Backward-stochastic-differential-equation approach to modeling of gene expression

• Type: Article in International Scientific Journal
• Date: 2017

Authors

Shamarova, E (Author) Other; Chertovskih, R (Author) FEUP; Ramos, AF (Author) Other; Paulo Aguiar (Author) FMUP

Journal

Title: Physical review. E

Vol. 95

ISSN: 2470-0045

Publisher: American Physical Society

Indexing

ISI Web of Knowledge - 5 Citations

Scopus - 5 Citations

Other information

Authenticus ID: P-00M-MZ1

DOI: 10.1103/physreve.95.032418

Abstract (EN): In this article, we introduce a backward method to model stochastic gene expression and protein-level dynamics. The protein amount is regarded as a diffusion process and is described by a backward stochastic differential equation (BSDE). Unlike many other SDE techniques proposed in the literature, the BSDE method is backward in time; that is, instead of initial conditions it requires the specification of end-point ("final") conditions, in addition to the model parametrization. To validate our approach we employ Gillespie's stochastic simulation algorithm (SSA) to generate (forward) benchmark data, according to predefined gene network models. Numerical simulations show that the BSDE method is able to correctly infer the protein-level distributions that preceded a known final condition, obtained originally from the forward SSA. This makes the BSDE method a powerful systems biology tool for time-reversed simulations, allowing, for example, the assessment of the biological conditions (e.g., protein concentrations) that preceded an experimentally measured event of interest (e.g., mitosis, apoptosis, etc.).

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 9