Promoter-mediated transcriptional dynamics

J Zhang, T Zhou - Biophysical journal, 2014 - cell.com
Genes in eukaryotic cells are typically regulated by complex promoters containing multiple
binding sites for a variety of transcription factors, but how promoter dynamics affect …

Exact distributions for stochastic gene expression models with arbitrary promoter architecture and translational bursting

M Chen, S Luo, M Cao, C Guo, T Zhou, J Zhang - Physical Review E, 2022 - APS
Gene expression in individual cells is inherently variable and sporadic, leading to cell-to-cell
variability in mRNA and protein levels. Recent single-cell and single-molecule experiments …

[HTML][HTML] A moment-convergence method for stochastic analysis of biochemical reaction networks

J Zhang, Q Nie, T Zhou - The Journal of chemical physics, 2016 - pubs.aip.org
Traditional moment-closure methods need to assume that high-order cumulants of a
probability distribution approximate to zero. However, this strong assumption is not satisfied …

Feedback-induced counterintuitive correlations of gene expression noise with bursting kinetics

L Huang, Z Yuan, P Liu, T Zhou - Physical Review E, 2014 - APS
Previous studies showed that a higher frequency of bursting results in lower expression
noise whereas a larger size of bursting leads to higher expression noise. Here, we show …

Decomposition and tunability of expression noise in the presence of coupled feedbacks

P Liu, Z Yuan, H Wang, T Zhou - Chaos: An Interdisciplinary Journal of …, 2016 - pubs.aip.org
Expression noise results in cell-to-cell variability in expression levels, and feedback
regulation may complicate the tracing of sources of this noise. Using a representative model …

Dynamical behavior of rumor spreading under a temporal random control strategy

X Yang, Y Wu, J Zhang, T Zhou - Journal of Statistical Mechanics …, 2019 - iopscience.iop.org
The propagation of rumors must be controlled due to their harm to society. Here, we analyze
a probability master equation model of rumor spreading, which considers a temporal …

Feedback-induced variations of distribution in a representative gene model

P Liu, Z Yuan, L Huang, T Zhou - International Journal of Bifurcation …, 2015 - World Scientific
Gene expression is inherently noisy, implying that the number of mRNAs or proteins is not
invariant rather than follows a distribution. This distribution can not only provide the exact …

Quantifying heterogeneity of stochastic gene expression

K Iida, N Obata, Y Kimura - Journal of Theoretical Biology, 2019 - Elsevier
The heterogeneity of stochastic gene expression, which refers to the temporal fluctuation in
a gene product and its cell-to-cell variation, has attracted considerable interest from …

Modeling and analytical solution of free energy of complex promoter structure

L Huang, P Liu, K Wen - Chinese Journal of Physics, 2021 - Elsevier
Based on the biological model of complex promoter structure, this paper establishes a
mathematical model, and maps the complex topological structures of promoter into a …

[PDF][PDF] Understanding the mechanisms of robustness in intracellular protein signalling cascades and gene expression

D Paul - 2018 - academia.edu
The term robustness provides an intuitive idea about failure or sustainability of a biological
or technical system under uncertainties and rapid changes in the environment of that …