SOMDE: a scalable method for identifying spatially variable genes with self-organizing map. - Minsheng Hao; Kui Hua; Xuegong Zhang (Bioinform., 2021)

xTrimoGene: An Efficient and Scalable Representation Learner for Single-Cell RNA-Seq Data. - Jing Gong; Minsheng Hao; Xingyi Cheng; Xin Zeng; Chiming Liu; Jianzhu Ma; Xuegong Zhang; Taifeng Wang; Le Song (NeurIPS, 2023)

Decoding functional cell-cell communication events by multi-view graph learning on spatial transcriptomics. - Haochen Li 003; Tianxing Ma; Minsheng Hao; Wenbo Guo 010; Jin Gu; Xuegong Zhang; Lei Wei (Briefings Bioinform., 2023)

scMulan: A Multitask Generative Pre-Trained Language Model for Single-Cell Analysis. - Haiyang Bian; Yixin Chen; Xiaomin Dong; Chen Li 001; Minsheng Hao; Sijie Chen; Jinyi Hu; Maosong Sun 001; Lei Wei; Xuegong Zhang (RECOMB, 2024)

MMA-RNN: A multi-level multi-task attention-based recurrent neural network for discrimination and localization of atrial fibrillation. - Yifan Sun 010; Jingyan Shen; Yunfan Jiang 002; Zhaohui Huang; Minsheng Hao; Xuegong Zhang (Biomed. Signal Process. Control., 2024)

scDiffusion: conditional generation of high-quality single-cell data using diffusion model. - Erpai Luo; Minsheng Hao; Lei Wei; Xuegong Zhang (CoRR, 2024)

QueST: Querying Functional and Structural Niches on Spatial Transcriptomics Data via Contrastive Subgraph Embedding. - Mo Chen; Minsheng Hao; Xuegong Zhang; Lei Wei (CoRR, 2024)

Current opinions on large cellular models. - Minsheng Hao; Lei Wei; Fan Yang 081; Jianhua Yao 001; Christina V. Theodoris; Bo Wang 044; Xin Li; Ge Yang 002; Xuegong Zhang (Quant. Biol., 2024)

Learning Multi-cellular Representations of Single-Cell Transcriptomics Data Enables Characterization of Patient-Level Disease States. - Tianyu Liu 001; Edward De Brouwer; Tony Kuo; Nathaniel Diamant; Alsu Missarova; Hanchen Wang 002; Minsheng Hao; Héctor Corrada Bravo; Gabriele Scalia; Aviv Regev; Graham Heimberg (RECOMB, 2025)

Towards Artificial Intelligence Research Assistant for Expert-Involved Learning. - Tianyu Liu 001; Simeng Han; Xiao Luo 001; Hanchen Wang 002; Pan Lu; Biqing Zhu; Yuge Wang; Keyi Li; Jiapeng Chen; Rihao Qu; Yufeng Liu; Xinyue Cui; et al. (CoRR, 2025)