USA 103:7304-7309. (Pubitemid 43727828)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.19
, pp. 7304-7309
-
-
Mettetal, J.T.1
Muzzey, D.2
Pedraza, J.M.3
Ozbudak, E.M.4
Van Oudenaarden, A.5
-
13
-
-
32844455250
-
A bottom-up approach to gene regulation
-
DOI 10.1038/nature04473, PII NATURE04473
-
Guido NJ, et al. (2006) A bottom-up approach to gene regulation. Nature 439:856-860. (Pubitemid 43255704)
-
(2006)
Nature
, vol.439
, Issue.7078
, 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
-
14
-
-
33751347484
-
The finite state projection algorithm for the solution of the chemical master equation
-
Munsky B, Khammash M (2006) The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys 124:044104.
-
(2006)
J Chem Phys
, vol.124
, pp. 044104
-
-
Munsky, B.1
Khammash, M.2
-
16
-
-
0017030517
-
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
-
Gillespie D (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22:403-434.
-
(1976)
J Comput Phys
, vol.22
, pp. 403-434
-
-
Gillespie, D.1
-
18
-
-
0001637131
-
On the use of the normal approximation in the treatment of stochastic processes
-
Whittle P (1957) On the use of the normal approximation in the treatment of stochastic processes. J Roy Stat Soc B Met 19:268-281.
-
(1957)
J Roy Stat Soc B Met
, vol.19
, pp. 268-281
-
-
Whittle, P.1
-
20
-
-
80555154070
-
Moment estimation for chemically reacting systems by extended Kalman filtering
-
Ruess J, Milias-Argeitis A, Summers S, Lygeros J (2011) Moment estimation for chemically reacting systems by extended Kalman filtering. J Chem Phys 135:165102.
-
(2011)
J Chem Phys
, vol.135
, pp. 165102
-
-
Ruess, J.1
Milias-Argeitis, A.2
Summers, S.3
Lygeros, J.4
-
21
-
-
79955753549
-
Transient activation of the HOG MAPK pathway regulates bimodal gene expression
-
Pelet S, et al. (2011) Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science 332:732-735.
-
(2011)
Science
, vol.332
, pp. 732-735
-
-
Pelet, S.1
-
22
-
-
53949098609
-
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
-
Shalem O (2008) Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol 4:4.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 4
-
-
Shalem, O.1
-
23
-
-
0036282743
-
Osmotic stress signaling and osmoadaptation in yeasts
-
Hohmann S (2002) Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66:300-372.
-
(2002)
Microbiol Mol Biol Rev
, vol.66
, pp. 300-372
-
-
Hohmann, S.1
-
25
-
-
0000025874
-
On structural identifiability
-
Bellman R, Astrom K (1970) On structural identifiability. Math Biosci 7:329-339.
-
(1970)
Math Biosci
, vol.7
, pp. 329-339
-
-
Bellman, R.1
Astrom, K.2
-
27
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
Gasch AP, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257.
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
-
28
-
-
0142215475
-
Global analysis of protein expression in yeast
-
DOI 10.1038/nature02046
-
Ghaemmaghami S, et al. (2003) Global analysis of protein expression in yeast. Nature 425:737-741. (Pubitemid 37314318)
-
(2003)
Nature
, vol.425
, Issue.6959
, pp. 737-741
-
-
Ghaemmaghami, S.1
Huh, W.-K.2
Bower, K.3
Howson, R.W.4
Belle, A.5
Dephoure, N.6
O'Shea, E.K.7
Weissman, J.S.8
-
29
-
-
67649669252
-
A systems-level analysis of perfect adaptation in yeast osmoregulation
-
Muzzey D, Gómez-Uribe Ca, Mettetal JT, van Oudenaarden A (2009) A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell 138:160-171.
-
(2009)
Cell
, vol.138
, pp. 160-171
-
-
Muzzey, D.1
Gómez-Uribe, Ca.2
Mettetal, J.T.3
Van Oudenaarden, A.4
-
30
-
-
77949729619
-
A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae
-
Zi Z, Liebermeister W, Klipp E (2010) A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae. PloS One 5:e9522.
-
(2010)
PloS One
, vol.5
-
-
Zi, Z.1
Liebermeister, W.2
Klipp, E.3
-
31
-
-
66149137998
-
Dynamic signaling in the Hog1 MAPK pathway relies on high basal signal transduction
-
Macia J, et al. (2009) Dynamic signaling in the Hog1 MAPK pathway relies on high basal signal transduction. Sci Signal 2:ra13.
-
(2009)
Sci Signal
, vol.2
-
-
Macia, J.1
-
32
-
-
84984933073
-
Structure and function of a transcriptional network activated by the MAPK Hog1
-
Capaldi AP, et al. (2008) Structure and function of a transcriptional network activated by the MAPK Hog1. Nat Genet 40:1300-1306.
-
(2008)
Nat Genet
, vol.40
, pp. 1300-1306
-
-
Capaldi, A.P.1
-
33
-
-
33745220278
-
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
-
Newman JRS, et al. (2006) Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature 441:840-846.
-
(2006)
Nature
, vol.441
, pp. 840-846
-
-
Newman, J.R.S.1
-
34
-
-
0033752944
-
Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry
-
Mateus C, Avery SV (2000) Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. Yeast 16:1313-1323.
-
(2000)
Yeast
, vol.16
, pp. 1313-1323
-
-
Mateus, C.1
Avery, S.V.2
-
35
-
-
23844449971
-
Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae
-
DOI 10.1128/EC.4.8.1343-1352.2005
-
Proft M, Gibbons F, Copeland M, Roth F, Struhl K (2005) Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. Eukaryot Cell 4:1343-1352. (Pubitemid 41176688)
-
(2005)
Eukaryotic Cell
, vol.4
, Issue.8
, pp. 1343-1352
-
-
Proft, M.1
Gibbons, F.D.2
Copeland, M.3
Roth, F.P.4
Struhl, K.5
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