He is the founding president of the New England Complex Systems Institute (NECSI), an independent research institution that studies complex systems science and its real-world applications.
Bar-Yam studies the unified properties of complex systems as a systematic strategy for answering basic questions about the world. His research is focused both on formalizing complex systems concepts and relating them to everyday problems. In particular, he studies the relationship between observations at different scales, formal properties of descriptions of systems, the relationship of structure and function, the representation of information as a physical quantity, and quantitative properties of the complexity of real systems.