-
1
-
-
34249950625
-
Stochastic simulation of chemical kinetics
-
(doi:10.1146/annurev.physchem.58.032806.104637
-
Gillespie DT. 2007 Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58, 35-55. (doi:10.1146/annurev.physchem.58.032806.104637)
-
(2007)
Annu. Rev. Phys. Chem
, vol.58
, pp. 35-55
-
-
Gillespie, D.T.1
-
2
-
-
79957743805
-
Sensitivity, robustness, and identifiability in stochastic chemical kinetics models
-
(doi:10.1073/pnas.1015814108
-
Komorowski M, Costa MJ, Rand DA, Stumpf MPH. 2011 Sensitivity, robustness, and identifiability in stochastic chemical kinetics models. Proc. Natl Acad. Sci. USA 108, 8645-8650. (doi:10.1073/pnas.1015814108)
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 8645-8650
-
-
Komorowski, M.1
Costa, M.J.2
Rand, D.A.3
Stumpf, M.P.H.4
-
3
-
-
30644460811
-
Continuous-time markov models for species interactions
-
(doi:10.1890/05-0029
-
Spencer M, Susko E. 2005 Continuous-time Markov models for species interactions. Ecology 86, 3272-3278. (doi:10.1890/05-0029)
-
(2005)
Ecology
, vol.86
, pp. 3272-3278
-
-
Spencer M Susko, E.1
-
4
-
-
0031191180
-
Traffic models in broadband networks
-
(doi:10.1109/35.601746
-
Adas A. 1997 Traffic models in broadband networks. Commun. Mag. IEEE 35, 82-89.(doi:10.1109/35.601746)
-
(1997)
Commun. Mag. IEEE
, vol.35
, pp. 82-89
-
-
Adas, A.1
-
5
-
-
44049109914
-
A rigorous derivation of the chemical master equation
-
(doi:10.1016/0378-4371(92)90283-V
-
Gillespie DT. 2005 A rigorous derivation of the chemical master equation. Phys. A: Stat. Mech. Appl. 188, 404-425. (doi:10.1016/0378-4371(92)90283-V)
-
(2005)
Phys. A: Stat. Mech. Appl
, vol.188
, pp. 404-425
-
-
Gillespie, D.T.1
-
6
-
-
41549140160
-
Bayesian inference for a discretely observed stochastic kinetic model
-
(doi:10.1007/s11222-007-9043-x
-
Boys RJ, Wilkinson DJ, Kirkwood TB. 2008 Bayesian inference for a discretely observed stochastic kinetic model. Stat. Comp. 18, 125-135. (doi:10.1007/s11222-007-9043-x)
-
(2008)
Stat. Comp
, vol.18
, pp. 125-135
-
-
Boys, R.J.1
Wilkinson, D.J.2
Kirkwood, T.B.3
-
8
-
-
77953839617
-
Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species
-
ra20. (doi:10.1126/ scisignal.2000517
-
Xu T et al. 2010 Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species. Sci. Signal. 3, ra20. (doi:10.1126/ scisignal.2000517)
-
(2010)
Sci. Signal
, vol.3
-
-
Xu, T.1
-
9
-
-
84859758552
-
Statistical analysis of nonlinear dynamical systems using differential geometric sampling methods
-
(doi:10.1098/rsfs. 2011.0051
-
Calderhead B, Girolami M. 2011 Statistical analysis of nonlinear dynamical systems using differential geometric sampling methods. Interface Focus 1, 821-835. (doi:10.1098/rsfs. 2011.0051)
-
(2011)
Interface Focus
, vol.1
, pp. 821-835
-
-
Calderhead, B.1
Girolami, M.2
-
10
-
-
85143463392
-
The diffusion approximation for markov processes
-
(eds I Lamprecht, AI Zotin), New York, NY:Walter de Gruyter & Co
-
van Kampen NG. 1982 The diffusion approximation forMarkov processes. In Thermodynamics & kinetics of biological processes (eds I Lamprecht, AI Zotin), pp. 181-195. New York, NY:Walter de Gruyter & Co.
-
(1982)
Thermodynamics & Kinetics of Biological Processes
, pp. 181-195
-
-
Van Kampen, N.G.1
-
11
-
-
0034225547
-
The chemical langevin equation
-
(doi:10.1063/1.481811
-
Gillespie DT. 2000 The chemical Langevin equation. J. Chem. Phys. 113, 297-306. (doi:10.1063/1.481811)
-
(2000)
J. Chem. Phys
, vol.113
, pp. 297-306
-
-
Gillespie, D.T.1
-
12
-
-
10244252366
-
On inference for partially observed nonlinear diffusion models using the metropolis-hastings algorithm
-
(doi:10.1093/biomet/88.3.603
-
Roberts GO, Stramer O. 2001 On inference for partially observed nonlinear diffusion models using the Metropolis-Hastings algorithm. Biometrika 88, 603-621. (doi:10.1093/ biomet/88.3.603)
-
(2001)
Biometrika
, vol.88
, pp. 603-621
-
-
Roberts, G.O.1
Stramer, O.2
-
13
-
-
84860901236
-
Bayesian parameter inference for stochastic biochemical network models using particle markov chain monte carlo
-
(doi:10.1098/rsfs.2011.0047
-
Golightly A, Wilkinson DJ. 2011 Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo. Interface Focus 1, 807-820. (doi:10.1098/rsfs.2011.0047)
-
(2011)
Interface Focus
, vol.1
, pp. 807-820
-
-
Golightly, A.1
Wilkinson, D.J.2
-
14
-
-
84867122511
-
The linear noise approximation is valid over limited times for any chemical system that is sufficiently large
-
(doi:10.1049/iet-syb.2011.0038
-
Wallace E, Gillespie D, Sanft K, Petzold L. 2012 The linear noise approximation is valid over limited times for any chemical system that is sufficiently large. IET Syst. Biol. 6, 102-115.(doi:10.1049/iet-syb.2011.0038)
-
(2012)
IET Syst. Biol
, vol.6
, pp. 102-115
-
-
Wallace, E.1
Gillespie, D.2
Sanft, K.3
Petzold, L.4
-
15
-
-
71749100925
-
Bayesian inference of biochemical kinetic parameters using the linear noise approximation
-
(doi:10.1186/1471-2105-10-343
-
Komorowski M, Finkenstadt B, Harper C, Rand D. 2009 Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinformatics 10, 343. (doi:10.1186/1471-2105-10-343)
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 343
-
-
Komorowski, M.1
Finkenstadt, B.2
Harper, C.3
Rand, D.4
-
17
-
-
0031285157
-
Weak convergence and optimal scaling of random walk metropolis algorithms
-
(doi:10.1214/aoap/1034625254
-
Roberts GO, Gelman A, Gilks WR. 1997 Weak convergence and optimal scaling of random walk Metropolis algorithms. Ann. Appl. Probab. 7, 110-120. (doi:10.1214/aoap/1034625254)
-
(1997)
Ann. Appl. Probab
, vol.7
, pp. 110-120
-
-
Roberts, G.O.1
Gelman, A.2
Gilks, W.R.3
-
18
-
-
15244341043
-
Langevin diffusions and metropolis-hastings algorithms
-
(doi:10.1023/A:1023562417138
-
Roberts GO, Stramer O. 2003 Langevin diffusions and Metropolis-Hastings algorithms. Methodol. Comp. Appl. Probab. 4, 337-358. (doi:10.1023/A: 1023562417138)
-
(2003)
Methodol. Comp. Appl. Probab
, vol.4
, pp. 337-358
-
-
Roberts, G.O.1
Stramer, O.2
-
19
-
-
4243137056
-
Hybrid monte carlo
-
(doi:10.1016/0370-2693(87)91197-X
-
Duane S, Kennedy AB, Pendleton JB, Roweth D. 1987 Hybrid Monte Carlo. Phys. Lett. B 195, 216-222. (doi:10.1016/0370-2693(87)91197-X)
-
(1987)
Phys. Lett. B
, vol.195
, pp. 216-222
-
-
Duane, S.1
Kennedy, A.B.2
Pendleton, J.B.3
Roweth, D.4
-
21
-
-
0000936678
-
Optimal scaling of discrete approximations to langevin diffusions
-
(doi:10.1111/1467-9868.00123
-
Roberts GO, Rosenthal JS. 1998 Optimal scaling of discrete approximations to Langevin diffusions. J. R. Stat. Soc. B (Stat. Methodol.) 60, 255-268. (doi:10.1111/1467-9868.00123)
-
(1998)
J. R. Stat. Soc. B (Stat. Methodol.
, vol.60
, pp. 255-268
-
-
Roberts, G.O.1
Rosenthal, J.S.2
-
22
-
-
79952295497
-
Riemann manifold langevin and hamiltonian monte carlo methods
-
(doi:10.1111/j.1467-9868.2010.00765.x
-
Girolami M, Calderhead B. 2011 Riemann manifold Langevin and Hamiltonian Monte Carlo methods. J. R. Stat. Soc. B (Stat. Methodol.) 73, 123-214. (doi:10.1111/j.1467-9868.2010.00765.x)
-
(2011)
J. R. Stat. Soc. B (Stat. Methodol.
, vol.73
, pp. 123-214
-
-
Girolami, M.1
Calderhead, B.2
-
23
-
-
38349133325
-
A hierarchy of approximations of the master equation scaled by a size parameter
-
(doi:10.1007/s10915-007-9179-z
-
Ferm L, Lötstedt P, Hellander A. 2008 A hierarchy of approximations of the master equation scaled by a size parameter. J. Sci. Comp. 34, 127-151. (doi:10.1007/s10915-007-9179-z)
-
(2008)
J. Sci. Comp
, vol.34
, pp. 127-151
-
-
Ferm, L.1
Lötstedt, P.2
Hellander, A.3
-
24
-
-
84950758368
-
The calculation of posterior distributions by data augmentation
-
(doi:10.2307/2289457
-
TannerMA,Wong WH. 1987 The calculation of posterior distributions by data augmentation. J. Am. Stat. Assoc. 82, 528-540. (doi:10.2307/2289457)
-
(1987)
J. Am. Stat. Assoc
, vol.82
, pp. 528-540
-
-
Tanner, M.A.1
Wong, W.H.2
-
25
-
-
77956889087
-
Reversible jump markov chain monte carlo computation and bayesian model determination
-
(doi:10.1093/biomet/82.4.711
-
Green PJ. 1995 Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82, 711-732. (doi:10.1093/biomet/82.4. 711)
-
(1995)
Biometrika
, vol.82
, pp. 711-732
-
-
Green, P.J.1
-
26
-
-
61949434787
-
Deterministic limit of stochastic chemical kinetics
-
(doi:10.1021/jp806431b
-
Gillespie DT. 2009 Deterministic limit of stochastic chemical kinetics. J. Phys. Chem. B 113, 1640-1644. (doi:10.1021/jp806431b)
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1640-1644
-
-
Gillespie, D.T.1
-
27
-
-
35748969565
-
Bayesian inference for dynamic transcriptional regulation; the hes1 system as a case study
-
(doi:10.1093/bioinformatics/btm367
-
Heron EA, Finkenstädt B, Rand DA. 2007 Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study. Bioinformatics 23, 2596-2603. (doi:10.1093/ bioinformatics/btm367)
-
(2007)
Bioinformatics
, vol.23
, pp. 2596-2603
-
-
Heron, E.A.1
Finkenstädt, B.2
Rand, D.A.3
-
29
-
-
33847643776
-
Quantification of mrna using real-time rt-pcr
-
(doi:10.1038/nprot.2006.236
-
Nolan T, Hands RE, Bustin SA. 2006 Quantification of mRNA using real-time RT-PCR. Nat. Protocols 1, 1559-1582. (doi:10.1038/nprot.2006.236)
-
(2006)
Nat. Protocols
, vol.1
, pp. 1559-1582
-
-
Nolan, T.1
Hands, R.E.2
Bustin, S.A.3
-
30
-
-
33746082065
-
Componentwise adaptation for high dimensional mcmc
-
(doi:10.1007/BF02789703
-
Haario H, Saksman E, Tamminen E. 2005 Componentwise adaptation for high dimensional MCMC. Comp. Stat. 20, 265-273. (doi:10.1007/BF02789703)
-
(2005)
Comp. Stat
, vol.20
, pp. 265-273
-
-
Haario, H.1
Saksman, E.2
Tamminen, E.3
-
31
-
-
57849088168
-
A tutorial on adaptive mcmc
-
(doi:10.1007/s11222-008-9110-y
-
Andrieu C, Thoms J. 2008 A tutorial on adaptive MCMC. Stat. Comp. 18, 343-373.(doi:10.1007/s11222-008-9110-y)
-
(2008)
Stat. Comp
, vol.18
, pp. 343-373
-
-
Andrieu, C.1
Thoms, J.2
-
32
-
-
23244440564
-
Differential geometry: Curves-surfaces-manifolds
-
Providence, RI: American Mathematical Society
-
Kühnel W. 2005 Differential geometry: curves-surfaces-manifolds, vol. 2. Student Mathematical Library. Providence, RI: American Mathematical Society.
-
(2005)
Student Mathematical Library
, vol.2
-
-
Kühnel, W.1
-
33
-
-
0038563932
-
An adaptive metropolis algorithm
-
(doi:10.2307/3318737
-
Haario H, Saksman E, Tamminen J. 2001 An adaptive Metropolis algorithm. Bernoulli 7, 223-242. (doi:10.2307/3318737)
-
(2001)
Bernoulli
, vol.7
, pp. 223-242
-
-
Haario, H.1
Saksman, E.2
Tamminen, J.3
|