CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes. - Victoria R. Li; Zijun Zhang 004; Olga G. Troyanskaya (Bioinform., 2021)

An automated framework for efficiently designing deep convolutional neural networks in genomics. - Zijun Zhang 004; Christopher Y. Park; Chandra L. Theesfeld; Olga G. Troyanskaya (Nat. Mach. Intell., 2021)

Interpretable neural architecture search and transfer learning for understanding sequence dependent enzymatic reactions. - Zijun Zhang 004; Adam R. Lamson; Michael J. Shelley; Olga G. Troyanskaya (CoRR, 2023)

Interpretable neural architecture search and transfer learning for understanding CRISPR-Cas9 off-target enzymatic reactions. - Zijun Zhang 004; Adam R. Lamson; Michael J. Shelley; Olga G. Troyanskaya (Nat. Comput. Sci., 2023)

A disease-specific language model for variant pathogenicity in cardiac and regulatory genomics. - Huixin Zhan; Jason H. Moore; Zijun Zhang 004 (Nat. Mac. Intell., 2025)