Xuegong Zhang, Ph.D.
Professor of Pattern
Recognition and Bioinformatics
Director,
Bioinformatics Division, TNLIST
Deputy
Director, MOE Key Laboratory of Bioinformatics
Department
of Automation
Phone: 86-10-6279-4919
Fax:
86-10-6278-6911
Email: zhangxg@tsinghua.edu.cn
Joint
Postdoc Positions at Tsinghua University and Sage Bionetworks
in
Computational Biology and Bioinformatics
Tsinghua University, Department of Automation and
the Bioinformatics Division of TNLIST is calling for applications to joint
postdoc positions with Sage Bionetworks
on Computational Biology and Bioinformatics. The recruited postdoc fellows will
work on large-scale omics data analysis and modeling in cancer study.
Applicants should own an earned Ph.D. degree on
relevant subjects, and have experiences in handling large data sets or in
cancer research. Applicants should have necessary knowledge in molecular
biology, have basic trainings in statistics or pattern recognition and machine
learning. Coding skills in at least one computer language is required. Reading
and writing skills in English are required. Applicants should be able to work
with fellow colleagues and/or collaborators efficiently.
Applicants should send personal statements, CV,
reprints of publications, as well as the names, phones and email addresses of 3
references to zhangxg@tsinghua.edu.cn,
or send by conventional mail to Ms. Haiyan Luo, 1-107 FIT Building, Tsinghua
University, Beijing 100084, China
Postdoc
Positions Open in Computational Biology and Bioinformatics
Applicants
should have earned a Ph.D. degree in one of the following fields: Pattern
Recognition, Machine Learning, Information Processing, Computer Science,
Software Engineering, Bioinformatics, Computational Biology, Molecular Biology,
Genetics, Statistics, Biostatistics
Last update：Jan. 12, 2010
Research
Experiences
Students
Publications
Research
Machine Learning and Pattern Recognition:
Theory, Methods and Applications:
SVM and Statistical
Learning Theory, Kernel Machines, Artificial Neural Networks and SOM, …
Bioinformatics, Computational Genomics
and Systems Biology:
Complex Diseases: Genomics and Proteomics analysis of complex diseases
Omics Data Analysis: Data mining, supervised and unsupervised classification, gene selection,
visualization, pattern discovery
Gene Regulation
Analysis: Transcription regulation, epigeomics regulation, RNA
regulation, post-translational regulation
Genotype and
Haplotype Analysis: haplotype block
and htSNPs analysis, recombination
Study on
alternative splicing and microRNA
Pattern Recognition
in Traditional Chinese Medicine
……
Education
March, 1994,
Ph.D. of Pattern Recognition and Intelligent Systems,
July, 1989, BS
of Industrial Automation,
Work Experiences
2003 – present Director,
Bioinformatics Division, TNLIST (Tsinghua National Laboratory of Information
Science and Technology)
2002 – present Professor of Pattern
Recognition and Bioinformatics, Department of Automation,
2002 – present Deputy
Director, MOE Key Laboratory of Bioinformatics
2007.Mar-Apr Visiting Scholar, MCB, USC
2006.Feb-Mar Visiting
Scientist,
2001 – 2002 Visiting Scholar, Harvard School of
Public Health
1999 – 2007 Director, Institute of Information
Processing, Department of Automation,
1996 – 2002 Associate Professor of Pattern
Recognition, Department of Automation,
1994 – 1996 Lecturer, Department of Automation,
Courses Given
Introductory Computational Molecular
Biology (graduate)
Introduction to Statistical Learning
Theory (graduate)
Scientific Ethics and Exposition
(graduate)
Fundamental Pattern Recognition
(undergraduate)
Awards
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
Ph.D. program：Zhengpeng
Wu, Xi Wang, Tao Ma, Xueya Zhou, Zhixing Feng, Feng Zeng, Chao Ye
MS
program: Lu Meng, Ruijuan Li, Bai Jiang
Postdoc
fellows: Dr. Yunfei Pei
Alumni：
Ph.D. Program:
Tingting Li, Shicai Fan, Xuesong Lu, Hui Yan, Jianhua Xu, Chaolin Zhang, Benoit
Valin, Zheng Ye
MS Program:
Ying Liu, Bo Jiang, Jun Li, Fang Fang, Jiangni Ao, Xi Ma, Jing Zhang, Shuhua Liu, Junwen
Wu, Haixin Ke, Xiang Wu, Yan Li, Zhenzhen Kou, Yunqian Ma
Postdoctoral
Fellows: Drs. Chenghai Xue, Li Wang, Fei Li, Ke Zhang, Gaojun Xiong, Tailin
Feng, Wenkai Lu
Selected Publications
2009
Likun Wang, Zhixing
Feng, Xi Wang, Xiaowo Wang, Xuegong
Zhang, DEGseq: an R package for identifying differentially expressed genes
from RNA-seq data, Bioinformatics, in
press (advanced access published
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, in
press
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,
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, 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
Invited Talks and Tutorials
1.
Xuegong Zhang, Putting more biology in learning machines, Planery Keynote Speech at APBC2008, Jan
14-17, 2008, Kyoto
2.
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
3.
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
4.
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
5.
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
6.
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
7.
Xuegong Zhang, Some new challenges for pattern recognition on
high-throughput genomics/proteomics data, ICCTA2007,
Kolkata, India, Mar 3-7, 2007
8.
Xuegong Zhang, Effects of re-mapping the oligo probes onto the
updated genome on high-level analyses of microarray data, BNI&IFBT2006, Beijing,
9.
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
10.
Fang
Fang, Xuegong Zhang and Michael Q.
Zhang, Computational studies in epigenetics, The First International
Conference on Computational Systems Biology, Shanghai,
11. Xuegong
Zhang, Building gene
networks by fusing literature and microarray data, Transcripteom 2005, Shanghai, Nov.5-9, 2005
12. Xuegong
Zhang, Computational
Analysis of Haplotype Blocks and Human Recombination Hotspots, Changchun International Bioinformatics
Workshop, Changchun,
13.
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
14.
Xuegong Zhang, Computation Analysis of Human Recombination
Hotspots, 1st International Workshop on
Computational and Systems Biology, Beijing,
15.
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
16.
Xuegong Zhang, Learning Specific Gene Relation Networks from
Literatures, 2005 Sina-German Workshop on
Networks: from Biology to Theory, Beijing,
17.
Xuegong Zhang, SVM and Its Application Examples in Computational
Biology, CSHL bioinformaics seminar,
18.
Xuegong Zhang, Computational Analysis of Haplotype Blocks and
Recombination Hotspots, Dr. Jun Liu’s lab
seminar at Harvard University,
19.
Xuegong
Zhang, Significance of
Gene Ranking for Classification of Microarray Samples, SRCCS 2004
International Workshop for Statistics, Seoul National University, Korea, June
2004
20.
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
Books and Book Chapters
1. 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
2. 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
3. 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
4.
张学工、刘业新编著, 《X Window /Motif编程速成》，清华大学出版社，1998.3
5.
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