Xie Group FOR Genetic Circuit Engineering

Tsinghua National Lab - Bioinformatics Division - Center for Synthetic and Systems Biology

  • Tingting Wang, Yue Xie, Aidi Tan, Shao Li and Zhen Xie*. Construction and Characterization of a Synthetic MicroRNA Cluster for Multiplex RNA Interference in Mammalian Cells. ACS Synthetic Biology 2015 Dec 22.

  • 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. Proceedings of the National Academy of Sciences of the U.S.A. 2015 Feb 23. pii: 201413896.

  • Yinqing Li#, Yun Jiang#, He Chen#, Weixi Liao, Zhihua Li, Ron Weiss* and Zhen Xie*. Modular construction of synthetic circuits using TALE transcriptional repressors in mammalian cells. Nature Chemical Biology 11(3):207-13.

  • Noah Davidsohn, Jacob Beal, Samira Kiani, Aaron Adler, Fusun Yaman, Yinqing Li, Zhen  Xie and Ron Weiss*. (2014) Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition. ACS Synthetic Biology

  • Jin Gu*, Yang Chen, Huiya Huang, Lingyun Yin, Zhen Xie, Michael Q. Zhang*. (2014) Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular Biosystems10(12):3249-54.

  • Samira Kiani, Jacob Beal, Mohammad R Ebrahimkhani, Jin Huh, Richard N. Hall, Zhen Xie, Yinqing Li and Ron Weiss*. (2014) CRISPR transcriptional repression devices and layered circuits in mammalian cells.Nature Methods 11, 723-6.

  • 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 30 2014, ISBN 978-3-527-33156-7-Wiley-VCH, Weinheim (Book chapter), Edited by Robert A. Meyers, 1-23.

  • Jonathan Leo Schmid-Burgk, Zhen Xie, Yaakov Benenson* (2014) Hierarchical ligation-independent assembly of PCR fragments. Methods Molecular Biology 1116:49-58.

  • 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.

  • 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.

  • Neha Kashyap, Bich Pham, Zhen Xie*, Leonidas Bleris* (2013). Transcripts for combined synthetic microRNA and gene delivery. Molecular Biosystems 9(7):1919-25.

  • 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.

  • Madeleine Leisner, Leonidas Bleris, Jason Lohmueller, Zhen Xie and Yaakov Benenson* MicroRNA circuits for transcriptional logic. (2012) Methods Molecular Biology 813:169-86.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • Zhen Xie, Paul Ruas and Qingxi J. Shen* (2005) Regulatory networks of phytohormone abscisic acid.Vitamins and Hormones 72, 235-269. (Book Chapter)

  • 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.

  • 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.

Equal contribution.
* Corresponding author.