Zemin Zhang

张泽民
研究员

  • E-mail:zemin#pku.edu.cn
  • 办公电话:+86-10-6276.8190
  • 办公地点:北京大学综合科研楼生物动态光学成像中心310室
  • 邮件地址:北京市海淀区颐和园路5号北京大学生物动态光学成像中心310室,100871

教育经历

  • 理学博士,美国宾州州立大学,1995,生物化学和分子生物学
  • 理学学士,南开大学,1988,遗传学

工作经历

  • 1995-1998,美国旧金山加州大学,博士后
  • 1998-2014,美国GENENTECH、ROCHE公司科研部,生物信息首席科学家
  • 2014-现在,北京大学BIOPIC,研究员
  • 2014-现在,北大-清华生命科学中心,高级研究员
  • 2014-现在,北京大学生命科学院,终身教授

获奖及荣誉

  • 2014年获得教育部“长江学者”荣誉;
  • 2014年获得国家中组部“千人计划”荣誉;
  • 1989年CUSBEA学者

代表性论文及论著

1. S. Z. Wang Z, Li Z, Duan J, Fu S, Liu Z, Bai H,Z. Zhang, Zhao J, Wang X, Wang J. Activation of the BMP-BMPR pathway conferred resistance to EGFR-TKIs in lung squamous cell carcinoma patients with EGFR mutations. . PNAS 112, 9990-9995 (2015).
2. C. Klijn, S. Durinck, E. W. 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, S. Jeffrey, S. Somasekar & Z. Zhang*. A comprehensive transcriptional portrait of human cancer cell lines. Nat Biotech 33, 306-312 (2015).
3. F. Gnad, S. Doll, G. Manning, D. Arnott & Z. Zhang*. Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer. BMC Genomics 16, S5-S5 (2015).
4. O. Mayba, F. Gnad, M. Peyton, F. A. N. Zhang, K. Walter, P. A. N. Du, M. A. Huntley, Z. Jiang, J. Liu, P. M. Haverty, R. C. Gentleman, R. Li, J. D. Minna, Y. Li, D. S. Shames & Z. Zhang*. INTEGRATIVE ANALYSIS OF TWO CELL LINES DERIVED FROM A NON-SMALL-LUNG CANCER PATIENT – A PANOMICS APPROACH. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 75-86 (2014).
5. O. Mayba, H. N. Gilbert, J. Liu, P. M. Haverty, S. Jhunjhunwala, Z. Jiang, C. Watanabe & Z. Zhang*. MBASED: allele-specific expression detection in cancer tissues and cell lines. Genome Biology 15, 405 (2014).
6. J. Liu, M. McCleland, E. W. Stawiski, F. Gnad, O. Mayba, P. M. Haverty, S. Durinck, Y.-J. Chen, C. Klijn, S. Jhunjhunwala, M. Lawrence, H. Liu, Y. Wan, V. Chopra, M. B. Yaylaoglu, W. Yuan, C. Ha, H. N. Gilbert, J. Reeder, G. Pau, J. Stinson, H. M. Stern, G. Manning, T. D. Wu, R. M. Neve, F. J. de Sauvage, Z. Modrusan, S. Seshagiri, R. Firestein & Z. Zhang*. Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer. Nature Communications 5, 3830 (2014).
7. G. Y. Lee, P. M. Haverty, L. Li, N. M. Kljavin, R. Bourgon, J. Lee, H. Stern, Z. Modrusan, S. Seshagiri, Z. Zhang, D. Davis, D. Stokoe, J. Settleman, F. J. de Sauvage & R. M. Neve. Comparative Oncogenomics Identifies PSMB4 and SHMT2 as Potential Cancer Driver Genes. Cancer Research 74, 3114-3126 (2014).
8. S. Jhunjhunwala, Z. Jiang, E. W. Stawiski, F. Gnad, J. Liu, O. Mayba, P. Du, J. Diao, S. Johnson, K.-F. Wong, Z. Gao, Y. Li, T. D. Wu, S. B. Kapadia, Z. Modrusan, D. M. French, J. M. Luk, S. Seshagiri & Z. Zhang. Diverse modes of genomic alteration in hepatocellular carcinoma. Genome Biology 15, 436 (2014).
9. A. S. Adler, M. L. McCleland, S. Yee, M. Yaylaoglu, S. Hussain, E. Cosino, G. Quinones, Z. Modrusan, S. Seshagiri, E. Torres, V. S. Chopra, B. Haley, Z. Zhang, E. M. Blackwood, M. Singh, M. Junttila, J.-P. Stephan, J. Liu, G. Pau, E. R. Fearon, Z. Jiang & R. Firestein. An integrative analysis of colon cancer identifies an essential function for PRPF6 in tumor growth. Genes & Development 28 (2014).
10. T. H. Hwang, G. Atluri, R. Kuang, V. Kumar, T. Starr, K. A. T. Silverstein, P. M. Haverty, Z. Zhang & J. Liu. Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers. BMC Genomics 14, 440-440 (2013).
11. F. Gnad, A. Baucom, K. Mukhyala, G. Manning & Z. Zhang*. Assessment of computational methods for predicting the effects of missense mutations in human cancers. BMC Genomics 14, S7-S7 (2013).
12. Z. Zhang*. Genomic landscape of liver cancer. Nat Genet 44, 1075-1077 (2012).
13. S. Seshagiri, E. W. Stawiski, S. Durinck, Z. Modrusan, E. 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. A. Huntley, J. D. Degenhardt, P. M. Haverty, R. Bourgon, W. Wang, H. Koeppen, R. Gentleman, T. K. Starr, Z. Zhang, D. A. Largaespada, T. D. Wu & F. J. de Sauvage. Recurrent R-spondin fusions in colon cancer. Nature 488, 660-664 (2012).
14. C. M. Rudin, S. Durinck, E. W. Stawiski, J. T. Poirier, Z. Modrusan, D. S. Shames, E. A. Bergbower, Y. Guan, J. Shin, J. Guillory, C. S. Rivers, C. K. 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 & S. Seshagiri. Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nature genetics 44, 1111-1116 (2012).
15. J. Liu, W. Lee, Z. Jiang, Z. Chen, S. Jhunjhunwala, P. M. Haverty, F. Gnad, Y. Guan, H. N. Gilbert, J. Stinson, C. Klijn, J. Guillory, D. Bhatt, S. Vartanian, K. Walter, J. Chan, T. Holcomb, P. Dijkgraaf, S. Johnson, J. Koeman, J. D. Minna, A. F. Gazdar, H. M. Stern, K. P. Hoeflich, T. D. Wu, J. Settleman, F. J. de Sauvage, R. C. Gentleman, R. M. Neve, D. Stokoe, Z. Modrusan, S. Seshagiri, D. S. Shames & Z. Zhang*. Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Research 22, 2315-2327 (2012).
16. Z. Jiang, S. Jhunjhunwala, J. Liu, P. M. Haverty, M. I. Kennemer, Y. Guan, W. Lee, P. Carnevali, J. Stinson, S. Johnson, J. Diao, S. Yeung, A. Jubb, W. Ye, T. D. Wu, S. B. Kapadia, F. J. de Sauvage, R. C. Gentleman, H. M. Stern, S. Seshagiri, K. P. Pant, Z. Modrusan, D. G. Ballinger & Z. Zhang*. The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Research 22, 593-601 (2012).
17. P. Yue, W. F. Forrest, J. S. Kaminker, S. Lohr, Z. Zhang & G. Cavet. Inferring the functional effects of mutation through clusters of mutations in homologous proteins. Human Mutation 31, 264-271 (2010).
18. 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 & Z. Zhang*. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473-477 (2010).
19. 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. H. 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 & S. Seshagiri. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature 466, 869-873 (2010).
20. W. Lee, Y. Zhang, K. Mukhyala, R. A. Lazarus & Z. Zhang*. Bi-Directional SIFT Predicts a Subset of Activating Mutations. PLoS ONE 4, e8311 (2009).
21. W. Lee, P. Yue & Z. Zhang*. Analytical methods for inferring functional effects of single base pair substitutions in human cancers. Human Genetics 126, 481-498 (2009).
22. L. S. Hon, Y. Zhang, J. S. Kaminker & Z. Zhang*. Computational prediction of the functional effects of amino acid substitutions in signal peptides using a model-based approach. Human Mutation 30, 99-106 (2009).
23. P. M. Haverty, L. S. Hon, J. S. Kaminker, J. Chant & Z. Zhang*. High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. BMC Medical Genomics 2, 21-21 (2009).
24. J. Liu, Y. Zhang, X. Lei & Z. Zhang*. Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective. Genome Biology 9, R69-R69 (2008).
25. H. Jin, R. Yang, Z. Zheng, M. Romero, J. Ross, H. Bou-Reslan, R. A. D. Carano, I. Kasman, E. Mai, J. Young, J. Zha, Z. Zhang, S. Ross, R. Schwall, G. Colbern & M. Merchant. MetMAb, the One-Armed 5D5 Anti-c-Met Antibody, Inhibits Orthotopic Pancreatic Tumor Growth and Improves Survival. Cancer Research 68, 4360-4368 (2008).
26. P. M. Haverty, J. Fridlyand, L. Li, G. Getz, R. Beroukhim, S. Lohr, T. D. Wu, G. Cavet, Z. Zhang* & J. Chant. High-resolution genomic and expression analyses of copy number alterations in breast tumors. Genes, Chromosomes and Cancer 47, 530-542 (2008).
27. Y. Zhang, S.-M. Luoh, L. S. Hon, R. Baertsch, W. I. Wood & Z. Zhang*. GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database. Nucleic Acids Research 35, W152-W158 (2007).
28. 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 & B. Vogelstein. The Genomic Landscapes of Human Breast and Colorectal Cancers. Science 318, 1108-1113 (2007).
29. X.-D. Wang, B.-E. Wang, R. Soriano, J. Zha, Z. Zhang, Z. Modrusan, G. R. Cunha & W.-Q. Gao. Expression profiling of the mouse prostate after castration and hormone replacement: implication of H-cadherin in prostate tumorigenesis. Differentiation 75, 219-234 (2007).
30. 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 & V. M. Dixit. A Deubiquitinase That Regulates Type I Interferon Production. Science 318, 1628-1632 (2007).
31. J. S. Kaminker, Y. Zhang, A. Waugh, P. M. Haverty, B. Peters, D. Sebisanovic, J. Stinson, W. F. Forrest, J. F. Bazan, S. Seshagiri & Z. Zhang*. Distinguishing Cancer-Associated Missense Mutations from Common Polymorphisms. Cancer Research 67, 465-473 (2007).
32. J. S. Kaminker, Y. Zhang, C. Watanabe & Z. Zhang*. CanPredict: a computational tool for predicting cancer-associated missense mutations. Nucleic Acids Research 35, W595-W598 (2007).
33. L. S. Hon & Z. Zhang*. The roles of binding site arrangement and combinatorial targeting in microRNA repression of gene expression. Genome Biology 8, R166-R166 (2007).
34. D. Gray, A. M. Jubb, D. Hogue, P. Dowd, N. Kljavin, S. Yi, W. Bai, G. Frantz, Z. Zhang, H. Koeppen, F. J. de Sauvage & D. P. Davis. Maternal Embryonic Leucine Zipper Kinase/Murine Protein Serine-Threonine Kinase 38 Is a Promising Therapeutic Target for Multiple Cancers. Cancer Research 65, 9751-9761 (2005).
35. Z. Zhang* & W. J. Henzel. Signal peptide prediction based on analysis of experimentally verified cleavage sites. Protein Science : A Publication of the Protein Society 13, 2819-2824 (2004).
36. E. D. Zhang Y, Frantz GD, Dowd P, Wu TD, Zhou Y, Watanabe C, Luoh SM, Polakis P, Hillan KJ, Wood WI, Zhang Z*. GEPIS–quantitative gene expression profiling in normal and cancer tissues.Bioinformatics. BIoinformatics 20, 2390-2398 (2004).
37. I. E. Wertz, K. M. O’Rourke, Z. Zhang, D. Dornan, D. Arnott, R. J. Deshaies & V. M. Dixit. Human De-Etiolated-1 Regulates c-Jun by Assembling a CUL4A Ubiquitin Ligase. Science 303, 1371-1374 (2004).
38. B. Desany & Z. Zhang*. Bioinformatics and cancer target discovery. Drug Discovery Today 9, 795-802 (2004).
39. Y. Zhou, S.-M. Luoh, Y. Zhang, C. Watanabe, T. D. Wu, M. Ostland, W. I. Wood & Z. Zhang*. Genome-wide Identification of Chromosomal Regions of Increased Tumor Expression by Transcriptome Analysis. Cancer Research 63, 5781-5784 (2003).
40. Z. Zhang*. a. W. I. Wood. A profile hidden Markov model for signal peptides generated by HMMER. Bioinformatics 19, 307-308 (2003).
41. J. LeCouter, R. Lin, G. Frantz, Z. Zhang, K. Hillan & N. Ferrara. Mouse Endocrine Gland-Derived Vascular Endothelial Growth Factor: A Distinct Expression Pattern from Its Human Ortholog Suggests Different Roles as a Regulator of Organ-Specific Angiogenesis. Endocrinology 144, 2606-2616 (2003).
42. K. M. L. Gaensler, Z. Zhang, C. Lin, S. Yang, K. Hardt & L. Flebbe-Rehwaldt. Sequences in the (A)γ–δ intergenic region are not required for stage-specific regulation of the human β-globin gene locus. Proceedings of the National Academy of Sciences of the United States of America 100, 3374-3379 (2003).
43. H. F. Clark, A. L. Gurney, E. Abaya, K. Baker, D. Baldwin, J. Brush, J. Chen, B. Chow, C. Chui, C. Crowley, B. Currell, B. Deuel, P. Dowd, D. Eaton, J. Foster, C. Grimaldi, Q. Gu, P. E. Hass, S. Heldens, A. Huang, H. S. Kim, L. Klimowski, Y. Jin, S. Johnson, J. Lee, L. Lewis, D. Liao, M. Mark, E. Robbie, C. Sanchez, J. Schoenfeld, S. Seshagiri, L. Simmons, J. Singh, V. Smith, J. Stinson, A. Vagts, R. Vandlen, C. Watanabe, D. Wieand, K. Woods, M.-H. Xie, D. Yansura, S. Yi, G. Yu, J. Yuan, M. Zhang, Z. Zhang, A. Goddard, W. I. Wood & P. Godowski. The Secreted Protein Discovery Initiative (SPDI), a Large-Scale Effort to Identify Novel Human Secreted and Transmembrane Proteins: A Bioinformatics Assessment. Genome Research 13, 2265-2270 (2003).
44. M. Yan, Z. Zhang, J. R. Brady, S. Schilbach, W. J. Fairbrother & V. M. Dixit. Identification of a Novel Death Domain-Containing Adaptor Molecule for Ectodysplasin-A Receptor that Is Mutated in crinkled Mice. Current Biology 12, 409-413 (2002).
45. 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 & N. Ferrara. Identification of an angiogenic mitogen selective for endocrine gland endothelium. Nature 412, 877-884 (2001).
46. M.-H. Xie, S. Aggarwal, W.-H. Ho, J. Foster, Z. Zhang, J. Stinson, W. I. Wood, A. D. Goddard & A. L. Gurney. Interleukin (IL)-22, a Novel Human Cytokine That Signals through the Interferon Receptor-related Proteins CRF2–4 and IL-22R. Journal of Biological Chemistry 275, 31335-31339 (2000).
47. A. Kishiyama, Z. Zhang & W. J. Henzel. Cleavage and Identification of Proteins:  A Modified Aspartyl−Prolyl Cleavage. Analytical Chemistry 72, 5431-5436 (2000).
48. Z. Zhang & A. R. Buchman. Identification of a member of a DNA-dependent ATPase family that causes interference with silencing. Molecular and Cellular Biology 17, 5461-5472 (1997).
49. S. Porcu, M. Kitamura, E. Witkowska, Z. Zhang, A. Mutero, C. Lin, J. Chang & K. M. L. Gaensler. The Human β Globin Locus Introduced by YAC Transfer Exhibits a Specific and Reproducible Pattern of Developmental Regulation in Transgenic Mice. Blood 90, 4602-4609 (1997).