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Volumn 371, Issue 1984, 2013, Pages

Markov chain monte carlo inference for markov jump processes via the linear noise approximation

Author keywords

Linear noise approximation; Markov chain Monte Carlo; Markov jump processes; Riemann manifold

Indexed keywords

ENGINEERING; INDUSTRIAL ENGINEERING; PHILOSOPHICAL ASPECTS;

EID: 84874160187     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2011.0541     Document Type: Article
Times cited : (40)

References (34)
  • 1
    • 34249950625 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 21
    • 0000936678 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


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