Application of combinatorial optimization strategies in synthetic biology

G Naseri, MAG Koffas - Nature communications, 2020 - nature.com
In the first wave of synthetic biology, genetic elements, combined into simple circuits, are
used to control individual cellular functions. In the second wave of synthetic biology, the …

Synthetic gene circuits: design with directed evolution

EL Haseltine, FH Arnold - Annu. Rev. Biophys. Biomol. Struct., 2007 - annualreviews.org
Synthetic circuits offer great promise for generating insights into nature's underlying design
principles or forward engineering novel biotechnology applications. However, construction …

Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression

AAK Nielsen, TH Segall-Shapiro, CA Voigt - Current opinion in chemical …, 2013 - Elsevier
Highlights•We review recent advances in the forward design of genetic circuits.•Advanced
circuit design concepts pave the way for more complex synthetic cellular regulation.•Part …

Synthetic biology: advancing the design of diverse genetic systems

YH Wang, KY Wei, CD Smolke - Annual review of chemical and …, 2013 - annualreviews.org
A major objective of synthetic biology is to make the process of designing genetically
encoded biological systems more systematic, predictable, robust, scalable, and efficient …

Computational tools and algorithms for designing customized synthetic genes

N Gould, O Hendy, D Papamichail - Frontiers in bioengineering and …, 2014 - frontiersin.org
Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits,
and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides …

Evolution-guided optimization of biosynthetic pathways

S Raman, JK Rogers, ND Taylor… - Proceedings of the …, 2014 - National Acad Sciences
Engineering biosynthetic pathways for chemical production requires extensive optimization
of the host cellular metabolic machinery. Because it is challenging to specify a priori an …

[HTML][HTML] The evolving art of creating genetic diversity: From directed evolution to synthetic biology

A Currin, S Parker, CJ Robinson, E Takano… - Biotechnology …, 2021 - Elsevier
The ability to engineer biological systems, whether to introduce novel functionality or
improved performance, is a cornerstone of biotechnology and synthetic biology. Typically …

Next-generation synthetic gene networks

TK Lu, AS Khalil, JJ Collins - Nature biotechnology, 2009 - nature.com
Synthetic biology is focused on the rational construction of biological systems based on
engineering principles. During the field's first decade of development, significant progress …

Large‐scale identification of genetic design strategies using local search

DS Lun, G Rockwell, NJ Guido, M Baym… - molecular systems …, 2009 - embopress.org
In the past decade, computational methods have been shown to be well suited to unraveling
the complex web of metabolic reactions in biological systems. Methods based on flux …

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks

J Beal, T Lu, R Weiss - PloS one, 2011 - journals.plos.org
Background The field of synthetic biology promises to revolutionize our ability to engineer
biological systems, providing important benefits for a variety of applications. Recent …