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)

MDEntropy: Information-Theoretic Analyses for Molecular Dynamics. - Carlos X. Hernández; Vijay S. Pande (J. Open Source Softw., 2017)

Using Deep Learning for Segmentation and Counting within Microscopy Data. - Carlos X. Hernández; Mohammad M. Sultan; Vijay S. Pande (CoRR, 2018)