His research focuses on developing new algorithms and mathematical methods in biophysics, nanotechnology, and informatics. His research projects include computational methods for modeling solvation in biomolecular systems, mathematical methods for mesoscale materials modeling, and development of methods for signature discovery. His research has been funded by the National Institutes of Health, U.S. Department of Energy, and National Science Foundation. Dr. Baker has served as co-principal investigator and project manager for the DOE Advanced Scientific Computing Research CM4: Collaboratory on Mathematics for Mesoscopic Modeling of Materials and as lead for the Signature Discovery Initiative at PNNL. He also managed the Applied Statistics and Computational Modeling Group at PNNL from 2013 to 2015, which comprised approximately 50 staff with expertise in statistics, mathematics, and operations research. Dr. Baker has served on review panels for various agencies, including as a member of the NIH Macromolecular Structure and Function D study section. He currently is an editorial board member for Biophysical Journal and serves on the editorial board for NPG Scientific Data. Dr. Baker previously served as associate editor for Biophysical Journal, editor-in-chief for Computational Science and Discovery, and section editor for Annual Reports in Computational Chemistry. He has authored more than 100 peer-reviewed publications.