张学工 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

通信地址:北京 清华大学自动化系(100084) FIT楼1-107
电话:010-62794919   Fax:010-62786911
电子邮件:zhangxg@tsinghua.edu.cn

教育背景

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

工作履历

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

研究领域

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

奖励与荣誉

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

期刊和会议论文:
2017

1. Xuegong Zhang*, Shansong Liu, Hongfei Cui, Ting Chen, Reading the underlying information from massive metagenomic sequencing data, Proceedings of the IEEE, 105(3): 459-473, 2017 doi: 10.1109/JPROC.2016.2604406

2016
2. Zhun Miao, Xuegong Zhang, Differential expression analyses for single-cell RNA-Seq: old questions on new data, Quantitative Biology, 4(4): 243-260, 2016

3. 张学工*,江瑞,汪小我,古槿,陈挺,从生物大数据到知识大发现,《科学通报》,61(36): 3869-3877, 2016

4. Yu Xue, Eric-Wubbo Lameijer, Kai Ye, Kunlin Zhang, Suhua Chang, Xiaoyue Wang, Jianmin Wu, Ge Gao, Fangqing Zhao, Jian Li, Chunsheng Han, Shuhua Xu, Jingfa Xiao, Xuerui Yang, Xiaomin Ying, Xuegong Zhang, Wei-Hua Chen, Yun Liu, Zhang Zhang, Kun Huang, Jun Yu, Precision medicine: what challenges are we facing? Genomics Proteomics Bioinformatics, 14: 253-261, 2016

5. Binbin Wang, Taoyun Ji, Xueya Zhou, Jing Wang, Xi Wang, Jingmin Wang, Dingliang Zhu, Xuejun Zhang, Pak Chung Sham, Xuegong Zhang, Xu Ma, Yuwu Jiang, CNV analysis in Chinese children of mental retardation highlights a sex differentiation in parental contribution to de novo and inherited mutational burdens, Scientific Reports, 6: 25954, 2016

6. Hui Chen, Xueya Zhou, Jing Wang, Xi Wang, Liyang Liu, Shinan Wu, Tenyan Li, Si Chen, Jingwen Yang, Pak Chung Sham, Guangming Zhu, Xuegong Zhang, Binbin Wang, Exome sequencing and gene prioritization correct misdiagnosis in a Chinese kindred with familial amyloid polyneuropathy, Scientific Reports, 6: 26362, 2016

7. Qifeng Xu, Xuegong Zhang*, The influence of the global gene expression shift on downstream analyses, PLoS ONE, 11(4): e0153903, 2016

8. Jing Li, Jing-Wen Li, Zhixing Feng, Juanjuan Wang, Haoran An, Yanni Liu, Yang Wang, Kailing Wang, Xuegong Zhang, Zhun Miao, Wenbo Liang, Robert Sebra, Guilin Wang, Wen-Ching Wang, Jing-Ren Zhang, Epigenetic switch driven by DNA inversions dictates phase variation in Streptococcus pneumonia, PLoS Pathogens, 12(7): e1005762, 2016

9. Lu Zhang, Xiaoqiao Liu, Xuegong Zhang*, Ronghua Chen*, Identification of important long non-coding RNAs and highly recurrent aberrant alternative splicing events in hepatocellular carcinoma through integrative analysis of multiple RNA-Seq datasets, Molecular Genetics and Genomics, 291(3): 1035-1051, 2016

10. Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michal Wojciech Szczesnik, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi, A survey of best practices for RNA-seq data analysis, Genome Biology, 17:13, 2016

11. Tatiana C. Mangericao, Zhanhao Peng, Xuegong Zhang*, Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls, BMC Systems Biology, 10(Suppl 1): 5, 2016

12. Aziz Khan & Xuegong Zhang*, dbSUPER: a database of super-enhancers in mouse and human genome, Nucleic Acids Research, 44(D1): D164-D171, Jan 2016

13. Hongfei Cui, Yingxue Li, Xuegong Zhang*, An overview of major metagenomic studies on human microbiomes in health and disease, Quantitative Biology, 4(3): 192-206, 2016

14. Huijuan Feng, Tingting Li, Xuegong Zhang*, Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-seq data, bioRxiv, doi: http://dx.doi.org/10.1101/061085, June 2016

2015
15. Huijuan Feng, Xuegong Zhang, Chaolin Zhang, mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data, Nature Communications, 6: 7836, 2015

16. 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

17. 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
18. 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

19. 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

20. 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

21. 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

22. Xavier Roge, Xuegong Zhang*, RNAseqViewer: visualization tool for RNA-Seq data, Bioinformatics, 30(6): 891-892, 2014

23. 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

24. 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

25. 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

26. 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 

27. 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

28. Qifeng Xu, Xuegong Zhang, Multiclass feature selection algorithms based on R-SVM, IEEE ChinaSIP, 525-529, 2014

29. 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
30. Eric E. Schadt, Onureena Banerjee, Gang Fangs, Zhixing Feng, Wing H. Wong, Xuegong Zhang, Andrey Kislyuk, Tyson A. Clark, Khai Luong, Alona Keren-Paz, Andrew Chess, Vipin Kumar, Alice Chen-Plotkin, Neal Sondheimer, Jonas Korlach, Andrew Kasarskis, Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases, Genome Research, 23: 129-141, 2013

31. Xuegong Zhang, Fengzhu Sun, Meeting report on RECOMB 2013 (the 17th Annual International Conference on Research in Computational Molecular Biology), Quantitative Biology, 1(2): 175-181, 2013

32. Yan Wang, Yi Zhang, Yan Li, Xueya Zhou, Xiaofeng Wang, Pingjin Gao, Li Jin, Xuegong Zhang, Dingliang Zhu, Common variants in the ATP2B1 gene are associated with hypertension and arterial stiffness in Chinese population, Molecular Biology Reports, 40: 1867-1873, 2013

33. Xueya Zhou, Suying Bao, Binbin Wang, Xuegong Zhang, You-Qiang Song, Short read mapping for exome sequencing, Chapter 6 of Noam Shomron (ed.), Deep Sequencing Data Analysis, Methods, in Molecular Biology, vol. 1038, NY: Springer, 2013

34. Suying Bao, Xueya Zhou, Liangcai Zhang, Jie Zhou, Kelvin Kai-Wang To, Binbin Wang, Liqiu Wang, Xuegong Zhang, You-Qiang Song, Prioritizing genes responsible for host resistance to influenza using network approaches, BMC Genomics, 14: 816, 2013

35. Chao Wu, Jun Zhu, Xuegong Zhang, Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma, BMC Bioinformatics, 14: 365, 2013

36. Hongfei Cui, Xuegong Zhang, Alignment-free supervised classification of metagenomes by recursive SVM, BMC Genomics, 14: 641, 2013

37. Qiongshi Lu, Siin Ren, Ming Lu, Yong Zhang, Dahai Zhu, Xuegong Zhang, Tingting Li, Computational prediction of associations between long non-coding RNAs and proteins, BMC Genomics, 14: 651, 2013

38. Huijuan Feng, Zhiyi Qin, Xuegong Zhang, Opportunities and methods for studying alternative splicing in cancer with RNA-Seq, Cancer Letters, 340: 179-191, 2013

39. Xinyun Ma, Xuegong Zhang, NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data, BMC Bioinformatics, 14: 220, 2013

40. 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 

41. 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

42. Yong Chen, Jingjing Hao, Wei Jiang, Tong He, Xuegong Zhang, Tao Jiang, Rui Jiang, Identifying potential cancer driver genes by genomic data integration, Scientific Reports, 3: 3538, 2013

43. 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

44. Hongshan Jiang, Ying Zhao, Wenguang Chen, Weimin Zheng, Xuegong Zhang, Improving cis-regulatory elements modeling by consensus scaffolded mixture models, Science in China - Information Sciences, 56: 012501:1-012501:11, 2013

2012
45. Bai Jiang, Kai Song, Jie Ren, Minghua Deng, Fengzhu Sun, Xuegong Zhang, Comparison of metagenomic samples using sequence signatures, BMC Genomics, 13: 730, 2012

46. 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

47. Chao Wu, Jun Zhu, Xuegong Zhang, Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes, BMC Bioinformatics, 13: 182, 2012

48. 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
49. Xi Wang, Xuegong Zhang, Pinpointing Transcription Factor Binding Sites from ChIP-seq Data with SeqSite, BMC Systems Biology, 5(Suppl 2): S3, 2011

50. 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

51. 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

52. Weichen Wang & Xuegong Zhang, Network-based group variable selection for detecting expression quantitative trait loci (eQTL), BMC Bioinformatics, 12: 269, 2011

53. N. Kato et al, Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians, Nature Genetics, 43(6): 531-538, 2011

54. Chao Ye, Ying Liu, Xuegong Zhang, Observations on shifted cumulative regulation, Genome Biology, 12:404, 2011

55. 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

56. Lu Meng, Fengzhu Sun, Xuegong Zhang, Michael S. Waterman, Sequence alignment as hypothesis testing, Journal of Computational Biology, 18(5): 677-691, May 2011

57. 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
58. 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

59. 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

60. Ting Zhang, Xuegong Zhang, Zhirong Sun, Global network analysis of lipid-raft-related proteins reveals their centrality in the network and their roles in multiple biological processes, Journal of Molecular Biology, 402(4): 761-773, 2010

61. 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

62. The MAQC Consortium, The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models, Nature Biotechnology, 28(8): 827-841, 2010

63. 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

64. 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

65. 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