Computational design of synthetic gene circuits with composable parts

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Computational design of synthetic gene circuits with composable parts

MOTIVATION In principle, novel genetic circuits can be engineered using standard parts with well-understood functionalities. However, no model based on the simple composition of these parts has become a standard, mainly because it is difficult to define signal exchanges between biological units as unambiguously as in electrical engineering. Corresponding concepts and computational tools for eas...

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Synthetic gene circuits: design with directed evolution.

Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Combining mathematical mod...

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Automatic Design of Digital Synthetic Gene Circuits

De novo computational design of synthetic gene circuits that achieve well-defined target functions is a hard task. Existing, brute-force approaches run optimization algorithms on the structure and on the kinetic parameter values of the network. However, more direct rational methods for automatic circuit design are lacking. Focusing on digital synthetic gene circuits, we developed a methodology ...

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Parts & Pools: A Framework for Modular Design of Synthetic Gene Circuits

Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the...

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Synthetic Gene Circuits

Barbara Jusiak1,2, Ramiz Daniel1,3, Fahim Farzadfard2–5, Lior Nissim1,3, Oliver Purcell2,3, Jacob Rubens1,3,5, and Timothy K. Lu1–6 1Massachusetts Institute of Technology, Research Laboratory of Electronics, Cambridge, MA 02139, USA 2Massachusetts Institute of Technology, Department of Biological Engineering, Cambridge, MA 02139, USA 3Massachusetts Institute of Technology, Synthetic Biology Cen...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2008

ISSN: 1460-2059,1367-4803

DOI: 10.1093/bioinformatics/btn330