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Stochastic Modelling in Life Sciences

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Inference for Diffusion Processes
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Abstract

Key mechanisms in life sciences can often be assessed by application of mathematical models. Moreover, real-world phenomena can particularly be captured when such a model allows for random events. This chapter motivates and reviews representative application fields from life sciences and appropriate mathematical models: for the spread of infectious diseases and for processes in molecular biology, biochemistry and genetics. These applications and models recur throughout the entire book. The chapter describes the dynamical evolution of the considered systems in terms of three established types of processes: stochastic jump processes, deterministic state-continuous processes and stochastic diffusion processes. Simulation of such models is explained, and the important role of randomness is discussed.

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References

  • Abbey H (1952) An examination of the Reed-Frost theory of epidemics. Hum Biol 24:201–233

    Google Scholar 

  • Allen L (2003) An introduction to stochastic processes with applications to biology. Pearson Prentice Hall, Upper Saddle River

    MATH  Google Scholar 

  • Alon U (2007) An Introduction to systems biology. Design principles of biological circuits. Chapman and Hall, Boca Raton

    Google Scholar 

  • Anderson R (1982) The population dynamics of infectious diseases. Chapman and Hall, London

    Book  Google Scholar 

  • Andersson H, Britton T (2000) Stochastic epidemic models and their statistical analysis. Lecture Notes in Statistics, vol 151. Springer, New York

    Book  Google Scholar 

  • Anderson R, May R (1985) Vaccination and herd immunity to infectious diseases. Nature 318:323–329

    Article  Google Scholar 

  • Anderson R, May R (1991) Infectious diseases of humans. Oxford University Press, Oxford

    Google Scholar 

  • Arkin A, Ross J, McAdams H (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics 149:1633–1648

    Google Scholar 

  • Arnaut L, Formosinho S, Burrows H (2007) Chemical kinetics: from molecular structure to chemical reactivity. Elsevier, Amsterdam/Oxford

    Google Scholar 

  • Bahcall O (2005) Single cell resolution in regulation of gene expression. Mol Syst Biol 1 (article number 2005.0015)

    Google Scholar 

  • Bailey N (1975) The mathematical theory of infectious diseases, 2nd edn. Charles Griffin, London

    MATH  Google Scholar 

  • Ball F (1983) The threshold behaviour of epidemic models. J Appl Probab 20:227–241

    Article  MathSciNet  MATH  Google Scholar 

  • Ball F (1986) A unified approach to the distribution of total size and total area under the trajectory of infectives in epidemic models. Adv in Appl Probab 18:289–310

    Article  MathSciNet  MATH  Google Scholar 

  • Ball F, Mollison D, Scalia-Tomba G (1997) Epidemics with two levels of mixing. Ann Appl Probab 7:46–89

    Article  MathSciNet  MATH  Google Scholar 

  • Bartlett M (1949) Some evolutionary stochastic processes. J R Stat Soc Ser B 11:211–229

    MathSciNet  MATH  Google Scholar 

  • Becker N (1989) Analysis of infectious disease data. Monographs on statistics and applied probability. Chapman and Hall, London

    Google Scholar 

  • Boys R, Wilkinson D, Kirkwood T (2008) Bayesian inference for a discretely observed stochastic kinetic model. Stat Comput 18:125–135

    Article  MathSciNet  Google Scholar 

  • Brauer F (2009) Mathematical epidemiology is not an oxymoron. BMC Public Health 9:S2

    Article  Google Scholar 

  • Costa Maia J (1952) Some mathematical developments on the epidemic theory formulated by Reed and Frost. Hum Biol 24:167–200

    Google Scholar 

  • Cunha B (2004) Historical aspects of infectious diseases, part I. Infect Dis Clin N Am 18(1):xi–xv

    Google Scholar 

  • Daley D, Gani J (1999) Epidemic modelling: an introduction. Cambridge studies in mathematical biology, vol 15. Cambridge University Press, Cambridge

    Google Scholar 

  • Demin O, Plyusnina T, Lebedeva G, Zobova E, Metelkin E, Kolupaev A, Goryanin I, Tobin F (2005) Kinetic modelling of the E. coli metabolism. In: Alberghina L, Westerhoff H (eds) Systems biology. Definitions and perspectives. Springer, Berlin/Heidelberg, pp 31–67

    Chapter  Google Scholar 

  • Diekmann O, Heesterbeek J (2000) Mathematical epidemiology of infectious diseases: model building, analysis and interpretation. Wiley, Chichester

    Google Scholar 

  • Dietz K (1967) Epidemics and rumours: a survey. J R Stat Soc Ser A 130:505–528

    Article  MathSciNet  Google Scholar 

  • Dobson A, Carper E (1996) Infectious diseases and human population history. Bioscience 46:115–126

    Article  Google Scholar 

  • Ehrenberg M, Elf J, Aurell E, Sandberg R, Tegnér J (2003) Systems biology is taking off. Genome Res 13:2377–2380

    Article  Google Scholar 

  • En’ko P (1889) On the course of epidemics of some infectious diseases. Vrach St Petersburg 10:1008–1010, 1039–1042, 1061–1063

    Google Scholar 

  • Fine P (1993) Herd immunity: history, theory, practice. Epidemiol Rev 15:265–302

    Google Scholar 

  • Galvani A, May R (2005) Dimensions of superspreading. Nature 438:293–295

    Article  Google Scholar 

  • Gibson M, Bruck J (2000) Efficient exact stochastic simulation of chemical systems with many species and many channels. J Phys Chem A 104:1876–1889

    Article  Google Scholar 

  • Gillespie D (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22:403–434

    Article  MathSciNet  Google Scholar 

  • Gillespie D (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81:2340–2361

    Article  Google Scholar 

  • Gillespie D (1992) A rigorous derivation of the chemical master equation. Phys A 188:404–425

    Article  Google Scholar 

  • Gillespie D (2007) Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 58:35–55

    Article  Google Scholar 

  • Goel N, Richter-Dyn N (1974) Stochastic models in biology. Academic, New York

    Google Scholar 

  • Greenwood M (1931) On the statistical measure of infectiousness. J Hyg 31:336–351

    Article  Google Scholar 

  • Hamer W (1906) The Milroy lectures on epidemic disease in England – the evidence of variability and of persistency of type (Lecture I). Lancet 167:569–574

    Article  Google Scholar 

  • Hethcote H (1994) A thousand and one epidemic models. In: Levin S (ed) Frontiers in mathematical biology, Lecture notes in biomathematics. Springer, Berlin, pp 504–515

    Chapter  Google Scholar 

  • Hethcote H (2000) The mathematics of infectious diseases. SIAM Rev 42:599–653

    Article  MathSciNet  MATH  Google Scholar 

  • Ireland J, Mestel B, Norman R (2007) The effect of seasonal host birth rates on disease persistence. Math Biosci 206:31–45

    Article  MathSciNet  MATH  Google Scholar 

  • Isham V (2004) Stochastic models for epidemics. Research Report No 263, Department of Statistical Science, University College London

    Google Scholar 

  • Jacquez J (1972) Compartmental analysis in biology and medicine. Elsevier, Amsterdam

    Google Scholar 

  • Keeling M, Rohani P (2008) Modeling infectious disease in humans and animals. Princeton University Press, Princeton

    Google Scholar 

  • Keener J, Sneyd J (1989) Mathematical physiology. Springer, New York

    Google Scholar 

  • Kelly H, Peck H, Laurie K, Wu P, Nishiura H, Cowling B (2011) The age-specific cumulative incidence of infection with pandemic influenza H1N1 2009 was similar in various countries prior to vaccination. PLoS ONE 6:e21 828

    Google Scholar 

  • Kermack W, McKendrick A (1927) A contribution to the mathematical theory of epidemics. Proc R Soc London Ser A 115:700–721

    Article  MATH  Google Scholar 

  • Kimura M (1964) Diffusion models in population genetics. J Appl Probab 1:177–232

    Article  MATH  Google Scholar 

  • Kramers H (1940) Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7:284–304

    Article  MathSciNet  MATH  Google Scholar 

  • Laidler K (1993) The world of physical chemistry. Oxford University Press, New York

    Google Scholar 

  • Lande R, Engen S, Sæther B (2003) Stochastic population dynamics in ecology and conservation. Oxford University Press, New York

    Book  Google Scholar 

  • Le Novère N, Shimizu T (2001) StochSim: modelling of stochastic biomolecular processes. Bioinformatics 17:575–576

    Article  Google Scholar 

  • Lloyd-Smith J, Schreiber S, Kopp P, Getz W (2005) Superspreading and the effect of individual variation on disease emergence. Nature 438:355–359

    Article  Google Scholar 

  • Manninen T, Linne ML, Ruohonena K (2006) Developing Itô stochastic differential equation models for neuronal signal transduction pathways. Comput Biol Chem 30:280–291

    Article  MATH  Google Scholar 

  • McKendrick A (1926) Application of mathematics to medical problems. Proc Edinb Math Soc 44:98–130

    Article  Google Scholar 

  • McNeill W (1976) Plagues and people. Anchor, New York

    Google Scholar 

  • McQuarrie D (1967) Stochastic approach to chemical kinetics. J Appl Probab 4:413–478

    Article  MathSciNet  MATH  Google Scholar 

  • Morton R, Wickwire K (1974) On the optimal control of a deterministic epidemic. Adv Appl Probab 6:622–635

    Article  MathSciNet  MATH  Google Scholar 

  • Neal P (2007) Coupling of two SIR epidemic models with variable susceptibilities and infectivities. J Appl Probab 44:41–57

    Article  MathSciNet  MATH  Google Scholar 

  • Oldstone M (2010) Viruses, plagues, and history: past, present and future. Oxford University Press, Oxford/New York

    Google Scholar 

  • Rao C, Wolf D, Arkin A (2002) Control, exploitation and tolerance of intracellular noise. Nature 420:231–237

    Article  Google Scholar 

  • Renshaw E (1991) Modelling biological populations in space and time. Cambridge University Press, Cambridge

    Book  MATH  Google Scholar 

  • Riley S (2007) Large-scale spatial-transmission models of infectious disease. Science 316:1298–1301

    Article  Google Scholar 

  • Ross R (1915) Some a priori pathometric equations. Br Med J 1:546–547

    Article  Google Scholar 

  • Rushton S, Mautner A (1955) The deterministic model of a simple epidemic for more than one community. Biometrika 42:126–132

    MathSciNet  MATH  Google Scholar 

  • Sattenspiel L (1987) Population structure and the spread of disease. Hum Biol 59:411–438

    Google Scholar 

  • Sattenspiel L, Dietz K (1995) A structured epidemic model incorporating geographic mobility among regions. Math Biosci 128:71–91

    Article  MATH  Google Scholar 

  • Sherman I (2006) The power of plagues. ASM Press, Washington, DC

    Google Scholar 

  • Smallman-Raynor M, Cliff A (2004) Impact of infectious diseases on war. Infect Dis Clin N Am 18:341–368

    Article  Google Scholar 

  • Sveiczer A, Tyson J, Novak B (2001) A stochastic, molecular model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in cycle time regulation. Biophys Chem 92:1–15

    Article  Google Scholar 

  • Tian T, Xu S, Gao J, Burrage K (2007) Simulated maximum likelihood method for estimating kinetic rates in gene expression. Bioinformatics 23:84–91

    Article  Google Scholar 

  • UNAIDS (2009) AIDS epidemic update: November 2009. WHO library cataloguing-in-publication data. Available at http://www.unaids.org

  • Vasold M (2008) Grippe, Pest und Cholera: eine Geschichte der Seuchen in Europa. Franz Steiner Verlag, Stuttgart

    Google Scholar 

  • Whittle P (1955) The outcome of a stochastic epidemic – a note on Bailey’s paper. Biometrika 42:116–122

    MathSciNet  MATH  Google Scholar 

  • WHO (2010) Pandemic (H1N1) 2009 – update 112 (from 6 August 2010). Available at http://www.who.int/csr/don/2010_08_06/en/index.html

  • Wilkinson D (2006) Stochastic modelling for systems biology. Chapman and Hall, Boca Raton

    MATH  Google Scholar 

  • Williams T (1971) An algebraic proof of the threshold theorem for the general stochastic epidemic. Adv Appl Probab 3:223

    Article  Google Scholar 

  • Zheng Q, Ross J (1991) Comparison of deterministic and stochastic kinetics for nonlinear systems. J Chem Phys 94:3644–3648

    Article  Google Scholar 

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Fuchs, C. (2013). Stochastic Modelling in Life Sciences. In: Inference for Diffusion Processes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25969-2_2

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