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Systems approaches for synthetic biology: a pathway toward mammalian design

By Rahul Rekhi and Amina A. Qutub

Abstract

We review methods of understanding cellular interactions through computation in order to guide the synthetic design of mammalian cells for translational applications, such as regenerative medicine and cancer therapies. In doing so, we argue that the challenges of engineering mammalian cells provide a prime opportunity to leverage advances in computational systems biology. We support this claim systematically, by addressing each of the principal challenges to existing synthetic bioengineering approaches—stochasticity, complexity, and scale—with specific methods and paradigms in systems biology. Moreover, we characterize a key set of diverse computational techniques, including agent-based modeling, Bayesian network analysis, graph theory, and Gillespie simulations, with specific utility toward synthetic biology. Lastly, we examine the mammalian applications of synthetic biology for medicine and health, and how computational systems biology can aid in the continued development of these applications

Topics: systems biology, synthetic biology, mammalian cell, computational biology, regenerative medicine, gene circuits, signaling network, multiscale modeling
Year: 2013
DOI identifier: 10.3389/fphys.2013.00285
OAI identifier: oai:scholarship.rice.edu:1911/78906
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