Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology

I Bervoets, D Charlier - FEMS microbiology reviews, 2019 - academic.oup.com
Gene expression occurs in two essential steps: transcription and translation. In bacteria, the
two processes are tightly coupled in time and space, and highly regulated. Tight regulation …

Systematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operons

DP Cetnar, HM Salis - ACS Synthetic Biology, 2021 - ACS Publications
mRNA degradation is a central process that affects all gene expression levels, and yet, the
determinants that control mRNA decay rates remain poorly characterized. Here, we applied …

Metabolic perceptrons for neural computing in biological systems

A Pandi, M Koch, PL Voyvodic, P Soudier… - Nature …, 2019 - nature.com
Synthetic biological circuits are promising tools for developing sophisticated systems for
medical, industrial, and environmental applications. So far, circuit implementations …

Systematic inference identifies a major source of heterogeneity in cell signaling dynamics: The rate-limiting step number

DW Kim, H Hong, JK Kim - Science advances, 2022 - science.org
Identifying the sources of cell-to-cell variability in signaling dynamics is essential to
understand drug response variability and develop effective therapeutics. However, it is …

Toward a systematic design of smart probiotics

R Choudhary, R Mahadevan - Current Opinion in Biotechnology, 2020 - Elsevier
Synthetic biology has been instrumental in turning microbes into cell-factories capable of
diverse processes. A recent application has been to convert them into living therapeutics …

Inferring delays in partially observed gene regulation processes

H Hong, MJ Cortez, YY Cheng, HJ Kim, B Choi… - …, 2023 - academic.oup.com
Motivation Cell function is regulated by gene regulatory networks (GRNs) defined by protein-
mediated interaction between constituent genes. Despite advances in experimental …

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

A Westbrook, X Tang, R Marshall… - Biotechnology and …, 2019 - Wiley Online Library
To build complex genetic networks with predictable behaviors, synthetic biologists use
libraries of modular parts that can be characterized in isolation and assembled together to …

Cell-free prototyping of AND-logic gates based on heterogeneous RNA activators

FX Lehr, M Hanst, M Vogel, J Kremer… - ACS synthetic …, 2019 - ACS Publications
RNA-based devices controlling gene expression bear great promise for synthetic biology, as
they offer many advantages such as short response times and light metabolic burden …

Bayesian inference of distributed time delay in transcriptional and translational regulation

B Choi, YY Cheng, S Cinar, W Ott, MR Bennett… - …, 2020 - academic.oup.com
Motivation Advances in experimental and imaging techniques have allowed for
unprecedented insights into the dynamical processes within individual cells. However, many …

Design and evaluation of synthetic RNA-based incoherent feed-forward loop circuits

S Hong, D Jeong, J Ryan, M Foo, X Tang, J Kim - Biomolecules, 2021 - mdpi.com
RNA-based regulators are promising tools for building synthetic biological systems that
provide a powerful platform for achieving a complex regulation of transcription and …