Algorithms in comparative genomics, transcriptome assembly, and metagenomics

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In this program, we will investigate three problems. Genomes of different species often share many genes, but these may occur in different orders in the genome sequence. Based on the principle that any two species share a common ancestor, the question of how to reconstruct the evolution of one genome into another, based on gene orders, have been studied intensively in recent years. One of the lingering problems is the difficulty of discriminating between the multitude of different evolution scenarios that are proposed by the current models. Based on previous results, we plan to find new answers by studying properties of special graphs associated to genome comparisons. In addition to this long term goal, we plan to rapidly develop software tools that can aid the construction of evolution scenarios.