Joe's research touches on a variety of research areas in community ecology, including invasion ecology, biogeography and spatial statistics. He has a particular interest in practical questions regarding invasive species control and management to protect threatened species.

He also works on theoretical questions regarding coexistence in fluctuating environments and the determinants of community assembly in terrestrial and aquatic ecosystems. He is involved in three NERP projects along with NERP Researcher Prof Hugh Possingham: