Citation: |
[1] |
A. Abdulle and A. Medivikov, Second order Chebyshev methods based on orthogonal polynomials, Numerische Mathematik, 90 (2001), 1-18.doi: 10.1007/s002110100292. |
[2] |
A. Abdulle and S. Cirilli, S-ROCK: Chebyshev methods for stiff stochastic differential equations, SIAM J. Sci. Comput., 30 (2008), 997-1014.doi: 10.1137/070679375. |
[3] |
U. Ala, F. A. Karreth, C. Bosia, A. Pagnani, R. Taulli, V. Léopold, Y. Tay, P. Provero, R. Zecchina and P. P. Pandolfi, Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments, PNAS, 110 (2013), 7154-7159.doi: 10.1073/pnas.1222509110. |
[4] |
C. T. H. Baker and E. Buckwar, Numerical analysis of explicit one-step methods for stochastic delay differential equations, LMS J. Comput. Math., 3 (2000), 315-335.doi: 10.1112/S1461157000000322. |
[5] |
M. Barrio, K. Burrage, A. Leier and T. Tian, Oscillatory Regulation of Hes1: Discrete stochastic delay modelling and simulation, PLoS Comput Biol, 2006. |
[6] |
D. P. Bartel, MicroRNAs: Genomics, biogenesis, mechanism, and function, Cell, 116 (2004), 281-297.doi: 10.1016/S0092-8674(04)00045-5. |
[7] |
D. P. Bartel, MicroRNAs: Target recognition and regulatory functions, Cell, 136 (2009), 215-233.doi: 10.1016/j.cell.2009.01.002. |
[8] |
K. Burrage, T. Tian and P. M. Burrage, A multi-scaled approach for simulating chemical reaction systems, Progress in Biophysics and Molecular Biology, 85 (2004), 217-234.doi: 10.1016/j.pbiomolbio.2004.01.014. |
[9] |
M. Carletti, Stochastic Modelling of Biological Processes, PhD Thesis, The University of Queensland, Brisbane, Australia, 2008. |
[10] |
A. Carracedo, A. Alimonti and P. P. Pandolfi, PTEN level in tumor suppression: How much is too little?, Cancer Res., 71 (2011), 629-633.doi: 10.1158/0008-5472.CAN-10-2488. |
[11] |
A. de Giorgio, J. Krell, V. Harding, J. Stebbing and L. Castellano, Emerging roles of competing endogenous RNAs in cancer: Insights from the regulation of PTEN, Mol Cell Biol., 33 (2013), 3976-3982.doi: 10.1128/MCB.00683-13. |
[12] |
M. Figliuzzi, E. Marinari and A. De Martino, MicroRNAs as a selective channel of communication between competing RNAs: A steady-state theory, Biophys J., 104 (2013), 1203-1213.doi: 10.1016/j.bpj.2013.01.012. |
[13] |
P. Garcia-Junco-Clemente and P. Golshani, PTEN: A master regulator of neuronal structure, function, and plasticity, Commun Integr Biol., 2014. |
[14] |
D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, J. Phys. Chem., 81 (1977), 2340-2361.doi: 10.1021/j100540a008. |
[15] |
D. T. Gillespie, Approximate accelerated stochastic simulation of chemically reacting systems, J. Chem. Phys., 115 (2001), 1716-1733.doi: 10.1063/1.1378322. |
[16] |
J. Goutsias, Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems, J. Chem. Phys., 122 (2005), 184102.doi: 10.1063/1.1889434. |
[17] |
D. Hernandez and R. Spigler, Convergence and stability of implicit Runge-Kutta methods for systems with multiplcative noise, BIT Num. Math., 33 (1993), 654-669.doi: 10.1007/BF01990541. |
[18] |
F. A. Karreth, Y. Tay, D. Perna, U. Ala, S. Mynn Tan, A. G. Rust, G. De Nicola, K. A. Webster, D. Weiss, P. A. P. Mancera, M. Krauthammer, R. Halaban, P. Provero, D. J. Adams, D. A. Tuveson and P. P. Pandolfi, In vivo identification of Tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma, Cell, 147 (2011), 382-395.doi: 10.1016/j.cell.2011.09.032. |
[19] |
A. Leier, T. T. Marquez-Lago and K. Burrage, Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise, J. Chem. Phys., 128 (2008), 205107. |
[20] |
S. Mukherji, M. S. Ebert , G. X. Zheng, J. S. Tsang, P. A. Sharz and A. van Oudenaarden, MicroRNAs can generate thresholds in target gene expression, Nat. Genet, 43 (2011), 854-859.doi: 10.1038/ng.905. |
[21] |
L. Poliseno, L. Salmena, J. Zhang, B. Carver, W. Haveman and P. P. Pandolfi, A coding-independent function of gene and pseudogene mRNAs regulates tumour biology, Nature, 465 (2010), 1033-1038.doi: 10.1038/nature09144. |
[22] |
P. Rue, J. Villa-Freixa and K. Burrage, Simulation methods with extended stability for stiff biochemical kinetics, BMC Systems Biology, (2010), p110. |
[23] |
P. Sumazin, X. Yang, H. S. Chiu, W. J. Chung, A. Iyer, D. Llobet-Navas, P. Rajbhandari, M. Bansal, P. Guarnieri, J. Silva and A. Califano, An extensive MicroRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in Glioblastoma, Cell, 147 (2011), 370-381.doi: 10.1016/j.cell.2011.09.041. |
[24] |
Y. Tay, L. Kats, L. Salmena, D. Weiss, S. M. Tan, U. Ala, F. Karreth, L. Poliseno, P. Provero, F. Di Cunto , J. Lieberman, I. Rigoutsos and P. P. Pandolfi, Coding Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs, Cell, 147 (2011), 344-357.doi: 10.1016/j.cell.2011.09.029. |
[25] |
Y. Tay, J. Rinn and P. P. Pandolfi, The multilayered complexity of ceRNA crosstalk and competition, Nature, 505 (2014), 344-352.doi: 10.1038/nature12986. |
[26] |
T. Tian, K. Burrage, P. M. Burrage and M. Carletti, Stochastic delay differential equations for genetic regulatory network, J. Comp App. Math., 205 (2007), 696-707.doi: 10.1016/j.cam.2006.02.063. |
[27] |
T. E. Turner, S. Schnell and K. Burrage, Stochastic approaches for modelling in vivo reactions Comput. Biol. and Chem., 28 (2004), 165-178.doi: 10.1016/j.compbiolchem.2004.05.001. |
[28] |
J. Xu, Z. Li, J. Wang, H. Chen and J. Y. Fang, Combined PTEN Mutation and Protein Expression Associate with Overall and Disease-Free Survival of Glioblastoma Patients, Transl Oncol., 7 (2014), 196-205.doi: 10.1016/j.tranon.2014.02.004. |