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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. Nature Medicine. 2024. 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 WX, Liu Q, Zitnik M. Efficient generation of protein pockets with PocketGen. Nature Machine Intelligence. 2024. doi: 10.1038/s42256-024-00920-9

Gao S, Fang A, Huang Y, Giunchiglia V, Noori A, Schwarz JR, Ektefaie Y, Kondic J, Zitnik M. Empowering biomedical discovery with AI agents. Cell. 2024. doi: 10.1016/j.cell.2024.09.022

Johnson R, Gottlieb U, Shaham G, Eisen L, Waxman J, Devons-Sberro S, Ginder CR, Hong P, Sayeed R, Reis BY, Balicer RD, Dagan N, Zitnik M. Unified Clinical Vocabulary Embeddings for Advancing Precision. medRxiv. 2024. doi: 10.1101/2024.12.03.24318322v2

Su X, Wang Y, Gao S, Liu X, Giunchiglia V, Clevert DA, Zitnik M. KGARevion. GitHub. 2025.

Gao S, Zhu R, Kong Z, Noori A, Su X, Ginder C, Tsiligkaridis T, Zitnik M. TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools. GitHub. 2025.

Su X, Wang Y, Gao S, Liu X, Giunchiglia V, Clevert DA, Zitnik M. KGARevion: An AI Agent for Knowledge-Intensive Biomedical QA. International Conference on Learning Representations, ICLR. 2025.

Gao S, Zhu R, Kong Z, Noori A, Su X, Ginder C, Tsiligkaridis T, Zitnik M. TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools. arXiv. 2025. doi: 10.48550/arXiv.2503.10970

Johnson R, Gottlieb U, Shaham G, Eisen L, Waxman J, Devons-Sberro S, Ginder CR, Hong P, Sayeed R, Su X, Reis BY, Balicer RD, Dagan N, Zitnik M. ClinVec: Unified Embeddings of Clinical Codes Enable Knowledge-Grounded AI in Medicine. medRxiv. 2024. doi: 10.1101/2024.12.03.24318322

Li MM, Li K, Ektefaie Y, Jin Y, Huang Y, Messica S, Cai T, Zitnik M. Controllable Sequence Editing for Biological and Clinical Trajectories. arXiv. 2025. doi: 10.48550/arXiv.2502.03569

Li MM, Reis BY, Rodman A, Cai T, Dagan N, Balicer RD, Loscalzo J, Kohane IS, Zitnik M. One Patient, Many Contexts: Scaling Medical AI Through Contextual Intelligence. arXiv. 2025.

Su X, Messica S, Huang Y, Johnson R, Fesser L, Gao S, Sahneh F, Zitnik M. Multimodal medical code tokenizer. arXiv. 2025. doi: 10.48550/arXiv.2502.04397

Huang Y, Su X, Ullanat V, Liang I, Clegg L, Olabode D, Ho N, John B, Gibbs M, Zitnik M. Multimodal AI predicts clinical outcomes of drug combinations from preclinical data. arXiv. 2025. doi: 10.48550/arXiv.2503.02781