Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook. - Sizhe Qiu; Aidong Yang; Hong Zeng 003 (PLoS Comput. Biol., 2023)

DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates. - Sizhe Qiu; Simiao Zhao; Aidong Yang (Briefings Bioinform., 2024)

Inferred regulons are consistent with regulator binding sequences in E. coli. - Sizhe Qiu; Xinlong Wan; Yueshan Liang; Cameron R. Lamoureux; Amir Akbari; Bernhard O. Palsson; Daniel C. Zielinski (PLoS Comput. Biol., 2024)

Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature. - Sizhe Qiu; Bozhen Hu; Jing Zhao; Weiren Xu; Aidong Yang (Briefings Bioinform., 2025)