His research deals with complex systems and anthropology, focusing on two topics. The first has to do with the role of Balinese water temple networks in the management of the island's rice terrace ecology, the subject of his books Priests and Programmers: Technologies of Power in the Engineered Landscape of Bali (1991; revised edition 2007) and  Perfect Order: Recognizing Complexity in Bali (2006).

In 2009, he helped the Government of Indonesia propose a new UNESCO World Heritage site to celebrate and protect the water temple system, with assistance from three graduate students at the Stockholm Resilience Centre (Anna Schmuki, Maria Fernanda Cedillo, Thomas Bergendorff).

A second project investigates the relationship between historical demography and the evolution of diseases in the Indonesian archipelago. The susceptibility of individuals to infectious disease is influenced by which genes they inherit and whether their ancestors underwent selection for resistant genotypes. The goal of this project is to elucidate the co-evolutionary history of humans and two infectious diseases, malaria and hepatitis B.

Using data from neutral genetic markers, historical linguistics, and archaeology for 68 villages on 13 islands, we reconstruct the history of village clusters. This provides the background for analysis of the evolutionary history of disease resistance markers. Because malaria and hepatitis differ in their patterns of transmission and response to environmental factors, studying both diseases in the same populations will help to clarify the diversity of host-parasite co-evolutionary dynamics.

This project continues an ongoing collaboration with the Eijkman Institute for Molecular Biology in Jakarta, which has overall responsibility for genetic research in Indonesia, and the Indonesian Public Health Service.