Leader: Alfonso Jaramillo.
This group works on several aspects of biological networks design and synthetic biology. Theses aspects include transcriptional networks, but also metabolic engineering and systems biology. The team develops computational methods to design bacterial RNA or transcriptional circuits which are then characterized in vivo. Finally, results from experiments feed models and thus close the loop.
The synth-bio group works on the design, synthesis and characterization of synthetic regulatory pathways. Our objective is to systematically construct models from scratch, either of synthetic protein, enzyme or nucleic acid parts, or of genetic devices (oscillators, inverters, amplifiers, digital devices, memory units...), taking special care to: the part characterization; the proteomic/transcriptomic analysis of the E. coli chassis and the re-use of that data in simulations to predict the final behaviour. This approach has the advantages of being quantitative, reproducible and it builds from the current knowledge of the rational design of parts and systems. We will take advantage of our automated computational design methodologies that could be later used with other model systems. We will also benefit from the increasingly available high-throughput data in structural and systems biology. We take advantage of MIT's biobrick database to experimentally construct and characterize our designs and we will incorporate back into the software the necessary design specifications that will arise from the experiments.
The design of more complex genetic devices will pose important questions such as the designability of biological networks, the scalability of the assembly of devices, the most appropriate way to model devices from modular components, or the robustness under noises or under evolutionary pressure. Our aim is to address such questions by extending our computational design methodology while working with concrete projects to be experimentally validated. We will work with an E. coli chassis implementing the different types of genetic devices (sensor, regulatory and metabolic) that would arise from the previous projects.
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