Foundations and Emerging Paradigms for Computing in Living Cells

Journal of Molecular Biology
Kevin C MaTimothy K Lu

Abstract

Genetic circuits, composed of complex networks of interacting molecular machines, enable living systems to sense their dynamic environments, perform computation on the inputs, and formulate appropriate outputs. By rewiring and expanding these circuits with novel parts and modules, synthetic biologists have adapted living systems into vibrant substrates for engineering. Diverse paradigms have emerged for designing, modeling, constructing, and characterizing such artificial genetic systems. In this paper, we first provide an overview of recent advances in the development of genetic parts and highlight key engineering approaches. We then review the assembly of these parts into synthetic circuits from the perspectives of digital and analog logic, systems biology, and metabolic engineering, three areas of particular theoretical and practical interest. Finally, we discuss notable challenges that the field of synthetic biology still faces in achieving reliable and predictable forward-engineering of artificial biological circuits.

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Citations

Feb 2, 2016·Journal of Molecular Biology·Timothy K LuHélène Hodak
Aug 9, 2016·Journal of Molecular Biology·Chieh HsuAttila Becskei
Mar 7, 2017·Biotechnology and Bioengineering·Allison Hoynes-O'ConnorTae Seok Moon
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Dec 5, 2017·Nature Methods·David AusländerMartin Fussenegger
Apr 28, 2017·Synthetic Biology·Chun Tung Chou
Dec 31, 2019·Molecular Systems Biology·Belén CallesVíctor de Lorenzo
Jan 14, 2021·Scientific Reports·Michael Taynnan BarrosSasitharan Balasubramaniam
Oct 5, 2021·Frontiers in Bioengineering and Biotechnology·Fernanda Miyuki KashiwagiMarcelo Müller-Santos

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