Publication 1: Mechanism-based and data-driven modeling in cell-free synthetic biology
Angelina Yurchenko, Gökçe Özkul, Natal A. W. van Riel, Jan C. M. van Hest and Tom F. A. de Greef | Chem. Commun., 2024,60, 6466-6475
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Publication abstract
Cell-free systems have emerged as a versatile platform in synthetic biology, finding applications in various areas such as prototyping synthetic circuits, biosensor development, and biomanufacturing. To streamline the prototyping process, cell-free systems often incorporate a modeling step that predicts the outcomes of various experimental scenarios, providing a deeper insight into the underlying mechanisms and functions. There are two recognized approaches for modeling these systems: mechanism-based modeling, which models the underlying reaction mechanisms; and data-driven modeling, which makes predictions based on data without preconceived interactions between system components. In this highlight, we focus on the latest advancements in both modeling approaches for cell-free systems, exploring their potential for the design and optimization of synthetic genetic circuits.