User:Xi Chen

Xi Chen
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.

Research
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 Although I have created a few unpublished RNA regulators that work minimally (by my standard), I mainly focused on the development of a method to directly select physiologically active ribozymes in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, Ellington AD, Chen X*. (2011) Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res.. doi: 10.1093/nar/gkr504
 * 2) 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
 * 3) Chen X, Ellington AD. (2010) Shaping up nucleic acid computation (Review). Curr Opin Biotechnol. 21(4):392-400
 * 4) Chen X, Ellington AD. (2009) Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes. PLoS Comput Biol. 5(12):e1000620
 * 5) Chen X, Denison L, Levy M, Ellington AD. (2009) Direct selection for ribozyme cleavage activity in cells RNA;15(11):2035-45
 * 6) Chen X, Li N, Ellington AD. (2007) Ribozyme catalysis of metabolism in the RNA world. (Review) Chem Biodivers. 4(4):633-55.
 * 7) 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.)

Contact
xichen at mail dot utexas dot edu