Georgia Institute of Technology College of Sciences

We have recently witnessed the tremendous progress in evolutionary and regulatory genomics of eukaryotes fueled by hundreds of sequenced eukaryotic genomes, including human and dozens of animal and plant genomes and culminating in the recent release of The Encyclopedia of DNA Elements (ENCODE) project. Yet, many interesting questions about the functional and structural organization of the genomic elements and their evolution remain unsolved. Computational genomics methods have become essential in addressing these questions working with the massive genomic data. In this presentation, I will talk about two interesting open problems in computational genomics. The first problem is related to identifying and characterizing long identical multispecies elements (LIMEs), the genomic regions that were slowed down through the course of evolution to their extremes. I will discuss our recent findings of the LIMEs shared across six animal as well as six plant genomes and the computational challenges associated with expanding our results towards other species. The second problem is finding genome rearrangements for a group of genomes. I will present out latest approach approach that brings together the idea of symbolic object representation and stochastic simulation of the evolutionary graphs.