THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. - Justin S. Diamond; Yang Zhang 040 (Database J. Biol. Databases Curation, 2018)

Improving Protein-peptide Interface Predictions in the Low Data Regime. - Justin S. Diamond; Markus A. Lill (CoRR, 2023)

Geometric Constraints in Probabilistic Manifolds: A Bridge from Molecular Dynamics to Structured Diffusion Processes. - Justin S. Diamond; Markus A. Lill (CoRR, 2023)

Neural SHAKE: Geometric Constraints in Graph Generative Models. - Justin S. Diamond; Markus A. Lill (ICANN (10), 2024)

Neural SHAKE: geometric constraints in neural differential equations. - Justin S. Diamond; Markus A. Lill (J. Cheminformatics, 2025)