The Salis Lab: De Novo Synthetic Biology
Biological functions are ultimately determined by their DNA sequences. By redesigning those sequences, micro-organisms can be engineered to become distributed sensor networks, active signal processing agents, chemically computing decision-makers, and multi-catalyst chemical factories.
In practice, there are an astronomical number of design choices (different DNA sequences), but only a few will be successful. In the Salis Lab, researchers develop and experimentally validate models and algorithms to rationally design the DNA sequences of micro-organisms, engineering sensors, genetic circuits, and metabolic pathways to reprogram their behavior.
Physics-based models are highly reductionist, focusing on specific biomolecular interactions that control transcription rate, translation rate, or their regulation. By combining several of those models together, the Salis Lab has created a DNA Compiler that inter-converts between DNA sequence instructions and biological outcomes. The lab has applied DNA Compiler to increase recombinant protein expression, design RNA-based sensors for diverse chemicals, efficiently optimize many-enzyme metabolic pathways, and program sophisticated decision-making genetic circuits. Through the popular web-interface, salislab.net/software, thousands of world-wide researchers have used the models and algorithms to design over one hundred thousand of their own DNA sequences for diverse biotechnological applications.
Current research focuses in the lab include:
- Biophysics of gene expression, regulation, and metabolism
- Engineering cellular sensors,circuits, and pathways
- Numerical methods and algorithm development