Concentration fluctuations due to size-dependent gene expression and cell-size control mechanisms

C Jia, A Singh, R Grima - BioRxiv, 2021 - biorxiv.org
Intracellular reaction rates depend on concentrations and hence their levels are often
regulated. However classical models of stochastic gene expression lack a cell size …

Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis

C Jia, A Singh, R Grima - PLoS computational biology, 2022 - journals.plos.org
Intracellular reaction rates depend on concentrations and hence their levels are often
regulated. However classical models of stochastic gene expression lack a cell size …

Division rate, cell size and proteome allocation: impact on gene expression noise and implications for the dynamics of genetic circuits

F Bertaux, S Marguerat… - Royal Society open …, 2018 - royalsocietypublishing.org
The cell division rate, size and gene expression programmes change in response to
external conditions. These global changes impact on average concentrations of biomolecule …

[PDF][PDF] Accuracy and limitations of extrinsic noise models to describe gene expression in growing cells

C Jia, R Grima - bioRxiv, 2022 - researchgate.net
The standard model describing the fluctuations of mRNA numbers in single cells is the
telegraph model which includes synthesis and degradation of mRNA, and switching of the …

[HTML][HTML] Connecting growth with gene expression: of noise and numbers

V Shahrezaei, S Marguerat - Current opinion in microbiology, 2015 - Elsevier
Highlights•Cellular growth, gene expression, and cell size are coordinated globally.•Cellular
growth is connected to protein numbers, noise, and gene networks dynamics.•Global …

Pyecolib: a python library for simulating stochastic cell size dynamics

C Nieto, SC Blanco, C Vargas-García, A Singh… - Physical …, 2023 - iopscience.iop.org
Recently, there has been an increasing need for tools to simulate cell size regulation due to
important applications in cell proliferation and gene expression. However, implementing the …

[HTML][HTML] Gene expression in growing cells: A biophysical primer

I Golding, A Amir - ArXiv, 2023 - ncbi.nlm.nih.gov
Cell growth and gene expression, two essential elements of all living systems, have long
been the focus of biophysical interrogation. Advances in experimental single-cell methods …

Transcription stochasticity of complex gene regulation models

A Schwabe, KN Rybakova, FJ Bruggeman - Biophysical Journal, 2012 - cell.com
Transcription is regulated by a multitude of factors that concertedly induce genes to switch
between activity states. Eukaryotic transcription involves a multitude of complexes that …

The chemical fluctuation theorem governing gene expression

SJ Park, S Song, GS Yang, PM Kim, S Yoon… - Nature …, 2018 - nature.com
Gene expression is a complex stochastic process composed of numerous enzymatic
reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell …

Frequency domain analysis of fluctuations of mRNA and protein copy numbers within a cell lineage: theory and experimental validation

C Jia, R Grima - Physical Review X, 2021 - APS
The stochasticity of gene expression is manifested in the fluctuations of messenger
ribonucleic acid and protein copy numbers within a cell lineage over time. While data of this …