Computational Methods in Synthetic Biology

Volume 1244 of the series Methods in Molecular Biology pp 167-178


Computationally Guided Design of Robust Gene Circuits

  • Najaf A. ShahAffiliated withGenomics and Computational Biology Graduate Group, Perelman School of Medicine, University of PennsylvaniaApplied Mathematics and Modeling, Informatics IT, Merck Research Labs
  • , Casim A. SarkarAffiliated withDepartment of Biomedical Engineering, College of Science and Engineering, University of Minnesota Email author 

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The inability to rationally design and construct circuits that robustly enable complex behaviors is perhaps the most fundamental challenge in synthetic biology. While systems modeling can aid this process and help reduce the space of design strategies, the unavailability and dynamic variability of kinetic parameters limits the utility of such models. Here, we present a general approach that employs an exhaustive enumeration of network architectures to suggest topologies that robustly enable a desired behavior.

Key words

Synthetic circuit design Systems modeling Network topology Topology search