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                張學工 教授

                清華信息★科學與技術國家實驗室(籌)生物信息〒學部主任
                生☆物信息學教育部重點實驗室副主任

                通信地址:北京 清華大學自動化系(100084) FIT樓1-107
                電話:010-62794919   Fax:010-62786911
                電子郵件:zhangxg@tsinghua.edu.cn

                展開
                教育背景

                1994年3月於清華大學獲模式識別※與智能系統專業工學博士學位

                1989年7月於清華大》學獲工業自動化專業工學學士學位

                工作履歷

                2003–今 清華信息科學與技術國家實驗室(籌)生物信息學部主任

                2002–今 清華大學自動化系 模式識別與生ζ 物信息學 教授

                2002–今 清華大學生物信息『學教育部重點實驗室 副主任

                2007.3-4 南加州大學分子與計◇算生物學系訪問學者

                2006.2-3 哈佛大學︽公共衛生學院訪問科學家

                2001–2002 哈佛大學公正在突破共衛生學院生物統計系高級訪問學者

                1999–2007 清華大學自動化系信息處理研究所 所長

                1996–2002 清華大學自動化系 模式識別理╲論及應用 副教授

                1994–1996 清華大學自動化系 講師

                研究領域

                機器學習與模式識別的理論、方』法與應用:

                支持向量機(SVM)與統計學習理論、核函數機器、人工神經網絡與自組織映射(SOM)、…

                生物信息學、計算功能基因組混蛋艾他这是不留余地學與系統生物學:

                組學數據分析:新一代測序數據處理與分析,基因表達數據挖掘,樣本和基因的監督與非監督分類→,基因選擇,可視化,基因表達數據中的隱藏模式發現

                基因調控分一副金光璀璨析:轉錄調控,表觀遺傳學調控,RNA調控,翻譯後修飾,特殊發育過程中的基因調控系統分析

                疾病基因組學:復雜疾病的計算系統生物學分析

                基因型與單倍型分就又是一个月析:Haplotype block分析與htSNP選擇,重組分析

                中醫藥現代化中的模式識別:中藥材產地與質ぷ量的自動鑒別、中藥藥效和作用機理的科學分析

                獎勵與√榮譽

                2009年國家教學成果二等獎

                2008年北京市教學成果一有字符元婴等獎

                2006年國我就不用了家傑出青年基金

                2004年教育部新世紀優秀人才支持計劃

                2002年國家科技進步二等獎

                2001年中國海洋石油總公司科技進步一等獎

                1995年國家教委科技進步二等獎

                學術成果

                期刊和會議論文:
                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. 張學工*,江瑞,汪小我,古槿,陳挺,從生物大數據到知識大發現】,《科學通報》,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: , 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序列數據可視化軟件[簡稱: RNASeqViewer] V1.0,中華人民共和國計算機◥軟件著作權登記,第0744989號,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,張學工,基於拷貝數變異的遺傳關聯研究,《科學通報》,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、馮智星、張學工,新一代高通量RNA測序數據嗤的處理與分析,《生物化學與生物物理進展》,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

                 

                 

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