Manifold denoising by Nonlinear Robust Principal Component Analysis. - He Lyu; Ningyu Sha; Shuyang Qin; Ming Yan 006; Yuying Xie 001; Rongrong Wang (NeurIPS, 2019)

Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares. - Yuning Hao; Ming Yan 006; Blake R. Heath; Yu L. Lei; Yuying Xie 001 (PLoS Comput. Biol., 2019)

Graph Neural Networks for Multimodal Single-Cell Data Integration. - Hongzhi Wen; Jiayuan Ding; Wei Jin 009; Yiqi Wang 001; Yuying Xie 001; Jiliang Tang (KDD, 2022)

Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data. - Zhiqian Zhai; Yu L. Lei; Rongrong Wang; Yuying Xie 001 (Bioinform., 2022)

Graph Neural Networks for Multimodal Single-Cell Data Integration. - Hongzhi Wen; Jiayuan Ding; Wei Jin 009; Yuying Xie 001; Jiliang Tang (CoRR, 2022)

Single-Cell Multimodal Prediction via Transformers. - Wenzhuo Tang; Hongzhi Wen; Renming Liu; Jiayuan Ding; Wei Jin 009; Yuying Xie 001; Hui Liu 031; Jiliang Tang (CIKM, 2023)

Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation. - Hongzhi Wen; Wenzhuo Tang; Wei Jin 009; Jiayuan Ding; Renming Liu; Feng Shi; Yuying Xie 001; Jiliang Tang (CoRR, 2023)

CellPLM: Pre-training of Cell Language Model Beyond Single Cells. - Hongzhi Wen; Wenzhuo Tang; Xinnan Dai; Jiayuan Ding; Wei Jin 009; Yuying Xie 001; Jiliang Tang (ICLR, 2024)

Cross-Domain Graph Data Scaling: A Showcase with Diffusion Models. - Wenzhuo Tang; Haitao Mao; Danial Dervovic; Ivan Brugere; Saumitra Mishra; Yuying Xie 001; Jiliang Tang (CoRR, 2024)

SpatialCTD: A Large-Scale Tumor Microenvironment Spatial Transcriptomic Dataset to Evaluate Cell Type Deconvolution for Immuno-Oncology. - Jiayuan Ding; Lingxiao Li; Qiaolin Lu; Julian Venegas; Yixin Wang 003; Lidan Wu; Wei Jin 009; Hongzhi Wen; Renming Liu; Wenzhuo Tang; Xinnan Dai; Zhaoheng Li; et al. (J. Comput. Biol., 2024)

Clustering and visualization of single-cell RNA-seq data using path metrics. - Andriana Manousidaki; Anna Little; Yuying Xie 001 (PLoS Comput. Biol., 2024)

Deep Learning in Single-cell Analysis. - Dylan Molho; Jiayuan Ding; Wenzhuo Tang; Zhaoheng Li; Hongzhi Wen; Yixin Wang 003; Julian Venegas; Wei Jin 009; Renming Liu; Runze Su; Patrick Danaher; Robert Yang; et al. (ACM Trans. Intell. Syst. Technol., 2024)