The Liberles Research Group works in the areas of computational comparative genomics, and molecular evolution. The central theme in the research group is the detection and characterization of the lineage-specific divergence of protein-encoding genes. Much of the work in the group is done in a phylogenetic context. Ultimately, we want to ask the question, “What makes each species unique at the genomic level?” and “what are the processes driving the functional divergence of genomes?”.
Theoretical and methodological work in the group involves the construction of mechanistic models for codon and amino acid substitution and for duplicate gene retention. Ultimately, we want to ask the question, “How do proteins change functions on evolutionary timescales?”. We build mechanistic mathematical models for processes, both to ask in simulation how the processes work as a function of underlying biological parameterization and for use in inference on genome scale data.
For example, the figure below on the left shows the evolutionary parameterization of a site-specific pseudoenergy function to evaluate amino acid substitution (from Proteins 86:218). The figure below on the right shows the expected time dependence of duplicate gene retention as mutations accumulate and selection acts according to combinations of different processes (neofunctionalization plus dosage constraints in A, subfunctionalization plus dosage constraints in B, from BMC EB 16:45).