清华合成与系统生物学中心
Tsinghua Center for Synthetic and Systems Biology
Micheal_Zhang_new
张奇伟 (Michael Q. Zhang)
教授,合成与系统生物学中心主任
清华大学国家实验室、医学院
首批“千人计划”获得者, 长江学者讲座教授





联系方式
电子邮件:
mzhang@cshl.edu; michaelqiweizhang@gmail.com

主要科研领域与方向  
      计算生物学与生物信息学,合成生物与系统生物学,特别是利用高通量组学技术和高性能计算机模拟,研究细胞发育、分化、凋亡的基因调控和代谢网络,以及它们在癌症等疾病、生物能源和环境中的应用。
教育背景及工作履历
  • 1977-1981 中科大近代力学系, 学士
  • 1981-1987 Rutgers U, 统计物理博士
  • 1987-1991 美国NYU Courant Inst.,应用数学博士后
  • 1991-1996 美国冷泉港实验室基因组研究Fellow
  • 1996-1998 美国冷泉港实验室,Assistant Staff
  • 1999-2001 美国冷泉港实验室,Associate Professor
  • 2002-2010 美国冷泉港实验室, Full Professor
  • 2009-至今 清华大学信息学院与医学院双聘教授,生命学院兼职教授, 博导,清华信息国家实验室合成与系统生物实验室主任
  • 2010-至今 美国UT Dallas,Cecil H. and Ida Green Distinguished Chair Professor, Director of Center for Systems Biology
发表论文及著作:  
  • Huang JF, Shang L, Zhang MQ, Wang H, Chen D, Tong JB, Huang H, Yan XX, Zeng LP, Xiong K. Differential neuronal expression of receptor interacting protein 3 in rat retina: involvement in ischemic stress response. BMC Neurosci. 2013 Feb 2;14:16. doi: 10.1186/1471-2202-14-16.
  • Kendrew SG, Petkovic H, Gaisser S, Ready SJ, Gregory MA, Coates NJ, Nur-E-Alam M, Warneck T, Suthar D, Foster TA, McDonald L, Schlingman G, Koehn FE, Skotnicki JS, Carter GT, Moss SJ, Zhang MQ, Martin CJ, Sheridan RM, Wilkinson B. Recombinant strains for the enhanced production of bioengineered rapalogs. Metab Eng. 2013 Jan;15:167-73. doi: 10.1016/j.ymben.2012.11.001. Epub 2012 Nov 17.
  • Hoffman MT, Doud MS, Williams L, Zhang MQ, Ding F, Stover E, Hall D, Zhang S, Jones L, Gooch M, Fleites L, Dixon W, Gabriel D, Duan YP. Heat treatment eliminates 'Candidatus Liberibacter asiaticus' from infected citrus trees under controlled conditions. Phytopathology. 2013 Jan;103(1):15-22. doi: 10.1094/PHYTO-06-12-0138-R.
  • Ouyang W, Will L, Luo CT, Yin N, Huse M, Kim MV, Peng M, Chan P, Ma Q, Mo Y, Meijer D, Zhao K, Rudensky AY, Atwal G, Zhang MQ*, Li MO* (2012) Novel Foxo1-dependent Transcriptional Programs Control Treg Cell Function. Nature. In press.
  • Xing H*, Mo Y, Liao W, Zhang MQ* (2012) Genomewide localization of protein-DNA binding and histone modification by BCP with ChIP-seq data. PLoS CB, 8(7): e1002613.
  • Sleumer MC, Wei G, Wang Y, Chang H, Xu T, Chen R, Zhang MQ (2012) Regulatory elements of Caenorhabditis elegans ribosomal protein genes. BMC Genomics. 13:433. PMID:22401550.
  • Li R, Guo W, Gu J, Zhang MQ, Wang XW (2012) Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics. [Epub ahead of print] PMID:22824656..
  • Zhang Z, Ma X, Zhang MQ (2012) Bivalent-like chromatin markers are predictive for transcription start site distribution in human. PLoS ONE, 7:e38112. PMID:22768038.
  • Chicas A*, Kapoor A*, Wang X*, Evertts AG, Benjam G, Zhang MQ, Bernstein E, Lowe SW, (2012) H3K4 demethylation by Jarid1a and Jarid1b contributes to RB-mediated gene silencing during cellular senescence. PNAS, 109:8971-6. PMID:22615382.
  • Zhang J, Wu Z, Gao C, Zhang MQ (2012) High-order interactions in Rheumatoid Arthritis detected by Bayesian method using GWAS data. American Medical Journal, 3:56-66.
  • Zhang C, Zhang MQ (2012) Identification of Splicing Factor Target Genes by High-throughput Sequencing. Chap. 51 in Alternative pre-mRNA Splicing: Theory and Protocols. Eds. Stamm S, Smith C, Luhrmann R. Wiley-Blackwell, Weinheim, Germany.
  • Zhang MQ (2012), Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data. Chap 12 in Bioinformatics for High Throughput Sequencing, eds. Rodriguez-Ezpeleta N, Hackenberg M, Aransay AM. p209. ISBN978-1-4614-0781-2, Springer.
  • Zhang J, Zhang Q, Lewis D, Zhang MQ (2012) A Bayesian Method for Disentangling Dependent Structure of Epistatic Interaction. Am. J. Biostat., 2:1-10.
  • He M, Liu Y, Wang X, Zhang MQ, Hannon GJ, Huang ZJ (2012) Cell-type based analysis of microRNA profiles in the mouse brain. Neuron. 73:35-48. PMID:22243745.
  • Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ (2012) POSMO: A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucl. Acid. Res. PMID:22228832.
  • Chen L, Zhang H, Li L, Yan Z, Wu DM, Liu Y, Liu K, Liu M, Hu L, Tu Q, Chang Y, Tan Y, Yang C, Song D, Fu J, Yang X, Feng Q, Chen H, Wu M, Yang H, Zhang MQ, Zhang Y, Wang J, Wang H (2011) Integrative whole genome analyses revealing clonal HBV integrations and abnormal enrichment of variable number tandem repeats in human hepatocellular carcinoma. J. Clinical Invest.
  • Ma X, Kulkarni A, Zhang Z, Xuan Z, Zhang MQ (2011) POSMO: A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.
  • Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ (2011) SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics, in press.
  • Dai Q, Lihua Li L, Liu X, Yao Y, Zhao F, Zhang M(2011) Integrating overlapping structures and background information of words significantly improves biological sequence comparison.
  • Shen M, Eyras E,Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S (2011) Direct cloning of double-stranded RNAs from RNAse protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. NAR, In press.
  • Watts JA, Zhang C, Klein-SzantoAJ,Kormish JD, Zhang MQ, Zaret K, (2011) Study of FoxA Pioneer Factor at Silent Genes Reveals Rfx-Repressed Enhancer at Cdx2 and a Potential Indicator of Esophageal Adenocarcinoma Development. PLoS Genet. In press.
  • Rajan P, Dalgliesh C, Carling P, Buist T, Zhang C, Grellscheid SN, Armstrong K, Stockley J, Simillion C, Gaughan L, Kalna G, Zhang MQ, Robson CN, Leung HY, Elliott DJ. (2011) Identification of novel androgen-related pathways and mRNAs isoforms through genome-wide exon-specific profiling of LNCaP transcriptome. Endocrine-Related Cancer.
  • Zhang Z, Zhang MQ (2011) Histone modification profiles are predictive for both protein-coding and microRNA gene’s tissue.cell-type specific expression. BMC Bioinformatics. In press.
  • Yang S, Yalamanchili HK, Li X, Yao K-M, Sham PC, Zhang MQ, Wang J. (2011) Correlated evolution of transcription factors and their binding sites. NAR, In press.
  • Qin J, Li M, Wang P, Zhang MQ, Wang J (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. NAR, in press.
  • Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ (2011) Inferring Haplotype of Copy Number variations from High-throughput data with Uncertainty. Genetics, In press.
  • Kato M, Yoon S, Hosono N, Leotta A, Sebat J, Tsunoda T, Zhang MQ (2011) Inferring Haplotype of Copy Number variations from High-throughput data with Uncertainty. Genetics, In press.
  • Valérie M. Renault, Pramod U. Thekkat, Kimmi L. Hoang, Jamie L. White, Colleen A. Brady, Daniela Kenzelmann, Ophelia S. Venturelli, Thomas M. Johnson, Zhenyu Xuan, Evan E. Santo, Michael Q. Zhang, Hannes Vogel, Laura D. Attardi, Anne Brunet (2011) The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene, In press.
  • Zhang MQ, (2011) Computational Promoter Prediction in a Vertebrate genome. Chap. In Handbook of Statistical Bioinformatics. Springer Handbooks of Computational Statistics. Lu H, Scholkopf B and Zhao H (Eds). In press. ISBN: 978-3-642-16344-9.
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