TY - BOOK AU - Szallasi, Z. AU - Stelling, J. AU - Periwal, V. PY - 2006 DA - 2006// TI - System Modeling in Cellular Biology UR - https://doi.org/10.7551/mitpress/9780262195485.001.0001 DO - 10.7551/mitpress/9780262195485.001.0001 ID - Szallasi2006 ER - TY - JOUR AU - Clodong, S. AU - Dühring, U. AU - Kronk, L. AU - Wilde, A. AU - Axmann, I. AU - Herzel, H. AU - Kollmann, M. PY - 2007 DA - 2007// TI - Functioning and robustness of a bacterial circadian clock JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100128 DO - 10.1038/msb4100128 ID - Clodong2007 ER - TY - JOUR AU - Shimoni, Y. AU - Friedlander, G. AU - Hetzroni, G. AU - Niv, G. AU - Altuvia, S. AU - Biham, O. AU - Margalit, H. PY - 2007 DA - 2007// TI - Regulation of gene expression by small non-coding RNAs: a quantitative view JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100181 DO - 10.1038/msb4100181 ID - Shimoni2007 ER - TY - JOUR AU - Calzone, L. AU - Thieffry, D. AU - Tyson, J. J. AU - Novak, B. PY - 2007 DA - 2007// TI - Dynamical modeling of syncytial mitotic cycles in Drosophila embryos JO - Mol Syst Biol VL - 3 UR - https://doi.org/10.1038/msb4100171 DO - 10.1038/msb4100171 ID - Calzone2007 ER - TY - JOUR AU - Gillespie, D. T. PY - 1976 DA - 1976// TI - A general method for numerically simulating the stochastic time evolution of coupled chemical reactions JO - Journal of Computational Physics VL - 22 UR - https://doi.org/10.1016/0021-9991(76)90041-3 DO - 10.1016/0021-9991(76)90041-3 ID - Gillespie1976 ER - TY - JOUR AU - Gibson, M. AU - Bruck, J. PY - 2000 DA - 2000// TI - Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels JO - Journal of Physical Chemistry A VL - 104 UR - https://doi.org/10.1021/jp993732q DO - 10.1021/jp993732q ID - Gibson2000 ER - TY - JOUR AU - Cao, Y. AU - Li, H. AU - Petzold, L. PY - 2004 DA - 2004// TI - Efficient formulation of the stochastic simulation algorithm for chemically reacting systems JO - J Chem Phys VL - 121 UR - https://doi.org/10.1063/1.1778376 DO - 10.1063/1.1778376 ID - Cao2004 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 - Cao, Y. AU - Gillespie, D. T. AU - Petzold, L. R. PY - 2005 DA - 2005// TI - Avoiding negative populations in explicit Poisson tau-leaping JO - J Chem Phys VL - 123 UR - https://doi.org/10.1063/1.1992473 DO - 10.1063/1.1992473 ID - Cao2005 ER - TY - JOUR AU - Cao, Y. AU - Gillespie, D. T. AU - Petzold, L. R. PY - 2006 DA - 2006// TI - Efficient step size selection for the tau-leaping simulation method JO - Journal of Chemical Physics VL - 124 UR - https://doi.org/10.1063/1.2159468 DO - 10.1063/1.2159468 ID - Cao2006 ER - TY - JOUR AU - Haseltine, E. L. AU - Rawlings, J. B. PY - 2002 DA - 2002// TI - Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics JO - The Journal of Chemical Physics VL - 117 UR - https://doi.org/10.1063/1.1505860 DO - 10.1063/1.1505860 ID - Haseltine2002 ER - TY - JOUR AU - Burrage, K. AU - Tian, T. AU - Burrage, P. PY - 2004 DA - 2004// TI - A multi-scaled approach for simulating chemical reaction systems JO - Prog Biophys Mol Biol VL - 85 UR - https://doi.org/10.1016/j.pbiomolbio.2004.01.014 DO - 10.1016/j.pbiomolbio.2004.01.014 ID - Burrage2004 ER - TY - JOUR AU - Vasudeva, K. AU - Bhalla, U. S. PY - 2004 DA - 2004// TI - Adaptive stochastic-deterministic chemical kinetic simulations JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg376 DO - 10.1093/bioinformatics/btg376 ID - Vasudeva2004 ER - TY - JOUR AU - Kiehl, T. R. AU - Mattheyses, R. M. AU - Simmons, M. K. PY - 2004 DA - 2004// TI - Hybrid simulation of cellular behavior JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg409 DO - 10.1093/bioinformatics/btg409 ID - Kiehl2004 ER - TY - JOUR AU - Salis, H. AU - Kaznessis, Y. PY - 2005 DA - 2005// TI - Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions JO - J Chem Phys VL - 122 UR - https://doi.org/10.1063/1.1835951 DO - 10.1063/1.1835951 ID - Salis2005 ER - TY - JOUR AU - Cao, Y. AU - Gillespie, D. AU - Petzold, L. PY - 2005 DA - 2005// TI - Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems JO - Journal of Computational Physics VL - 206 UR - https://doi.org/10.1016/j.jcp.2004.12.014 DO - 10.1016/j.jcp.2004.12.014 ID - Cao2005 ER - TY - JOUR AU - Chiam, K. H. AU - Tan, C. M. AU - Bhargava, V. AU - Rajagopal, G. PY - 2006 DA - 2006// TI - Hybrid simulations of stochastic reaction-diffusion processes for modeling intracellular signaling pathways JO - Phys Rev E Stat Nonlin Soft Matter Phys VL - 74 UR - https://doi.org/10.1103/PhysRevE.74.051910 DO - 10.1103/PhysRevE.74.051910 ID - Chiam2006 ER - TY - JOUR AU - Harris, L. A. AU - Clancy, P. PY - 2006 DA - 2006// TI - A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics JO - J Chem Phys VL - 125 UR - https://doi.org/10.1063/1.2354085 DO - 10.1063/1.2354085 ID - Harris2006 ER - TY - JOUR AU - Puchalka, J. AU - Kierzek, A. M. PY - 2004 DA - 2004// TI - Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks JO - Biophys J VL - 86 UR - https://doi.org/10.1016/S0006-3495(04)74207-1 DO - 10.1016/S0006-3495(04)74207-1 ID - Puchalka2004 ER - TY - JOUR AU - Rao, C. V. AU - Arkin, A. P. PY - 2003 DA - 2003// TI - Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm JO - The Journal of Chemical Physics VL - 118 UR - https://doi.org/10.1063/1.1545446 DO - 10.1063/1.1545446 ID - Rao2003 ER - TY - JOUR AU - Cao, Y. AU - Gillespie, D. T. AU - Petzold, L. R. PY - 2004 DA - 2004// TI - Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems JO - Journal of Computational Physics VL - 206 UR - https://doi.org/10.1016/j.jcp.2004.12.014 DO - 10.1016/j.jcp.2004.12.014 ID - Cao2004 ER - TY - JOUR AU - Salis, H. AU - Kaznessis, Y. N. PY - 2005 DA - 2005// TI - An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks JO - J Chem Phys VL - 123 UR - https://doi.org/10.1063/1.2131050 DO - 10.1063/1.2131050 ID - Salis2005 ER - TY - JOUR AU - Cao, Y. AU - Gillespie, D. T. AU - Petzold, L. R. PY - 2005 DA - 2005// TI - The slow-scale stochastic simulation algorithm JO - J Chem Phys VL - 122 UR - https://doi.org/10.1063/1.1824902 DO - 10.1063/1.1824902 ID - Cao2005 ER - TY - JOUR AU - Goutsias, J. PY - 2005 DA - 2005// TI - Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems JO - J Chem Phys VL - 122 UR - https://doi.org/10.1063/1.1889434 DO - 10.1063/1.1889434 ID - Goutsias2005 ER - TY - JOUR AU - Samant, A. AU - Vlachos, D. G. PY - 2005 DA - 2005// TI - Overcoming stiffness in stochastic simulation stemming from partial equilibrium: a multiscale Monte Carlo algorithm JO - J Chem Phys VL - 123 UR - https://doi.org/10.1063/1.2046628 DO - 10.1063/1.2046628 ID - Samant2005 ER - TY - JOUR AU - Samant, A. AU - Ogunnaike, B. A. AU - Vlachos, D. G. PY - 2007 DA - 2007// TI - A hybrid multiscale Monte Carlo algorithm (HyMSMC) to cope with disparity in time scales and species populations in intracellular networks JO - BMC Bioinformatics VL - 8 UR - https://doi.org/10.1186/1471-2105-8-175 DO - 10.1186/1471-2105-8-175 ID - Samant2007 ER - TY - JOUR AU - Hoops, S. AU - Sahle, S. AU - Gauges, R. AU - Lee, C. AU - Pahle, J. AU - Simus, N. AU - Singhal, M. AU - Xu, L. AU - Mendes, P. AU - Kummer, U. PY - 2006 DA - 2006// TI - COPASI-a COmplex PAthway SImulator JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl485 DO - 10.1093/bioinformatics/btl485 ID - Hoops2006 ER - TY - JOUR AU - Ramsey, S. AU - Orrell, D. AU - Bolouri, H. PY - 2005 DA - 2005// TI - Dizzy: stochastic simulation of large-scale genetic regulatory networks JO - J Bioinform Comput Biol VL - 3 UR - https://doi.org/10.1142/S0219720005001132 DO - 10.1142/S0219720005001132 ID - Ramsey2005 ER - TY - JOUR AU - Gillespie, C. S. AU - Wilkinson, D. J. AU - Proctor, C. J. AU - Shanley, D. P. AU - Boys, R. J. AU - Kirkwood, T. B. L. PY - 2006 DA - 2006// TI - Tools for the SBML Community JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btk042 DO - 10.1093/bioinformatics/btk042 ID - Gillespie2006 ER - TY - JOUR AU - Kierzek, A. M. PY - 2002 DA - 2002// TI - STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm JO - Bioinformatics VL - 18 UR - https://doi.org/10.1093/bioinformatics/18.3.470 DO - 10.1093/bioinformatics/18.3.470 ID - Kierzek2002 ER - TY - JOUR AU - Li, H. AU - Cao, Y. AU - Petzold, L. AU - Gillespie, D. PY - 2008 DA - 2008// TI - Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems JO - Biotechnol Prog VL - 24 UR - https://doi.org/10.1021/bp070255h DO - 10.1021/bp070255h ID - Li2008 ER - TY - JOUR AU - Adalsteinsson, D. AU - McMillen, D. AU - Elston, T. C. PY - 2004 DA - 2004// TI - Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-24 DO - 10.1186/1471-2105-5-24 ID - Adalsteinsson2004 ER - TY - JOUR AU - Hucka, M. AU - Finney, A. AU - Sauro, H. M. AU - Bolouri, H. AU - Doyle, J. C. AU - Kitano, H. AU - Arkin, A. P. AU - Bornstein, B. J. AU - Bray, D. AU - Cornish-Bowden, A. AU - Cuellar, A. A. AU - Dronov, S. AU - Gilles, E. D. AU - Ginkel, M. AU - Gor, V. AU - Goryanin, I. I. AU - Hedley, W. J. AU - Hodgman, T. C. AU - Hofmeyr, J. H. AU - Hunter, P. J. AU - Juty, N. S. AU - Kasberger, J. L. AU - Kremling, A. AU - Kummer, U. AU - Novère, N. L. AU - Loew, L. M. AU - Lucio, D. AU - Mendes, P. AU - Minch, E. AU - Mjolsness, E. D. AU - Nakayama, Y. AU - Nelson, M. R. AU - Nielsen, P. F. AU - Sakurada, T. AU - Schaff, J. C. AU - Shapiro, B. E. AU - Shimizu, T. S. AU - Spence, H. D. AU - Stelling, J. AU - Takahashi, K. AU - Tomita, M. AU - Wagner, J. AU - Wang, J. AU - SBML, F. o. r. u. m. PY - 2003 DA - 2003// TI - The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg015 DO - 10.1093/bioinformatics/btg015 ID - Hucka2003 ER - TY - JOUR AU - Funahashi, A. AU - Tanimura, N. AU - Morohashi, M. AU - Kitano, H. PY - 2003 DA - 2003// TI - CellDesigner: a process diagram editor for gene-regulatory and biochemical networks JO - BIOSILICO VL - 1 UR - https://doi.org/10.1016/S1478-5382(03)02370-9 DO - 10.1016/S1478-5382(03)02370-9 ID - Funahashi2003 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. AU - Amin, N. AU - Schwikowski, B. AU - Ideker, T. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER - TY - JOUR AU - Kierzek, A. M. AU - Zaim, J. AU - Zielenkiewicz, P. PY - 2001 DA - 2001// TI - The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression JO - J Biol Chem VL - 276 UR - https://doi.org/10.1074/jbc.M006264200 DO - 10.1074/jbc.M006264200 ID - Kierzek2001 ER - TY - JOUR AU - Kennell, D. AU - Riezman, H. PY - 1977 DA - 1977// TI - Transcription and translation initiation frequencies of the Escherichia coli lac operon JO - J Mol Biol VL - 114 UR - https://doi.org/10.1016/0022-2836(77)90279-0 DO - 10.1016/0022-2836(77)90279-0 ID - Kennell1977 ER - TY - JOUR AU - Lee, D. Y. AU - Zimmer, R. AU - Lee, S. Y. AU - Park, S. PY - 2006 DA - 2006// TI - Colored Petri net modeling and simulation of signal transduction pathways JO - Metab Eng VL - 8 UR - https://doi.org/10.1016/j.ymben.2005.10.001 DO - 10.1016/j.ymben.2005.10.001 ID - Lee2006 ER - TY - JOUR AU - Evans, T. W. AU - Gillespie, C. S. AU - Wilkinson, D. J. PY - 2008 DA - 2008// TI - The SBML Discrete Stochastic Models Test Suite JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btm566 DO - 10.1093/bioinformatics/btm566 ID - Evans2008 ER -