Dr. Yu led his group to develop the concept of “3D structurally-resolved interactome networks”, where they integrate multi-scale structural modeling, machine learning, and high-throughput genomics/proteomics experiments to determine protein interactions/complexes and their structures and dynamics on the whole proteome scale. The Yu group has established many cutting-edge experimental methodologies in structural proteomics, cross-linking mass spectrometry, and quantitative proteomics, and built innovative analysis pipelines using machine learning (deep learning) and rigorous statistical models in these areas.