Biography
Zemin Zhang received his bachelor degree in Biology Department of Nankai University in 1988 and went to USA by CUSBEA. He obtained his PhD in Biochemistry and Molecular Biology Department of Penn State University in 1995. After the postdoc training in University of California, San Francisco from 1995 to 1998, he worked in GENENTECH, USA, where he served as postdoctoral supervisor, department director, and the principal scientist of bioinformatics. His previous achievements include the first whole-genome sequencing study of solid tumor, the first systematic assessment of viral insertion on liver cancer, and the first computational method to discriminate cancer driver mutations from passenger mutations. His studies led to the discovery of multiple cancer-specific drug targets and 60 US patents granted. In 2014, he joined Peking University. He was awarded the Bollinger Ingelheim Fellow Award in 2017 and the Bayer Investigator Award in 2019, and his research achievements have been selected in the Top Ten Biological Science Advances of China in 2017, the Top Ten Biomedical Advances of China in 2017, the Cell Press Paper of the Year Award in China for 2017 and 2019, the Top Ten Bioinformatics Progresses of China in 2018 and 2019, the Cell Press 2020 Best of Cell.
Representative Peer-Reviewed Publications
1. S. Cheng, Z. Li, R. Gao, B. Xing, Y. Gao, Y. Yang, S. Qin, L. Zhang, H. Ouyang, P. Du, L. Jiang, B. Zhang, Y. Yang, X. Wang, X. Ren, J. Bei, X. Hu, Z. Bu*, J. Ji*, and Z Zhang*. (2021) A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells. Cell, 184:792-809
2. L. Zheng and Z. Zhang*. (2021) Decoding the genetic basis of anti-tumor immunity. Immunity, 54:199-201,
3. X. Ren, W. Wen, X. Fan, W. Hou, B. Su, P.i Cai, J. Li, Y. Liu, F. Tang, F. Zhang, Y. Yang, J. He, W. Ma, J. He, P. Wang, … P. Zhou*, Q. Jiang*, Z. Huang*, J-X Bei*, L. Wei*, X-W Bian*, X. Liu*, T Cheng*, X. Li*, P. Zhao*, F-S Wang*, H. Wang*, B. Su*, Z. Zhang*, K. Qu*, X. Wang*, J. Chen*, R. Jin*, Z. Zhang*, (2021) COVID-19 immune features revealed by a large-scale single cell transcriptome atlas, Cell, https://doi.org/10.1016/j.cell.2021.01.053
4. B. Liu, C. Li, Z. Li, D. Wang, X. Ren, and Z. Zhang*. (2020) An entropy-based metric for assessing the purity of single cell populations, Nature Communications, 11:3155
5. X. Ren*, G. Zhong, Q. Zhang, L. Zhang, Y. Sun and Z. Zhang*. (2020) Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly, Cell Research, 30:763-778
6. Q. Zhang and Z. Zhang. (2020) Stepwise immune alterations in multiple myeloma progression. Nature Cancer, 1:477-479
7. L. Zhang, Z. Li, K. M. Skrzypczynska, Q. Fang, W. Zhang, S. A. O’Brien, Y. He, L. Wang, Q. Zhang, A. Kim, R. Gao, J. Orf, T. Wang, D. Sawant, J. Kang, D. Bhatt, D. Lu, C-M Li, A. Rapaport, K. Perez, Y. Ye, S. Wang, X. Hu, X. Ren, W. Ouyang, Z. Shen*, J. G. Egen*, Z Zhang*, and X. Yu*. (2020) Single-cell analyses inform mechanisms of myeloid-targeted therapies in colon cancer. Cell, 181:442-459
8. C. Li, B. Liu, B. Kang, Z. Liu, Y. Liu, C. Chen, X. Ren*, and Z. Zhang*. (2020) SciBet as a portable and fast single cell type identifier. Nature Communications, 11:1818
9. PCAWG Transcriptome Core Group, C. Calabrese, N. R. Davidson, D. Demircioğlu, N. A. Fonseca, Y. He, A. Kahles, K-V Lehmann, F. Liu, Y. Shiraishi, C. M. Soulette, L. Urban, L. Greger, S. Li, D. Liu, M. D. Perry, Q. Xiang, F. Zhang, J. Zhang, P. Bailey, S. Erkek, K. A. Hoadley, Y. Hou, M. R. Huska, H. Kilpinen, J. O. Korbel, M. G. Marin, J. Markowski, T. Nandi, Q. Pan-Hammarström, C. S. Pedamallu, R. Siebert, S. G. Stark, H. Su, P. Tan, S. M. Waszak, C. Yung, S. Zhu, P. Awadalla, C. J. Creighton, M. Meyerson, B. F. Ouellette, K. Wu, H. Yang, PCAWG Transcriptome Working Group, A. Brazma*, A. N. Brooks*, J. Göke*, G. Rätsch*, R. F. Schwarz*, O. Stegle*, Z. Zhang* & PCAWG Consortium. (2020) Genomic basis for RNA alterations in cancer. Nature, 578:129-136
10. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020) Pan-cancer analysis of whole genomes. Nature, 578:82–93
11. Y. Zhang, F. Chen, N. A. Fonseca, Y. He, M. Fujita, H. Nakagawa, Z. Zhang, A. Brazma; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, C. J. Creighton; PCAWG Consortium. (2020) High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nature Communications, 11:736
12. R. Bernards, E. Jaffee, J. A. Joyce, S. W. Lowe, E. R. Mardis, S. J. Morrison, K. Polyak, C. L. Sears, K. H. Vousden, and Z. Zhang. (2020) A roadmap for the next decade in cancer research. Nature Cancer, 1:12-17
13. R. Yang, S. Cheng, N. Luo, R. Gao, K. Yu, B. Kang, L. Wang, Q. Zhang, Q. Fang, L. Zhang, C. Li, A. He, X. Hu, J. Peng*, X. Ren*, and Z. Zhang*. (2020) Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis. Genome Biology, 21:2
14. Y. Zhang and Z. Zhang*. (2020) The history and advances in cancer immunotherapy: understanding the characteristics of tumor-infiltrating immune cells and their therapeutic implications. Cellular & Molecular Immunology, 17(8):807-821
15. F. Liu, Y. Zhang, L. Zhang, Z. Li, Q. Fang, R. Gao, and Z. Zhang. (2019) Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data. Genome Biology, 20:242
16. Q. Zhang, Y. He, N. Luo, S. J. Patel, Y. Han, R. Gao, M. Modak, S. Carotta, C. Haslinger, D. Kind, G. W. Peet, G. Zhong, S. Lu, W. Zhu, Y. Mao, M. Xiao, M. Bergmann, X. Hu, S. P. Kerkar, A. B. Vogt, S. Pflanz, K. Liu*, J. Peng*, X. Ren*, and Z. Zhang* (2019) Landscape and dynamics of single immune cells in hepatocellular carcinoma. Cell, 179:829-845.
17. H. Yang, L. Xia, J. Chen, S. Zhang, V. Martin, Q. Li, S. Lin, J. Chen, J. Calmette, M. Lu, L. Fu, J. Yang, Z. Pan, K. Yu, J. He, E.Morand, G. Schlecht-Louf, R. Krzysiek, L. Zitvogel, B. Kang, Z. Zhang, A. Leader, P. Zhou, L. Lanfumey, M. Shi, G. Kroemer, and Y. Ma. (2019) Stress–glucocorticoid–TSC22D3 axis compromises therapy-induced antitumor immunity. Nature Medicine, 26:1428-1441.
18. R. Xu, S. Yu, D. Zhu, X. Huang, Y. Xu, Y. Lao, Y. Tian, J. Zhang, Z. Tang, Z. Zhang, J. Yi, H. Zhu, and X. Zheng. (2019) hCINAP regulates the DNA-damage response and mediates the resistance of acute myelocytic leukemia cells to therapy. Nature Communications, 10: 3812.
19. Z. Tang, B. Kang, C. Li, T. Chen, and Z. Zhang. (2019) GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Research, 47:W556-W560
20. L. Zhang and Z. Zhang. (2019) Recharacterizing tumor-infiltrating lymphocytes by single-cell RNA sequencing. Cancer Immunology Research, 7:1040-1046.
21. L. Zhang, X. Yu, L. Zheng, Y. Zhang, Y. Li, Q. Fang, R. Gao, B. Kang, Q. Zhang, J.Y. Huang, H. Konno, X. Guo, Y. Ye, S. Gao, S. Wang, X. Hu, X. Ren, Z. Shen*, W. Ouyang*, and Z. Zhang*. (2018) Lineage tracking reveals dynamic relationships of T cells in colorectal cancer. Nature, 564:268-272
22. X. Guo, Y. Zhang, L. Zheng, C. Zheng, J. Song, Q. Zhang, B. Kang, Z. Liu, L. Jin,R. Xing, R. Gao, L. Zhang, M. Dong, X. Hu, X. Ren, D. Kirchhoff, H. G. Roider, T. Yan*, and Z. Zhang*. (2018) Global characterization of T cells in non-small cell lung cancer by single-cell sequencing. Nature Medicine, 24:978-985
23. X. Ren*, B. Kang, and Z. Zhang*. (2018) Understanding tumor ecosystems by single-cell sequencing: promises and limitations. Genome Biology, 19:211
24. C. Zheng, L. Zheng, J.-K. Yoo, H. Guo, Y. Zhang, X. Guo, B. Kang, R. Hu, J. Y. Huang, Q. Zhang, Z. Liu, M. Dong, X. Hu, W. Ouyang*, J. Peng*, and Z. Zhang*. (2017) Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing. Cell, 169(7), 1342–1356
25. Z. Tang, C. Li, B. Kang, G. Gao, C. Li, and Z. Zhang. (2017) GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Research, 45(W1):W98-W102
26. X. Hu and Z. Zhang. (2016) Understanding the genetic mechanisms of cancer drug resistance using genomic approaches. Trends in Genetics, 32(2):127-37
27. 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
28. 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
29. 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 Communications, 5:3830
30. 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
31. Z. Zhang (2012), Genomic landscape of liver cancer. Nature Genetics, 44: 1075-1077
32. 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, Z. Zhang (2012) Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Research, 22:2315-2327
33. 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
34. 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, Z. Zhang (2012) The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients. Genome Research, 22:593-601
35. 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
36. 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
37. 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
38. 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
39. 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
40. 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
41. 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
42. 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
43. 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
44. 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
45. I. 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
46. 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
Laboratory Introduction
Zhang Lab is devoted to using the cutting-edge genomics and bioinformatics technologies to study critical issues of cancer biology, including revealing the genetic and immune factors underlying tumorigenesis, tumor microenvironment and drug resistance. The current main research directions include: 1) applying single cell sequencing technology to dissect tumor microenvironment, especially the accurate composition and functional status of tumor-infiltrating immune cells; 2) dissecting the heterogeneity of tumor and the impact on cancer biology and drug resistance; 3) developing innovative bioinformatics tools and resources to analyze, integrate, and visualize single-cell genomic data and large-scale cancer genomic data to reveal novel targets as well as the genomic mechanisms underlying tumor heterogeneity and immune response differences.
