Akademik Veri Yönetim Sistemi
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, cilt.15, sa.3, ss.813-827, 2018 (SCI-Expanded)
This paper proposes aggregation-based, three-stage algorithms to overcome the numerical problems encountered in computing stationary distributions and mean first passage times for multi-modal birth-death processes of large state space sizes. The considered birth-death processes which are defined by Chemical Master Equations are used in modeling stochastic behavior of gene regulatory networks. Computing stationary probabilities for a multi-modal distribution from Chemical Master Equations is subject to have numerical problems due to the probability values running out of the representation range of the standard programming languages with the increasing size of the state space. The aggregation is shown to provide a solution to this problem by analyzing first reduced size subsystems in isolation and then considering the transitions between these subsystems. The proposed algorithms are applied to study the bimodal behavior of the lac operon of E. coli described with a one-dimensional birth-death model. Thus, the determination of the entire parameter range of bimodality for the stochastic model of lac operon is achieved.