ProFunc: a server for predicting protein function from 3D structure. - Roman A. Laskowski; James D. Watson; Janet M. Thornton (Nucleic Acids Res., 2005)

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale. - Jason W. Bohland; Caizhi Wu; Helen Barbas; Hemant Bokil; Mihail Bota; Hans C. Breiter; Hollis T. Cline; John C. Doyle 001; Peter J. Freed; Ralph J. Greenspan; Suzanne N. Haber; Michael Hawrylycz; et al. (PLoS Comput. Biol., 2009)

Computational complexity of the ground state energy density problem. - James D. Watson; Toby S. Cubitt (STOC, 2022)

The Complexity of Translationally Invariant Problems Beyond Ground State Energies. - James D. Watson; Johannes Bausch; Sevag Gharibian (STACS, 2023)

Exponentially Reduced Circuit Depths Using Trotter Error Mitigation. - James D. Watson; Jacob Watkins (CoRR, 2024)

Polynomial-Time Classical Simulation of Noisy IQP Circuits with Constant Depth. - Joel Rajakumar; James D. Watson; Yi-Kai Liu 001 (SODA, 2025)