Transcriptional bursting in gene expression: analytical results for general stochastic models

N Kumar, A Singh, RV Kulkarni - PLoS computational biology, 2015 - journals.plos.org
Gene expression in individual cells is highly variable and sporadic, often resulting in the
synthesis of mRNAs and proteins in bursts. Such bursting has important consequences for …

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 …

Intercellular variability in protein levels from stochastic expression and noisy cell cycle processes

M Soltani, CA Vargas-Garcia, D Antunes… - PLoS computational …, 2016 - journals.plos.org
Inside individual cells, expression of genes is inherently stochastic and manifests as cell-to-
cell variability or noise in protein copy numbers. Since proteins half-lives can be comparable …

Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics

S Luo, Z Wang, Z Zhang, T Zhou… - Nucleic Acids …, 2023 - academic.oup.com
Gene expression in mammalian cells is highly variable and episodic, resulting in a series of
discontinuous bursts of mRNAs. A challenge is to understand how static promoter …

Quantifying intrinsic and extrinsic variability in stochastic gene expression models

A Singh, M Soltani - Plos one, 2013 - journals.plos.org
Genetically identical cell populations exhibit considerable intercellular variation in the level
of a given protein or mRNA. Both intrinsic and extrinsic sources of noise drive this variability …

Mitigating long queues and waiting times with service resetting

OL Bonomo, A Pal, S Reuveni - PNAS nexus, 2022 - academic.oup.com
What determines the average length of a queue, which stretches in front of a service station?
The answer to this question clearly depends on the average rate at which jobs arrive at the …

Inferring transcriptional bursting kinetics from single-cell snapshot data using a generalized telegraph model

S Luo, Z Zhang, Z Wang, X Yang… - Royal Society …, 2023 - royalsocietypublishing.org
Gene expression has inherent stochasticity resulting from transcription's burst manners.
Single-cell snapshot data can be exploited to rigorously infer transcriptional burst kinetics …

Analytical results for a multistate gene model

T Zhou, J Zhang - SIAM Journal on Applied Mathematics, 2012 - SIAM
Gene expression is a complicated multistep process where transcription depends on a
chromatin template that can be characterized by stochastic transitions between active and …

Inferring entropy production rate from partially observed Langevin dynamics under coarse-graining

A Ghosal, G Bisker - Physical Chemistry Chemical Physics, 2022 - pubs.rsc.org
The entropy production rate (EPR) measures time-irreversibility in systems operating far
from equilibrium. The challenge in estimating the EPR for a continuous variable system is …

Delayed protein synthesis reduces the correlation between mRNA and protein fluctuations

T Gedeon, P Bokes - Biophysical journal, 2012 - cell.com
Recent experimental results indicate that, in single Escherichia coli cells, the fluctuations in
mRNA level are uncorrelated with those of protein. However, a basic two-stage model for …