Unsupervised manifold alignment for single-cell multi-omics data. - Ritambhara Singh; Pinar Demetci; Giancarlo Bonora; Vijay Ramani; Choli Lee; He Fang; Zhi-jun Duan; Xinxian Deng; Jay Shendure; Christine Disteche; William Stafford Noble (BCB, 2020)

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. - Hyeon-Jin Kim; Galip Gürkan Yardimci; Giancarlo Bonora; Vijay Ramani; Jie Liu 045; Ruolan Qiu; Choli Lee; Jennifer Hesson; Carol B. Ware; Jay Shendure; Zhi-jun Duan; William Stafford Noble (PLoS Comput. Biol., 2020)

ACE: Explaining cluster from an adversarial perspective. - Yang Young Lu; Timothy C. Yu; Giancarlo Bonora; William Stafford Noble (ICML, 2021)