Genetic circuit design and biodesign automation towards programmable cellular computers


   School of Biological Sciences

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  Dr Baojun Wang  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Bacterial cells live in an ever changing environment and therefore are equipped with specific genetically-encoded sensors and signalling networks to continuously perceive and process the various environmental signals. In this sense, cells can be viewed as replicating living computers but with biochemical inputs and outputs. This project aims to streamline the typical design, build and test cycle of large-scale gene circuits to program live bacterial cells with designer functions, in particular for advanced sensing, computing, information processing and control of multiple cellular and environmental signals with applications, for example, in cell-based biosensing and biomanufacturing.
You will be guided to design, build, test and model various genetic programs including novel sensors, genetic logic gates, amplifiers, computing and memory circuits. The layering and integration of these circuit modules will lead to a programmable biological computer. The biological computer will then enable the programmed cells to have a range of intelligent capabilities for application in areas including biosensing, biomanufacturing and biotherapies. By example, the engineered tools can be applied to significantly enhance the production yields of some difficult-to-express, large or toxic therapeutic proteins in industrial scale bioreactors. You will be guided to develop new biological circuit design principles by exploiting design principles in other engineering disciplines such as modularity, orthogonality, systematic characterization, modelling and simulation to increase the predictability and scalability of gene circuit design and assembly. In addition, you will have the opportunity to develop efficient Bio-CAD software and tools to automate the design and diagnosis of large-scale genetic circuits.
The project will provide the student a comprehensive training of advanced molecular biology, innovative microbiology and synthetic biology techniques, and computational modelling and programming skills. The research thus gives the student an inter-disciplinary research experience and cutting edge technologies exposure to prepare well for his/her future research career. The student may also benefit from the opportunity to work collaboratively with some of our blue-chip industrial partners (e.g. Microsoft Research). It is expected that the student either have wet-related (bioengineering, molecular biology, biochemistry, microbiology or synthetic biology) or a dry-related background (e.g. computing science, software design, electronic circuit design, bioinformatics or computational biology) to drive either of the two synergistic aspects of the project.

Further information about the lab can be found at http://wang.bio.ed.ac.uk/ and informal enquiries may be made to [Email Address Removed].

The School of Biological Sciences is committed to Equality & Diversity: https://www.ed.ac.uk/biology/equality-and-diversity




Funding Notes

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References

Wan et al., “Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals”, Nature Chemical Biology, 2019, 15(5):540–548
Wang et al. “Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology”, Nature Communications, 2011, 2:508
Nielsen et al., "Genetic circuit design automation." Science, 2016, 352:aac7341.

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