张学工 博士
模式识别与生物信息学 教授
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
北京100084 清华大学自动化系
电话：86-10-6279-4919
传真：86-10-6278-6911
研究方向
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：
疾病基因组学：复杂疾病的基因组学与蛋白质组学分析
组学数据分析： 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
基因型与单倍型分析：Haplotype block分析与htSNP选择，重组分析
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
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
……
学历
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
工作经历
2007.3-4 南加州大学分子与计算生物学系访问学者
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
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
开设课程
计算分子生物学引论（研究生，2002秋，2003秋，2004秋）
统计学习理论导论（研究生，2000秋，2002秋，2003秋，2004秋）
科学精神、道德与表达（研究生，2005夏）
模式识别基础（本科生，1998-2004秋）
曾获奖励
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
博士生：李婷婷、武征鹏、裴云飞、凡时财、王曦、马涛、冯智星
硕士生：周雪崖、刘莹、孟璐
本科生：郑荣获
校友：
博士生：吕雪松、张朝林、阎辉、许建华、Benoit Valin、叶铮
硕士生：蒋博、李俊、方芳、敖江昵、马熹、张晶、刘沭华、吴君文、柯海昕、吴翔、李岩、寇真真、马云潜
合作博士后：薛成海、汪莉、李飞、章珂、熊高君、冯太林、陆文凯
特邀报告与讲座
Xuegong Zhang, Putting more biology in learning machines, Planery Keynote Speech at APBC2008, Jan
14-17, 2008, Kyoto
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
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
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
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
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
Xuegong Zhang, Some new challenges for pattern recognition on
high-throughput genomics/proteomics data, ICCTA2007, Kolkata, India, Mar 3-7,
2007
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
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
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
Xuegong
Zhang, Building gene
networks by fusing literature and microarray data, Transcripteom 2005, Shanghai, Nov.5-9, 2005
Xuegong
Zhang, Computational
Analysis of Haplotype Blocks and Human Recombination Hotspots, Changchun International Bioinformatics
Workshop, Changchun,
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
Xuegong
Zhang, Computation
Analysis of Human Recombination Hotspots, 1st
International Workshop on Computational and Systems Biology, Beijing,
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
Xuegong
Zhang, Learning Specific
Gene Relation Networks from Literatures, 2005
Sina-German Workshop on Networks: from Biology to Theory, Beijing,
Xuegong
Zhang, SVM and Its
Application Examples in Computational Biology, CSHL bioinformaics seminar,
Xuegong
Zhang, Computational
Analysis of Haplotype Blocks and Recombination Hotspots, Dr. Jun Liu’s lab seminar at Harvard University,
Xuegong Zhang, Significance of Gene Ranking for Classification of Microarray
Samples, SRCCS 2004 International Workshop for Statistics, Seoul National
University, Korea, June 2004
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
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
主要学术论文
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, in
press
Xiaowo Wang, Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of microRNAs in Vertebrates, Science in China, in press
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, in press (published online: 6 Aug 2007)
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
2003
李岩，张学工，应用图像处理方法自动检测路口车辆排队长度，《计算机应用与软件》，vol.20, n.12, pp.47-49, 2003
Jianhua Xu, Xuegong Zhang, Yanda Li, Sparse training procedure for kernel neuron, IEEE Int. Conf. Neural Networks & Signal Processing, Nanjing, China, Dec.14-17, 2003, pp49-53
Xiaotong Shen, George C. Tseng, Xuegong Zhang, Wing Hung Wong, On psi-learning, Journal of the American Statistical Association, vol.98: number: 463, pp.724-734, Sept. 2003
李梢，张学工，季梁，李衍达，复杂性疾病生物信息学研究的策略与方法，《世界华人消化杂志》（World Chinese Journal Digestology）, v.11, n.10, 1465-1469，Oct. 2003
O'Hagan RC, Brennan CW, Strahs A, Zhang X, Kannan K, Donovan M, Cauwels C, Sharpless NE, Wong WH, Chin L., Array Comparative Genome Hybridization for Tumor Classification and Gene Discovery in Mouse Models of Malignant Melanoma. Cancer Res. 63(17):5352-5356, Sept.1, 2003
Wenkai Lu, Xuegong Zhang, Yanda Li, Multiple removal based on detection and estimation of localized coherent signal, Geophysics, vol.68, no.2, pp.745-750, Mar. 2003
许建华，张学工，李衍达，基于核函数的非线性口袋算法，《电子学报》，vo.31, no.4, 612-615, 2003.4
吴翔，谭李，陆文凯，张学工，提高超大规模SVM训练计算速度的研究，《模式识别与人工智能》，vol.16, no.1, 2003, pp.46-49
2002
许建华，张学工，李衍达，经典线性算法核化研究的新进展，第十二届全国神经计算学术大会（特邀论文），pp.117-122，2002
许建华，张学工，李衍达，基于最小二乘支持向量机的油气判别技术，《模式识别于人工智能》，v.15, n.4, 507-509, 2002年12月
吴君文，张学工，应用小波变换和PCA进行车辆的静态图像检测，《清华大学学报》，v.42, n.11, 2002, pp.1560-1564
熊高君，张学工，贺振华，吴正伯，三维定位原理与三维反射波长模拟，《矿物岩石》，vol.22, no.3, pp.93-97, 2002
阎辉，张学工，马云潜，李衍达，“基于变异函数的径向基核函数参数估计”，《自动化学报》，vol.28, no.3, 2002, pp.450-455
许建华，张学工，李衍达，“一种基于核函数的非线性感知器算法”，《计算机学报》，v.25, n.7, 2002, pp.689-695
Kou, Z., Ji, Liang & Zhang, X., Karyotyping of comparative genomic hybridization human metaphases by using support vector machines, Cytometry, v.47, n.1, pp.17-23, 2002
Kai Yu, Liang Ji, Xuegong Zhang, Kernel nearest-neighbor algorithm, Neural Processing Letters, vol.15, no.2, 2002, pp.147-156
阎辉，张学工，李衍达，“基于核函数的最大间隔聚类算法”，《清华大学学报（自然科学版）》，v.42, n.1, 2002, pp.132-134
许建华，张学工，李衍达，“应用核Fisher判别技术预测油气储集层”，《石油地球物理勘探》，vol.37, n.2, 2002, pp.170-174
2001
阎辉，张学工，李衍达，“支持向量机与最小二乘法的关系研究”，《清华大学学报（自然科学版）》，v.41, n.9, 2001, pp.77-80
冯占林，张学工，李衍达，“基于小波变换的地震勘探数据压缩的工程分析”，《清华大学学报（自然科学版）》，v.41, n.4/5, April, 2001, pp.170-173
阎辉，张学工，张贤达，“基于小波变换的自适应多井对比技术”，《石油物探》，vol.40, n.1, 2001.3, pp.49-55
陆文凯，张学工，李衍达，何汉漪，温书亮，刘永江，“时间域零炮检距地震道拟合”，《石油地球物理勘探》，vol.36, n.1, 2001, pp.56-59
冯太林，张学工，李衍达，白天成，李云，杨贵祥，陆修莲，“折射波地震记录叠加成像方法研究”，《地球物理学报》，v.44, n.1, 2001, pp.129-134
Jianhua XU, Xuegong ZHANG, Yanda LI. Kernel Neuron and its Training Algorithm. Proc. of 8th Intl Conf on Neural Information Processing, Vol.2, pp. 861-866, Shanghai, China, Nov., 2001
Zhenzhen Kou, Jianhua Xu, Xuegong Zhang, Liang Ji，