User:Xi Chen

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Xi Chen

Xi Chen (UT-Austin)

I am currently a post-doc fellow in the lab of Andrew D. Ellington in the University of Texas at Austin. I am also a visiting fellow of the Yin Lab in Wyss Institute of Harvard University, and will move to the Yin Lab in Sep 2012 as a full-time Jane Coffin Childs postdoctoral fellow.


The first 3 years of my graduate study were spent primarily on engineering ribozyme-based RNA regulators in mammalian cells. Although I have created a few unpublished RNA regulators that work minimally (by my standard), I mainly focused on the development of a method to directly select physiologically active ribozymes in mammalian cells, and a kinetic model to analyze and direct such selections. I then extended this kinetic model to analyze and predict the performance of ribozyme- and deoxyribozyme-based sensors in vitro and in vivo.

Since late 2008, I became interested in enzyme-free DNA circuits initially developed by the Winfree Lab and the Pierce Lab in Caltech. I have started designing and executing similar circuits for the purpose of biosensing, pattern formation, and chemical synthesis.

After graduation, I stayed in the Ellington Lab to keep working on DNA circuits.

Selected Publications

(Note: * denotes corresponding author or co-corresponding author)

  1. Li B, Jiang Y, Chen X*, Ellington AD. (2012) Probing Spatial Organization of DNA Strands Using Enzyme-Free Hairpin Assembly Circuits. J. Am. Chem. Soc. (in press) doi:10.1021/ja300984b
  2. Chen X*. (2012) Expanding the Rule Set of DNA Circuitry with Associative Toehold Activation. J. Am. Chem. Soc. 134(1):263-71.
  3. Li B, Ellington AD, Chen X*. (2011) Rational, Modular Adaptation of Enzyme-free DNA Circuits to Multiple Detection Methods. Nucleic Acids Res. 39(16):e110.
  4. Eckhoff G, Codrea V, Ellington AD, Chen X*. (2010) Beyond Allostery: Catalytic Regulation of a Deoxyribozyme Through an Entropy-driven DNA Amplifier. J. Syst. Chem. 1:13
  5. Chen X, Ellington AD. (2010) Shaping up Nucleic Acid Computation. (Review) Curr. Opin. Biotechnol. 21(4):392-400
  6. Chen X, Ellington AD. (2009) Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes. PLoS Comput. Biol. 5(12):e1000620
  7. Chen X, Denison L, Levy M, Ellington AD. (2009) Direct Selection for Ribozyme Cleavage Activity in Cells. RNA 15(11):2035-45
  8. Chen X, Li N, Ellington AD. (2007) Ribozyme Catalysis of Metabolism in the RNA World. (Review) Chem. Biodivers. 4(4):633-55.
  9. Chen X, Wang Y, Liu Q, Zhang Z, Fan C, He L. (2006) Construction of Molecular Logic Gates with a DNA-cleaving Deoxyribozyme. Angew. Chem. Int. Ed. Engl. 45(11):1759-62.

(This link is left here formating examples.)


xichen at mail dot utexas dot edu


Scientific interest

Synthetic Biology Library

Personal life