Feature Selection Methods for Improving Protein Structure Prediction with Rosetta. - Ben Blum; Michael I. Jordan; David E. Kim; Rhiju Das; Philip Bradley; David Baker 001 (NIPS, 2007)

How do amino acid mismatches affect the outcome of hematopoietic cell transplants?: a structural perspective. - Chen Yanover; Mari Malkki; Ted Gooley; Effie W. Petersdorf; Philip Bradley (BCB, 2010)

Rational design of α-helical tandem repeat proteins with closed architectures. - Lindsey Doyle; Jazmine Hallinan; Jill Bolduc; Fabio Parmeggiani; David Baker 001; Barry L. Stoddard; Philip Bradley (Nat., 2015)

Better together: Elements of successful scientific software development in a distributed collaborative community. - Julia Koehler Leman; Brian D. Weitzner; P. Douglas Renfrew; Steven M. Lewis; Rocco Moretti; Andrew M. Watkins; Vikram Khipple Mulligan; Sergey Lyskov; Jared Adolf-Bryfogle; Jason W. Labonte; Justyna Krys; RosettaCommons Consortium; et al. (PLoS Comput. Biol., 2020)

Learning the shape of protein micro-environments with a holographic convolutional neural network. - Michael N. Pun; Andrew Ivanov; Quinn Bellamy; Zachary Montague; Colin H. LaMont; Philip Bradley; Jakub Otwinowski; Armita Nourmohammad (CoRR, 2022)

Comparing T cell receptor repertoires using optimal transport. - Branden J. Olson; Stefan A. Schattgen; Paul G. Thomas; Philip Bradley; Frederick A. Matsen IV (PLoS Comput. Biol., 2022)

Neural network models for sequence-based TCR and HLA association prediction. - Si Liu; Philip Bradley; Wei Sun (PLoS Comput. Biol., 2023)

T-cell receptor specificity landscape revealed through de novo peptide design. - Gian Marco Visani; Michael N. Pun; Anastasia A. Minervina; Philip Bradley; Paul Thomas; Armita Nourmohammad (CoRR, 2025)