Stochastic modeling of autoregulatory genetic feedback loops: A review and comparative study
Autoregulatory feedback loops are one of the most common network motifs. A wide variety of
stochastic models have been constructed to understand how the fluctuations in protein …
stochastic models have been constructed to understand how the fluctuations in protein …
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 …
Statistical and computational challenges for whole cell modelling
MPH Stumpf - Current Opinion in Systems Biology, 2021 - Elsevier
Mathematical modelling of whole biological cells opens up new opportunities for
fundamental and applied biology. In particular in the context of synthetic biology, it opens up …
fundamental and applied biology. In particular in the context of synthetic biology, it opens up …
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 …
[HTML][HTML] Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition
In this study, we obtain an exact time-dependent solution of the chemical master equation
(CME) of an extension of the two-state telegraph model describing bursty or non-bursty …
(CME) of an extension of the two-state telegraph model describing bursty or non-bursty …
Dynamical phase diagram of an auto-regulating gene in fast switching conditions
While the steady-state behavior of stochastic gene expression with auto-regulation has been
extensively studied, its time-dependent behavior has received much less attention. Here …
extensively studied, its time-dependent behavior has received much less attention. Here …
A stochastic model of gene expression with polymerase recruitment and pause release
Transcriptional bursting is a major source of noise in gene expression. The telegraph model
of gene expression, whereby transcription switches between on and off states, is the …
of gene expression, whereby transcription switches between on and off states, is the …
110th Anniversary: An Overview on Learning-Based Model Predictive Control for Batch Processes
Batch processes repeatedly execute a given set of tasks over a finite duration, whose
versatility and ability to adapt to rapidly changing markets make it prevalent in a multitude of …
versatility and ability to adapt to rapidly changing markets make it prevalent in a multitude of …
Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities
Biochemical systems consist of numerous elementary reactions governed by the law of
mass action. However, experimentally characterizing all the elementary reactions is nearly …
mass action. However, experimentally characterizing all the elementary reactions is nearly …
Corrected Hill function in stochastic gene regulatory networks
ME Hernández-García, J Velázquez-Castro - arXiv preprint arXiv …, 2023 - arxiv.org
Describing reaction rates in stochastic bio-circuits is commonly done by directly introducing
the deterministically deduced Hill function into the master equation. However, when …
the deterministically deduced Hill function into the master equation. However, when …