Speaker:Huy Nguyen

Reconstruction of Ancestral Gene Block Using Event-based Method and its Application

The evolution of complex systems is an open problem in biology.  To better understand how complex systems evolve, we focus on the problem of the evolution of orthologous gene blocks and operons in bacteria. Several models have been proposed to explain gene block and operon evolution. Previously, we proposed a method that explains the evolution of orthoblocks and operons as a combination of events that take place in vertical evolution from common ancestors. In the
evolution of an orthoblock, the different gene blocks may gain or lose genes, have genes duplicated, or have them split off. By determining the frequency of the events for any orthoblock in a studied clade, we can determine a cost for each event, and thus create a cost function to determine an optimal vertical path for the evolution of orthoblocks. In this talk, I will discuss about using orthoblock evolution distance to reconstruct ancestral gene blocks. In the first part, I provide motivation, background and my method to reconstruct ancestral gene block in my recent paper.  In the second part, I employ our method to characterise gene loss, split of gene block of the Gibberellin gene block. Finally, I formalize the problem of finding the best (smallest evolution cost) orthologous gene block of a target to a reference operon. Then, I briefly show this problem is NP-Hard by reducing it to Set Cover.
 

Committee: Oliver Eulenstein (major professor), Iddo Friedberg (major professor), David Fernandez-Baca, Xiaoqiu Huang, & Dennis Lavrov