Michael Q. Zhang
Michael Q. Zhang
Dept of MCB, Center for Systems Biology, UT Dallas, USA
Email: michael.zhang AT utdallas.edu

Guest Professor in both school of Information Science and Technology and Medical School
Adjunct professor in Life School
Doctoral Supervisor
Director of Center for Synthetic and Systems Biology, Tsinghua U., Beijing
Qian Ren Ji Hua Distinguished Adjunct Professor
Chang Jiang Chair Professor
Email: michaelzhang AT tsinghua.edu.cn

Research  Top

Computational Biology, Synthetic biology and system biology, especially high-throughput technology and high performance computational researches, focus on gene regulation network and metabolic network during the cell developing, differentiation and apoptosis, and the application in cancer, bioenergy and environment.

Publications  Top


  • Djekidel MN, Liang ZY, Wang Q, Hu Z, Li G, Chen Y, Zhang MQ, (2015) 3CPET: Finding Co-factor Complexes from ChIA-PET data by using Hierarchical Dirichlet Process. Genome Biol. In press.
  • Zhang H*, Zhu C*, Zhao Y*, Li M, Wu L, Yang X, Wan X, Wang A, Zhang MQ+, Sang X+, Zhao H+ (2015) Long non-coding RNA expression profiles of Hepatitis Cvirus-related dysplasia and hepatocellular carcinoma. Oncotarget, DOI: 10.18632/oncotarget.6087.
  • Zhao, Yi; Li, Hui; Fang, shuangsang; Kang, Yue; Wu, Wei; Hao, Yajing; Li, Ziyang; Bu, Dechao; Sun, Ninghui; Zhang MQ*; Chen, Runsheng* (2015) NONCODE 2016: an informative and valuable data source of long noncoding RNAs. NAR, In press
  • Wu D, Wang D, Zhang MQ, Jin Gu (2015) Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification. MBC Genomics, In press.
  • Sathe, A.; Zhang, Yu-An; Ma, X.; Ray, P.; Cadinu, D.; Wang, Yi-Wei; Yao, X.; Liu, Xiao-Yun; Tang, H.; Wang, Y.; Huang, Y.; Liu, C.; Gu, J.; Akerman, M.; Mo, Y.; Cheng, C.; Xuan, Z.; Chen, L.; Xiao, G.; Xie, Y.; Girard, L.; Wang, H.; Lam, S.; Wistuba, I.I.; Zhang, L.; Gazdar, A.F.; Zhang MQ. (2015) "SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers," in Life Sciences Letters, IEEE , vol.PP, no.99, pp.1-1. doi: 10.1109/LLS.2015.2488438
  • Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park I, Kim TH (2015) Histone deacetylases positively regulate transcription through the elongation machinery. Cell Rep. in press.
  • Mehta, H. H., Liu, Y., Zhang MQ, & Spiro, S. (2015). Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073. Microbial Genomics, 1(4).
  • He C, Zhang MQ, Wang X (2015) MICC: an R package for identifying chromatin interactions from ChIA-PET data. Bioinformatics, in press.
  • Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, Ren B, Krainer AR, Maniatis T, Wu Q (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell 162:900-10. PMID: 26276636.
  • Ehrhardt K, Guinn MT, Quarton T, Zhang MQ, Bleris L (2015) Reconfigurable hybrid interface for molecular marker diagnostics and in-situ reporting. Biosens Bioelectron. 74:744-750. PMID: 26210472
  • Hu L, Di C, Kai M, Yang Y-C, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ (2015) A common set of distinct features that characterize noncoding RNAs across multiple species. NAR. 43:104-14. PMID: 25505163, PMCID: PMC4288202.
  • Orozco LD, Marco Morselli M, Rubbi L, Guo W, Go J, Shi H, Lopez D, Furlotte NA, Bennett BJ, Charles R. Farber CR, Ghazalpour A, Zhang MQ, Bahous R, Rozen R, Lusis AJ, Pellegrini M (2015) Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice. Cell Metabolism, 21:905-17. PMID: 26039453, PMCID: PMC4454894.
  • Sun G, Hu Z, Min Z, Yan X, Guan Z, Su H, Fu Y, Ma X, Chen Y-G, Zhang MQ*, Tao Q*, Wu W* (2015) Small C-terminal Domain Phosphatase 3 Dephosphorylates the Linker Sites of Receptor-regulated Smads (R-Smads) to Ensure Transforming Growth Factor β (TGFβ)-mediated Germ Layer Induction in Xenopus Embryos. JBC, 290:17239-49. PMID: 26013826, PMCID: PMC4498063.
  • Akerman M, Fregoso O, Das S, Ruse C, Jensen MA, Pappin DL, Zhang MQ, Krainer A. (2015) Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biol. 16:119. PMID: 26047612, PMCID: PMC4502471.
  • Wang T, Xiao G; Chu Y, Zhang MQ, Corey D, Xie Y (2015) Design and bioinformatics analysis of genome-wide CLIP experiments. NAR, PMID:25958398.
  • Huo W, Adams HM, Zhang MQ, Palmer KL (2015) Genome modification in Enterococcus faecalisOG1RF assessed by bisulfite sequencing and single molecule real time sequencing. J. Bacteriology 197:1939-51. PMID:25825433.
  • Yuan Y, Liu B, Xie P, Zhang MQ, Li Y, Zhen X, Wang X (2015) Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit. PNAS, 112:3158-63. PMID:25713348.
  • Raodmap Epigenomics Consortium (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518:317-30. PMID:25693563
  • Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B (2015) Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature, 518:350-4. PMID:25693566
  • Li L, Tang J, Zhang B, Yang W, Liugao M, Wang R, Tan Y, Fan J, Chang Y, Fu J, Jiang F, Chen C, Yang Y, Gu J, Wu D, Guo L, Cao D, Li H, Cao G, Wu M, Zhang MQ, Chen L, Wang H (2015) Epigenetic modification of MiR-429 promotes liver tumour-initiating cell properties by targeting Rb binding protein 4. Gut 64:156-67. PMID: 24572141.

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Updated on Nov. 20, 2015