Unsupervised embedding of single-cell Hi-C data. - Jie Liu 045; Dejun Lin; Galip Gürkan Yardimci; William Stafford Noble (Bioinform., 2018)

HiCRep.py: fast comparison of Hi-C contact matrices in Python. - Dejun Lin; Justin Sanders; William Stafford Noble (Bioinform., 2021)

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)

Optimizing Data Distribution and Kernel Performance for Efficient Training of Chemistry Foundation Models: A Case Study with MACE. - Jesun Firoz; Franco Pellegrini; Mario Geiger; Darren Hsu; Jenna A. Bilbrey; Han-Yi Chou; Maximilian Stadler; Markus Hoehnerbach; Tingyu Wang; Dejun Lin; Emine Küçükbenli; Henry W. Sprueill; et al. (CoRR, 2025)