Approximation and inference methods for stochastic biochemical kinetics—a tutorial review
D Schnoerr, G Sanguinetti… - Journal of Physics A …, 2017 - iopscience.iop.org
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important
examples include gene expression and enzymatic processes in living cells. Such systems …
examples include gene expression and enzymatic processes in living cells. Such systems …
Misuse of the Michaelis–Menten rate law for protein interaction networks and its remedy
For over a century, the Michaelis–Menten (MM) rate law has been used to describe the rates
of enzyme-catalyzed reactions and gene expression. Despite the ubiquity of the MM rate …
of enzyme-catalyzed reactions and gene expression. Despite the ubiquity of the MM rate …
Linear mapping approximation of gene regulatory networks with stochastic dynamics
The presence of protein–DNA binding reactions often leads to analytically intractable
models of stochastic gene expression. Here we present the linear-mapping approximation …
models of stochastic gene expression. Here we present the linear-mapping approximation …
Beyond the Michaelis-Menten equation: Accurate and efficient estimation of enzyme kinetic parameters
Examining enzyme kinetics is critical for understanding cellular systems and for using
enzymes in industry. The Michaelis-Menten equation has been widely used for over a …
enzymes in industry. The Michaelis-Menten equation has been widely used for over a …
Markovian approaches to modeling intracellular reaction processes with molecular memory
J Zhang, T Zhou - Proceedings of the National Academy of …, 2019 - National Acad Sciences
Many cellular processes are governed by stochastic reaction events. These events do not
necessarily occur in single steps of individual molecules, and, conversely, each birth or …
necessarily occur in single steps of individual molecules, and, conversely, each birth or …
Markovian dynamics on complex reaction networks
J Goutsias, G Jenkinson - Physics reports, 2013 - Elsevier
Complex networks, comprised of individual elements that interact with each other through
reaction channels, are ubiquitous across many scientific and engineering disciplines …
reaction channels, are ubiquitous across many scientific and engineering disciplines …
Nonmodular oscillator and switch based on RNA decay drive regeneration of multimodal gene expression
Periodic gene expression dynamics are key to cell and organism physiology. Studies of
oscillatory expression have focused on networks with intuitive regulatory negative feedback …
oscillatory expression have focused on networks with intuitive regulatory negative feedback …
Comprehensive review of models and methods for inferences in bio-chemical reaction networks
The key processes in biological and chemical systems are described by networks of
chemical reactions. From molecular biology to biotechnology applications, computational …
chemical reactions. From molecular biology to biotechnology applications, computational …
Stochastic simulation of biomolecular networks in dynamic environments
Simulation of biomolecular networks is now indispensable for studying biological systems,
from small reaction networks to large ensembles of cells. Here we present a novel approach …
from small reaction networks to large ensembles of cells. Here we present a novel approach …
Small protein number effects in stochastic models of autoregulated bursty gene expression
A stochastic model of autoregulated bursty gene expression by Kumar et al.[Phys. Rev. Lett.
113, 268105 (2014)] has been exactly solved in steady-state conditions under the implicit …
113, 268105 (2014)] has been exactly solved in steady-state conditions under the implicit …