Comprehensive review of models and methods for inferences in bio-chemical reaction networks

P Loskot, K Atitey, L Mihaylova - Frontiers in genetics, 2019 - frontiersin.org
The key processes in biological and chemical systems are described by networks of
chemical reactions. From molecular biology to biotechnology applications, computational …

Precise parameter synthesis for stochastic biochemical systems

M Češka, F Dannenberg, N Paoletti, M Kwiatkowska… - Acta Informatica, 2017 - Springer
We consider the problem of synthesising rate parameters for stochastic biochemical
networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of …

Condition-based maintenance planning for multi-state systems under time-varying environmental conditions

J Hu, A Xu, B Li, H Liao - Computers & Industrial Engineering, 2021 - Elsevier
Abstract Systems commonly operate under time-varying environmental condition (EC).
Since the EC can affect the degradation process of a system, maintenance planning can be …

Polynomial-time verification of PCTL properties of MDPs with convex uncertainties

A Puggelli, W Li, AL Sangiovanni-Vincentelli… - … Aided Verification: 25th …, 2013 - Springer
We address the problem of verifying Probabilistic Computation Tree Logic (PCTL) properties
of Markov Decision Processes (MDPs) whose state transition probabilities are only known to …

Exploring parameter space of stochastic biochemical systems using quantitative model checking

L Brim, M Češka, S Dražan, D Šafránek - International Conference on …, 2013 - Springer
We propose an automated method for exploring kinetic parameters of stochastic
biochemical systems. The main question addressed is how the validity of an a priori given …

Syntax-guided optimal synthesis for chemical reaction networks

L Cardelli, M Češka, M Fränzle, M Kwiatkowska… - … Aided Verification: 29th …, 2017 - Springer
We study the problem of optimal syntax-guided synthesis of stochastic Chemical Reaction
Networks (CRNs) that plays a fundamental role in design automation of molecular devices …

Reliability performance for dynamic multi-state repairable systems with K regimes

J Shen, L Cui - IISE Transactions, 2017 - Taylor & Francis
It is well known that many factors can influence the rate at which a machine degrades. In this
article, we study a multi-state repairable system subject to continuous degradation and …

Bayesian estimation for stochastic gene expression using multifidelity models

HD Vo, Z Fox, A Baetica, B Munsky - The Journal of Physical …, 2019 - ACS Publications
The finite state projection (FSP) approach to solving the chemical master equation has
enabled successful inference of discrete stochastic models to predict single-cell gene …

Bayesian inference of stochastic reaction networks using multifidelity sequential tempered Markov chain Monte Carlo

TA Catanach, HD Vo, B Munsky - International journal for …, 2020 - dl.begellhouse.com
Stochastic reaction network models are often used to explain and predict the dynamics of
gene regulation in single cells. These models usually involve several parameters, such as …

Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks

J Ruess, J Lygeros - ACM Transactions on Modeling and Computer …, 2015 - dl.acm.org
Continuous-time Markov chains are commonly used in practice for modeling biochemical
reaction networks in which the inherent randomness of the molecular interactions cannot be …