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1. Huiya Huang#, Yiqi Liu#, Weixi Liao#, Yubing Cao, Qiang Liu, Yakun Guo, Yinying Lu and Zhen Xie*. Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy, Nature Communications, 2019, 10(1):4801
2. Yucheng Guo†, Chen Bao†, Dacheng Ma, Yubing Cao, Yanda Li, Zhen Xie*, Shao Li*. Network-Based Combinatorial CRISPR-Cas9 Screens Identify Synergistic Modules in Human Cells, ACS Synthetic Biology, 2019, 8(3):482-490.
3. Dacheng Ma, Zhimeng Xu, Zhaoyu Zhang, Xi Chen, Xiangzhi Zeng, Yiyang Zhang, Tingyue Deng, Mengfei Ren, Zheng Sun, Rui Jiang, Zhen Xie*. Engineer chimeric Cas9 to expand PAM recognition based on evolutionary information, Nature Communications, 2019, 10(1):560.
4. Jiahui Guo, Tianmin Wang, Changge Guan, Bing Liu, Cheng Luo, Zhen Xie, Chong Zhang*, Xin-Hui Xing. Improved sgRNA design in bacteria via genome-wide activity profiling, Nucleic Acids Research, 2018, 46(14):7052-7069.
5. Tianmin Wang, Changge Guan, Jiahui Guo, Bing Liu, Yinan Wu, Zhen Xie, Chong Zhang*, Xin-Hui Xing. Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance, Nature Communications, 2018, 9(1):2475.
6. Dacheng Ma, Shuguang Peng, Weiren Huang, Zhiming Cai, Zhen Xie*. (2018) Rational Design of Mini-Cas9 for Transcriptional Activation, ACS Synthetic Biology, 2018, 7(4):978-985.
7. Weixi Liao†, Bing Liu†, Che Lin, Bor-Sen Chen, Zhen Xie*, Functional characterization of insulators in non-integrated synthetic gene circuits, ACS Synthetic Biology, 2018, 7(2):412-418.
8. Jianying Guo, Dacheng Ma, Rujin Huang, Jia Ming, Min Ye, Kehkooi Kee, Zhen Xie, Jie Na, An inducible CRISPR-ON system for controllable gene activation in human pluripotent stem cells, Protein and Cell, 2017, 8(5):379-393
9. Shuguang Peng and Zhen Xie*, Smart therapeutics based on synthetic gene circuits. Sheng Wu Gong Cheng Xue Bao. 2017, 33(3):456-466.
10. Dacheng Ma†, Shuguang Peng†, Zhen Xie*, Integration and exchange of split dCas9 domains for transcriptional controls in mammalian cells, Nature Communications, 2016, 7:13056
11. Tingting Wang, Yue Xie, Aidi Tan, Shao Li, Zhen Xie*, Construction and characterization of synthetic microRNA cluster for multiplex RNA interference in mammalian cells, ACS Synthetic Biology, 2016, 5 (11), pp 1193–1200
12. Yingting Yu, Yi Yao, Han Yan, Rui Wang, Zhenming Zhang, Xiaodan Sun, Lingyun Zhao, Xiang Ao, Zhen Xie, and Qiong Wu. (2016). A Tumor-specific MicroRNA Recognition System Facilitates the Accurate Targeting to Tumor Cells by Magnetic Nanoparticles. Molecular Therapy Nucleic Acids 5, e318
13. Yinqing Li†, Yun Jiang†, He Chen†, Weixi Liao, Zhihua Li, Weiss, Ron*, Zhen Xie*, Modular construction of mammalian gene circuits using TALE transcriptional repressors, Nature Chemical Biology, 2015, 11(3): 207-213
14. Ye Yuan†, Bing Liu†, Peng Xie, Michael Q. Zhang, Yanda Li, Zhen Xie*, Xiaowo Wang*, Model-guided quantitative analysis of microRNA- mediated regulation on competing endogenous RNAs using a synthetic gene circuit, PNAS (Proceedings of the National Academy of Sciences of the United States of America), 2015, 10: 3158-3163
15. Noah Davidsohn, Jacob Beal, Samira Kiani, Aaron Adler, Fusun Yaman, Yinqing Li, Zhen Xie, and Ron Weiss. (2015). Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition. ACS Synthetic Biology 4, 673–681.
16. Jin Gu, Yang Chen, Huiya Huang, Lingyun Yin, Zhen Xie, and Michael Q. Zhang. (2014). Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular BioSystem 10, 3249–3254.
17. Samira Kiani, Jacob Beal, Mohammad R Ebrahimkhani, Jin Huh, Richard N. Hall1, Zhen Xie, Yinqing Li and Ron Weiss*. (2014) CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nature Methods 11, 723-6.
18. Jonathan Leo Schmid-Burgk, Zhen Xie, Yaakov Benenson* (2014) Hierarchical ligation-independent assembly of PCR fragments. Methods Molecular Biology 1116:49-58.
19. Zhen Xie, Liliana Wroblewska and Ron Weiss*. (2014) RNAi synthetic logic circuits for sensing, information processing and actuation. RNA Regulation, Encyclopedia of Molecular Cell Biology and Molecular Medicine. Edition April 2014, ISBN 978-3-527-33156-7-Wiley-VCH, Weinheim (Book chapter).
20. Yi-Ying Lee, Chih-Yuan Hsu, Ling-Jiun Lin, Chih-Chun Chang, Hsiao-Chun Cheng, Tsung-Hsien Yeh, Rei-Hsing Hu, Che Lin, Zhen Xie, Bor-Sen Chen* (2013) Systematic design methodology for robust genetic transistors based on I/O specifications via promoter-RBS libraries. BMC System Biology 7:109.
21. Taek Kang, Jacob T. White, Zhen Xie, Yaakov Benenson, Eduardo Sontag, & Leonidas Bleris* (2013). Reverse Engineering Validation using a Benchmark Synthetic Gene Circuit in Human Cells. ACS Synthetic Biology 2(5):255-62.
22. Neha Kashyap, Bich Pham, Zhen Xie*, Leonidas Bleris* (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular Biosystems 9(7):1919-25.
23. Jonathan Leo Schmid-Burgk, Zhen Xie, Stefan Frank, Sebastian Virreira Winter, Sibylle Mitschka, Waldemar Kolanus, Andrew Murray, Yaakov Benenson* Rapid hierarchical assembly of medium-size DNA cassettes. (2012) Nucleic Acids Research 40(12):e92.
24. Madeleine Leisner, Leonidas Bleris, Jason Lohmueller, Zhen Xie and Yaakov Benenson* MicroRNA circuits for transcriptional logic. (2012) Methods Molecular Biology 813:169-86.
25. Zhen Xie, Liliana Wroblewska, Laura Prochazka, Ron Weiss*, Yaakov Benenson* Multi-input RNAi-based logic circuit for identification of specific cancer cells. (2011) Science 333(6047):1307-11.
26. Leonidas Bleris, Zhen Xie, David Glass, Asa Adadey, Eduardo Sontag and Yaakov Benenson* Synthetic incoherent feed-forward circuits show adaptation to the amount of their genetic template. (2011) Molecular Systems Biology 7, 519.
27. Madeleine Leisner, Leonidas Bleris, Jason Lohmueller, Zhen Xie and Yaakov Benenson* (2010) Rationally designed logic integration of regulatory signals in mammalian cells. Nature Nanotechnology 5(9), 666-70.
28. Zhen Xie, Siyuan John Liu, Leonidas Bleris and Yaakov Benenson* (2010) Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Research 38, 2692-2701.
29. Zhen Xie†, Zhong-Lin Zhang†, Shane Hanzlik, Everett Cook and Qingxi J. Shen* (2007) Salicylic acid inhibits gibberellin-induced alpha-amylase expression and seed germination via a pathway involving an abscisic-acid-inducible WRKY gene. Plant Molecular Biology 64(3), 293-303.
30. Zhen Xie†, Zhong-Lin Zhang†, Xiaolu Zou, Guangxiao Yang, Setsuko Komatsu and Qingxi J. Shen* (2006) Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Plant Journal 46, 231-242.
31. Zhen Xie, Paul Ruas and Qingxi J. Shen* (2005) Regulatory networks of phytohormone abscisic acid. Vitamins and Hormones 72, 235-269. (Book Chapter)
32. Zhen Xie†, Zhong-Lin Zhang†, Xiaolu Zou, Jie Huang, Paul Ruas, Daniel Thompson and Qingxi J. Shen* (2005) Annotations and functional analyses of the rice WRKY gene superfamily reveal positive and negative regulators of abscisic acid signaling in aleurone cells. Plant Physiology 137, 176-189.
33. Zhong-Lin Zhang†, Zhen Xie†, Xiaolu Zou, Jose Casaretto, Tuan-hua David Ho and Qingxi J. Shen* (2004) A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiology 134, 1500-1513.
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