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ZHANG, Zemin
Title:
Professor
Office Address: Integrated Science Research Center,Peking University, No.5 Yiheyuan Road, Haidian District,Beijing, P.R.China 100871
Lab Address: Integrated Science Research Center,Peking University, No.5 Yiheyuan Road, Haidian District,Beijing, P.R.China 100871
Lab Homepage: http://cancer-pku.cn/
Personal Homepage: http://
Resume
Biography
Dr. Zhang obtained his Bachler degree in Genetics from Nankai University, and PhD in Biochemistry and Molecular Biology from Penn State University. He received additional training in Information Technology from UC Berkeley and postdoctoral trainings in Laboratory Medicine from UC San Francisco.

Prior to joining Peking University, Dr. Zhang spent over 16 years at Genentech/Roche, leading the cancer genomics and bioinformatics group to discover anticancer targets and biomarkers using new technologies such as machine learning and high throughput sequencing. He has pioneered multiple research directions in computational cancer biology and cancer genomics including the first ever whole genome tumor sequencing. He is also an inventor for 60 issued US patents, and has directly contributed to the initial finding of the molecular targets of multiple cancer therapeutic agents in clinical trials. He is on the editorial boards for journals including Cell Systems, Genome Medicine, and Cancer Informatics. He is a CUSBEA Scholar, a recipient of the 1000 Talents program, and also a Cheung Kong Scholar.
Representative Peer-Reviewed Publications
1. 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

2. C. Li, B. Liu, B. Kang, Z. Liu, Y. Liu, C. Chen, X. Ren*, and Z. Zhang*. SciBet as a portable and fast single cell type identifier. Nature Communication, 11:1818

3. 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

4. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020) Pan-cancer analysis of whole genomes. Nature, 578:82–93

5. 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

6. 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

7. 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

8. 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.

9. 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

10. L. Zhang and Z. Zhang. (2019) Recharacterizing tumor-infiltrating lymphocytes by single-cell RNA sequencing. Cancer Immunology Research, 7:1040-1046.

11. 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

12. 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

13. X. Ren*, B. Kang, and Z. Zhang*. (2018) Understanding tumor ecosystems by single-cell sequencing: promises and limitations. Genome Biology, 19:211

14. 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

15. 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

16. X. Hu and Z. Zhang. (2016) Understanding the genetic mechanisms of cancer drug resistance using genomic approaches. Trends in Genetics, 32(2):127-37

17. C. Klijn, S. Durinck, …, 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

18. S. Jhunjhunwala, Z. Jiang, …, S. Seshagiri, and Z. Zhang (2014) Diverse modes of genomic alterations in hepatocellular carcinoma. Genome Biology, 15:436

19. J. Liu, M. McCleland, …, S. Seshagiri, R. Firestein, and Z. Zhang (2014), Integrated exome and transcriptome sequencing reveals ZAK isoform usage in gastric cancer. Nature Communication, 5:3830

20. O. Mayba, H. N. Gilbert, …, C. Watanabe, and Z. Zhang (2014) Allele specific expression detection in cancer tissues and cell lines by MBASED. Genome Biology, 15:405

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

22. J. Liu, W. Lee, …, D. S. Shames, Z. Zhang (2012) Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Research, 22:2315-2327

23. S. Seshagiri, E. Stawiski, …, 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

24. Z. Jiang*, S. Jhunihunwala*, …, 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

25. W. Lee, Z. Jiang, …, 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

26. Z. Kan, B. S. Jaiswal, J…, 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

27. N. Kayagaki, Q. Phung, …, 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

28. 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

Laboratory Introduction