TDC

Velez-Arce A, Lin X, Li MM, Huang K, Gao W, Fu T, Pentelute BL, Kellis M, Zitnik M. Therapeutics Data Commons. GitHub. 2024.

ProCyon: A Multimodal Foundation Model for Protein Phenotypes

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 M, Zitnik M. ProCyon: A multimodal foundation model for protein phenotypes. bioRxiv. 2024. doi:10.1101/2024.12.10.627665

Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics

Velez-Arce A, Lin X, Li MM, Huang K, Gao W, Fu T, Pentelute BL, Kellis M, Zitnik M. Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics. NeurIPS AIDrugX. 2024.

Generalizable AI Predicts Immunotherapy Outcomes Across Cancers and Treatments

Shen W, Nguyen TH, Li MM, Huang Y, Moon I, Nair N, Marbach D, Zitnik M. Generalizable AI predicts immunotherapy outcomes across cancers and treatments. medRxiv. 2025.

SPATIA: Multimodal Model for Prediction and Generation of Spatial Cell Phenotypes

Kong Z, Qiu M, Boesen J, Lin X, Yun S, Chen T, Kellis M, Zitnik M. SPATIA: Multimodal Model for Prediction and Generation of Spatial Cell Phenotypes. arXiv. 2025.

Learning Universal Representations of Intermolecular Interactions with ATOMICA

Fang A, Desgagné M, Zhang Z, Zhou A, Loscalzo J, Pentelute, BL, Zitnik M. Learning Universal Representations of Intermolecular Interactions with ATOMICA. bioRxiv. 2025. doi: 10.1101/2025.04.02.646906