[HTML][HTML] Single-cell transcriptional dynamics in a living vertebrate

E Eck, B Moretti, BH Schlomann, J Bragantini, M Lange… - bioRxiv, 2024 - ncbi.nlm.nih.gov
The ability to quantify transcriptional dynamics in individual cells via live imaging has
revolutionized our understanding of gene regulation. However, such measurements are …

Optimization-based synthesis of stochastic biocircuits with statistical specifications

Y Sakurai, Y Hori - Journal of The Royal Society …, 2018 - royalsocietypublishing.org
Model-guided design has become a standard approach to engineering biomolecular circuits
in synthetic biology. However, the stochastic nature of biomolecular reactions is often …

High cooperativity in negative feedback can amplify noisy gene expression

P Bokes, YT Lin, A Singh - Bulletin of Mathematical Biology, 2018 - Springer
Burst-like synthesis of protein is a significant source of cell-to-cell variability in protein levels.
Negative feedback is a common example of a regulatory mechanism by which such …

Quantitative control of noise in mammalian gene expression by dynamic histone regulation

D Tan, R Chen, Y Mo, S Gu, J Ma, W Xu, X Lu, H He… - Elife, 2021 - elifesciences.org
Fluctuation ('noise') in gene expression is critical for mammalian cellular processes.
Numerous mechanisms contribute to its origins, yet the mechanisms behind large …

The influence of nuclear compartmentalisation on stochastic dynamics of self-repressing gene expression

M Sturrock, S Li, V Shahrezaei - Journal of theoretical biology, 2017 - Elsevier
Gene expression is an inherently noisy process. This noise is generally thought to be
deleterious as precise internal regulation of biochemical reactions is essential for cell growth …

[HTML][HTML] Oscillations in well-mixed, deterministic feedback systems: Beyond ring oscillators

KM Page - Journal of Theoretical Biology, 2019 - Elsevier
A ring oscillator is a system in which one species regulates the next, which regulates the
next and so on until the last species regulates the first. In addition, the number of the …

Promoters architecture-based mechanism for noise-induced oscillations in a single-gene circuit

N Guisoni, D Monteoliva, L Diambra - PLoS One, 2016 - journals.plos.org
It is well known that single-gene circuits with negative feedback loop can lead to oscillatory
gene expression when they operate with time delay. In order to generate these oscillations …

Multiple binding sites for transcriptional repressors can produce regular bursting and enhance noise suppression

IM Lengyel, LG Morelli - Physical Review E, 2017 - APS
Cells may control fluctuations in protein levels by means of negative autoregulation, where
transcription factors bind DNA sites to repress their own production. Theoretical studies have …

Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network

A Dhawan, AL Harris, FM Buffa, JG Scott - Journal of Theoretical Biology, 2019 - Elsevier
Oscillations are crucial to the normal function of living organisms, across a wide variety of
biological processes. In eukaryotes, oscillatory dynamics are thought to arise from …

Postponing production exponentially enhances the molecular memory of a stochastic switch

P Bokes - European Journal of Applied Mathematics, 2022 - cambridge.org
Delayed production can substantially alter the qualitative behaviour of feedback systems.
Motivated by stochastic mechanisms in gene expression, we consider a protein molecule …