清华合成与系统生物学中心
Tsinghua Center for Synthetic and Systems Biology
Xuegong photo
张学工 (Xuegong Zhang)
教授,合成与系统生物学中心副主任
清华大学自动化系、医学院
国家杰出青年基金获得者
清华信息科学与技术国家实验室(筹)生物信息学部主任
生物信息学教育部重点实验室副主任


联系方式
通信地址:北京 清华大学自动化系(100084) FIT楼1-107
电话:86-10-6279-4919   传真:86-10-6278-6911
电子邮件:
zhangxg@tsinghua.edu.cn

教育背景及工作履历
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

2003 – 今 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

主要科研领域方向
机器学习与模式识别的理论、方法与应用:
支持向量机(SVM)与统计学习理论、核函数机器、人工神经网络与自组织映射(SOM)、…
生物信息学、计算功能基因组学与系统生物学:
组学数据分析:新一代测序数据处理与分析,基因表达数据挖掘,样本和基因的监督与非监督分类,基因选择,可视化,基因表达数据中的隐藏模式发现
基因调控分析:转录调控,表观遗传学调控,RNA调控,翻译后修饰,特殊发育过程中的基因调控系统分析
疾病基因组学:复杂疾病的计算系统生物学分析
基因型与单倍型分析:Haplotype block分析与htSNP选择,重组分析
中医药现代化中的模式识别:中药材产地与质量的自动鉴别、中药药效和作用机理的科学分析
主要荣誉
2009年国家教学成果二等奖
2008年北京市教学成果一等奖
2006年国家杰出青年基金
2004年教育部新世纪优秀人才支持计划
2002年国家科技进步二等奖
2001年中国海洋石油总公司科技进步一等奖
1995年国家教委科技进步二等奖

学术成果
主要学术论文
 2010
周雪崖,张学工,基于拷贝数变异的遗传关联研究,《科学通报》,in press
Zhengpeng Wu, Xi Wang, Xuegong Zhang, Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq, Bioinformatics, in press, 2010
Xi Wang, Zhengpeng Wu, Xuegong Zhang, Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq, Journal of Bioinformatics and Computational Biology, 8(Suppl.1): 177-192, 2010
Ting Zhang, Xuegong Zhang, Zhirong Sun, Identifying changed protein-protein interactions in biological processes by gene coexpression analysis, Chinese Science Bulletin, 55(14): 1396-1402, 2010
王曦、汪小我、王立坤、冯智星、张学工,新一代高通量RNA测序数据的处理与分析,《生物化学与生物物理进展》,37(8): 834-846, 2010
The MAQC Consortium, The MAQC-II project: a comprehensive study of common practices for the development and validation of microarray-based predictive models, Nature Biotechnology, 28(8): 827-841, 2010
Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang, Xuegong Zhang, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26(1): 136-138, 2010
PEI YunFei, WANG ZhiMin, Fei Fei, SHAO ZhiMing, HUANG Wei, ZHANG XueGong. Bioinformatics study indicates possible microRNA-regulated pathways in the differentiation of breast cancer, Chinese Science Bulletin, 55(10): 927-93, 2010
Tingting Li, Bingbing Wan, Jian Huang, Xuegong Zhang, Comparison of gene expression in hepatocellular carcinoma, liver development and liver regeneration, Mol Genet Genomics, 283: 485-492, 2010
 2009
Ying Liu, Bo Jiang, Xuegong Zhang, Gene set analysis identifies master transcription factors in developmental courses, Genomics, 94: 1-10, 2009 (cover story)
Tingting Li, Jian Huang, Ying Jiang, Yan Zeng, Fuchu He, Michael Q. Zhang, Zeguang Han, Xuegong Zhang, Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development, Genomics, 93: 235-242, 2009
Shicai Fan, Xuegong Zhang, CpG island methylation pattern in different human tissues and its correlation with gene expression, BBRC, 383(2009): 421-425
Yunfei Pei, Ting Zhang, Victor Renault, Xuegong Zhang, An overview of hepatocellular carcinoma study by omics-based methods, Acta Biochimica et Biophysica Sinica, 41(1): 1-15, 2009
YunfeiPei, Xi Wang, Xuegong Zhang, Predicting the fate of microRNA target genes based on sequence features, Journal of Theoretical Biology, 261: 17-22, 2009
凡时财,张学工,DNA甲基化的生物信息学研究进展, 《生物化学与生物物理进展》,36(2): 143-150, 2009
Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang, Introduction: the seventh Asia Pacific Bioinformatics Conference (APBC2009), BMC Bioinformatics, 10(Suppl 1): S1, 2009
Li Zhu, Wanwan Tang, Guisen Li, Jicheng Lv, Jiaxiang Ding, Lei Yu, Minghui Zhao, Yanda Li, Xuegong Zhang, Yan Shen, Hong Zhang, Haiyan Wang, Interaction between variants of two glycosyltransferase genes in IgA nephropathy, Kidney International, 76: 190-198, 2009
 2008
Bo Jiang, Xuegong Zhang, Tianxi Cai, Estimating the confidence interval for prediction errors of support vector machine classifiers, Journal of Machine Learning Research, 9(March): 521-540, 2008
Xuesong Lu, Xin Lu, Zhigang C. Wang, J. Dirk Iglehart, Xuegong Zhang and Andrea L. Richardson, Predicting features of breast cancer with gene expression patterns, Breast Cancer Research and Treatment, 108(2): 191-201, March 2008 (published online: May, 2007)  (4.671)
Tingting Li, Fei Li, Xuegong Zhang, Prediction of kinase-specific phosphorylation sites with sequence features by a log-odds ratio approach, Proteins: Structure, Function, and Bioinformatics, 70: 404-414, 2008
李婷婷,蒋博,汪小我,张学工,转录因子结合位点的计算分析方法,《生物物理学报》,24(5): 334-346, 2008
Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Xuegong Zhang, Michael Zhang, Multiobjective fuzzy biclustering in microarray data: method and a new performance measure, IEEE Congress on Evolutionary Computation 2008 (CEC2008), pp. 1536-1543, June 1-6, 2008
Shicai Fan, Michael Q. Zhang, Xuegong Zhang, Histone methylation marks play important roles in predicting the methylation status of CpG islands, Biochemical and Biophysical Research Communications, 374: 559-564, 2008
Tao Peng, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang and Yanda Li, Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse, BMC Genomics, 9: 191, 2008
Xiaowo Wang, Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of microRNAs in Vertebrates, Science in China, 51(6):552-9, 2008
 2007
Yonghong Peng, Xuegong Zhang, Guest Editorial: Integrative data mining in systems biology: from text to network mining, Artificial Intelligence in Medicine, 41(2): 83-86, 2007
Tingting Li, Hu Fu, and Xuegong Zhang, Prediction of kinase-specific phosphorylation sites by one-class SVMs, Proceedings of 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM2007), pp. 217-222, 2007
Xi Wang, Sanghamitra Bandyopadhyay, Zhenyu Xuan, Xiaoyue Zhao, Michael Q. Zhang, Xuegong Zhang, Prediction of transcription start site based on feature selection using AMOSA, CSB2007 Conference Proceedings, volume 6, pp.183-193, San Diego, Aug 13-17, 2007
Bo Jiang, Michael Q. Zhang, Xuegong Zhang, OSCAR: one-class SVM for accurate recognition of cis-elements, Bioinformatics, 23(5): 531-537, 2007
Shicai Fan, Fang Fang, Xuegong Zhang, Michael Q. Zhang, Putative zinc finger protein binding sites are enriched in the boundaries of methylation-resistant CpG islands in the human genome, PLoS ONE, 2(11): e1184, 2007
Jin Gu, Hu Fu, Xuegong Zhang, Yanda Li, Identifications of conserved 7-mers in the 3’-UTRs and microRNAs in Drosophila, BMC Bioinformatics, 8:432, 2007
S Li, ZQ Zhang, LJ Wu, XG Zhang, YD Li, YY Wang Understanding ZHENG in Traditional Chinese Medicine in the context of neuro-endocrine-immune network, IEE Systems Biology, 1(1): 51-60, 2007
Jing Zhang, Bo Jiang, Ming Li, John Tromp, Xuegong Zhang and Michael Q. Zhang, Computing exact P-values for DNA motifs, Bioinformatics, 23(5): 531-537, 2007
Jian Huang, Pei Hao, Yun-Li Zhang, Fu-Xing Deng, Qing Deng, Yi Hong, Xiao-Wo Wang, Yun Wang, Ting-Ting Li, Xue-Gong Zhang, Yi-Xue Li, Pen-Yuan Yang, Hong-Yang Wang, Ze-Guang Han, Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS), BMC Genomics, 8: 207, 2007
Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Neighbor number, valley seeking and clustering, Pattern Recognition Letters, 28: 173-180, 2007
 2006
Jun Li, Michael Q. Zhang, Xuegong Zhang, A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data, American Journal of Human Genetics, 79: 628-639, Oct 2006
Shao Li, Ruiqin Wang, Yulong Zhang, Xuegong Zhang, A. Joseph Layon, Yanda Li and Mingzhe Chen, Symptom combinations associated with outcome and therapeutic effects in a cohort of cases with SARS, The American Journal of Chinese Medicine, 34(6): 937-947, 2006
Jin Gu, Tao He, Yunfei Pei, Fei Li, Xiaowo Wang, Jing Zhang, Xuegong Zhang, Yanda Li, Primary transcripts and expressions of mammal intergenic microRNAs detected by mapping ESTs to their flanking seqeuences, Mammalian Genome, 17: 1033-1041, 2006
Chaolin Zhang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Neighbor number, valley seeking and clustering, Pattern Recognition Letters, 28: 173-180, 2006
Fang Fang, Shicai Fan, Xuegong Zhang and Michael Q. Zhang, Predicting methylation status of CpG islands in the human brain, Bioinformatics, 22(18): 2204-2209, 2006
Xuesong Lu, Xuegong Zhang, The effect of GeneChip gene definitions on the microarray study of cancers, BioEssays, 28(7): 739-746, 2006
Chaolin Zhang, Xuesong Lu, Xuegong Zhang, Significance of gene ranking for classification of microarray samples, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3(3): 312-320, 2006
Xuegong Zhang, Xin Lu, Qian Shi, Xiu-qin Xu, Hon-chiu E Leung, Lyndsay N Harris, James D Iglehart, Alexander Miron, Jun S Liu and Wing H Wong, Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data, BMC Bioinformatics, 7:197, 2006 (10Apr2006)  
刘沭华,张学工,周群,孙素琴,近红外漫反射光谱法和模式识别技术鉴别中药材产地,《光谱学与光谱分析》,26(4): 629-632, Apr. 2006
许建华,张学工,经典线性算法的非线性核形式,《控制与决策》,vol.21, no.1, pp. 1-12, 2006
Xu Jian-hua, Zhang, Xue-gong, Li Yan-da, Regularized kernel forms of minimum squared error method, Front. Electr. Electron. Eng. China, (2006)1: 1-7
Jianhua XU, Xuegong Zhang, Suqin Sun. Tuning SVM Parameters for Classifying Geographical Origins of Chinese Medical Herbs. International Journal of Wavelet, Multimedia and Information Processing, 2006, 4(3)
 2005
Shicai Fan & Xuegong Zhang, Characterizing the microenvironment surrounding phosphorylated protein sites, Genomics, Proteomics & Bioinformatics, 3(4): 213-217, 2005
S. Weng, C. Zhang, Z. Liu, and X. Zhang, Mining the structural knowledge of high-dimensional medical data using Isomap, Medical & Biological Engineering & Computing, 43(3): 410-412, 2005
Jianhua Xu, Xuegong Zhang. A Multiclass Kernel Perceptron Algorithm. In: Proceedings of International Conference on Neural Networks and Brain (Mingsheng Zhao and Zhongzhi Shi, editors). Vol. 2, pp. 717-721, Oct. 13-15, 2005, Beijing, China. New York: IEEE Press
Chenghai Xue, Fei Li, Tao He, Guoping Liu, Yanda Li, Xuegong Zhang, Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine, BMC Bioinformatics, 6: 310, 2005
Xiangqing Sun, Zhongqi Zhang, Yulong Zhang, Xuegong Zhang, Yanda Li, Multi-locus penetrance variance analysis method for association study in complex diseases, Human Heredity, 60(3): 143-149, 2005
Xiaowo Wang, Jing Zhang, Fei Li, Jin Gu, Tao He, Xuegong Zhang, Yanda Li, MicroRNA identification based on sequence and structure alignment, Bioinformatics, 21(18): 3610-3614, 2005
Jianning Bi, Huiyu Xia, Fei Li, Xuegong Zhang, Yanda Li, The effect of U1 snRNA binding free energy on the selection of 5' splice sites, Biochemical and Biophysical Research Communications, 333: 64-69, 2005
刘沭华,张学工,周群,孙素琴,模式识别和红外光谱法相结合鉴别中药材产地,《光谱学与光谱分析》,2005,v.25, no.6, 878-881  (Use of FTIR and pattern recognition to detemine geographical origins of Chinese midical herbs, Spectroscopy and Spectral Analysis)
Shuhua Liu, Xuegong Zhang, Suqin Sun, Discrimination and feature selection of geographic origins of traditional Chinese medicine herbs with NIR spectroscopy, Chinese Science Bulletin, 50(2): 179-184, 2005
Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang, htSNPer1.0: software for haplotype block partition and htSNPs selection, BMC Bioinformatics, 6:38, 2005 (1 March 2005)
Keyue Ding, Kaixin Zhou, Jing Zhang, Joanne Knight, Xuegong Zhang, Yan Shen, The effect of haplotype block definations on inference of haplotype block structure and htSNPs selection, Molecular Biology and Evolution, 22(1): 148-159, 2005
 2004
Jing Zhang, Fei Li, Jun Li, Michael Q. Zhang, Xuegong Zhang, Evidence and characteristics of putative human alpha recombination hotspots, Human Molecular Genetics, 13(22): 2823-2828, 2004
Xi Ma, Jun Cai, Wei Hu, Yimin Zhang, Yanda Li, Xuegong Zhang, Discovering possible context dependences around SNP Sites in human genes with Bayesian wetwork learning, ICARCV 2004, pp.1315-1319, Dec.2004
Xuesong Lu, Yanda Li, Xuegong Zhang, A simple strategy for detecting outlier samples in microarray data, ICARCV 2004, pp.1331-1335, Dec.2004
孙向青,贾彦彬,张学工,许琪,沈岩,李衍达,多巴胺通路的基因与精神分裂症风险的多位点关联研究,《中国科学》(C辑),34(5): 465-470, 2004
X-Q. Xu, C.K. Leow, X. Lu, X. Zhang, J.S. Liu, W.H. Wong, A. Asperger, S. Deininger, H.E. Leung, Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics, Proteomics, 4: 3235-3245, 2004
Jianhua Xu, Xuegong Zhang, A learning algorithm with Gaussian regularizer for kernel neuron, Advances in Neural Networks – ISNN 2004, part I, pp.252-257, Dalian, Aug., 2004
Jianhua Xu, Xuegong Zhang, Kernels based on weighted Levenshtein distance, IJCNN2004, pp.3015-3018, Budapest, July 2004
许建华,张学工,李衍达,支持向量机的新发展,《控制与决策》,vol.19,no.5, pp.481-484, 2004年5月
李衍达,张学工,李飞,生命信息技术前沿热点—小RNA基因及基因组非编码区的信息挖掘,中国科学院《2004高技术发展报告》,科学出版社,2004年3月 pp. 124-131
Fang Wen, Fei Li, Huiyu Xia, Xin Lu, Xuegong Zhang (corresponding author), Yanda Li, The impact of very short alternative splicing on protein structures and functions in the human genome, Trends in Genetics, vol.20, no.5, May 2004, pp.232-236
Xuesong Lu, Xing Wang, Ying Huang, Wei Hu, Guang R. Gao, Yanda Li, Xuegong Zhang, On some choices in Bayesian network learning for reconstructing regulatory networks, Proceedings of RECOMB04, March 2004, pp. 126-127
Chaolin Zhang, Yanda Li, Xuegong Zhang, gMap: extracting and interactively visualizing nonlinear relationships of genes from expression, Proceedings of RECOMB04, March 2004, pp. 228-229   
许建华,张学工,李衍达,最小平方误差算法的正则化核形式,《自动化学报》,vol.30, no.1, Jan. 2004, pp.27-36
 
特邀报告与讲座
 1.    Xuegong Zhang, Computational prediction of miRNA-regulated pathways in the differentiation of histological grades in breast cancer, ACM-HK Bioinformatics Symposium, March 27, HK, 2010
2.    Xuegong Zhang, Estimating variances of pattern classifiers’ performances with given samples, ISciDE (Sino-foreign-interchange Workshop on Intelligence Science and Intelligent Data Engineering), June 3-5, Harbin, 2010
3.    Xuegong Zhang, Estimating gene expression values from RNA-seq data, IEEE International Conference on Bioinformatics & Biomedicine (BIBM2010), HK, Dec.18-21, 2010
4.    Xuegong Zhang, Estimating gene expression values from RNA-seq data, The 8th ICSA International Conference: Frontiers of Interdisciplinary and Methodological Statistical Research, Guangzhou, Dec.19-22, 2010
5.    Xuegong Zhang, Computational prediction of microRNA-regulated pathways in the differentiation of histological grades in breast cancer, Opportunities for Integrative Bionetworks to Enable Dynamic Models of Diseases – Beijing Summit, Beijing, Nov.20, 2009
6.    Xuegong Zhang, Putting more biology in learning machines, Planery Keynote Speech at APBC2008, Jan 14-17, 2008, Kyoto
7.    Xuegong Zhang, Studying molecular features of breast cancer with learning machines, invited talk at CAS International Symposium on Developmental Systems Biology, May 18-20, 2008, Beijing
8.    Xuegong Zhang, Bioinformatics Study of the Molecular Features of Breast Cancer, invited keynote talk at the 5th International Conference on Information Technology and Applications in Biomedicine (ITAB’08), May 30-31, 2008, Shenzhen
9.    Xuegong Zhang, Learning Biology with Machines: examples from alternative splicing and DNA methylation, invited talk at 2008 International Bioinformatics Workshop, June 7-9, 2008, Kunming
10.  Xuegong Zhang, Understanding lymph node metastasis in breast cancers: a case study of microarray data analysis, invited talk, NSF Sponsored International Conference on Bioinformatics, June 10-14, 2007, Hangzhou
11.  Xuegong Zhang, A bioinformatics study on lymph node metastasis of breast cancers, invited talk, International Symposium on Biochip Technology and Molecular Classification of Disease, May 6-8, Shanghai, 2007
12.  Xuegong Zhang, Some new challenges for pattern recognition on high-throughput genomics/proteomics data, ICCTA2007, Kolkata, India, Mar 3-7, 2007
13.  Xuegong Zhang, Effects of re-mapping the oligo probes onto the updated genome on high-level analyses of microarray data, BNI&IFBT2006, Beijing, Oct. 10, 2006
14.  Xuegong Zhang, Machine learning in high-throughput genomics and proteomics, Tutorial at ICONIP2006 (
http://iconip2006.cse.cuhk.edu.hk/program/Tutorial-3), Hong Kong, Oct.3, 2006
15.  Fang Fang, Xuegong Zhang and Michael Q. Zhang, Computational studies in epigenetics, The First International Conference on Computational Systems Biology, Shanghai, July 20-23, 2006
16.  Xuegong Zhang, Building gene networks by fusing literature and microarray data, Transcripteom 2005, Shanghai, Nov.5-9, 2005
17.  Xuegong Zhang, Computational Analysis of Haplotype Blocks and Human Recombination Hotspots, Changchun International Bioinformatics Workshop, Changchun, July 5-7, 2005
18.  张学工,再看高通量表达数据的机器学习分析,东方科技论坛:计算生物学最新进展,上海,2005年7月2日
19.  Xuegong Zhang, Computation Analysis of Human Recombination Hotspots, 1st International Workshop on Computational and Systems Biology, Beijing, May 23, 2005
20.  张学工, 生物信息学中的若干计算问题,中国计算机学会青年计算机科技论坛,2005年4月22日
21.  Xuegong Zhang, Learning Specific Gene Relation Networks from Literatures, 2005 Sina-German Workshop on Networks: from Biology to Theory, Beijing, Apr 4-8, 2005
22.  Xuegong Zhang, SVM and Its Application Examples in Computational Biology, CSHL bioinformaics seminar, Feb 9, 2005
23.  Xuegong Zhang, Computational Analysis of Haplotype Blocks and Recombination Hotspots, Dr. Jun Liu’s lab seminar at Harvard University, Feb 1, 2005
24.  Xuegong Zhang, Significance of Gene Ranking for Classification of Microarray Samples, SRCCS 2004 International Workshop for Statistics, Seoul National University, Korea, June 2004
25.  Xuegong Zhang, Considerations on Sample Classification and Gene Selection with Microarray Data using Machine Learning Approaches, Statistical Method in Microarray Analysis Workshop at NUS, Singapore, Jan 2004
26.  张学工,基因表达数据中模式识别问题的一些特点,中国科协中国科学青年科学家论坛第81次论坛“生物信息学中的若干前沿问题的探讨”,2003年11月28-29日
 
教材、专著与章节
1.   张学工,《模式识别》(第三版),清华大学出版社,2010.8
2.    V. Vapnik著,许建华、张学工译,《统计学习理论》,电子工业出版社,2004.6
3.    边肇祺、张学工等编著,《模式识别》(第二版),清华大学出版社,2000.1
4.    V. Vapnik著,张学工译,《统计学习理论的本质》,清华大学出版社,2000.8
5.    张学工、刘业新编著, 《X Window /Motif编程速成》,清华大学出版社,1998.3
6.    Xuegong Zhang and Yanda Li, The application of artificial neural networks in editing noisy seismic data, Chapter 7, in F.Aminzadeh & M. Jamshidi eds., Soft Computing: Fuzzy Logic, Neural Networks, and Distributed Artificial Intelligence, PTR Prentice Hall, NY, 1994
 
开设课程
计算分子生物学引论(研究生,2002-2009秋)
统计学习理论导论(研究生,2000秋,2002-2009秋)
科学精神、道德与表达(研究生,2005-2007夏)
模式识别基础(本科生,1998-2009秋,国家级精品课)

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