Gao's research lies at the intersection between computer science and biology. His work has two main focuses: 1) developing theory and methodology in the fields of machine learning and algorithms; and 2) solving key open problems in biological and medical fields through building computational models, developing machine-learning techniques, and designing effective and efficient algorithms. In particular, he aims to solve problems that occur along the path from protein amino acid sequences to their three-dimensional structures and functions that ultimately lead to their undesirable expression in complex biological networks.