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.
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(3):792-809
2. D. Wang*, S. Hou, L. Zhang, X. Wang, B. Liu, and Z. Zhang*. (2021) iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks. Genome Biology, 22, 63
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*, and Z. Zhang*, (2021) COVID-19 immune features revealed by a large-scale single cell transcriptome atlas, Cell, 184:1895-1913
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. 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
7. 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
8. 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
9. 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.
10. 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
11. 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
12. 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
