메뉴 건너뛰기




Volumn 23, Issue 1, 2007, Pages 84-91

Simulated maximum likelihood method for estimating kinetic rates in gene expression

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ALGORITHM; GENETIC REGULATION; INTERMETHOD COMPARISON; MATHEMATICAL MODEL; MAXIMUM LIKELIHOOD METHOD; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROBABILITY; REGULATORY MECHANISM; SIMULATION; STATISTICS; SYSTEMS BIOLOGY;

EID: 33845875759     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl552     Document Type: Article
Times cited : (80)

References (48)
  • 1
    • 0033737840 scopus 로고    scopus 로고
    • Inferring qualitative relations in genetic networks and metabolic pathways
    • Akutsu,T. et al. (2000) Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics, 16, 727-734.
    • (2000) Bioinformatics , vol.16 , pp. 727-734
    • Akutsu, T.1
  • 2
    • 4444305178 scopus 로고    scopus 로고
    • A genetic estimation algorithm for parameters of stochastic ordinary differential equations
    • Alcock,J. and Burrage,K. (2004) A genetic estimation algorithm for parameters of stochastic ordinary differential equations. Comput. Stat. Data An., 47, 255-275.
    • (2004) Comput. Stat. Data An. , vol.47 , pp. 255-275
    • Alcock, J.1    Burrage, K.2
  • 3
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
    • Arkin,A. et al. (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics, 149, 1633-1684.
    • (1998) Genetics , vol.149 , pp. 1633-1684
    • Arkin, A.1
  • 4
    • 22344449669 scopus 로고    scopus 로고
    • Constructing transcriptional regulatory networks
    • Blais,A. and Dynlacht,B.D. (2005) Constructing transcriptional regulatory networks. Gene Dev., 19, 1499-1511.
    • (2005) Gene Dev. , vol.19 , pp. 1499-1511
    • Blais, A.1    Dynlacht, B.D.2
  • 5
    • 27544481184 scopus 로고    scopus 로고
    • SPLINDID: A semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles
    • Bhasi,K. et al. (2005) SPLINDID: A semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles. Bioinformatics, 21, 3873-3879.
    • (2005) Bioinformatics , vol.21 , pp. 3873-3879
    • Bhasi, K.1
  • 6
    • 1542512456 scopus 로고    scopus 로고
    • Numerical methods for strong solutions of stochastic differential equations: An overview
    • Burrage,K. et al. (2004a) Numerical methods for strong solutions of stochastic differential equations: An overview. Proc. R. Soc. A-Math. Phys. Eng. Sci., 460, 373-402.
    • (2004) Proc. R. Soc. A-Math. Phys. Eng. Sci. , vol.460 , pp. 373-402
    • Burrage, K.1
  • 7
    • 2442438819 scopus 로고    scopus 로고
    • A multi-scaled approach for simulating chemical reaction systems
    • Burrage,K. et al. (2004b) A multi-scaled approach for simulating chemical reaction systems. Prog. Biophys. Mol. Bio., 85, 217-234.
    • (2004) Prog. Biophys. Mol. Bio. , vol.85 , pp. 217-234
    • Burrage, K.1
  • 8
    • 23944491675 scopus 로고    scopus 로고
    • Avoiding negative populations in explicit Poisson tau-leaping
    • Cao,Y. et al. (2005) Avoiding negative populations in explicit Poisson tau-leaping. J. Phys. Chem., 123, 054104.
    • (2005) J. Phys. Chem. , vol.123 , pp. 054104
    • Cao, Y.1
  • 9
    • 0038402506 scopus 로고    scopus 로고
    • Computational Modeling and experimental analysis of nonsense-mediated delay in yeast
    • Cao,D. and Parker,R. (2003) Computational Modeling and experimental analysis of nonsense-mediated delay in yeast. Cell, 113, 533-545.
    • (2003) Cell , vol.113 , pp. 533-545
    • Cao, D.1    Parker, R.2
  • 10
    • 22944469465 scopus 로고    scopus 로고
    • Binomial distribution based tau-leap accelerated stochastic simulation
    • Chatterjee,A. et al. (2005a) Binomial distribution based tau-leap accelerated stochastic simulation. J. Phys. Chem., 122, 024112.
    • (2005) J. Phys. Chem. , vol.122 , pp. 024112
    • Chatterjee, A.1
  • 11
    • 18744405416 scopus 로고    scopus 로고
    • Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method
    • Chatterjee,A. et al. (2005b) Time accelerated Monte Carlo simulations of biological networks using the binomial tau-leap method. Bioinformatics, 21, 2136-2137.
    • (2005) Bioinformatics , vol.21 , pp. 2136-2137
    • Chatterjee, A.1
  • 13
    • 3142617691 scopus 로고    scopus 로고
    • Mathematical and computational techniques to deduce complex biochemical reaction mechanisms
    • Crampin,E.J. et al. (2004) Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog. Biophys. Mol. Bio., 86, 77-112.
    • (2004) Prog. Biophys. Mol. Bio. , vol.86 , pp. 77-112
    • Crampin, E.J.1
  • 14
    • 25444510601 scopus 로고    scopus 로고
    • Iterative approach to model identification of biological system
    • Gadkar,K.G. et al. (2005) Iterative approach to model identification of biological system. BMC Bioinformatics, 6, 155.
    • (2005) BMC Bioinformatics , vol.6 , pp. 155
    • Gadkar, K.G.1
  • 15
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner,T.S. et al. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature, 403, 339-342.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1
  • 16
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie,D.T. (1977) Exact stochastic simulation of coupled chemical reactions, J. Phys. Chem., 81, 2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 17
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting systems
    • Gillespie,D.T. (2001) Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys., 115, 1716-1733.
    • (2001) J. Chem. Phys. , vol.115 , pp. 1716-1733
    • Gillespie, D.T.1
  • 18
    • 28944434119 scopus 로고    scopus 로고
    • Real-time kinetics of gene activity in individual bacteria
    • Golding,I. et al. (2005) Real-time kinetics of gene activity in individual bacteria. Cell, 123, 1025-1036.
    • (2005) Cell , vol.123 , pp. 1025-1036
    • Golding, I.1
  • 19
    • 0024456475 scopus 로고
    • The role of mRNA and protein stability in gene expression
    • Hargrove,J.L. and Schmidt,F.H. (1989) The role of mRNA and protein stability in gene expression. FASEB. J., 3, 2360-2370.
    • (1989) FASEB. J. , vol.3 , pp. 2360-2370
    • Hargrove, J.L.1    Schmidt, F.H.2
  • 20
    • 0037109565 scopus 로고    scopus 로고
    • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    • Haseltine,E.L. and Rawlings,J.B. (2002) Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J. Chem. Phys, 117, 6959-6969.
    • (2002) J. Chem. Phys , vol.117 , pp. 6959-6969
    • Haseltine, E.L.1    Rawlings, J.B.2
  • 21
    • 0034050722 scopus 로고    scopus 로고
    • Noise-based switches and amplifiers for gene expression
    • Hasty,J. et al. (2000) Noise-based switches and amplifiers for gene expression. Proc. Natl. Acad. Sci. USA, 97, 2075-2080.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 2075-2080
    • Hasty, J.1
  • 22
    • 0036578786 scopus 로고    scopus 로고
    • Translating the noise
    • Hasty,J. and Collins,J.J. (2002) Translating the noise. Nat. Genet., 31, 13-14.
    • (2002) Nat. Genet. , vol.31 , pp. 13-14
    • Hasty, J.1    Collins, J.J.2
  • 23
    • 0003340616 scopus 로고    scopus 로고
    • Estimating the parameters of stochastic differential equations
    • Hurn,A.S. and Lindsay,K.A. (1999) Estimating the parameters of stochastic differential equations. Math. Comput. Simulat., 48, 373-384.
    • (1999) Math. Comput. Simulat. , vol.48 , pp. 373-384
    • Hurn, A.S.1    Lindsay, K.A.2
  • 24
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating 'omics' data sets
    • Joyce,A.R. and Palsson,B.Ø. (2006) The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell Biol., 7, 198-210.
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.Ø.2
  • 25
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: From theories to phenotypes
    • Kærn,M. et al. (2005) Stochasticity in gene expression: From theories to phenotypes. Nat. Rev. Genet., 6, 451-464.
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 451-464
    • Kærn, M.1
  • 26
    • 2942614884 scopus 로고    scopus 로고
    • Programmable cells: Interfacing natural and engineered gene networks
    • Kobayashi,H. et al. (2004) Programmable cells: Interfacing natural and engineered gene networks. Proc. Natl Acad. Sci. USA, 101, 8414-8419.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 8414-8419
    • Kobayashi, H.1
  • 27
    • 33644959172 scopus 로고    scopus 로고
    • Metabolomics, modelling and machine learning in systems biology - Towards an understanding of the languages of cells
    • Kell,D.B. (2006) Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells. FEBS J., 273, 873-894.
    • (2006) FEBS J. , vol.273 , pp. 873-894
    • Kell, D.B.1
  • 28
    • 0036204115 scopus 로고    scopus 로고
    • STOCKS: Stochastic kinetic simulations of biochemical systems with Gillespie algorithm
    • Kierzek,A.M. (2002) STOCKS: Stochastic kinetic simulations of biochemical systems with Gillespie algorithm. Bioinformatics, 18, 470-481.
    • (2002) Bioinformatics , vol.18 , pp. 470-481
    • Kierzek, A.M.1
  • 29
    • 5044245706 scopus 로고    scopus 로고
    • Probabilistic representation of gene regulatory networks
    • Mao,L. and Resat,H. (2004) Probabilistic representation of gene regulatory networks. Bioinformatics, 20, 2258-2269.
    • (2004) Bioinformatics , vol.20 , pp. 2258-2269
    • Mao, L.1    Resat, H.2
  • 30
    • 0033083733 scopus 로고    scopus 로고
    • It's a noisy business! Genetic regulation at the nanomolar scale
    • McAdams,H.H. and Arkin,A. (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet., 15, 65-69.
    • (1999) Trends Genet. , vol.15 , pp. 65-69
    • McAdams, H.H.1    Arkin, A.2
  • 31
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: A comparison of global optimization methods
    • Moles,C.G. et al. (2003) Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Res., 13, 2467-2474.
    • (2003) Genome Res. , vol.13 , pp. 2467-2474
    • Moles, C.G.1
  • 32
    • 1542345686 scopus 로고    scopus 로고
    • Bridging the gap between stochastic and deterministic regimes in the kinetic simulation of the biochemical reaction systems
    • Puchalka,J. and Kierzek,A.M. (2004) Bridging the gap between stochastic and deterministic regimes in the kinetic simulation of the biochemical reaction systems. Biophys. J., 86, 1357-1372.
    • (2004) Biophys. J. , vol.86 , pp. 1357-1372
    • Puchalka, J.1    Kierzek, A.M.2
  • 33
    • 0037444724 scopus 로고    scopus 로고
    • Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
    • Rao,C.V. and Arkin,A.P. (2003) Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. J. Chem. Phys., 118, 4999-5010.
    • (2003) J. Chem. Phys. , vol.118 , pp. 4999-5010
    • Rao, C.V.1    Arkin, A.P.2
  • 34
    • 0037078982 scopus 로고    scopus 로고
    • Control, exploitation and tolerance of intracellular noise
    • Rao,C.V. et al. (2002) Control, exploitation and tolerance of intracellular noise. Nature, 420, 231-237.
    • (2002) Nature , vol.420 , pp. 231-237
    • Rao, C.V.1
  • 35
    • 33746582040 scopus 로고    scopus 로고
    • Parameter estimation in stochastic chemical reactions
    • Reinker,S. et al. (2006) Parameter estimation in stochastic chemical reactions. IEE Proc. Sys. Biol., 153, 168-178.
    • (2006) IEE Proc. Sys. Biol. , vol.153 , pp. 168-178
    • Reinker, S.1
  • 36
    • 22944451159 scopus 로고    scopus 로고
    • Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions
    • Salis,H. and Kaznessis,Y. (2005) Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. J. Chem. Phys., 122, 054103.
    • (2005) J. Chem. Phys. , vol.122 , pp. 054103
    • Salis, H.1    Kaznessis, Y.2
  • 37
    • 33645465102 scopus 로고    scopus 로고
    • Multiscale Hy3S: Hybrid stochastic simulation for supercomputers
    • Salis,H. et al. (2006) Multiscale Hy3S: Hybrid stochastic simulation for supercomputers. BMC Bioinformatics, 7, 93.
    • (2006) BMC Bioinformatics , vol.7 , pp. 93
    • Salis, H.1
  • 38
    • 26944450876 scopus 로고    scopus 로고
    • Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm
    • Samant,A. and Vlachos,D.G. (2005) Overcoming stiffness in stochastic simulation stemming from partial equilibrium: A multiscale Monte Carlo algorithm. J. Chem. Phys., 123, 144114.
    • (2005) J. Chem. Phys. , vol.123 , pp. 144114
    • Samant, A.1    Vlachos, D.G.2
  • 40
    • 17044395470 scopus 로고    scopus 로고
    • Reverse engineering of biochemical equations from time-course data by means of genetic programming
    • Sugimoto,M. et al. (2005) Reverse engineering of biochemical equations from time-course data by means of genetic programming. Biosystems, 80, 155-164.
    • (2005) Biosystems , vol.80 , pp. 155-164
    • Sugimoto, M.1
  • 41
    • 0036790975 scopus 로고    scopus 로고
    • Intrinsic and extrinsic contributions to stochasticity in gene expression
    • Swain,P.S. et al. (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl Acad. Sci. USA, 99, 12795-12800.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 12795-12800
    • Swain, P.S.1
  • 43
    • 33744811457 scopus 로고    scopus 로고
    • Stochastic models for regulatory networks of the genetic toggle switch
    • Tian,T. and Burrage,K. (2006) Stochastic models for regulatory networks of the genetic toggle switch. Proc. Natl Acad. Sci. USA, 103, 8372-8377.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 8372-8377
    • Tian, T.1    Burrage, K.2
  • 44
    • 1442335476 scopus 로고    scopus 로고
    • Bistability and switching in the lysis/lysogeny genetic regulatory network of Bacteriophage lambda
    • Tian,T. and Burrage,K. (2004a) Bistability and switching in the lysis/ lysogeny genetic regulatory network of Bacteriophage lambda. J. Theor. Biol., 227, 229-237.
    • (2004) J. Theor. Biol. , vol.227 , pp. 229-237
    • Tian, T.1    Burrage, K.2
  • 45
    • 3142543968 scopus 로고    scopus 로고
    • Binomial leap methods for simulating stochastic chemical kinetics
    • Tian,T. and Burrage,K. (2004b) Binomial leap methods for simulating stochastic chemical kinetics. J. Chem. Phys., 121, 10356-10364.
    • (2004) J. Chem. Phys. , vol.121 , pp. 10356-10364
    • Tian, T.1    Burrage, K.2
  • 46
    • 27744516835 scopus 로고    scopus 로고
    • Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates
    • Weinan,E. et al. (2005) Nested stochastic simulation algorithm for chemical kinetic systems with disparate rates. J. Chem. Phys., 123, 194107.
    • (2005) J. Chem. Phys. , vol.123 , pp. 194107
    • Weinan, E.1
  • 47
    • 0041523923 scopus 로고    scopus 로고
    • Deacy rates of human mRNAs: Correlation with functional characteristics and sequence attributes
    • Yang,E. et al. (2003) Deacy rates of human mRNAs: Correlation with functional characteristics and sequence attributes. Genome Res., 13, 1863-1872.
    • (2003) Genome Res. , vol.13 , pp. 1863-1872
    • Yang, E.1
  • 48
    • 33645033645 scopus 로고    scopus 로고
    • Probing gene expression in live cells, one protein molecule at a time
    • Yu,J. et al. (2006) Probing gene expression in live cells, one protein molecule at a time. Science, 311, 1600-1603.
    • (2006) Science , vol.311 , pp. 1600-1603
    • Yu, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.