Zemin Zhang
Cheung Kong Professor (PI)

  • E-mail:zemin#pku.edu.cn
  • Tel:+86-10-6276.8190
    Office:Rm. 310, Biodynamic Optical Imaging Center, Integrated Science Research Center, Peking University
    Mailing Address:Biodynamic Optical Imaging Center, Integrated Science Research Center, Peking University, Yiheyuan Rd., No. 5, Haidian District, Beijing, 100871
    Website:
  • Sc.D. Pennsylvania State University, 1995, Biochemistry and Molecular Biology
    B.S., Nankai University, 1988, Genetics

    Professional Experiences
  • 2014-PresentTenured Full Professor, Peking University, School of Life Sciences

    2014-PresentPeking University-Tsinghua University Center of Life Sciences, Senior Principle Investigator

    2014-PresentBIOPICPeking University, Principal Investigator

    1998-2014, Genentech Inc., South San Francisco, CA

    1995-1998 Postdoctoral Fellow, Howard Hughes Medical Institute (Laboratory of Yuet Wai Kan) University of California, San Francisco, CA, 


    Research Interests
  • Almost all characteristics of cancer cells, including how they respond to anti-cancer drugs, are determined by genetic and epigenetic alterations in the cancer genome. The Zhang Laboratory aims at understanding oncogenesis and developing novel therapies based on genomic characterization of tumors and cancer models. First, we will apply advanced bioinformatics methods to the tremendous cancer genomics data generated by us and various public efforts (such as TCGA and ICGC), with the goal to reveal cancer subtypes and subtype-specific cancer driving events. Second, we will build a large collection of cancer cell lines, with the initial focus on gastric and liver cancers, and study how cell lines with different genetic background might exhibit distinct responses to therapeutic agents. Third, we will collaborate with our colleagues at PKU and associated hospitals to investigate how cutting edge technologies such as single cell sequencing can be utilized for studying tumor heterogeneity and drug resistance.
    Awards and Honors
  • 2014-Present,Cheung Kong Scholar, Professor of Bioinformatics, School of Life Sciences, Peking University, China
    2014-Present, 1000 Talent Plan Scholar
    1988-1989 CUSBEA (China-US Biochemistry Exchange Program) training program

    Selected Publication
  • 34. R. Xue, R. Li, H. Guo, L. Guo, Z. Su, X. Ni, L. Qi, T. Zhang, Q. Li, Z. Zhang, X.S. Xie, F. Bai, and N. Zhang. (2016) Variable Extent of Intra-tumor Heterogeneity Revealed by Genomic Sequencing of Multiple Lesions in Patients with Hepatocellular Carcinoma. Gastroenterology. pii: S0016-5085(15)01861-2

    33. Z. Wang, Z. Shen, Z. Li, J. Duan, S. Fu, Z. Liu, H. Bai, Z. Zhang, J. Zhao, X. Wang, J. Wang (2015) Activation of the BMP-BMPR pathway conferred resistance to EGFR-TKIs in lung squamous cell carcinoma patients with EGFR mutations. Proc Natl Acad Sci U S A. 112:9990-5

    32. X. Hu and Z. Zhang. (2016) Understanding the Genetic Mechanisms of Cancer Drug Resistance Using Genomic Approaches. Trends In Genetics. 32(2):127-37.

    31. R. Xue, R. Li, H. Guo, L. Guo, Z. Su, X. Ni, L. Qi, T. Zhang, Q. Li, Z. Zhang, X.S. Xie, F. Bai, and N. Zhang. (2016) Variable Extent of Intra-tumor Heterogeneity Revealed by Genomic Sequencing of Multiple Lesions in Patients with Hepatocellular Carcinoma. Gastroenterology. pii: S0016-5085(15)01861-2

    30. C. Klijn, S. Durinck, E. Stawiski, P. M. Haverty, Z. Jiang, H. Liu, J. Degenhardt, O. Mayba, F. Gnad, J. Liu, G. Pau, J. Reeder, Y. Cao, K. Mukhyala, S. K. Selvaraj, M. Yu, G. J. Zynda, M. J. Brauer, T. D. Wu, R. C. Gentleman, G. Manning, R. L. Yauch, R. Bourgon, D. Stokoe, Z. Modrusan, R. M. Neve, F. J. de Sauvage, J. Settleman*, S. Seshagiri*, and Z. Zhang* (2015) A comprehensive transcriptional portrait of human cancer cell lines. Nature Biotechnology, 33:305-315

    29. Z. Wang, Z. Shen, Z. Li, J. Duan, S. Fu, Z. Liu, H. Bai, Z. Zhang, J. Zhao, X. Wang, J. Wang (2015) Activation of the BMP-BMPR pathway conferred resistance to EGFR-TKIs in lung squamous cell carcinoma patients with EGFR mutations. Proc Natl Acad Sci U S A. 112:9990-5

    28. F. Gnad*, S. Doll, G. Manning, D. Arnott, Z. Zhang* (2015) Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. BMC Genomics. 16:S5

    27. S. Jhunjhunwala, Z. Jiang, E. W. Stawiski, F. Gnad, J. Liu, O. Mayba, P. Du, J. Diao, C. Santos, K-F Wong, Z. Gao, Y. Li, S. Johnson, H. M. Stern, T. D. Wu, S. B. Kapadia, Z. Modrusan, J. M. Luk, D. M. French, S. Seshagiri, and Z. Zhang. (2014) Diverse modes of genomic alterations in hepatocellular carcinoma. Genome Biology, 15:436

    26. J. Liu, M. McCleland, E. Stawiski, F. Gnad, P. M. Haverty, S. Durinck, Y-J. Chen, C. Klijn, O. Mayba, S. Jhunjhunwala, M. Lawrence, H. Liu, Y. Wan, V. Chopra, W. Yuan, C. Ha, H. Gilbert, J. Reeder, G. Pau, J. Stinson, H. Stern, G. Manning, T. D. Wu, R. Neve, F. J. de Sauvage, Z. Modrusan, S. Seshagiri, R. Firestein, and Z. Zhang. (2014) Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer. Nature Communication, 5:3830, doi: 10.1038/ncomms4830

    25. O. Mayba, H. N. Gilbert, J. Liu, P. M. Haverty, S. Jhunjhunwala, Z. Jiang, C. Watanabe, and Z. Zhang. (2014) Allele specific expression detection in cancer tissues and cell lines by MBASED. Genome Biology, 15:405

    24. G. Lee, P. M. Haverty, L. Li, N. Kljavin, R. Bourgon, J. Lee, H. M. Stern, Z. Modrusan, S. Seshagiri, Z. Zhang, D. Davis, D. Stokoe, J. Settleman, F. J. de Sauvage, and R. M. Neve. (2014) Comparative oncogenomics identifies PSMB4 and SHMT2 as potential cancer driver genes. Cancer Research, 74:3114-26

    23. A. Adler, V. Chopra, M.L. McCleland, S. Hussain, G. Quinones, Z. Modrusan, S. Seshagiri, E. Torres, B. Haley, Z. Zhang, E.M. Blackwood, M. Singh, M. Junttila, J. Stephan, E. Fearson, Z. Jiang, and R. Firestein. (2014) An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth. Genes and Development, 28:1068-84

    22. F. Gnad, A. Baucom, K. Mukhyala, G. Manning, and Z. Zhang. (2013) Assessment of computational methods for predicting the effects of missense mutations in human cancers. BMC Genomics, 14:S7

    21. Z. Zhang* (2012), Genomic landscape of liver cancer. Nature Genetics, 44: 1075-1077

    20. J. Liu, W. Lee, Z. Chen, Z. Jiang, S. Jhunjhunwala, P. M Haverty, F. Gnad, Y. Guan, H. Gilbert, J. Stinson, C. Klijn, J. Guillory, D. Bhatt, S. Vartanian, K. Walter, J. Chan, P. Dijkgraaf, S. Johnson, J. Koeman, J. Minna, A. Gazdar, H. M. Stern, K. P. Hoeflich, T. D. Wu, F. J. de Sauvage, R. C. Gentleman, R. M. Neve, D. Stokoe, Z. Modrusan, S. Seshagiri, D. S. Shames, and Z. Zhang* (2012) Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Research, 22:2315-2327

    19. Z. Jiang, S. Jhunihunwala, J. Liu, P. Haverty, K. Pant, M. I. Kennemer, P. Carnevali, Y. Guan, J. Stinson, P. Dijkgraaf, J. Rae, S. Johnson, C. Watanabe, J. Diao, S. Kapadia, F. de Sauvage, R. Gentleman, H. Stern, S. Seshagiri, Z. Modrusan, D. Ballinger, and Z. Zhang* (2012) The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Research, 22:593-601

    18. C. M. Rudin, S. Durinck, E. W. Stawiski, J. T. Poirier, Z. Modrusan, D. Shames, E. A. Bergbower, Y. Guan, J. Shin, J. Guillory, C. S. Rivers, C. Foo, D. Bhatt, J. Stinson, F. Gnad, P. M. Haverty, R. Gentleman, S. Chaudhuri, V. Janakiraman, B. S. Jaiswal, C. Parikh, W. Yuan, Z. Zhang, H. Koeppen, T. D. Wu, H. M Stern, R. L. Yauch, K. E. Huffman, D. D. Paskulin, P. B. Illei, M. Varella-Garcia, A. F. Gazdar, F. J. de Sauvage, R. Bourgon, J. D. Minna, M. V. Brock, and S. Seshagiri (2012) Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small cell lung cancer. Nature Genetics, 44: 1111-1116

    17. S. Seshagiri, E. Stawiski, S. Durinck, Z. Modrusan, E. Storm, C. B. Conboy, S. Chaudhuri, Y. Guan, V. Janakiraman, B. S. Jaiswal, J. Guillory, C. Ha, G. J. P. Dijkgraaf, J. Stinson, F. Gnad, M. Huntley, J. D. Degenhardt, P. M. Haverty, R. Bourgon, W. Wang, H. Koeppan, R. Gentleman, T. K. Starr, Z. Zhang, D. A. Largaespada, T. D. Wu, and F. J. de Sauvage (2012) Recurrent R-spondin fusions in colon cancer. Nature, 488, 660–664

    16. W. Lee, Z. Jiang, J. Liu, P. M. Haverty, Y. Guan, J. Stinson, P. Yue, Y. Zhang, K. P. Pant, D. Bhatt, C. Ha, S. Johnson., M. I. Kennemer, S. Mohan, I. Nazarenko, C. Watanabe, A. B. Sparks, D. S. Shames, R. Gentleman, F. J. de Sauvage, H. Stern, A. Pandita, D. G. Ballinger, R. Drmanac, Z. Modrusan, S. Seshagiri, and Z. Zhang* (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature, 465:473-477

    15. Z. Kan, B. S. Jaiswal, J. Stinson, V. Janakiraman, D. Bhatt, H. M. Stern, P. Yue, P. M. Haverty, R. Bourgon, J. Zheng, M. Moorhead, S. Chaudhuri, L. P. Tomsho, B. A. Peters, K. Pujara, S. Cordes, D. P. Davis, V. E. Carlton, W. Yuan, L. Li, W. Wang, C. Eigenbrot, J. S. Kaminker, D. A. Eberhard, P. Waring, S. C. Schuster, Z. Modrusan, Z. Zhang, D. Stokoe, F. J. de Sauvage, M. Faham and S. Seshagiri. (2010) Diverse somatic mutation patterns and pathway alterations in human cancers. Nature, 466: 869-873

    14. W. Lee, P. Yue, and Z. Zhang*. (2009) Analytical methods for inferring functional effects of single base-pair substitutions in human cancers. Human Genetics, 126:481-498

    13. L. S. Hon, Y. Zhang, J. S. Kaminker, and Z. Zhang*. (2009) Computational prediction of the functional effects of amino acid substitutions in signal peptides using a model-based approach. Human Mutation, 30 (1): 99-106

    12. J. Liu, Y. Zhang, X. Lei, and Z. Zhang*. (2008) Natural selection of protein structural and functional properties: a SNP perspective. Genome Biology, 9(4): R69

    11. L. D. Wood, D. W. Parsons, S. Jones, J. Lin, T. Sj?blom, R. J. Leary, D. Shen, S. M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P. A. Wilson, J. S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J. K. V. Willson, S. Sukumar, K. Polyak, B. H. Park, C. L. Pethiyagoda, P. V. K. Pant, D. G. Ballinger, A. B. Sparks, J. Hartigan, D. R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S. D. Markowitz, G. Parmigiani, K. W. Kinzler, V. E. Velculescu, and B. Vogelstein. (2007) The genomic landscapes of human breast and colorectal cancers. Science, 318: 1108-1113

    10. N. Kayagaki, Q. Phung, S. Chan, R. Chaudhari, C. Quan, K. M. O'Rourke, M. Eby, E. Pietras, G. Cheng, J. F. Bazan, Z. Zhang, D. Arnott, and V. M. Dixit. (2007) DUBA: a deubiquitinase that regulates type I interferon production. Science, 318: 1628-1632

    9. L. S. Hon and Z. Zhang*. (2007) The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biology, 8 (8): R166

    8. J. S. Kaminker, Y. Zhang, C. Watanabe, and Z. Zhang*. (2007) CanPredict: A computational tool for predicting missense cancer-associated mutations. Nucleic Acids Research, 35: W595-598

    7. Y. Zhang, S-M Luoh, L. S. Hon, R. Baertsch, W. I. Wood and Z. Zhang*. (2007) GeneHub-GEPIS: Digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Research, 35: W152-158

    6. J. S. Kaminker, Y. Zhang, A. Waugh, P. Haverty, J. Stinson, B. Peters, D. Sebisanovic, W. F. Forrest, J. F. Bazan, S. Seshagiri, and Z. Zhang*. (2007) Distinguishing cancer associated missense mutations from common polymorphisms. Cancer Research, 67: 465-473

    5. Z. Zhang* and W. J. Henzel. (2004) Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Science, 13: 2819-2824

    4. Y. Zhang, D. Eberhard, G. D. Frantz, P. Dowd, T. D. Wu, C. Watanabe, Y. Zhou, P. Polakis, K. J. Hillan, W. I. Wood, and Z. Zhang*. (2004) GEPIS – Quantitative gene expression profiling in normal and cancer tissues. Bioinformatics, 20: 2390-2398

    3. E. Wertz, K. M. O’Rourke, Z. Zhang, D. Dornan, D. Arnott, R. J. Deshaies, and V. M. Dixit. (2004) Human De-etiolated-1 regulates c-Jun by assembling a CUL4A ubiquitin ligase. Science, 303: 1371-1374

    2. Y. Zhou, S-M. Luoh, Y. Zhang, C. Watanabe, T. D. Wu, M. Ostland, W. I. Wood, and Z. Zhang*. (2003) Genome-wide identification of chromosome regions of increased tumor expression by transcriptome analysis. Cancer Research, 63: 5781-5784

    1. J. LeCouter, J. Kowalski, J. Foster, P. Hass, Z. Zhang, L. Dillard-Telm, G. Frantz, L. Rangell, L. DeGuzman, G-A. Keller, F. Peale, A. Gurney, K. J. Hillan, and N. Ferrara. (2001) Identification of an angiogenic mitogen selective for endocrine gland endothelium. Nature, 412: 877-884