Structure-aware models and algorithms for reconstructing the evolution and ancestral states of genes and genomes

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This is a computational genomics research program aimed at solving algorithmic and computational problems in order to improve our understanding of genome evolution. Currently, most genome evolution reconstruction methods are limited to the use of sequence-conserved portions of genomes, paying less attention to the structure of components. However, current discoveries in the life sciences are shedding new light on the complexity of gene structure and its importance for gene function and evolution. In particular, the secondary structure of non-coding RNAs (ncRNAs) and the architecture of eukaryotic coding genes constitute valuable information for the reconstruction of gene evolution and ancestral states.