Doyne began his academic career doing research in dynamical systems theory, and particularly chaotic dynamics, as part of the UCSC Dynamical Systems Collective. He then worked at Los Alamos for ten years, where he was an Oppenheimer Fellow at the Center for Nonlinear Studies and founded the Complex Systems Group in the Theoretical Division. While at Los Alamos he did research on nonlinear time series prediction, artificial life, and theoretical biology. In 1991 he co-founded Prediction Company, a Santa Fe firm that does automatic trading of stocks using mathematical methods. He is currently the McKinsey Professor at the Santa Fe Institute, where he studies economics and financial markets.