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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
Shamarova, Evelina ; Chertovskih, Roman ; Ramos, Alexandre F. ; Aguiar, Paulo
Total Authors: 4
Document type: Journal article
Source: Physical Review E; v. 95, n. 3 MAR 29 2017.
Web of Science Citations: 1
Abstract

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.). (AU)

FAPESP's process: 13/01242-8 - Generation of large-scale magnetic field by Rayleigh-Bénard convection
Grantee:Roman Chertovskikh
Support Opportunities: Scholarships in Brazil - Post-Doctorate