MIT EECS Undergraduate Research and Innovation Scholar
Algorithms For E.Coli Genome Engineering
Timothy K. Lu
E.Coli is one of the most important species in synthetic biology since it is a model organism in studying genetic manipulation. The genome of E.coli is manipulated by the integration of synthetic constructs. For the insertion we want to choose regions that are minimally disruptive to the surrounding genes and the function of the organism and that the surrounding DNA does not affect our insert. There are some integration sites that have been discovered experimentally but the technique is not robust enough to scale to more complex organisms and might potentially also not be the most ideal sites. My project would focus on developing an algorithm to score potential integration sites in E. coli in order to systematically generate a list of regions in the genome for integration that would be minimally disruptive. Once the technique is experimentally verified, it can be used to generate similar lists for any organism as long as the genome has been completely sequenced.
I have done several UROPs that have helped me prepare for the superUROP. As a freshman, I studied the pathway of uptake of Exotoxin A in the Whitehead institute. I have also been working on understanding oxygenation patterns in neonates at the HST with professor Heldt. Additionally, I spent the last year working in the Lu lab developing the algorithm.