Publications

2021

Jiang, X.*, Dimas, R.P.*, Chan, C.T.Y., and Morcos, F. (2021). Coevolutionary methods enable robust design of modular repressors by reestablishing intra-protein interactions. Nature Communications. 12:5592.

2019

Dimas, R.P.*, Jiang, X.*, Alberto de la Paz, J., Morcos, F., and Chan, C.T.Y. (2019). Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset. Nucleic Acids Research. 47(10):5449-5463.

Dimas, R.P.*, Jordan, B.R.*, Jiang, X., Martini, C., Glavy, J.S., Patterson, D.P., Morcos, F., and Chan, C.T.Y. (2019). Engineering DNA recognition and allosteric response properties of TetR family proteins by using a module-swapping strategy. Nucleic Acids Research. 47(16):8913–8925.

2018

Lee, J.W.*, Chan, C.T.Y.*, Slomovic, S., Collins, J.J. (2018). Next-generation biocontainment systems for engineered organisms. Nature Chemical Biology. 14:530-537.

Selected Publications before 2017

Chan, C.T.Y.*, Lee, J.W.*, Cameron, D.E.*, Bashor, C.J., and Collins, J.J. (2016). “Deadman” and “passcode” microbial kill switches for bacterial containment.  Nature Chemical Biology. 12(2):82-86.
•  Highlighted in Nature. 528(7581):166-167. Kill switches limit modified microbes. Sutter, P. (2015).
•  Highlighted in Science. 351(6272):462-463. Engineering a 
bacterial “Deadman” walking. Vinson, V. (2016).
•  Highlighted in Nature Review Genetics. 17(2):67. Synthetic biology: Genetic kill switches – a matter of life or death. Osorio, J. (2016).
•  Highlighted in Chemical & Engineering News, Top Research of 2015. Keeping GMOs on a leash. Everts, S. (2015).
•  Accompanying News & Views article in Nature Chemical Biology. 12(2):55-56. Building genetic containment. Haynes, K.A. (2016).

 

Chan, C.T.Y.*, Deng, W.*, Li, F., DeMott, M.S., Babu, I.R., Begley, T.J., and Dedon, P.C. (2015). Highly predictive reprogramming of tRNA modifications is linked to selective expression of codon-biased genes. Chemical Research in Toxicology. 28(5):978-988.

 

Dwyer, D.J., Belenky, P.A., Yang, J.H., MacDonald, I.C., Martell, J.D., Takahashi, N., Chan, C.T.Y., Lobritz, M.A., Braff, D., Schwarz, E.G., Ye, J.D., Pati, M., Vercruysse, M., Ralifo, P.S., Allison, K.R., Khalil, A.S., Ting, A.Y., Walker, G.C., and Collins, J.J. (2014). Antibiotics induce redox-related physiological alterations as part of their lethality. Proceedings of the National Academy of Sciences of the U.S.A. 111(20):E2100-E2109.

 

Su, D., Chan, C.T.Y., Gu, C., Lim, K.S., Chionh, Y.H., McBee, M.E., Russell, B.S., Babu, I.R., Begley, T.J., and Dedon, P.C. (2014). Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Nature Protocols. 9(4):828-841.

 

Mandal, D., Köhrer, C. Su, D., Babu, I.R., Chan, C.T.Y., Liu, Y., Söll, D., Blum, P., Kuwahara, M., Dedon, P.C., and Rajbhandary, U.L. (2014). Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs. RNA. 20(2):177-188.

 

Begley, J., Sosa, M.S., Avivar-Valderas, A., Patil, A., Endres, L., Estrada, Y., Chan, C.T.Y., Su, D., Dedon, P.C., Aguirre-Ghiso, J.A., and Begley, T.J. (2013). A human tRNA methyltransferase 9-like protein prevents tumour growth by regulating LIN9 and HIF1-α. EMBO Molecular Medicine. 5(3):366-383.

 

Patil, A., Dyavaiah, M., Joseph, F., Rooney, J.P., Chan, C.T.Y., Dedon P.C., and Begley, T.J. (2012). Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response. Cell Cycle. 11(19):3656-3665.

 

Patil, A., Chan, C.T.Y., Dyavaiah, M., Rooney, J.P., Dedon, P.C., and Begley, T.J. (2012). Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications. RNA Biology. 9(7):990-1001.

 

Chan, C.T.Y., Pang, Y.L., Deng, W., Babu, I.R., Dyavaiah, M., Begley, T.J., and Dedon, P.C. (2012). Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nature Communications. 3:937.

 

Chan, C.T.Y., Chionh, Y.H., Ho, C, Lim, K.S., Babu, I.R., Ang, E., Lin, W., Alonso, S., and Dedon P.C. (2011). Identification of N6,N6-dimethyladenosine in transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin. Molecules. 16(6):5168-5181.
 

Chan C.T.Y., Dyavaiah M., DeMott M.S., Taghizadeh K., Dedon P.C., and Begley T.J. (2010).  A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genetics. 6(12):e1001247.
•  Highlighted in Nature Methods. 8(2):108-109. Better living through biochemistry. Eisenstein, M. (2011).
•  Highlighted in Nature Review Genetics. 12(2):77. In brief: translational control – a quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. Muers, M. (2012).

 

Fu, D., Brophy J.A., Chan, C.T.Y., Atmore, K.A., Begley, U., Paules, R.S., Dedon, P.C., Begley, T.J., and Samson, L.D. (2010). Human AlkB homolog ABH8 is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Molecular and Cellular Biology. 30(10):2449-2459.

 

Seyedsayamdost, M.R., Xie, J., Chan, C.T.Y., Alfonta, L., Schultz, P.G., and Stubbe, J. (2009). Genetic incorporation of 3-aminotyrosine into reductases. U.S. patent. Publication number:20090208994.

 

Seyedsayamdost, M.R., Chan, C.T.Y., Mugnaini, V., Stubbe, J. and Bennati, M. (2007).  PELDOR spectroscopy with DOPA−α2 and NH2Y−β2: distance measurements between residues involved in the radical propagation pathway of E. coli ribonucleotide reductase. Journal of American Chemical Society. 129:15748-15749. 

 

Seyedsayamdost, M.R., Xie, J., Chan, C.T.Y., Schultz, P.G., and Stubbe, J. (2007).  Site-specific insertion of 3-aminotyrosine into subunit α2 of E. coli ribonucleotide reductase: direct evidence for involvement of Y730 and Y731 in radical propagation. Journal of American Chemical Society. 129:15060-15071.
 

 

Note: * Authors with equal contribution; ‡ Co-corresponding authors