João F. Rocha

According to our database, João F. Rocha authored at least 6 papers between 2024 and 2026.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2026

scShapeBench: Discovering geometry from high dimensional scRNAseq data.

Andrew J. Steindl, João F. Rocha, Brian Tshilengi Di Bassinga, Zachary Warren, Matthew Scicluna, César Miguel Valdez Córdova, Shabarni Gupta, Leire Torices, Daniel Neumann, Timothy J. Mann, Ihuan Gunawan, Dhananjay Bhaskar, John G. Lock, Christine L. Chaffer, Guy Wolf, Smita Krishnaswamy

CoRR, May, 2026

MIOFlow 2.0: A unified framework for inferring cellular stochastic dynamics from single cell and spatial transcriptomics data.

Xingzhi Sun, João F. Rocha, Brett Phelan, Dhananjay Bhaskar, Guillaume Huguet, Yanlei Zhang, Daniel Sumner Magruder, Alexander Tong, Ke Xu, Oluwadamilola Fasina, Mark Gerstein, Guy Wolf, Natalia Ivanova, Christine L. Chaffer, Smita Krishnaswamy

CoRR, March, 2026

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, June, 2025

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics.

João F. Rocha, Ke Xu, Xingzhi Sun, Ananya Krishna, Dhananjay Bhaskar, Blanche Mongeon, Morgan Craig, Mark Gerstein, Smita Krishnaswamy

Proceedings of the 20th Machine Learning in Computational Biology (MLCB), 2025

Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics.

Xingzhi Sun, Charles Xu, João F. Rocha, Chen Liu, Benjamin Hollander-Bodie, Laney Goldman, Marcello DiStasio, Michael Perlmutter, Smita Krishnaswamy

Proceedings of the 2025 IEEE International Conference on Acoustics, 2025

2024

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