For billions of years, nature has been conducting the greatest experiment of all time. Imagine one-day gaining access to the detailed notes from these experiments. Today, with worldwide expeditions to collect samples from all habitats, single-cell sequencing of unculturable microbes and the rapid drop in sequencing costs, we can finally tap into nature and gain access to these notes.
Making use of this data, our lab is interested in:
(1) Developing a unified statistical model of protein evolution that integrates phylogenetics, genomic, structural, and functional constraints.
(2) Explicit modeling of the protein conformational (and/or folding) landscape for protein structure prediction and design.
(image credit Basile Wicky)
(3) Applying the models to mine metagenomic “dark matter” sequences to discover new protein families, functions, and protein-protein interactions. Probing evolution of multicellularity through comparison of structures and interactions in the early tree of life.