Xuegong Zhang,  Ph.D.

Professor of Pattern Recognition and Bioinformatics

Director, Bioinformatics Division, TNLIST

Deputy Director, MOE Key Laboratory of Bioinformatics

Department of Automation, FIT 1-107, Tsinghua University, Beijing 100084, China

Phone: 86-10-62794919,  Fax: 86-10-62786911,  Email: zhangxg@tsinghua.edu.cn

 Education

Ph.D. of Pattern Recognition and Intelligent Systems, Tsinghua University, 1994

B.S. of Industrial Automation, Tsinghua University, 1989 

  Working Experience

Director, Bioinformatics Division, TNLIST (Tsinghua National Laboratory of Information Science and Technology), 2003-present

Professor of Pattern Recognition and Bioinformatics, Department of Automation, Tsinghua University, 2002-present

Director, Institute of Information Processing, Department of Automation, Tsinghua University, 1999-2007

Associate Professor of Pattern Recognition, Department of Automation, Tsinghua University, 1996-2002

Lecturer, Department of Automation, Tsinghua University, 1994-1996

  Expertise and Research Interests

Machine Learning and Pattern Recognition: Theory, Methods and Applications;

Bioinformatics, Computational Genomics and Systems Biology

  Academic/Social Activities and Memberships

Associate Editor, BMC Bioinformatics

Associate Editor, Chinese Science Bulletin

Associate Editor, Acta Automatica Sinica

Deputy Director, Committee of Bioinformatics and Theoretical Biophysics, Chinese Association of Biophysics

Deputy Director, Committee of Bioinformatics and Artificial Life, Chinese Association of Artificial Intelligence

   Grants and Contracts / Research Projects

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

   Honors and Awards

2nd Prize of National Award for Excellence in Education Achievements, 2009

National Science Fund for Distinguished Young Scholars, 2006

2nd Prize of National Award for Advances in Science and Technology, 2001

   Academic Achievements

SELECTED RECENT PUBLICATIONS:

2010

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

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

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

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)  

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

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

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

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