个人简历

教育背景\r
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\r
1989年7月于清华大学获工业自动化专业工学学士学位\r
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工作履历\r
2018–今 北京信息科学技术国家研究中心生物信息学部主任\r
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\r
2002–今 清华大学自动化系 模式识别与生物信息学 教授\r
2002–今 清华大学生物信息学教育部重点实验室 副主任\r
2007.3-4 南加州大学分子与计算生物学系访问学者\r
2006.2-3 哈佛大学公共卫生学院访问科学家\r
2001–2002 哈佛大学公共卫生学院生物统计系高级访问学者\r
1999–2007 清华大学自动化系信息处理研究所 所长\r
1996–2002 清华大学自动化系 模式识别理论及应用 副教授\r
1994–1996 清华大学自动化系 讲师\r
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学术兼职\r
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主任\r
中国生物工程学会常务理事、计算生物学与生物信息学专委会常务副主任\r
国际计算生物学学会理事（ISCB Board of Directors）\r
Quantitative Biology执行主编

研究领域

"机器学习与生物和医学大数据分析\r
人类细胞图谱与人体系统数字孪生\r
单细胞生物信息学分析"

近期论文

张学工、汪小我编著，《模式识别》(第4版)，清华大学出版社，2021.9\r
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Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang*, A method for generating synthetic electronic medical record text, IEEE TCBB, 18(1):173-182, 2021\r
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Minsheng Hao, Kui Hua*, Xuegong Zhang*, SOMDE: a scalable method for identifying spatially variable genes with self-organizing map, Bioinformatics, 2021\r
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Sijie Chen, Yanting Luo, Haoxiang Gao, Fanhong Li, Jiaqi Li, Yixin Chen, 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*, A human ensemble cell atlas (hECA) enables in data cell sorting, bioRxiv 2021.07.21.453289;\r
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Sijie Chen, (陈斯杰), Yanting Luo, (罗燕婷), Haoxiang Gao, (高浩翔), Fanhong Li, (李范红), Jiaqi Li, (李嘉骐), Yixin Chen, (陈奕鑫), Renke You, (尤仁科), Hairong Lv, (闾海荣), Kui Hua, (花奎), Rui Jiang, (江瑞), Xuegong Zhang, (张学工), Toward a unified information framework for cell atlas assembly, National Science Review, 2021;, nwab179\r
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Yue Hu, Xi Xi, Qian Yang, Xuegong Zhang*, SCeQTL: an R package for indentifying eQTL from single-cell parallel sequencing data, BMC Bioinformatics, 21: 184, 2020 https://doi.org/10.1186/s12859-020-3534-6\r
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Wendao Liu, Xuegong Zhang*, Single-cell alternative splicing analysis reveals dominance of single transcript variant, Genomics, 112: 2418-2425, 2020\r
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Qin Yu, Geng Chen, Jiaqi Li, Xiaolong Liu, Xuegong Zhang, Haiming Lu, Predicting microvascular invasion of hepatocellular carcinoma by texture analysis of multi-phase MR image, Eulenstein & Al-Mubaid (eds.) BICOB 2020 (EPiC Series in Computing, vol.70), pp.238-246, 2020\r
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Yixin Chen, Sijie Chen, Xuegong Zhang*, Using DenseFly algorithm for cell searching on massive scRNA-seq datasets, BMC Genomics, 21 (Suppl 5): 222, 2020\r
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Najeebullah Shah, Jiaqi Li, Fanhong Li, Wenchang Chen, Haoxiang Gao, Sijie Chen, Kui Hua, Xuegong Zhang*, An experiment on ab initio discovery of biological knowledge from scRNA-seq data using machine learning, Patterns, 1: 100071, 2020 https://doi.org/10.1016/j.patter.2020.100071\r
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Jiaqi Li, Haiming Lu, Xiang Fang, Sijie Chen, Xuegong Zhang*, Pixel-level clustering reveals intra-tumor heterogeneity in non-small cell lung cancer, IEEE BIBM 2019, pp.1536-1939\r
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Jiaxing Cui, Hongfei Cui, Mingran Yang, Shiyu Du, Junfeng Li, Yingxue Li, Liyang Liu, Xuegong Zhang*, Shao Li*, Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade, Protein Cell, 10(7): 496-509, 2019\r
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Sijie Chen, Yixin Chen, Fengzhu Sun, Michael S. Waterman, Xuegong Zhang*, A new statistic for efficient detection of repetitive sequences, Bioinformatics, 35(22): pp.4596-4606, 2019\r
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Xuegong Zhang, QB: Embracing the future of quantitative understanding and engineering of life, Quantitative Biology, 7(1): 1-2, 2019\r
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Aziz Khan & Xuegong Zhang, Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers, Scientific Reports, 9: 2877, 2019\r
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Kui Hua, Xuegong Zhang, Estimating the total genome length of a metagenomic sample using k-mers, BMC Genomics, 20 (Suppl 2):183, 2019\r
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Kui Hua, Xuegong Zhang, A case study on the detailed reproducibility of a human cell altas project, Quantitative Biology, 7(2): 162-169, 2019\r
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Huijuan Feng, Tingting Li, Xuegong Zhang*, Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-seq data, BMC Genomics, 19 (Suppl 6): S64, 2019\r
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Chao Zhang, Xing Sun, Kang Dang, Ke Li, Xiao-wei Gao, Zong-qiao Yu, Fei-yue Huang, Yun-sheng Wu, Zhu Liang, Zai-yi Liu, Xue-gong Zhang, Xing-lin Gao, Shao-hong Huang, Jie Qin, Wei-neng Feng, Tao Zhou, Yan-bin Zhang, Wei-jun Fang, Ming-fang Zhao, Xue-ning Yang, Qing Zhou, Yi-long Wu, Wen-zhao Zhong, Toward an expert level of lung cancer detection and classification using a deep convolutional neural network, The Oncologist, 24: 1-7, 2019\r
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胡越，罗东阳，花奎，路海明，张学工，关于深度学习的综述与讨论，《智能系统学报》， 14(1): 1-18, 2019\r
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Jiaqi Guan, Runzhe Li, Sheng Yu, Xuegong Zhang*, Generation of synthetic electronic medical record text, Proc. IEEE BIBM2018, pp.374-380, 2018\r
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S.M. Weyn-Vanhentenryck, H. Feng, D. Ustianenko, R. Duffie, Q. Yan, M. Jacko, J.C. Martinez, M. Goodwin, X. Zhang, U. Hengst, S. Lomvardas, M.S. Swanson, C. Zhang, Precise temporal regulation of alternative splicing during neural development, Nature Communications, 9: 2189, 2018\r
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Aziz Khan, Anthony Mathelier, Xuegong Zhang, Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers, Epigenetics, 2018\r
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Jing-Ren Zhang, Lihong He, Dongyang Luo, Fan Yang, Chris Li, Xuegong Zhang, and Haiteng Deng, Multiple Domains of Bacterial and Human Lon Proteases Define Substrate Selectivity, Emerging Microbes & Infections, in press\r
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Aziz Khan & Xuegong Zhang*, Making genome browsers portable and personal, Genome Biology, 19: 93, 2018\r
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Zhun Miao, Ke Deng, Xiaowo Wang, Xuegong Zhang*, DEsingle for detecting three types of differential expression in single-cell RNA-seq data, Bioinformatics, 34(18): 3223-3224, 2018\r
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Zhiyi Qin, Peter Stoilov, Xuegong Zhang*, Yi Xing*, SEASTAR: systematic evaluation of alternative transcription start sites in RNA, NAR, 46(8): e45, 2018\r
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Shansong Liu, Kui Hua, Sijie Chen, Xuegong Zhang*, Comprehensive simulation of metagenomics sequencing data with non-uniform sampling distribution, Quantitative Biology, 6(2): 175-185, 2018