Understanding Protein Dynamics with L1-Regularized Reversible Hidden Markov Models. - Robert McGibbon; Bharath Ramsundar; Mohammad Sultan; Gert Kiss; Vijay S. Pande (ICML, 2014)

Theano: A Python framework for fast computation of mathematical expressions. - Rami Al-Rfou; Guillaume Alain; Amjad Almahairi; Christof Angermüller; Dzmitry Bahdanau; Nicolas Ballas; Frédéric Bastien; Justin Bayer; Anatoly Belikov; Alexander Belopolsky; Yoshua Bengio; Arnaud Bergeron; et al. (CoRR, 2016)

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)

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)

Efficient hyperparameter optimization by way of PAC-Bayes bound minimization. - John J. Cherian; Andrew G. Taube; Robert T. McGibbon; Panagiotis Angelikopoulos; Guy Blanc; Michael Snarski; Daniel D. Richman; John L. Klepeis; David E. Shaw (CoRR, 2020)

SOAP: A Python Package for Calculating the Properties of Galaxies and Halos Formed in Cosmological Simulations. - Robert McGibbon; John C. Helly; Joop Schaye; Matthieu Schaller; Bert Vandenbroucke (J. Open Source Softw., 2025)