The Flamio Lab investigates how vertebrate immune systems detect and respond to microorganisms. We study the evolution, regulation, and function of innate immune pathways using comparative genomics, transcriptomics, microbiology, and computational biology.

Our research focuses on how immune receptors and their regulatory elements evolve across vertebrates, with particular interest in gene architecture, transcript isoforms, untranslated regions (UTRs), and noncoding RNAs that shape immune signaling. We use Toll-like receptor (TLR) pathways as model systems to understand how conserved mechanisms of microbial recognition diversify across evolutionary time.

Our work integrates genome assembly, full-length transcriptomics, comparative immunogenomics, and microbial genomics to investigate host–microbe interactions in model and non-model vertebrates, including conservation-relevant fish species. We also apply these approaches to selected human inflammatory disease datasets to identify conserved mechanisms underlying immune regulation and dysfunction.

Through this research, we aim to uncover general principles governing innate immunity and immune evolution while training students in genomics, bioinformatics, microbiology, and reproducible computational biology.