个人简历:
1989年 获清华大学自动化系学士学位
1994年 获清华大学模式识别与智能系统专业博士学位
2001--2002年 哈佛大学公共卫生学院高级访问学者
现为清华大学自动化系教授、生命学院和医学院兼职教授
主要科研领域及方向:
主要研究方向是模式识别、生物信息学与系统生物学。在高通量组学数据处理与分析方法、RNA测序与选择性剪接调控、宏基因组分析、生物大数据机器学习与精准医学应用方面取得多项成果。。
代表论文:
2015
Aziz Khan & Xuegong Zhang, dbSUPER: a database of super-enhancers in mouse and human genome, Nucleic Acids Research, advanced access Oct.4, 2015
Huijuan Feng, Xuegong Zhang, Chaolin Zhang, mRNA for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data, Nature Communications, 6: 7836, 2015
Junfeng Li, Junyi Zhang, Liyang Liu, Yucai Fan, Lianshuo Li, Yunfeng Yang, Zuhong Lu, Xuegong Zhang, Annual periodicity in planktonic bacterial and archaeal community composition of eutrophic Lake Taihu,Scientific Reports, 5: 15488, 2015
Chao Ye, Bo Jiang, Xuegong Zhang, Jun S. Liu, dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis, Bioinformatics, 31(11): 1842-1844, 2015
2014
Zhixing Feng, Jing Li, Jing-Ren Zhang, Xuegong Zhang, qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data, Nucleic Acids Research, 42(22): 13488-13499, 2014
Leying Guan, Qian Yang, Mengting Gu, Liang Chen, Xuegong Zhang, Exon expression QTL (eeQTL) analysis highlights distant genomic variations associated with splicing regulation, Quantitative Biology, 2(2): 71-79, 2014
Guang-Zhong Wang, Simone Marini, Xinyun Ma, Qiang Yang, Xuegong Zhang, Yan Zhu*, Improvement of Dscam hemophilic binding affinity throughout Drosophila evolution, BMC Evolutionary Biology, 4: 186, 2014
YingXue Li, XueNing Liu, XiaoWo Wang, Xuegong Zhang, Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 57(1): 52-58, 2014
Xavier Roge, Xuegong Zhang, RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892, 2014
Yong Chen, Yunfeng Ding, Yi Yang, Jinhai Yu, Guiing Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, Peng Zhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Alexander Steinbuchel, Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu, Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic Acids Research, 42(2): 1042-1064, 2014
Shufang Zhang, Xueya Zhou, Shengnan Liu, Tingting Bai, Yingai Zhang, Jing Wang, Shunlan Wang, Xuegong Zhang, Binbin, Wang, MYH9‑related disease: description of a large Chinese pedigree and a survey of reported mutations, Acta Haematologica, 132: 193-198, 2014
Jing Cheng, Xueya Zhou, Yu Lu, Jing Chen, Bing Han, Yuhua Zhu, Liyang Liu, Kwong‑Wai Choy, Dongyi Han, Pak C. Sham, Michael Q. Zhang, Xuegong Zhang, Huijun Yuan, Exom sequencing identifies a novel frameshift mutation of MYO6 as the cause of autosomal dominant nonsyndromic hearing loss in a Chinese Family, Annals of Human Genetics, 78: 410-423, 2014
Yu Lu, Xueya Zhou, Zhanguo Jin, Jing Cheng, Weidong Shen, Fei Ji, Liyang Liu, Xuegong Zhang, Michael Zhang, Ye Cao, Dongyi Han, KwongWai Choy, Huijun Yuan, Resolving the genetic heterogeneity of prelingual hearing loss within one family: performance comparison and application of two targeted next generation sequencing approaches, Journal of Human Genetics, 59: 599-607, 2014
Chao Ye, Xuegong Zhang, A simulation study on gene expression regulation via stochastic model, Proceedings of the 33rd Chinese Control Conference, pp. 6885-6888, July 28-30, 2014, Nanjing, China
Qifeng Xu, Xuegong Zhang, Multiclass feature selection algorithms based on R-SVM, IEEE ChinaSIP, 525-529, 2014
RNA序列数据可视化软件[简称: RNASeqViewer] V1.0，中华人民共和国计算机软件著作权登记，第0744989号，2014.6.11
2013
Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric Schadt, Detecting DNA modification from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic, PLoS Computational Biology, 9(3): e1002935, March 2013
Weichen Wang, Zhiyi Qin, Zhixing Feng, Xi Wang, Xuegong Zhang, Identifying differentially spliced genes from two groups of RNA-seq samples, GENE, 518: 164-170, 2013
Ali Nowrouze, Wing T. Cheung, Tingting Li, Xuegong Zhang, Anne Arens, Anna Paruzynski, Simon N. Waddington, Emma Osejindu, Safia Reja, Christof von Kalle, Yoahe Wang, Faisal Al-Allaf, Lisa Gregory, Matthew Themis, Maxine Holder, Niraja Dighe, Alaine Ruthe, Suzanne MK Buckley, Brian Bigger, Eugenio Montini, Adrian J. Thrasher, Robert Andrews, Terry P. Roberts, Robert F. Newbold, Charles Coutelle, Manfred Schmidt, Mike Themis, The fetal mouse is a sensitive genotoxicity model that exposes lentiviral-associated mutagenesis resulting in liver oncogenesis, Molecular Therapy, 21: 324-337, Feb. 2013
2012
Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang, Comparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012
Bai Jiang, Xujun Liang, Yang Chen, Tao Ma, Liyang Liu, Junfeng Li, Rui Jiang, Ting Chen, Xuegong Zhang, Shao Li, Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome, Scientific Reports, 2: 936, 2012
Huijuan Feng, Zhiyi Qin, Xuegong Zhang, Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer Letters, doi: http://dx.doi.org/10.1016/j.canlet.2012.11.010, 2012
Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang, Cmoparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012
Chao Wu, Jun Zhu, Xuegong Zhang, Inegrating gene expression and protein-protein interaction network to prioritize cancer-associated genes, BMC Bioinformatics, 13: 182, 2012
Tingting Li, Yipeng Du, Likun Wang, Lei Huang, Wenlin Li, Ming Lu, Xuegong Zhang, Wei-Guo Zhu, Characterization and prediction of lysine(k)-acetyl-transferase specific acetylation sites, Molecular & Cellular Proteomics, 11(1): M111.011080, Jan 2012
2011
Xi Wang, Xuegong Zhang, Pinpointing Transcription Factor Binding Sites from ChIP-seq Data with SeqSite, BMC Systems Biology, 5(Suppl 2): S3, 2011
周雪崖，张学工，基于拷贝数变异的遗传关联研究，《科学通报》，56(6): 370-382, 2011
Chao Ye, Linxi Liu, Xi Wang, Xuegong Zhang, Observations on potential novel transcripts from RNA-Seq data, Front. Electr. Electron. Eng. China,6(2): 275-282, 2011
Weichen Wang & Xuegong Zhang, Network-based group variable selection for detecting expression quantitative trait loci (eQTL), BMC Bioinformatics, 12: 269, 2011
N. Kato et al, Meta-analysis of genome-wide association studies identifies five novel variants associated with blood pressure in east Asians, Nature Genetics, 43(6): 531-538, 2011
Chao Ye, Ying Liu, Xuegong Zhang, Observations on shifted cumulative regulation, Genome Biology, 12:404, 2011
Likun Wang, Xiaowo Wang, Xi Wang, Yanchun Liang, Xuegong Zhang, Observations on novel splice junctions from RNA sequencing data, Biochemical and Biophysical Research Communications, 409: 299-303, 2011
Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman, Sequence alignment as hypothesis testing, Journal of Computational Biology, 18(5): 677-691, May 2011
Zhengpeng Wu, Xi Wang, Xuegong Zhang, Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq, Bioinformatics, 27(4): 502-508, 2011
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
联系方式:
清华大学自动化系
北京100084，中国
电话：+86-10-62794919
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