Journal
FEBS LETTERS
Volume 586, Issue 15, Pages 2037-2042Publisher
WILEY
DOI: 10.1016/j.febslet.2012.02.031
Keywords
Computational design; Regulatory network; In silico evolution; Optimization; Synthetic biology
Funding
- BACTOCOM [FP7-ICT-043338]
- CADMAD [FP7-ICT-265505]
- ATIGE-Genopole
- Fondation pour la Recherche Medicale grants
- EMBO
- Marie Curie actions [ALTF-1177-2011]
- AXA Research Fund
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Automatic design is based on computational modeling and optimization methods to provide prototype designs to targeted problems in an unsupervised manner. For biological circuits, we need to produce quantitative predictions of cell behavior for a given genotype as consequence of the different molecular interactions. Automatic design techniques aim at solving the inverse problem of finding the sequences of nucleotides that better fit a targeted behavior. In the post-genomic era, our molecular knowledge and modeling capabilities have allowed to start using such methodologies with success. Herein, we describe how the emergence of this new type of tools could enable novel synthetic biology applications. We highlight the essential elements to develop automatic design procedures for synthetic biology pointing out their advantages and bottlenecks. We discuss in detail the experimental difficulties to overcome in the in vivo implementation of designed networks. The use of automatic design to engineer biological networks is starting to emerge as a new technique to perform synthetic biology, which should not be neglected in the future. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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