ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics. - Siddharth Viswanath; Dhananjay Bhaskar; David R. Johnson; João F. Rocha; Egbert Castro; Jackson D. Grady; Alex T. Grigas; Michael A. Perlmutter; Corey S. O'Hern; Smita Krishnaswamy (CoRR, 2024)

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics. - Xingzhi Sun 003; Charles Xu 004; João F. Rocha; Chen Liu 020; Benjamin Hollander-Bodie; Laney Goldman; Marcello DiStasio; Michael Perlmutter; Smita Krishnaswamy (ICASSP, 2025)

HEIST: A Graph Foundation Model for Spatial Transcriptomics and Proteomics Data. - Hiren Madhu; João F. Rocha; Tinglin Huang; Siddharth Viswanath; Smita Krishnaswamy; Rex Ying (CoRR, 2025)

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics. - João F. Rocha; Ke Xu 010; Xingzhi Sun 003; Ananya Krishna; Dhananjay Bhaskar; Blanche Mongeon; Morgan Craig; Mark Gerstein; Smita Krishnaswamy (CoRR, 2025)