Bioinformatic promoter predictions and theoretical modeling of gene circuits in bacteria

Purpose of the project is to develop novel bioinformatic methods, and to generate fundamental understanding necessary for biotechnology applications. This will be achieved through integration of physical and mathematical modeling with biological experiments. The topic of the project is control of gene expression in bacteria, and we will: i) Develop a novel bioinformatic method for promoter prediction in bacterial genome. The algorithm will be based on our recently developed quantitative model of transcription initiation, and is expected to significantly improve low accuracy of the existing algorithms. This will, in turn, improve our ability to analyze transcription regulation and significantly impact other bioinformatic applications such as gene and operon detection. Our promoter prediction method will be experimentally tested. ii)Theoretically analyze strategies that allow expression of toxic, but otherwise useful, molecules in bacterial cells. Systems to be studied are bacterial gene circuits involved in defense against bacterial viruses: specifically, we will analyze restriction modification systems, and the newly discovered CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems. The study will provide guidelines on how to design useful synthetic biology circuits.