-
1
-
-
84859739489
-
A Bayesian approach to targeted experiment design
-
Vanlier J, Tiemann CA, Hilbers PA, van Riel NA (2012) A Bayesian approach to targeted experiment design. Bioinformatics 28(8):1136-1142.
-
(2012)
Bioinformatics
, vol.28
, Issue.8
, pp. 1136-1142
-
-
Vanlier, J.1
Tiemann, C.A.2
Hilbers, P.A.3
Van Riel, N.A.4
-
2
-
-
73449142148
-
Optimal experimental design for parameter estimation of a cell signaling model
-
Bandara S, Schlöder JP, Eils R, Bock HG, Meyer T (2009) Optimal experimental design for parameter estimation of a cell signaling model. PLOS Comput Biol 5(11):e1000558.
-
(2009)
PLOS Comput Biol
, vol.5
, Issue.11
-
-
Bandara, S.1
Schlöder, J.P.2
Eils, R.3
Bock, H.G.4
Meyer, T.5
-
3
-
-
77950841799
-
Parameter estimation and model selection in computational biology
-
Lillacci G, Khammash M (2010) Parameter estimation and model selection in computational biology. PLOS Comput Biol 6(3):e1000696.
-
(2010)
PLOS Comput Biol
, vol.6
, Issue.3
-
-
Lillacci, G.1
Khammash, M.2
-
5
-
-
40149112059
-
Stimulus design for model selection and validation in cell signaling
-
Apgar JF, Toettcher JE, Endy D, White FM, Tidor B (2008) Stimulus design for model selection and validation in cell signaling. PLOS Comput Biol 4(2):e30.
-
(2008)
PLOS Comput Biol
, vol.4
, Issue.2
-
-
Apgar, J.F.1
Toettcher, J.E.2
Endy, D.3
White, F.M.4
Tidor, B.5
-
7
-
-
34247236577
-
Biology by numbers: Mathematical modelling in developmental biology
-
Tomlin CJ, Axelrod JD (2007) Biology by numbers: Mathematical modelling in developmental biology. Nat Rev Genet 8(5):331-340.
-
(2007)
Nat Rev Genet
, vol.8
, Issue.5
, pp. 331-340
-
-
Tomlin, C.J.1
Axelrod, J.D.2
-
8
-
-
4444226267
-
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data
-
Sontag E, Kiyatkin A, Kholodenko BN (2004) Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 20(12):1877-1886.
-
(2004)
Bioinformatics
, vol.20
, Issue.12
, pp. 1877-1886
-
-
Sontag, E.1
Kiyatkin, A.2
Kholodenko, B.N.3
-
9
-
-
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
-
10
-
-
49549094042
-
Sloppiness, robustness, and evolvability in systems biology
-
Daniels BC, Chen YJ, Sethna JP, Gutenkunst RN, Myers CR (2008) Sloppiness, robustness, and evolvability in systems biology. Curr Opin Biotechnol 19(4):389-395.
-
(2008)
Curr Opin Biotechnol
, vol.19
, Issue.4
, pp. 389-395
-
-
Daniels, B.C.1
Chen, Y.J.2
Sethna, J.P.3
Gutenkunst, R.N.4
Myers, C.R.5
-
12
-
-
84861443923
-
Moment-based inference predicts bimodality in transient gene expression
-
Zechner C, et al. (2012) Moment-based inference predicts bimodality in transient gene expression. Proc Natl Acad Sci USA 109(21):8340-8345.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.21
, pp. 8340-8345
-
-
Zechner, C.1
-
13
-
-
84895072562
-
Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings
-
Zechner C, Unger M, Pelet S, Peter M, Koeppl H (2014) Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings. Nat Methods 11(2):197-202.
-
(2014)
Nat Methods
, vol.11
, Issue.2
, pp. 197-202
-
-
Zechner, C.1
Unger, M.2
Pelet, S.3
Peter, M.4
Koeppl, H.5
-
14
-
-
77955187053
-
Global parameter estimation methods for stochastic biochemical systems
-
Poovathingal SK, Gunawan R (2010) Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics 11:414-425.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 414-425
-
-
Poovathingal, S.K.1
Gunawan, R.2
-
15
-
-
84883481038
-
The signal within the noise: Efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations
-
Lillacci G, Khammash M (2013) The signal within the noise: Efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinformatics 29(18):2311-2319.
-
(2013)
Bioinformatics
, vol.29
, Issue.18
, pp. 2311-2319
-
-
Lillacci, G.1
Khammash, M.2
-
16
-
-
84896591356
-
Designing experiments to understand the variability in biochemical reaction networks
-
Ruess J, Milias-Argeitis A, Lygeros J (2013) Designing experiments to understand the variability in biochemical reaction networks. J R Soc Interface 10(88):20130588.
-
(2013)
J R Soc Interface
, vol.10
, Issue.88
, pp. 20130588
-
-
Ruess, J.1
Milias-Argeitis, A.2
Lygeros, J.3
-
17
-
-
84874225515
-
Optimal variational perturbations for the inference of stochastic reaction dynamics
-
IEEE, Maui, HI
-
st Annual Conference on Decision and Control (CDC) (IEEE, Maui, HI), pp 5336-5341.
-
(2012)
Proceedings of the IEEE 51st Annual Conference on Decision and Control (CDC)
, pp. 5336-5341
-
-
Zechner, C.1
Nandy, P.2
Unger, M.3
Koeppl, H.4
-
18
-
-
84873801555
-
Systematic identification of signal-activated stochastic gene regulation
-
Neuert G, et al. (2013) Systematic identification of signal-activated stochastic gene regulation. Science 339(6119):584-587.
-
(2013)
Science
, vol.339
, Issue.6119
, pp. 584-587
-
-
Neuert, G.1
-
19
-
-
0036789439
-
A light-switchable gene promoter system
-
Shimizu-Sato S, Huq E, Tepperman JM, Quail PH (2002) A light-switchable gene promoter system. Nat Biotechnol 20(10):1041-1044.
-
(2002)
Nat Biotechnol
, vol.20
, Issue.10
, pp. 1041-1044
-
-
Shimizu-Sato, S.1
Huq, E.2
Tepperman, J.M.3
Quail, P.H.4
-
20
-
-
83255165732
-
In silico feedback for in vivo regulation of a gene expression circuit
-
Milias-Argeitis A, et al. (2011) In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol 29(12):1114-1116.
-
(2011)
Nat Biotechnol
, vol.29
, Issue.12
, pp. 1114-1116
-
-
Milias-Argeitis, A.1
-
21
-
-
84897954571
-
Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals
-
Olson EJ, Hartsough LA, Landry BP, Shroff R, Tabor JJ (2014) Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat Methods 11(4):449-455.
-
(2014)
Nat Methods
, vol.11
, Issue.4
, pp. 449-455
-
-
Olson, E.J.1
Hartsough, L.A.2
Landry, B.P.3
Shroff, R.4
Tabor, J.J.5
-
22
-
-
84902823142
-
Optogenetic characterization methods overcome key challenges in synthetic and systems biology
-
Olson EJ, Tabor JJ (2014) Optogenetic characterization methods overcome key challenges in synthetic and systems biology. Nat Chem Biol 10(7):502-511.
-
(2014)
Nat Chem Biol
, vol.10
, Issue.7
, pp. 502-511
-
-
Olson, E.J.1
Tabor, J.J.2
-
23
-
-
79956204640
-
Analysis, design and implementation of a novel scheme for in vivo control of synthetic gene regulatory networks
-
Menolascina F, Di Bernardo M, Di Bernardo D (2011) Analysis, design and implementation of a novel scheme for in vivo control of synthetic gene regulatory networks. Automatica 47(6):1265-1270.
-
(2011)
Automatica
, vol.47
, Issue.6
, pp. 1265-1270
-
-
Menolascina, F.1
Di Bernardo, M.2
Di Bernardo, D.3
-
24
-
-
84865536748
-
Long-term model predictive control of gene expression at the population and single-cell levels
-
Uhlendorf J, et al. (2012) Long-term model predictive control of gene expression at the population and single-cell levels. Proc Natl Acad Sci USA 109(35):14271-14276.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.35
, pp. 14271-14276
-
-
Uhlendorf, J.1
-
25
-
-
79957743805
-
Sensitivity, robustness, and identifiability in stochastic chemical kinetics models
-
Komorowski M, Costa MJ, Rand DA, Stumpf MP (2011) Sensitivity, robustness, and identifiability in stochastic chemical kinetics models. Proc Natl Acad Sci USA 108(21):8645-8650.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.21
, pp. 8645-8650
-
-
Komorowski, M.1
Costa, M.J.2
Rand, D.A.3
Stumpf, M.P.4
-
27
-
-
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(4):403-434.
-
(1976)
J Comput Phys
, vol.22
, Issue.4
, pp. 403-434
-
-
Gillespie, D.1
-
29
-
-
77952492425
-
Tuning and controlling gene expression noise in synthetic gene networks
-
Murphy KF, Adams RM, Wang X, Balázsi G, Collins JJ (2010) Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res 38(8):2712-2726.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.8
, pp. 2712-2726
-
-
Murphy, K.F.1
Adams, R.M.2
Wang, X.3
Balázsi, G.4
Collins, J.J.5
-
30
-
-
84866083176
-
Dynamics of protein noise can distinguish between alternate sources of gene-expression variability
-
Singh A, Razooky BS, Dar RD, Weinberger LS (2012) Dynamics of protein noise can distinguish between alternate sources of gene-expression variability. Mol Syst Biol 8:607.
-
(2012)
Mol Syst Biol
, vol.8
, pp. 607
-
-
Singh, A.1
Razooky, B.S.2
Dar, R.D.3
Weinberger, L.S.4
-
31
-
-
79953666361
-
Noise contributions in an inducible genetic switch: A whole-cell simulation study
-
Roberts E, Magis A, Ortiz JO, Baumeister W, Luthey-Schulten Z (2011) Noise contributions in an inducible genetic switch: A whole-cell simulation study. PLOS Comput Biol 7(3):e1002010.
-
(2011)
PLOS Comput Biol
, vol.7
, Issue.3
-
-
Roberts, E.1
Magis, A.2
Ortiz, J.O.3
Baumeister, W.4
Luthey-Schulten, Z.5
|