This is a completely incomplete but hopefully useful small collection of references related to the topic.

• B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, J.D. Watson, Molecular Biology of the Cell, Gerland Science, 2002
• Adam P. Arkin and John Ross and Harley H. McAdams, Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells, Genetics 149 (1998), pp. 1633-1648
  
• Christopher P. Fall, Eric S. Marland, John M. Wagner und John J. Tyson, Computational Cell Biology, Springer Serie Interdisciplinary Applied Mathematics, New York, 2002
  
• Daniel T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, J Comput Phys 22 (1976), pp. 403-434
• James P. Keener and James Sneyd, Mathematical Physiology, Springer Serie "Interdisciplinary Applied Mathematics", New York, 1998
• Harley H. McAdams and Adam P. Arkin, Stochastic mechanisms in gene expression, PNAS 94 (1997), pp. 814-819
• Nature Insight Computational Biology, Vol. 420, 2002, in particular Computational Biology Insight
  
• R. Srivastava and L. You and J. Summer and J. Yin, Stochastic vs. deterministic modeling of intracellular viral kinetics, J theor Biol 218 (2002), pp. 309-321
  
• T. E. Turner and S. Schnell and K. Burrage, Stochastic approaches for modelling in vivo reactions, Comp Bio Chem 28 (2004), pp. 165-178