Systematic molecular evolution enables robust biomolecule discovery

EA DeBenedictis, EJ Chory, DW Gretton, B Wang… - Nature …, 2022 - nature.com
Evolution occurs when selective pressures from the environment shape inherited variation
over time. Within the laboratory, evolution is commonly used to engineer proteins and RNA …

[HTML][HTML] Adaptive circuits in synthetic biology

T Frei, M Khammash - Current Opinion in Systems Biology, 2021 - Elsevier
One of the most remarkable features of biological systems is their ability to adapt to the
constantly changing environment. By harnessing principles of control theory, synthetic …

Dynamical allocation of cellular resources as an optimal control problem: novel insights into microbial growth strategies

N Giordano, F Mairet, JL Gouzé… - PLoS computational …, 2016 - journals.plos.org
Microbial physiology exhibits growth laws that relate the macromolecular composition of the
cell to the growth rate. Recent work has shown that these empirical regularities can be …

Fast, cheap and somewhat in control

AP Arkin, DA Fletcher - Genome biology, 2006 - Springer
Efforts to manipulate living organisms have raised the question of whether engineering
principles of hierarchy, abstraction and design can be applied to biological systems. Here …

Downward causation by information control in micro-organisms

L Jaeger, ER Calkins - Interface Focus, 2012 - royalsocietypublishing.org
The concepts of functional equivalence classes and information control in living systems are
useful to characterize downward (or top-down) causation by feedback information control in …

Evolutionary rescue: linking theory for conservation and medicine

HK Alexander, G Martin, OY Martin… - Evolutionary …, 2014 - Wiley Online Library
Evolutionary responses that rescue populations from extinction when drastic environmental
changes occur can be friend or foe. The field of conservation biology is concerned with the …

Dynamically reshaping signaling networks to program cell fate via genetic controllers

KE Galloway, E Franco, CD Smolke - Science, 2013 - science.org
Introduction Engineering of cell fate through synthetic gene circuits requires methods to
precisely implement control around native decision-making pathways and offers the …

Tradeoffs and optimality in the evolution of gene regulation

FJ Poelwijk, MGJ De Vos, SJ Tans - Cell, 2011 - cell.com
Cellular regulation is believed to evolve in response to environmental variability. However,
this has been difficult to test directly. Here, we show that a gene regulation system evolves to …

Understanding biology by reverse engineering the control

CJ Tomlin, JD Axelrod - Proceedings of the National …, 2005 - National Acad Sciences
Faced with the problem of con-trolling a physical system, an en-gineer will identify a model
for the system, and then use this model to design a process for automatically actuating some …

Achieving optimal growth through product feedback inhibition in metabolism

S Goyal, J Yuan, T Chen, JD Rabinowitz… - PLoS computational …, 2010 - journals.plos.org
Recent evidence suggests that the metabolism of some organisms, such as Escherichia coli,
is remarkably efficient, producing close to the maximum amount of biomass per unit of …