Interpretability analysis on a pathology foundation model reveals biologically relevant embeddings across modalities. - Le, Nhat; Shen, Ciyue; Shah, Chintan; Martin, Blake; Shenker, Daniel; Padigela, Harshith; Hipp, Jennifer A.; Grullon, Sean; Abel, John; Pokkalla, Harsha; Juyal, Dinkar (CoRR, 2024)

Inference of cell dynamics on perturbation data using adjoint sensitivity. - Ji, Weiqi; Yuan, Bo; Shen, Ciyue; Regev, Aviv; Sander, Chris; Deng, Sili (CoRR, 2021)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah; Shapira, Ofer; Tiao, Grace; Hornshøj, Henrik; Hess, Julian M.; Juul, Randi Istrup; Lin, Ziao; Feuerbach, Lars; Sabarinathan, Radhakrishnan; et al. (Nat., 2020)