Unified dimensionless transformation in enzyme kinetics: Application to mathematical analyses of ten biochemical reaction systems
Sign Up to like & getrecommendations! Published in 2020 at "Analytical Biochemistry"
DOI: 10.1016/j.ab.2020.113794
Abstract: Abstract A novel general principle was proposed to transform enzyme kinetic equations into unified dimensionless forms. The principle consists of six steps. The principle was applied to ten complex biochemical reaction systems and their characteristics… read more here.
Keywords: unified dimensionless; reaction systems; mathematical analyses; enzyme ... See more keywords
Analysis of stochastic multimolecular biochemical reaction model with lévy jumps
Sign Up to like & getrecommendations! Published in 2019 at "Physica A: Statistical Mechanics and its Applications"
DOI: 10.1016/j.physa.2019.04.218
Abstract: Abstract In this paper, a stochastic multimolecular biochemical reaction model with levy jumps is investigated. Firstly, we prove the existence and uniqueness of the global positive solution. Then we derive the conditions when the reaction… read more here.
Keywords: stochastic multimolecular; reaction; multimolecular biochemical; reaction model ... See more keywords
Parameter estimation for biochemical reaction networks using Wasserstein distances
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Physics A: Mathematical and Theoretical"
DOI: 10.1088/1751-8121/ab5877
Abstract: We present a method for estimating parameters in stochastic models of biochemical reaction networks by fitting steady-state distributions using Wasserstein distances. We simulate a reaction network at different parameter settings and train a Gaussian process… read more here.
Keywords: reaction networks; reaction; biochemical reaction; parameter estimation ... See more keywords
CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa241
Abstract: MOTIVATION Signaling pathways capable of switching between two states are ubiquitous within living organisms. They provide the cells with the means to produce reversible or irreversible decisions. Switch-like behavior of biological systems is realized through… read more here.
Keywords: biochemical reaction; reaction networks; python package; reaction ... See more keywords
SBbadger: biochemical reaction networks with definable degree distributions
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac630
Abstract: MOTIVATION An essential step in developing computational tools for the inference, optimization, and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the… read more here.
Keywords: reaction; sbbadger biochemical; degree distributions; reaction networks ... See more keywords
Quasi-robust control of biochemical reaction networks via stochastic morphing
Sign Up to like & getrecommendations! Published in 2021 at "Journal of the Royal Society Interface"
DOI: 10.1098/rsif.2020.0985
Abstract: One of the main objectives of synthetic biology is the development of molecular controllers that can manipulate the dynamics of a given biochemical network that is at most partially known. When integrated into smaller compartments,… read more here.
Keywords: control biochemical; robust control; networks via; biochemical reaction ... See more keywords
Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks
Sign Up to like & getrecommendations! Published in 2022 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1010183
Abstract: Quantifying biochemical reaction rates within complex cellular processes remains a key challenge of systems biology even as high-throughput single-cell data have become available to characterize snapshots of population variability. That is because complex systems with… read more here.
Keywords: reaction rates; reaction; population variability; quantifying biochemical ... See more keywords
A framework for deriving analytic steady states of biochemical reaction networks
Sign Up to like & getrecommendations! Published in 2023 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1011039
Abstract: The long-term behaviors of biochemical systems are often described by their steady states. Deriving these states directly for complex networks arising from real-world applications, however, is often challenging. Recent work has consequently focused on network-based… read more here.
Keywords: analytic steady; framework deriving; reaction networks; steady states ... See more keywords
WinBEST-KIT: Biochemical Reaction Simulator for Analyzing Multi-Layered Metabolic Pathways
Sign Up to like & getrecommendations! Published in 2021 at "Bioengineering"
DOI: 10.3390/bioengineering8080114
Abstract: We previously developed the biochemical reaction simulator WinBEST-KIT. In recent years, research interest has shifted from analysis of individual biochemical reactions to analysis of metabolic pathways as systems. These large-scale and complicated metabolic pathways can… read more here.
Keywords: reaction simulator; biochemical reaction; metabolic pathways; winbest kit ... See more keywords
Quantifying Information of Dynamical Biochemical Reaction Networks
Sign Up to like & getrecommendations! Published in 2023 at "Entropy"
DOI: 10.3390/e25060887
Abstract: A large number of complex biochemical reaction networks are included in the gene expression, cell development, and cell differentiation of in vivo cells, among other processes. Biochemical reaction-underlying processes are the ones transmitting information from… read more here.
Keywords: information; reaction; amount information; reaction networks ... See more keywords