Yves Gendrault

University of Strasbourg | UNISTRA · Systèmes microsystèmes hétérogènes

Synthetic biology is an emerging science that aims to create new biological functions that do not exist in nature, based on the knowledge acquired in life science over the last century. Since the beginning of this century, several projects in synthetic biology have emerged. The complexity of the developed artificial bio-functions is relatively low...

The topic of this article is the development of an open-source automated design framework for synthetic biology, specifically for the design of artificial gene regulatory networks based on a digital approach. In opposition to other tools, GeNeDA is an open-source online software based on existing tools used in microelectronics that have proven thei...

Synthetic biology is a new field of biotechnology which aims to apply engineering design processes for the development of new artificial biological functions. In this domain, the development of automated design tools is a big challenge. This paper deals with a new approach based on the description of elementary biological mechanisms through fuzzy l...

Synthetic biology is an emerging field at the interface between biotechnology and engineering sciences. It aims at designing new biological functions by assembling elementary parts (DNA sequences) based on design approaches inspired from those used for the design of complex microsystems. The development of efficient tools to support the design is t...

Nowadays, synthetic biology is a hot research topic. Each day, progresses are made to improve the complexity of artificial biological functions in order to tend to complex biodevices and biosystems. Up to now, these systems are handmade by bioengineers, which require strong technical skills and leads to nonreusable development. Besides, scientific...

The interaction of a ligand with a macromolecule has been modeled following different theories. The tenants of the induced fit model consider that upon ligand binding, the protein-ligand complex undergoes a conformational change. In contrast, the allosteric model assumes that only one among different coexisting conformers of a given protein is suit...

Synthetic biology, or biological engineering, is a new science which may take advantage of the know-how of engineering science in order to build new in-vivo biological functions. The complete design process implies lots of modeling and simulation tasks. The design flow for this technology uses “digital” models at high level of abstraction as well a...

The topic of this paper is to develop an open-source framework to help bio-engineers through the different stages of a top-down design process for new artificial biosystems (synthetic biology). The presented tools address the upstream stages of the design, starting from a high-level behavioral description of the targeted biological function and end...

This paper deals with the development of a new simulator that will be very helpful to establish new accurate and predictive design-oriented models for the BioBricks used in synthetic biology. The simulator uses the principle of the game-of-life: molecules can move on a grid and, at every iteration, binding and dissociation rules are applied when tw...

Synthetic bio-systems become increasingly more complex and their development is lengthy and expensive. In the same way, in microelectronics, the design process of very complex circuits has benefited from many years of experience. It is now partly automated through Electronic Design Automation tools. Both areas present analogies that can be used to...

The development of computer-aided design tools for synthetic biology is currently a hot research topic. However the field is not mature enough to provide a generic, adaptable and reliable tool for potential applications. The purpose of this paper is to present a system designers approach. We highlight, through the work carried out by our team in re...

In microelectronics, the design of new systems is based on a proven time-tested design flow. The goal of this paper is to determine to what extend this design flow can be adapted to biosystem design. The presented methodology is based on a top-down approach and consists of starting with a behavioral description of the system to progressively refine...

Synthetic biology is a science resulting from the connection between biotechnology and engineering sciences. It aims to design and build new biological systems and functions. The ability to design a new biological function according to given specifications includes many steps. One of the big issues is to formalize a design methodology and to develo...

Synthetic biology is an emerging area of biotechnology for which main applications are in the field of Health and Environment. However, it suffers from a lack of adapted CAD tools and methodology in order to fulfill efficiently and quickly to the needs of these domains. In this paper, the strong relationship between circuits design in microelectron...