title: Global parameter identification of stochastic reaction networks from single trajectories.
abstract: We consider the problem of inferring the unknown parameters of a stochastic biochemical network model from a single measured time-course of the concentration of some of the involved species. Such measurements are available, e.g., from live-cell fluorescence microscopy in image-based systems biology. In addition, fluctuation time-courses from, e.g., fluorescence correlation spectroscopy (FCS) provide additional information about the system dynamics that can be used to more robustly infer parameters than when considering only mean concentrations. Estimating model parameters from a single experimental trajectory enables single-cell measurements and quantification of cell-cell variability. We propose a novel combination of an adaptive Monte Carlo sampler, called Gaussian Adaptation (GaA), and efficient exact stochastic simulation algorithms (SSA) that allows parameter identification from single stochastic trajectories. We benchmark the proposed method on a linear and a non-linear reaction network at steady state and during transient phases. In addition, we demonstrate that the present method also provides an ellipsoidal volume estimate of the viable part of parameter space and is able to estimate the physical volume of the compartment in which the observed reactions take place.
authors.affiliation: Institute of Theoretical Computer Science and Swiss Institute of Bioinformatics, ETH Zurich, CH-8092 Zurich, Switzerland. christian.mueller@inf.ethz.ch
authors.forename: Christian L
authors.initials: CL
authors.lastname: Müller
authors.forename: Rajesh
authors.initials: R
authors.lastname: Ramaswamy
authors.forename: Ivo F
authors.initials: IF
authors.lastname: Sbalzarini
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D008856:Microscopy, Fluorescence; D008954:Models, Biological; D008956:Models, Chemical; D009010:Monte Carlo Method; D015203:Reproducibility of Results; D015398:Signal Transduction / Q000502:physiology*; D059010:Single-Cell Analysis / Q000379:methods; D013269:Stochastic Processes; D049490:Systems Biology / Q000379:methods*