Our research combines comparative genomics and computational structural biology to address fundamental questions in molecular evolution, spanning genome dynamics, protein structure–function relationships, and lineage-specific adaptive diversification. We employ a diverse range of computational approaches to investigate various biological systems, guided by evolutionary logic and inference as a unifying framework.

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Guided by the principle that evolutionary thinking provides a powerful framework for interpreting molecular diversity and innovation, our work is grounded in the idea that nature—through billions of genetic experiments across evolutionary time—has continuously shaped a dynamic landscape of molecular evolution. Comparative and evolutionary genomics enable us to dissect this landscape and uncover fundamental principles, including divergence, constraint, convergence, and related forces that drive molecular innovation and functional diversification.

 

At the molecular level, we examine sequence–structure relationships across protein domains and families, trace lineage-specific gene expansions, and identify patterns of diversification that scale from molecular change to organismal adaptation and evolutionary novelty. These approaches enable us to uncover molecular strategies spanning prokaryotic defense systems against selfish genetic elements to major eukaryotic transitions driven by gene family expansions and whole-genome duplications. We are also broadly interested in the evolution of protein folds, exploring how their inherent evolutionary malleability facilitates functional adaptation, diversification, and repurposing across diverse biological contexts, and how such transitions can be systematically traced and predicted using computational frameworks.

 

Unified by a central interest in the evolution of molecular systems, our research themes apply evolutionary reasoning to understand how proteins and genomes diversify, adapt, and innovate across diverse biological contexts.

 

The following sections highlight the major research themes currently pursued in our group

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• Prokaryotic Defense Systems

• Lineage-Specific Expansions (LSEs) of Gene Families in Metazoans

• Genome Sequencing of Invertebrates to Study the LSEs and Other Adaptive Diversifications

• Comparative Genomics of Lipid-Binding GPCRs: Evolution, Specificity, and Human Variation

• Adaptive Evolution of Diverse Protein Folds and Domains and Their Functional Diversification in Prokaryotes