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Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…

Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first genetic circuits -- the repressilator and the toggle switch -- were designed and implemented, many advances have been made in this area of research.…

Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…

Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies,…

This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model…

Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…

Mathematical modelling is a cornerstone of computational biology. While mechanistic models might describe the interactions of interest of a system, they are often difficult to study. On the other hand, abstract models might capture key…

Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of…

The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…

One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of…

With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…

A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to…

Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide invaluable insight into the function and design of both natural and synthetic biomolecular…

Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…

Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling techniques in conjunction with molecular…

Advances in science and engineering often reveal the limitations of classical approaches initially used to understand, predict, and control phenomena. With progress, conceptual categories must often be re-evaluated to better track recently…

The focus of this thesis is on the applications of nonlinear dynamical systems in bioengineering which are mainly used in large-scale and generally categorised into two groups: (1) dynamical systems from biology (2) dynamical systems for…

In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…

Associative learning is one of the key mechanisms displayed by living organisms in order to adapt to their changing environments. It was early recognized to be a general trait of complex multicellular organisms but also found in "simpler"…