signac: Data Management and Workflows for Computational Researchers. - Bradley D. Dice; Brandon L. Butler; Vyas Ramasubramani; Alyssa Travitz; Michael M. Henry; Hardik Ojha; Kelly L. Wang; Carl S. Adorf; Eric Jankowski; Sharon C. Glotzer (SciPy, 2021)

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. - Peter K. Eastman; Raimondas Galvelis; Raúl P. Peláez; Charlles R. A. Abreu; Stephen E. Farr; Emilio Gallicchio; Anton Gorenko; Michael M. Henry; Frank Hu; Jing Huang 004; Andreas Krämer; Julien Michel; et al. (CoRR, 2023)

Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations. - Benjamin Ries; Richard J. Gowers; Hannah M. Baumann; David W. H. Swenson; Michael M. Henry; James R. B. Eastwood; Irfan Alibay; David L. Mobley (J. Chem. Inf. Model., 2024)