Unsupervised embedding of single-cell Hi-C data. - Jie Liu 045; Dejun Lin; Galip Gürkan Yardimci; William Stafford Noble (Bioinform., 2018)

Jointly Embedding Multiple Single-Cell Omics Measurements. - Jie Liu 045; Yuanhao Huang; Ritambhara Singh; Jean-Philippe Vert; William Stafford Noble (WABI, 2019)

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)

scHiCTools: A computational toolbox for analyzing single-cell Hi-C data. - Xinjun Li; Fan Feng; Hongxi Pu; Wai Yan Leung; Jie Liu 045 (PLoS Comput. Biol., 2021)

NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps. - Yuanhao Huang; Bingjiang Wang; Jie Liu 045 (PLoS Comput. Biol., 2022)

Characterizing collaborative transcription regulation with a graph-based deep learning approach. - Zhenhao Zhang; Fan Feng; Jie Liu 045 (PLoS Comput. Biol., 2022)

GenomicKB: a knowledge graph for the human genome. - Fan Feng; Feitong Tang; Yijia Gao; Dongyu Zhu; Tianjun Li; Shuyuan Yang 006; Yuan Yao; Yuanhao Huang; Jie Liu 045 (Nucleic Acids Res., 2023)

CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images. - Yicheng Tao 002; Fan Feng; Xin Luo; Conrad V. Reihsmann; Alexander L. Hopkirk; Jean-Philippe Cartailler; Marcela Brissova; Stephen C. J. Parker; Diane C. Saunders; Jie Liu 045 (PLoS Comput. Biol., 2024)