Li MM, Huang Y, Sumathipala M, Liang MQ, Valdeolivas A, Ananthakrishnan A, Liao K, Marbach D, Zitnik M. Contextual AI models for single-cell protein biology. GitHub. 2024

Su X, Wang Y, Gao S, Liu X, Guinchiglia V, Clevert DA, Zitnik M. Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine. arXiv. 2024. doi: doi.org/10.48550/arXiv.2410.04660

Huang K, Chandak P, Wang Q, Havaldar S, Vaid A, Leskovec J, Nadkarni G, Glicksberg BS, Gehlenborg N, Zitnik M. A foundation model for clinician-centered drug repurposing. 2024. Nature Medicine. doi: 10.1038/s41591-024-03233-x

Lin MM, Huang Y, Sumathipala M, Liang MQ, Valdeolivas A, Ananthakrishnan AN, Liao K, Marbach D, Zitnik M. Contextual AI models for single-cell protein biology. Nature Methods. 2024. doi:10.1038/s41592-024-02341-3

Zhang, Z., Shen, W.X., Liu, Q. et al. Efficient generation of protein pockets with PocketGen. Nat Mach Intell6, 1382–1395 (2024). https://doi.org/10.1038/s42256-024-00920-9

Queen O, Huang Y, Calef R, Giunchiglia V, Chen T, Dasoulas G, Tai L, Ektefaie Y, Noori A, Brown J, Cobley T, Hrovatin K, Hartvigsen T, Theis FJ, Pentelute B, Khurana V,Kellis, Zitnik M. ProCyon: A multimodal foundation model for protein phenotypes. bioRxiv. 2024. doi:10.1101/2024.12.10.627665