Yan’s expertise lies in comparative genomics, co-evolution, divergence time estimation, and horizontal gene transfer (HGT) in the field of fungal evolution. He applied molecular phylogenetic methods to help establish a new fungal genus Zancudomyces and reconstruct ancestral state characters to assist the delimitation of one cosmopolitan taxonomic group Smittium. He used state-of-the-art genomic methods to identify an inter-kingdom HGT event of the polyubiquitin coding gene from the mosquito host to its gut fungal symbiont. His comparative genomic study between insect fungal pathogens and commensals leads to the finding of a general fungus-insect symbiotic core-gene toolbox.
As a postdoc, Yan is involved in two collaborative projects focusing on the early-diverging fungi—the Zygomycetes Genealogy of Life (http://zygolife.org/) and the Phylogenomics of the anaerobic gut fungi (Neocallimastigomycota). He is responsible for the divergence time estimation of these fungal groups using genome-wide data with calibration of multiple fossil records. In addition, he uses comparative method to analyze the protein family enrichment patterns of over 100 fungal genome sequences and identify unique enzymes in certain clades to explain their autapomorphic characters.