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Inference for Diffusion Processes pp 305–369Cite as

Application II: Analysis of Molecular Binding

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Abstract

The genetic material of humans and mammals is mainly contained in their cell nuclei, where most genome regulatory processes like DNA replication or transcription take place. These processes are controlled by complex protein networks.

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References

  • Akaike H (1973) Information theory and an extension of the maximum likelihood principle. In: Petrov B, Csaki F (eds) 2nd international symposium on information theory, Akademiai Kiado, pp 267–281. Reprinted, with an introduction by J. deLeeuw, in Breakthroughs in Statistics, Volume I, edited by Samuel Kotz and Norman L. Johnson. Springer, 1992, pp. 599-624

    Google Scholar 

  • Beaudouin J, Mora-Bermúdez F, Klee T, Daigle N, Ellenberg J (2006) Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins. Biophys J 90:1878–1894

    Article  Google Scholar 

  • Carrero G, Crawford E, Hendzel MJ (2004) Characterizing fluorescence recovery curves for nuclear proteins undergoing binding events. Bull Math Biol 66:1515–1545

    Article  MathSciNet  Google Scholar 

  • Chen MH, Shao QM (1999) Monte Carlo estimation of Bayesian credible and hpd intervals. J Comput Graph Stat 8:69–92

    MathSciNet  Google Scholar 

  • Chib S (1995) Marginal likelihood from the Gibbs output. J Am Stat Assoc 90:1313–1321

    Article  MathSciNet  MATH  Google Scholar 

  • Elerian O, Chib S, Shephard N (2001) Likelihood inference for discretely observed nonlinear diffusions. Econometrica 69:959–993

    Article  MathSciNet  MATH  Google Scholar 

  • Fahrmeir L, Kneib T, Lang S (2009) Regression. Modelle, Methoden und Anwendungen, 2nd edn. Springer, Heidelberg

    Google Scholar 

  • Garcia-Parajo M, Segers-Nolten G, Veerman J, Greve J, van Hulst N (2000) Real-time light-driven dynamics of the fluorescence emission in single green fluorescent protein molecules. Proc Natl Acad Sci U S A 97:7237–7242

    Article  Google Scholar 

  • Gorski S, Misteli T (2005) Systems biology in the cell nucleus. J Cell Sci 118:4083–4092

    Article  Google Scholar 

  • Jeffreys H (1961) Theory of probability. Prentice Hall, Princeton

    MATH  Google Scholar 

  • Kass R, Raftery A (1995) Bayes factors. J Am Stat Assoc 90:773–795

    Article  MATH  Google Scholar 

  • Kuch D, Schermelleh L, Manetto S, Leonhardt H, Carell T (2008) Synthesis of DNA dumbbell based inhibitors for the human DNA methyltransferase Dnmt1. Angew Chem Int Ed 47:1515–1518

    Article  Google Scholar 

  • Lambert N (2009) Uncoupling diffusion and binding in FRAP experiments. Nat Methods 6:183

    Article  Google Scholar 

  • McNally J (2008) Quantitative FRAP in analysis of molecular binding dynamics in vivo. Method Cell Biol 85:329–351

    Article  Google Scholar 

  • Mueller F, Wach P, McNally J (2008) Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantitative fluorescence recovery after photobleaching. Biophys J 94:3323–3339

    Article  Google Scholar 

  • Nelder J, Mead R (1965) A simplex method for function minimization. Comput J 7:308–313

    Article  MATH  Google Scholar 

  • Phair R, Gorski S, Misteli T (2004a) Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Method Enzymol 375:393–414

    Article  Google Scholar 

  • Phair R, Scaffidi P, Elbi C, Vecerová J, Dey A, Ozato K, Brown D, Hager G, Bustin M, Misteli T (2004b) Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol Cell Biol 24:6393–6402

    Article  Google Scholar 

  • Polson N, Roberts G (1994) Bayes factors for discrete observations from diffusion processes. Biometrika 81:11–26

    Article  MathSciNet  MATH  Google Scholar 

  • Schneider K (2009) Analysis of cell cycle dependent kinetics of Dnmt1 by FRAP and kinetic modeling. Diploma Thesis, LMU Munich

    Google Scholar 

  • Schneider K, Fuchs C, Dobay A, Rottach A, Qin W, Álvarez-Castro J, Nalaskowski M, Schmid V, Leonhardt H, Schermelleh L (2012) Dissection of cell cycle dependent dynamics of Dnmt1 by FRAP and diffusion-coupled modeling (in preparation)

    Google Scholar 

  • Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6:461–464

    Article  MATH  Google Scholar 

  • Sprague B, McNally J (2005) FRAP analysis of binding: proper and fitting. Trends Cell Biol 15:84–91

    Article  Google Scholar 

Download references

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Authors and Affiliations

  1. Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany

    Christiane Fuchs

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  1. Christiane Fuchs
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Fuchs, C. (2013). Application II: Analysis of Molecular Binding. In: Inference for Diffusion Processes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25969-2_9

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