His research is primarily focused on construction of genetic networks that include but are not limited to collaborative networks, coexpression networks and multi-layered hierarchical gene regulatory networks. He proposed the concept of collaborative networks and then developed multiple algorithms to construct and then decompose the collaborative network into subnetworks from which regulatory genes that control a biological process or complex trait can be identified. In addition, his group has developed multiple algorithms to construct a multi-layered hierarchical gene regulatory network operating above a biological process or pathway, from which the critical hierarchical regulators can be identified.