Noise propagation in synthetic gene circuits for metabolic control

DA Oyarzun, JB Lugagne, GBV Stan - ACS synthetic biology, 2015 - ACS Publications
Dynamic control of enzyme expression can be an effective strategy to engineer robust
metabolic pathways. It allows a synthetic pathway to self-regulate in response to changes in …

Impact of negative feedback in metabolic noise propagation

A Borri, P Palumbo, A Singh - IET Systems Biology, 2016 - Wiley Online Library
Synthetic biology combines different branches of biology and engineering aimed at
designing synthetic biological circuits able to replicate emergent properties useful for the …

Synthetic gene circuits for metabolic control: design trade-offs and constraints

DA Oyarzún, GBV Stan - Journal of the Royal Society …, 2013 - royalsocietypublishing.org
A grand challenge in synthetic biology is to push the design of biomolecular circuits from
purely genetic constructs towards systems that interface different levels of the cellular …

Noise suppression in stochastic genetic circuits using pid controllers

S Modi, S Dey, A Singh - PLoS Computational Biology, 2021 - journals.plos.org
Inside individual cells, protein population counts are subject to molecular noise due to low
copy numbers and the inherent probabilistic nature of biochemical processes. We …

On the attenuation and amplification of molecular noise in genetic regulatory networks

BS Chen, YC Wang - BMC bioinformatics, 2006 - Springer
Background Noise has many important roles in cellular genetic regulatory functions at the
nanomolar scale. At present, no good theory exists for identifying all possible mechanisms of …

Frequency domain analysis of noise in autoregulated gene circuits

ML Simpson, CD Cox… - Proceedings of the …, 2003 - National Acad Sciences
We describe a frequency domain technique for the analysis of intrinsic noise within
negatively autoregulated gene circuits. This approach is based on the transfer function …

Dynamics of complex feedback architectures in metabolic pathways

M Chaves, DA Oyarzún - Automatica, 2019 - Elsevier
Cellular metabolism contains intricate arrays of feedback control loops. These are a key
mechanism by which cells adapt and survive environmental disturbances. Gene regulation …

Automated design of synthetic gene circuits in the presence of molecular noise

C Sequeiros, C Vázquez, JR Banga… - ACS Synthetic …, 2023 - ACS Publications
Microorganisms (mainly bacteria and yeast) are frequently used as hosts for genetic
constructs in synthetic biology applications. Molecular noise might have a significant effect …

Tuning and controlling gene expression noise in synthetic gene networks

KF Murphy, RM Adams, X Wang, G Balazsi… - Nucleic acids …, 2010 - academic.oup.com
Synthetic gene networks can be used to control gene expression and cellular phenotypes in
a variety of applications. In many instances, however, such networks can behave unreliably …

Negative autoregulation matches production and demand in synthetic transcriptional networks

E Franco, G Giordano, PO Forsberg… - ACS synthetic …, 2014 - ACS Publications
We propose a negative feedback architecture that regulates activity of artificial genes, or
“genelets”, to meet their output downstream demand, achieving robustness with respect to …