To adapt their physiology to gradual and sudden changes occurring in the host environment or during inter-individual transmissions, commensals exhibit remarkable genetic variation diversity at a population level. I am interested in the genetic variations of gut microbes and how the variations are beneficial for their effective colonization and successful survival. I am developing tools and mining genetic variations from isolate genomes and metagenomic data.
Single nucleotide variation
I am working with long-dense longitudinal metagenomic data to identify the SNVs that differentiated strains of same species to track strain-levels dynamics in microbiome.
I am particularly interested in DNA inversion and how these inversions generate hybrid proteins, shuffling domains between genes and rearranging operon structure.
Mobile genetic elements
I developed a Split Read Insertion Detection (SRID) method to detect mobile genetic elements in the microbiome and created ImmeDB, a database dedicated to the collection, classification, and annotation of mobile genetic elements (MGEs) from gut microbiome.