Quantitative Biology / Gene Expression in Development & Disease Seminar

Friday, 11 January 2013 at 11:30am

Room 1400 Biomedical and Physical Sciences Bldg.

Refreshments at 11:15

Speaker:  David A. Liberles, Department of Molecular Biology, University of Wyoming

Title:  Computational Approaches for Linking Comparative Genomics to Biochemistry and Evolution

Standard bioinformatics pipelines for the comparative genomic data analysis of protein-encoding gene families typically include steps like multiple sequence alignment, phylogenetic tree reconstruction, calculation of the ratio of rates of nonsynonymous to synonymous nucleotide substitution (dN/dS), and gene tree-species tree reconciliation. Models for amino acid substitution used in these processes assume that each site evolves independently according to average properties in the absence of a protein structural or functional context. Models for duplicate gene retention assume that the process is evolutionarily neutral and do not consider functional or mechanistic underpinnings. A model for duplicate gene retention that would allow for mechanistic differentiation between nonfunctionalization, neofunctionalization, subfunctionalization, and dosage balance based upon differences in expected time-dependent retention profiles is presented. Two characterizations of amino acid substitution are also presented. One approach extends a population genetic model to inter-specific genomic data and a second approach evaluates the effects of selection for protein folding and protein-protein interaction on sequence evolution. These approaches reflect an in progress strategy for increasing biochemical and evolutionary realism in bioinformatics.