Evolution of Molecular Complexity
Our computational lab explores the evolution of molecular complexity, focusing on the organization of interconnected systems such as protein complexes, metabolic networks, and transcriptional units. We address two fundamental trajectories: how complexity emerges from simpler origins through the incremental integration of individual units, and how it is reduced through the loss of components in specialized lineages, such as parasites. To decode these processes, we integrate comparative genomics, structural biology, and metabolism.
We ask a series of fundamental questions at the interface of biochemistry, genomics, and evolutionary biology. These questions are all centered around the origin and evolution of complex biological systems composed of interconnected building blocks. We study three types of systems:
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(1) Protein complexes: protein subunits are building blocks; connected through direct physical association.
(2) Genome architecture, genes are building blocks; linearly connected through DNA continuity.
(3) Metabolic networks, enzymes are building blocks; connected through sequences of chemical reactions.
For each of these systems, we investigate the evolutionary origins of its building blocks and their connectivity. As such, we study how present-day complex systems originated from simpler beginnings in the deep past. We also study the reverse process: how ancestral complex systems were simplified in parasites and endosymbionts through reductive evolution. We pursue these questions using a combination of carefully selected model systems and computational frameworks.​​​​
To study these phenomena, on one hand, we employ phylogenetic methods to reconstruct the evolutionary history of gene gain, loss, fission, fusion, duplication, and miniaturization events. We integrate the phylogenetic data with biochemical properties of these systems.