Osprey: Hyperparameter Optimization for Machine Learning. - Robert T. McGibbon; Carlos X. Hernández; Matthew P. Harrigan; Steven Kearnes; Mohammad M. Sultan; Stanislaw Jastrzebski; Brooke E. Husic; Vijay S. Pande (J. Open Source Softw., 2016)

MSMExplorer: Data Visualizations for Biomolecular Dynamics. - Carlos X. Hernández; Matthew P. Harrigan; Mohammad M. Sultan; Vijay S. Pande (J. Open Source Softw., 2017)

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. - Peter K. Eastman; Jason M. Swails; John D. Chodera; Robert McGibbon; Yutong Zhao; Kyle Beauchamp; Lee-Ping Wang; Andrew C. Simmonett; Matthew P. Harrigan; Chaya D. Stern; Rafal P. Wiewiora; Bernard R. Brooks; et al. (PLoS Comput. Biol., 2017)

Expressing and Analyzing Quantum Algorithms with Qualtran. - Matthew P. Harrigan; Tanuj Khattar; Charles Yuan; Anurudh Peduri; Noureldin Yosri; Fionn D. Malone; Ryan Babbush; Nicholas C. Rubin (CoRR, 2024)