[1] H. Kitano, “Computational Systems Biology,” Nature, Vol. 420, No. 6912, 2002, pp. 206-210. doi:10.1038/nature01254
[2] M. B. Elowitz and S. Leibler, “A Synthetic Oscillatory Network of Transcriptional Regulators,” Nature, Vol. 403, No. 6767, 2000, pp. 335-338. doi:10.1038/35002125
[3] A. P. Arkin, J. Ross and H. H. McAdams, “Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage-Infected Escherichia coli Cells,” Genetics, Vol. 149, 1998, pp. 1633-1648.
[4] W. J. Blake, M. Kaern, C. R. Cantor and J. J. Collins, “Noise in Eukaryotic Gene Expression,” Nature, Vol. 422, No. 6932, 2003, pp. 633-637. doi:10.1038/nature01546
[5] N. Federoff and W. Fontana, “Small Numbers of Big Molecules,” Science, Vol. 297, No. 5584, 2002, pp. 1129-1131. doi:10.1126/science.1075988
[6] M. B. Elowitz, A. J. Levine, E. D. Siggia and P. S. Swain, “Stochastic Gene Expression in a Single Cell,” Science, Vol. 297, No. 5584, 2002, pp. 1183-1186. doi:10.1126/science.1070919
[7] D. T. Gillespie, “A Rigorous Derivation of the Chemical Master Equation,” Physica A, Vol. 188, No. 1-3, 1992, pp. 402-425. doi:10.1016/0378-4371(92)90283-V
[8] D. T. Gillespie, “A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions,” Journal of Computational Physics, Vol. 22, No. 4, 1976, pp. 403-434. doi:10.1016/0021-9991(76)90041-3
[9] D. T. Gillespie, “Exact Stochastic Simulation of Coupled Chemical Reactions,” Journal of Physical Chemistry, Vol. 81, No. 25, 1977, pp. 2340-2361. doi:10.1021/j100540a008
[10] Y. Cao, D. T. Gillespie and L. Petzold, “The Slow-Scale Stochastic Simulation Algorithm,” Journal of Computational Physics, Vol. 122, No. 1, 2005, pp. 01411601-01411618. doi:10.1063/1.1824902
[11] D. T. Gillespie, “Approximate Accelerated Stochastic Simulation of Chemically Reacting Systems,” Journal of Chemical Physics, Vol. 115, No. 4, 2001, pp. 1716-1733. doi:10.1063/1.1378322
[12] T. Li, “Analysis of Explicit Tau-Leaping Schemes for Simulating Chemically Reacting Systems,” SIAM Multiscale Modeling & Simulation, Vol. 6, No. 2, 2007, pp. 417-436.
[13] C. V. Rao and A. P. Arkin, “Stochastic Chemical Kinetics and the Quasi-Steady-State Assumption: Application to the Gillespie Algorithm,” Journal of Chemical Physics, Vol. 118, No. 11, 2003, pp. 4999-5010. doi:10.1063/1.1545446
[14] A. Samant and D. Vlachos, “Overcoming Stiffness in Stochastic Simulation Stemming from Partial Equilibrium: A Multiscale Monte-Carlo Algorithm,” Journal of Chemical Physics, Vol. 123, No. 14, 2005, pp. 144114-144122. doi:10.1063/1.2046628
[15] D. T. Gillespie, “The Chemical Langevin Equation,” Journal of Chemical Physics, Vol. 113, No. 1, 2000, pp. 297-306. doi:10.1063/1.481811
[16] S. Ilie and A. Teslya, “An Adaptive Stepsize Method for the Chemical Langevin Equation,” Journal of Chemical Physics, Vol. 136, No. 18, 2012, pp. 184101-184115. doi:10.1063/1.4711143
[17] S. Ilie, “Variable Time-Stepping in the Pathwise Numerical Solution of the Chemical Langevin Equation,” Journal of Chemical Physics, Vol. 137, No. 23, 2012, pp. 234110-234119. doi:10.1063/1.4771660
[18] S. Ilie, W. H. Enright and K. R. Jackson, “Numerical Solution of Stochastic Models of Biochemical Kinetics,” Canadian Applied Mathematics Quarterly, Vol. 17, No. 3, 2009, pp. 523-554.
[19] C. W. Gardiner, “Stochastic Methods: A Handbook for the Natural and Social Sciences,” Springer, Berlin, 2009.
[20] P. E. Kloeden and E. Platen, “Numerical Solution of Stochastic Differential Equations,” Springer-Verlag, Berlin, 1992.
[21] K. Burrage, P. M. Burrage and T. Tian, “Numerical Methods for Strong Solutions of Stochastic Differential Equations: An Overview,” Proceedings of the Royal Society A, Vol. 460, No. 2041, 2004, pp. 373-402. doi:10.1098/rspa.2003.1247
[22] MATLAB, “The Language of Technical Computing,” 2009. www.mathworks.com.
[23] D. J. Wilkinson, “Stochastic Modelling for Systems Biology,” Chapman & Hall/CRC, London, 2006.