1994年3月于清华大学获模式识别与智能系统专业工学博士学位
1989年7月于清华大学获工业自动化专业工学学士学位
2018–2023 北京信息科学技术国家研究中心生物信息学部主任
2003–2018 清华信息科学与技术国家实验室（筹）生物信息学部主任
2002–今 清华大学自动化系 模式识别与生物信息学 教授
2002–今 清华大学生物信息学教育部重点实验室 副主任
2007.3-4 南加州大学分子与计算生物学系访问学者
2006.2-3 哈佛大学公共卫生学院访问科学家
2001–2002 哈佛大学公共卫生学院生物统计系高级访问学者
1999–2007 清华大学自动化系信息处理研究所 所长
1996–2002 清华大学自动化系 模式识别理论及应用 副教授
1994–1996 清华大学自动化系 讲师
中国人工智能学会常务理事、生物信息学与人工生命专委会名誉主任
中国自动化学会智能健康与生物信息专委会主任
中国生物工程学会常务理事
国际计算生物学学会副主席（ISCB Vice President）、ISCB中国理事会创始主席
Quantitative Biology共同主编
生命基础模型与数基生命系统
机器学习与生物医学大数据分析
单细胞生物信息学、人体细胞图谱与数字孪生
2024年当选ISCB Vice President（国际计算生物学学会副主席）
2022年获教育部高等学校科学研究优秀成果奖自然科学奖一等奖
2020年当选ISCB Fellow（国际计算生物学学会会士）
2020年当选中国人工智能学会会士
2017年成为国家自然科学基金创新群体负责人
2016年被评为全国优秀科技工作者
2009年获国家教学成果奖
2024
1. Chen Li#, Haoxiang Gao#, Yuli She#, Haiyang Bian, Qing Chen, Kai Liu*, Lei Wei*, Xuegong Zhang*, Benchmarking AI models for in silico gene preturbation of cells, bioRxiv, https://doi.org/10.1101/2024.12.20.629581, 2024
2. Najeebullah Shah, Qiuchen Meng, Ziheng Zou, Xuegong Zhang*, Bioinformatics Advances, 2024, 00, vbae 109, https://doi.org/10.1093/bioadv/vbae109, 2024
3. Chuxi Xiao#, Yixin Chen#, Qiuchen Meng, Lei Wei*, Xuegong Zhang, Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data, Briefings in Bioinformatics, 25(2): bbae095, https://doi.org/10.1093/bib/bbae095, 2024
4. Haochen Li#, Tianxing Ma#, Zetong Zhao#, Yixin Chen, Xi Xi, Xiaofei Zhao, Xiaoxiang Zhou, Yibo Gao, Lei Wei*, Xuegong Zhang, scTML: a pan-cancerl single-cell landscape of multiple mutation types, Nucleic Acids Research, https://doi.org/10.1093/nar/gkae898, 2024,
5. Haiyang Bian, Yixin Chen, Erpai Luo, Xinze Wu, Minsheng Hao, Lei Wei, Xuegong Zhang*, General-purpose pre-trained large cellular models for single-cell transcriptomics, National Science Review, 11: nwae340, 2024
6. Wenbo Guo, Xinqi Li, Dongfang Wang, Nan Yan, Qifan Hu, Fan Yang, Xuegong Zhang, Jin Gu*, scStateDynamics: deciphering the drug-responsive tumor cell state dynamics by modeling single-cell level expression changes, Genome Biology, 25: 297, 2024
7. Shihua Dou#, Zhuofeng Li#, Zhenbin Qiu#, Jing Zhang, Yaxi Chen, Shuyuan You, Mengmin Wang, Hongsheng Xie, Xiaoxiang Huang, Yun Yi Li, Jingjing Liu, Yuxin Wen, Jingshan Gong, Fanli Peng, Wenzhao Zhong*, Xuegong Zhang*, Lin Yang*, Improving prediction accuracy of spread through air spaces in clinical-stage T1N0 lung adenocarinoma using computed tomography imaging models, JTCVS Open, https://doi.org/10.1016/j.xjon.2024.07.018, 2024
8. Wenrui Li, Wei Zhang, Qinghao Zhang, Xuegong Zhang, Xiaowo Wang*, Weakly-supervised causal discovery based on fuzzy knowledge and complex data complementarity, IEEE Transactions on Fuzzy Systems, 32(12): 7002-7014, 2024
9. Erpai Luo#, Minsheng Hao#, Lei Wei, Xuegong Zhang*, scDiffusion: conditional generation of high-quality single-cell data using diffusion model, Bioinformatics, 40(9), btae518, 2024
10. Minsheng Hao, Lei Wei, Fan Yang, Jianhua Yao*, Christina V. Theodoris*, Bo Wang*, Xin Li*, Ge Yang*, Xuegong Zhang*, Current opinions on large cellular models, Quantitative Biology, 12:433-443, 2024
11. Minsheng Hao, Jing Gong, Xin Zeng, Chiming Liu, Yucheng Guo, Xingyi Cheng, Taifeng Wang, Jianzhu Ma*, Xuegong Zhang*, Le Song*, Large-scale foundation model on single-cell transcriptomics, Nature Methods, 21: 1481-1491, Aug. 2024
12. Rui Jiang, Xiaoxu Yin, Pengshuai Yang, Lingchao Cheng, Juan Hu, Jiao Yang, Ying Wang, Xiaodan Fu, Li Shang, Liling Li, Wei Lin, Huan Zhou, Fufeng Chen, Xuegong Zhang*, Zhongliang Hu*, Hairong Lv*, A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of giomas, Nature Machine Intelligence, 6: 876-891, 2024
13. Xinyue Chen, Yin Huang, Liangfeng Huang, Ziliang Huang, Zhao-Zhe Hao, Lahong Xu, Nana Xu, Zhi Li, Yonggao Mou, Mingli Ye, Renke You, Xuegong Zhang, Sheng Liu*, Zhichao Miao*, A brain cell atlas integrating single-cell transcriptomes across human brain regions, Nature Medicine, 2024 https://doi.org/10.1038/s41591-024-03150-z
14. Xue Bai, Sijie Chen, Xinxin Chi, Bowen Xie, Xinyi Guo, Han Feng, Peng Wei, Di Zhang, Shan Xie, Tian Xie, Yongzhen Chen, Mengting Gou, Qin Qiao, Xinwei Liu, Wei Jin, Wei Xu, Zixuan Zhao, Qi Xing, Xiaohu Wang, Xuegong Zhang, Chen Dong*, Reciprocal regulation of T follicular helper cells and dendritic cells drives colitis development, Nature Immunology, https://doi.org/10.1038/s41590-024-01882-1
15. Haiyang Bian#, Yixin Chen#, Xiaomin Dong#, Chen Li, Minsheng Hao, Sijie Chen, Jinyi Hu, Maosong Sun, Lei Wei*, Xuegong Zhang*, scMulan: a multitask generative pre-trained language model for single-cell analysis, in J. Ma (Ed.): RECOMB 2024, LNCS 14758, pp. 479-482, 2024
16. Minsheng Hao, Erpai Luo, Yixin Chen, Yanhong Wu, Chen Li, Sijie Chen, Haoxiang Gao, Haiyang Bian, Jin Gu, Lei Wei*, Xuegong Zhang*, STEM enables mapping of single-cell and spatial transcriptomics data with transfer learning, Communications Biology, 7:56, 2024
17. Haoxiang Gao#, Kui Hua#, Xinze Wu#, Lei Wei, Sijie Chen, Qijin Yin, Rui Jiang, Xuegong Zhang*, Building a learnable universal coordinate system for single-cell atlas with a joint-VAE model, Communications Biology, 7: 977, 2024
18. Tianyu Zhang, Chengbin Hou*, Rui Jiang, Xuegong Zhang, Chenghu Zhou, Ke Tang, Hairong Lv*, Label informed constrastive pretraining for node importance estimation on knowledge graphs, IEEE Transactions on Neural Networks and Machine Learning, in press, 2024
19. Tianxing Ma, Zetong Zhao, Haochen Li, Lei Wei, Xuegong Zhang*, NeoHunter: flexible software for systematically detecting neoantigens from sequencing data, Quantitative Biology, http://doi.org/10.1002/qub2.28, 2024
20. Yifan Sun, jingyan Shen, Yunfan Jiang, Zhaohuii Huang, Minsheng Hao, Xuegong Zhang*, MMA-RNN: a multi-level multi-task attention-based recurrent neural network for discrimination and localization of atrial fibrillation, Biomedical Signal Processing and Control, 89(2024): 105747, 2024
21. Qiuchen Meng, Lei Wei*, Kun Ma, Ming Shi, Xinyi Lin, Joshua W.K. Ho, Yinqing Li*, Xuegong Zhang, scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq, Briefings in Bioinformatics, 25(2): 1-10, 2024
22. Gan Liu#*, Qifan Hu#, Shuguang Peng#, Hui Ning#, Jiajia Mai, Xi Chen, Minzhen Tao, Qiang Liu, Huiya Huang, Yun Jiang, Yanhua Ding*, Xuegong Zhang*, Jin Gu*, Zhen Xie*, The spatial and single-cell analysis reveals remodeled immune miscroenvironment induced by synthetic oncolytic adenovirus treatment, Cancer Letters, 581: 216485, 2024
23. Jiachen Liu#, Jiaoyan Lv#, Sijie Chen#, Jie Ma#, Jiaying Yao#, Zan Yuan, Chunyuan Yang, Xiao Li, Xuegong Zhang*, Yunping Zhu*, Jianhong Zhang*, Li Wu*, Single-cell profiling highlight pathogenic myeloid features in house dust mite-induced murine model of airway inflammation, Allergy, 2024
24. Gan Liu*, Qifan Hu, Shuguang Peng, Hui Ning, Jiajia Mai, Xi Chen, Minzhen Tao, Qiang Liu, Huiya Huang, Yun Jiang, Yanhua Ding*, Xuegong Zhang*, Jin Gu*, Zhen Xie*, The spatial and single-cell analysis reveals remodeled immune microenvironment induced by synthetic oncolytic adenovirus treatment, Cancer Letters, 581: 216485, 2024
2023
25. Xuegong Zhang*, Lei Wei, Rui Jiang, Xiaowo Wang, Jin Gu, Zhen Xie, Hairong Lv, Building digital life systems for future biology and medicine, Quantitative Biology 11(3): 207-213, 2023
26. Zhan Wang#, Haiyang Bian#, Jiaqi Li, Jin Xu, Haining Fan, Xinze Wu, Yuntai Cao, Bin Guo, Xiaole Xu, Haiju Wang, Liangqiang Zhang, Hu Zhou, Jianfeng Fan, Youyou Ren, Yunping Geng, Xiaobin Feng, Luming Li, Lei Wei, Xuegong Zhang*, Detecting and subtyping of hepatic echinococcosis from plan CT images with deep learning: a retrospective, muticentre study, The Lancet Digit Health, 5(11): e754-e762, 2023
27. Haochen Li, Tianxing Ma, Minsheng Hao, Wenbo Guo, Jin Gu, Xuegong Zhang*, Lei Wei*, Decoding functinoal cell-cell communication events by multi-view graph learning on spatial transcriptomics, Briefings in Bioinformatics, 24(6): 1-13, 2023
28. Jing Gong#, Minsheng Hao#, Xingyi Cheng*, Xin Zeng, Chiming Liu, Jianzhu Ma, Xuegong Zhang, Taifeng Wang, Le Song*, xTrimoGene: An efficient and scalable representation learner for single-cell RNA-seq data, NeurIPS, 2023
29. Yifan Zhou, Yusra B. Medik, Bhakti Patel, Daniel B. Zamler, Sijie Chen, Thomas Chapman, Sarah Schneider, Elizabeth M. Park, Rachel L. Babcock, Taylor T. Chrisikos, Laura M. Kahn, Allison M. Dyevoich, Josue E. Pineda, Matthew C. Wong, Aditya K. Mishra, Samuel H. Cass, Alexandria P. Cogdill, Daniel H. Johnson, Sarah B. Johnson, Khalida Wani, Debora A. Ledesma, Courtney W. Hudgens, Jingjing Wang, Md Abdul Wadud Khan, Christine B. Peterson, Aron Y. Joon, Weiyi Peng, Haiyan S. Li, Reetakshi Arora, Ximing Tang, Maria Gabriela Raso, Xuegong Zhang, Wai Chin Foo, Michael T. Tetzlaff, Gretchen E. Diehl, Karen Clise-Dwyer, Elizabeth M. Whitley, Matthew M. Gubin, James P. Allison, Patrick Hwu, Nadim J. Ajami, Adi Diab, Jennifer A. Wargo, and Stephanie S. Watowich, Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration, Journal of Experimental Medicine, 220(2): e20221333, 2023 https://doi.org/10.1084/jem.20221333
30. Jiaqi Li, Zhenbin Qiu, Chao Zhang, Sijie Chen, Mengmin Wang, Qiuchen Meng, Haiming Lu, Lei Wei, Hairong Lv, Wenzhao Zhong*, Xuegong Zhang*, ITHscore: comprehensive quantification of intra-tumor heterogeneity in NSCLC by multi-scale radiomic features, European Radiology, 33:893-903, 2023 https://doi.org/10.1007/s00330-022-09055-0
31. Jiaqi Li, Zhuofeng Li, Lei Wei, Xuegong Zhang*, Machine learning in lung cancer radiomics, Machine Intelligence Research, 20: 753-782, 2023 https://doi.org/10.1007/s11633-022-1364-x
2022
32. Weili Fu#*, Sijie Chen#, Runze Yang, Chen Li, Haoxiang Gao, Jian Li, Xuegong Zhang*, Cellular features of localized microenvironments in human meniscal degeneration: a single-cell transcriptomic study, eLife 2022; 11:e79585, https://doi.org/10.7554/eLife.79585
33. Tianxing Ma, Haochen Li, Xuegong Zhang*, Discovering single-cell eQTLs from scRNA-seq data only, Gene, 829(2022): 146520, April 2022
34. Sijie Chen#, Yanting Luo#, Haoxiang Gao#, Fanhong Li#, Yixin Chen#, Jiaqi Li#, Renke You, Minsheng Hao, Haiyang Bian, Xi Xi, Wenrui Li, Weiyu Li, Mingli Ye, Qiuchen Meng, Ziheng Zou, Chen Li, Haochen Li, Yangyuan Zhang, Yanfei Cui, Lei Wei, Fufeng Chen, Xiaowo Wang, Hairong Lv, Kui Hua, Rui Jiang, Xuegong Zhang*, hECA: The cell-centric assembly of a cell atlas, iScience, 25: 104318, 2022 https://doi.org/10.1016/j.isci.2022.104318
35. Xiaoyang Chen, Shengquan Chen, Shuang Song, Zijiang Gao, Lin Hou, Xuegong Zhang, Hairong Lv, Rui Jiang*, Cell type annotation of single-cell chromatin accessibility data via supervised Bayesian embedding, Nature Machine Intelligence, 4: 116-126, Feb, 2022, https://doi.org/10.1038/s42256-021-00432-w
36. Liang Chen#, Kui Hua#, Ningning Zhang, Jingyu Wang, Jian Meng, Zhenliang Hu, Haoxiang Gao, Fanhong Li, Yang Chen, Jie Ren, Liyang Liu, Qiming Zhou, Jin Gu, Jiangping Song*, Xuegong Zhang*, and Shengshou Hu*, Multifaceted spatial and functional zonation of cardiac cells in adult human heart, Circulation, 145: 315-318, 2022 (https://doi.org/10.1161/CIRCULATIONAHA.121.055690)
37. Sijie Chen#, Yanting Luo#, Haoxiang Gao#, Fanhong Li#, Jiaqi Li#, Yixin Chen, Renke You, Hairong Lv, Kui Hua, Rui Jiang, Xuegong Zhang*, Toward a unified information framework for cell atlas assembly, National Science Review, 9: nwab179, https://doi.org/10.1093/nsr/nwab179, 27 Sept, 2021
2021及以前
见http://xglab.tech/member/Publications.html
