Principles of genetic circuit design

JAN Brophy, CA Voigt - Nature methods, 2014 - nature.com
Cells navigate environments, communicate and build complex patterns by initiating gene
expression in response to specific signals. Engineers seek to harness this capability to …

[HTML][HTML] Roles for microRNAs in conferring robustness to biological processes

MS Ebert, PA Sharp - Cell, 2012 - cell.com
Biological systems use a variety of mechanisms to maintain their functions in the face of
environmental and genetic perturbations. Increasing evidence suggests that, among their …

Overflow metabolism in Escherichia coli results from efficient proteome allocation

M Basan, S Hui, H Okano, Z Zhang, Y Shen… - Nature, 2015 - nature.com
Overflow metabolism refers to the seemingly wasteful strategy in which cells use
fermentation instead of the more efficient respiration to generate energy, despite the …

Identification and consequences of miRNA–target interactions—beyond repression of gene expression

J Hausser, M Zavolan - Nature Reviews Genetics, 2014 - nature.com
Comparative genomics analyses and high-throughput experimental studies indicate that a
microRNA (miRNA) binds to hundreds of sites across the transcriptome. Although the …

Small RNAs in bacteria and archaea: who they are, what they do, and how they do it

EGH Wagner, P Romby - Advances in genetics, 2015 - Elsevier
Small RNAs are ubiquitously present regulators in all kingdoms of life. Most bacterial and
archaeal small RNAs (sRNAs) act by antisense mechanisms on multiple target mRNAs …

[HTML][HTML] Regulation by small RNAs in bacteria: expanding frontiers

G Storz, J Vogel, KM Wassarman - Molecular cell, 2011 - cell.com
Research on the discovery and characterization of small, regulatory RNAs in bacteria has
exploded in recent years. These sRNAs act by base pairing with target mRNAs with which …

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

R Balakrishnan, M Mori, I Segota, Z Zhang… - Science, 2022 - science.org
Protein concentrations are set by a complex interplay between gene-specific regulatory
processes and systemic factors, including cell volume and shared gene expression …

Functional roles for noise in genetic circuits

A Eldar, MB Elowitz - Nature, 2010 - nature.com
The genetic circuits that regulate cellular functions are subject to stochastic fluctuations, or
'noise', in the levels of their components. Noise, far from just a nuisance, has begun to be …

A quasi-integral controller for adaptation of genetic modules to variable ribosome demand

HH Huang, Y Qian, D Del Vecchio - Nature communications, 2018 - nature.com
The behavior of genetic circuits is often poorly predictable. A gene's expression level is not
only determined by the intended regulators, but also affected by changes in ribosome …

MicroRNAs can generate thresholds in target gene expression

S Mukherji, MS Ebert, GXY Zheng, JS Tsang… - Nature …, 2011 - nature.com
MicroRNAs (miRNAs) are short, highly conserved noncoding RNA molecules that repress
gene expression in a sequence-dependent manner. We performed single-cell …