Lab


Lab

Zemin Zhang

Computational Genomics

Center For Biolnformatics, School of Life Sciences, Peking University

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

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

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

2014-Present,BIOPIC,Peking University, Principal Investigator

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

2014-Present,Tenured Full Professor, Peking University, School of Life Sciences

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

1. 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 kinase isoform usage in gastric cancer. Nature Communication, 5:3830, doi: 10.1038/ncomms4830 (* denotes corresponding author)

2. 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 (in press)

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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

13. L. D. Wood, D. W. Parsons, S. Jones, J. Lin, T. Sjöblom, 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

14. 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

15. 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

16. 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

17. 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

18. 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

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

20. 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

21. 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

22. 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

23. 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