TY - JOUR AU - Tan, C. AU - Song, H. AU - Niemi, J. AU - You, L. PY - 2007 DA - 2007// TI - A synthetic biology challenge: making cells compute JO - Mol Biosyst VL - 3 UR - https://doi.org/10.1039/b618473c DO - 10.1039/b618473c ID - Tan2007 ER - TY - JOUR AU - Poovathingal, S. K. AU - Gunawan, R. PY - 2010 DA - 2010// TI - Global parameter estimation methods for stochastic biochemical systems JO - BMC Bioinf VL - 11 UR - https://doi.org/10.1186/1471-2105-11-414 DO - 10.1186/1471-2105-11-414 ID - Poovathingal2010 ER - TY - JOUR AU - Moles, C. G. AU - Mendes, P. AU - Banga, J. R. PY - 2003 DA - 2003// TI - Parameter estimation in biochemical pathways: a comparison of global optimization methods JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1262503 DO - 10.1101/gr.1262503 ID - Moles2003 ER - TY - JOUR AU - Wang, Y. AU - Christley, S. AU - Mjolsness, E. AU - Xie, X. PY - 2010 DA - 2010// TI - Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent JO - BMC Syst Biol VL - 4 UR - https://doi.org/10.1186/1752-0509-4-99 DO - 10.1186/1752-0509-4-99 ID - Wang2010 ER - TY - JOUR AU - McAdams, H. H. AU - Arkin, A. PY - 1997 DA - 1997// TI - Stochastic mechanisms in gene expression JO - Proc Natl Acad Sci USA VL - 94 UR - https://doi.org/10.1073/pnas.94.3.814 DO - 10.1073/pnas.94.3.814 ID - McAdams1997 ER - TY - JOUR AU - McAdams, H. H. AU - Arkin, A. PY - 1999 DA - 1999// TI - It’s a noisy business! Genetic regulation at the nanomolar scale JO - Trends Genet VL - 15 UR - https://doi.org/10.1016/S0168-9525(98)01659-X DO - 10.1016/S0168-9525(98)01659-X ID - McAdams1999 ER - TY - JOUR AU - Tan, C. AU - Marguet, P. AU - You, L. PY - 2009 DA - 2009// TI - Emergent bistability by a growth-modulating positive feedback circuit JO - Nat Chem Biol VL - 5 UR - https://doi.org/10.1038/nchembio.218 DO - 10.1038/nchembio.218 ID - Tan2009 ER - TY - JOUR AU - Vilar, J. M. G. AU - Kueh, H. Y. AU - Barkai, N. AU - Leibler, S. PY - 2002 DA - 2002// TI - Mechanisms of noise-resistance in genetic oscillators JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.092133899 DO - 10.1073/pnas.092133899 ID - Vilar2002 ER - TY - CHAP AU - El-Samad, H. AU - Khammash, M. PY - 2006 DA - 2006// TI - Coherence Resonance: A Mechanism for Noise Induced Stable Oscillations in Gene Regulatory Networks BT - Decision and Control, 2006 45th IEEE Conference on ID - El-Samad2006 ER - TY - JOUR AU - Munsky, B. AU - Khammash, M. PY - 2010 DA - 2010// TI - Identification from stochastic cell-to-cell variation: a genetic switch case study JO - IET Syst Biol VL - 4 UR - https://doi.org/10.1049/iet-syb.2010.0013 DO - 10.1049/iet-syb.2010.0013 ID - Munsky2010 ER - TY - JOUR AU - Gillespie, D. T. PY - 1977 DA - 1977// TI - Exact stochastic simulation of coupled chemical reactions JO - J Phys Chem VL - 81 UR - https://doi.org/10.1021/j100540a008 DO - 10.1021/j100540a008 ID - Gillespie1977 ER - TY - JOUR AU - Tian, T. AU - Xu, S. AU - Gao, J. AU - Burrage, K. PY - 2007 DA - 2007// TI - Simulated maximum likelihood method for estimating kinetic rates in gene expression JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl552 DO - 10.1093/bioinformatics/btl552 ID - Tian2007 ER - TY - CHAP AU - Horváth, A. AU - Manini, D. PY - 2008 DA - 2008// TI - Parameter Estimation of Kinetic Rates in Stochastic Reaction Networks by the EM Method BT - BMEI (1) ID - Horváth2008 ER - TY - JOUR AU - Boys, R. J. AU - Wilkinson, D. J. AU - Kirkwood, T. B. L. PY - 2008 DA - 2008// TI - Bayesian inference for a discretely observed stochastic kinetic model JO - Stat Comput VL - 18 UR - https://doi.org/10.1007/s11222-007-9043-x DO - 10.1007/s11222-007-9043-x ID - Boys2008 ER - TY - JOUR AU - Rubinstein, R. Y. PY - 1997 DA - 1997// TI - Optimization of computer simulation models with rare events JO - Eur J Operational Res VL - 99 UR - https://doi.org/10.1016/S0377-2217(96)00385-2 DO - 10.1016/S0377-2217(96)00385-2 ID - Rubinstein1997 ER - TY - JOUR AU - Glasserman, P. AU - Heidelberger, P. AU - Shahabuddin, P. AU - Zajic, T. PY - 1999 DA - 1999// TI - Multilevel splitting for estimating rare event probabilities JO - Operations Res VL - 47 UR - https://doi.org/10.1287/opre.47.4.585 DO - 10.1287/opre.47.4.585 ID - Glasserman1999 ER - TY - BOOK AU - Rubino, G. AU - Tuffin, B. PY - 2009 DA - 2009// TI - Rare Event Simulation Using Monte Carlo methods PB - Wiley CY - Chichester UR - https://doi.org/10.1002/9780470745403 DO - 10.1002/9780470745403 ID - Rubino2009 ER - TY - JOUR AU - Daigle Jr, B. J. AU - Roh, M. K. AU - Gillespie, D. T. AU - Petzold, L. R. PY - 2011 DA - 2011// TI - Automated estimation of rare event probabilities in biochemical systems JO - J Chem Phys VL - 134 UR - https://doi.org/10.1063/1.3522769 DO - 10.1063/1.3522769 ID - Daigle Jr2011 ER - TY - JOUR AU - Caffo, B. S. AU - Jank, W. AU - Jones, G. L. PY - 2005 DA - 2005// TI - Ascent-based Monte Carlo expectation-maximization JO - J R Stat Soc Ser B VL - 67 UR - https://doi.org/10.1111/j.1467-9868.2005.00499.x DO - 10.1111/j.1467-9868.2005.00499.x ID - Caffo2005 ER - TY - JOUR AU - Gillespie, D. T. PY - 2007 DA - 2007// TI - Stochastic simulation of chemical kinetics JO - Annu Rev Phys Chem VL - 58 UR - https://doi.org/10.1146/annurev.physchem.58.032806.104637 DO - 10.1146/annurev.physchem.58.032806.104637 ID - Gillespie2007 ER - TY - BOOK AU - Wilkinson, D. J. PY - 2006 DA - 2006// TI - Stochastic modelling for systems biology PB - Taylor and Francis CY - Chapman and Hall/CRC mathematical and computational biology series, Boca Raton ID - Wilkinson2006 ER - TY - JOUR AU - Dempster, A. P. AU - Laird, N. M. AU - Rubin, D. B. PY - 1977 DA - 1977// TI - Maximum likelihood from incomplete data via the EM Algorithm JO - J R Stat Soc Series B (Methodological) VL - 39 ID - Dempster1977 ER - TY - BOOK AU - Robert, C. P. AU - Casella, G. PY - 2004 DA - 2004// TI - Monte Carlo Statistical Methods PB - Springer CY - New York UR - https://doi.org/10.1007/978-1-4757-4145-2 DO - 10.1007/978-1-4757-4145-2 ID - Robert2004 ER - TY - JOUR AU - Wei, G. AU - Tanner, M. PY - 1990 DA - 1990// TI - A Monte-Carlo implementation of the EM Algorithm and the poor man’s data Augmentation Algorithms JO - J Am Stat Assoc VL - 85 UR - https://doi.org/10.1080/01621459.1990.10474930 DO - 10.1080/01621459.1990.10474930 ID - Wei1990 ER - TY - BOOK AU - Rubinstein, R. Y. AU - Kroese, D. P. PY - 2004 DA - 2004// TI - The Cross-Entropy Method: A Unified Approach to Combinatorial Optimization, Monte-Carlo Simulation, and Machine Learning PB - Springer CY - New York UR - https://doi.org/10.1007/978-1-4757-4321-0 DO - 10.1007/978-1-4757-4321-0 ID - Rubinstein2004 ER - TY - BOOK AU - Homem-de Mello, T. AU - Rubinstein, R. Y. PY - 2002 DA - 2002// TI - Rare event estimation for static models via cross-entropy and importance sampling ID - Homem-de Mello2002 ER - TY - JOUR AU - Ionides, E. L. AU - Bretó, C. AU - King, A. A. PY - 2006 DA - 2006// TI - Inference for nonlinear dynamical systems JO - Proc Natl Acad Sci USA VL - 103 UR - https://doi.org/10.1073/pnas.0603181103 DO - 10.1073/pnas.0603181103 ID - Ionides2006 ER - TY - BOOK AU - Tanner, M. A. PY - 1996 DA - 1996// TI - Tools for statistical inference: methods for the exploration of posterior distributions and likelihood functions PB - Springer CY - New York UR - https://doi.org/10.1007/978-1-4612-4024-2 DO - 10.1007/978-1-4612-4024-2 ID - Tanner1996 ER - TY - JOUR AU - Gillespie, D. T. PY - 2001 DA - 2001// TI - Approximate accelerated stochastic simulation of chemically reacting systems JO - J Chem Phys VL - 115 UR - https://doi.org/10.1063/1.1378322 DO - 10.1063/1.1378322 ID - Gillespie2001 ER - TY - JOUR AU - Drawert, B. AU - Lawson, M. J. AU - Petzold, L. AU - Khammash, M. PY - 2010 DA - 2010// TI - The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation JO - J Chem Phys VL - 132 UR - https://doi.org/10.1063/1.3310809 DO - 10.1063/1.3310809 ID - Drawert2010 ER - TY - JOUR AU - Toni, T. AU - Welch, D. AU - Strelkowa, N. AU - Ipsen, A. AU - Stumpf, M. P. H. PY - 2009 DA - 2009// TI - Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems JO - J R Soc Interface VL - 6 UR - https://doi.org/10.1098/rsif.2008.0172 DO - 10.1098/rsif.2008.0172 ID - Toni2009 ER -