title: A data-integrated method for analyzing stochastic biochemical networks.
abstract: Variability and fluctuations among genetically identical cells under uniform experimental conditions stem from the stochastic nature of biochemical reactions. Understanding network function for endogenous biological systems or designing robust synthetic genetic circuits requires accounting for and analyzing this variability. Stochasticity in biological networks is usually represented using a continuous-time discrete-state Markov formalism, where the chemical master equation (CME) and its kinetic Monte Carlo equivalent, the stochastic simulation algorithm (SSA), are used. These two representations are computationally intractable for many realistic biological problems. Fitting parameters in the context of these stochastic models is particularly challenging and has not been accomplished for any but very simple systems. In this work, we propose that moment equations derived from the CME, when treated appropriately in terms of higher order moment contributions, represent a computationally efficient framework for estimating the kinetic rate constants of stochastic network models and subsequent analysis of their dynamics. To do so, we present a practical data-derived moment closure method for these equations. In contrast to previous work, this method does not rely on any assumptions about the shape of the stochastic distributions or a functional relationship among their moments. We use this method to analyze a stochastic model of a biological oscillator and demonstrate its accuracy through excellent agreement with CME/SSA calculations. By coupling this moment-closure method with a parameter search procedure, we further demonstrate how a model's kinetic parameters can be iteratively determined in order to fit measured distribution data.
authors.affiliation: Department of Biochemistry and Biophysics, California Institute for Quantitative Biosciences, University of California San Francisco, 1700, 4th Street, San Francisco, California 94143-2542, USA. Michael.Chevalier@ucsf.edu
authors.forename: Michael W
authors.initials: MW
authors.lastname: Chevalier
authors.forename: Hana
authors.initials: H
authors.lastname: El-Samad
mesh_terms: D001683:Biological Clocks; D003198:Computer Simulation; D007700:Kinetics; D008954:Models, Biological; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D013269:Stochastic Processes; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D014157:Transcription Factors