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 …
Studying stochastic systems biology of the cell with single-cell genomics data
Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …
promise for systems biology. However, rigorously probing the biology of living cells requires …
Analytical distributions for detailed models of stochastic gene expression in eukaryotic cells
The stochasticity of gene expression presents significant challenges to the modeling of
genetic networks. A two-state model describing promoter switching, transcription, and …
genetic networks. A two-state model describing promoter switching, transcription, and …
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 …
Phenotypic switching in gene regulatory networks
Noise in gene expression can lead to reversible phenotypic switching. Several experimental
studies have shown that the abundance distributions of proteins in a population of isogenic …
studies have shown that the abundance distributions of proteins in a population of isogenic …
Exact distributions for stochastic gene expression models with bursting and feedback
Stochasticity in gene expression can give rise to fluctuations in protein levels and lead to
phenotypic variation across a population of genetically identical cells. Recent experiments …
phenotypic variation across a population of genetically identical cells. Recent experiments …
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 …
Exact solution of stochastic gene expression models with bursting, cell cycle and replication dynamics
The bulk of stochastic gene expression models in the literature do not have an explicit
description of the age of a cell within a generation and hence they cannot capture events …
description of the age of a cell within a generation and hence they cannot capture events …
Extrinsic noise and heavy-tailed laws in gene expression
Noise in gene expression is one of the hallmarks of life at the molecular scale. Here we
derive analytical solutions to a set of models describing the molecular mechanisms …
derive analytical solutions to a set of models describing the molecular mechanisms …