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


  • Jingyu Wang, Fengling Chen, Longwei Liu, Chunxiao Qi, Bingjie Wang, Xiaojun Yan, Chenyu Huang, Wei Hou, Michael Q. Zhang, Yang Chen, Yanan Du, Engineering EMT using 3D micro-scaffold to promote hepatic functions for drug hepatotoxicity evaluation. Biomaterials, 2016. 91: p. 11-22.
  • Guipeng Li, Yang Chen, Michael P. Snyder and Michael Q. Zhang, ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis. Nucleic Acids Res, 2016. doi: 10.1093/nar/gkw809
  • Chao He*, Guipeng Li*, Diekidel M. Nadhir, Yang Chen, Xiaowo Wang and Michael Q. Zhang, Advances in computational ChIA-PET data analysis. Quantitative Biology, 2016. 4(3): p. 217-225.
  • Juntao Gao, Xusan Yang, Mohamed Nadhir Djekidel, Yang Wang, Peng Xi and Michael Q. Zhang, Developing bioimaging and quantitative methods to study 3D genome. Quantitative Biology, 2016. 4(2): p. 129-147.
  • Karl Zhanghao, Long Chen, Xusan Yang, Miaoyan Wang, Zhenli Jing, Hongbin Han, Michael Q. Zhang, Dayong Jin, Juntao Gao and Peng Xi, Super-resolution Dipole Orientation Mapping via Polarization Demodulation. Light: Science & Applications, 2016. 5: p. e16166.
  • Weilong Guo, Michael Q. Zhang and Hong Wu, Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Sci Rep, 2016. 6: p. 32207.
  • Xiaopeng Ma, Ge Zhan, Monica C. Sleumer, Siyu Chen, Weihong Liu, Michael Q. Zhang and Xiao Liu, Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT). Nucleic Acids Res, 2016.
  • Yang Yang, Lei Chen, Jin Gu,Hanshuo Zhang, Jiapei Yuan, Qiuyu Lian, Michael Q. Zhang, Zhi John Lu, et al, Recurrently deregulated lncRNAs associated with HCC tumorigenesis and metastasis revealed by genomic, epigenomic, and transcriptomic profiling in paired primary tumor and PVTT samples. Nature Comm, 2016.
  • Yanli Zhang, Jun Tang, Ning Yang, Qiang Liu, Qingchao Zhang, Yanxu Zhang, Ning Li, Yan Zhao, Shunwang Li, Song Liu, Huandi Zhou, Xiao Li, Mingyao Tian, Jiejie Deng, Peng Xie, Yang Sun, Huijun Lu, Zhang MQ, Ningyi Jin and Chengyu Jiang, FAT10 Is Critical in Influenza A Virus Replication by Inhibiting Type I IFN. J Immunol, 2016. 197(3): p. 824-33.
  • Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Zhang MQ and Runsheng Chen, NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res, 2016. 44(D1): p. D203-8.
  • Yong Chen, Yunfei Wang, Zhenyu Xuan, Min Chen and Zhang MQ, De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. Nucleic Acids Res, 2016. 44(11): p. e106.
  • Yu-An Zhang, Xiaotu Ma, Adwait Sathe, Junya Fujimoto, Ignacio I. Wistuba, Stephen Lam, Yasushi Yatabe, Yi-Wei Wang, Victor Stastny, Boning Gao, Jill E. Larsen, Luc Girard, Xiaoyun Liu, Kai Song, Carmen Behrens, Neda Kalhor, Yang Xie, Zhang MQ, John D. Minna, Adi F. Gazdar, Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers. J Thorac Oncol, 2016. 11(3): p. 346-60.


  • Djekidel, M.N., Liang, Z., Wang, Q., Hu, Z., Li, G., Chen, Y. and Zhang, M.Q. (2015) 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome biology, 16, 288.
  • 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.
  • Wu, D., Wang, D.,Zhang MQ and Gu, J. (2015) Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification. BMC genomics, 16, 1022.
  • 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, btv445.
  • 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 Dec. 12, 2016