PB-AM: An open-source, fully analytical linear poisson-boltzmann solver. - Lisa E. Felberg; David H. Brookes; Eng-Hui Yap; Elizabeth Jurrus; Nathan A. Baker; Teresa Head-Gordon (J. Comput. Chem., 2017)

Design by adaptive sampling. - David H. Brookes; Jennifer Listgarten (CoRR, 2018)

Conditioning by adaptive sampling for robust design. - David H. Brookes; Hahnbeom Park; Jennifer Listgarten (ICML, 2019)

A view of estimation of distribution algorithms through the lens of expectation-maximization. - David H. Brookes; Akosua Busia; Clara Fannjiang; Kevin Murphy 002; Jennifer Listgarten (GECCO Companion, 2020)

Beyond the training set: an intuitive method for detecting distribution shift in model-based optimization. - Farhan Damani; David H. Brookes; Theodore Sternlieb; Cameron Webster; Stephen Malina; Rishi Jajoo; Kathy Lin; Sam Sinai (CoRR, 2023)

Contrastive losses as generalized models of global epistasis. - David H. Brookes; Jakub Otwinowski; Sam Sinai (NeurIPS, 2024)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - Peter St. John; Dejun Lin; Polina Binder; Malcolm Greaves; Vega Shah; John St. John; Adrian Lange; Patrick D. Hsu; Rajesh Illango; Arvind Ramanathan; Anima Anandkumar; David H. Brookes; et al. (CoRR, 2024)