Z. Weinberg, Lünse, C. E., Corbino, K., Ames, T. D., Nelson, J. W., Roth, A., Perkins, K., Sherlock, M. E., and Breaker, R. R., “Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions”, Nucleic Acids Research, 2017.
J. W. Nelson, Plummer, M. S., Blount, K. F., Ames, T. D., and Breaker, R. R., “Small molecule fluoride toxicity agonists.”, Chem Biol, vol. 22, no. 4, pp. 527-34, 2015.
A. Roth, Weinberg, Z., G Y Chen, A., Kim, P. B., Ames, T. D., and Breaker, R. R., “A widespread self-cleaving ribozyme class is revealed by bioinformatics.”, Nat Chem Biol, vol. 10, no. 1, pp. 56-60, 2014.
T. D. Ames and Breaker, R. R., “Bacterial aptamers that selectively bind glutamine.”, RNA Biol, vol. 8, no. 1, pp. 82-9, 2011.
T. D. Ames, Rodionov, D. A., Weinberg, Z., and Breaker, R. R., “A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate.”, Chem Biol, vol. 17, no. 7, pp. 681-5, 2010.
T. D. Ames and Breaker, R. R., “Bacterial Riboswitch Discovery and Analysis”, in The Chemical Biology of Nucleic Acids, 2010.
K. D. Smith, Lipchock, S. V., Ames, T. D., Wang, J., Breaker, R. R., and Strobel, S. A., “Structural basis of ligand binding by a c-di-GMP riboswitch.”, Nat Struct Mol Biol, vol. 16, no. 12, pp. 1218-23, 2009.
E. Poiata, Meyer, M. M., Ames, T. D., and Breaker, R. R., “A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria.”, RNA, vol. 15, no. 11, pp. 2046-56, 2009.
M. M. Meyer, Ames, T. D., Smith, D. P., Weinberg, Z., Schwalbach, M. S., Giovannoni, S. J., and Breaker, R. R., “Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.”, BMC Genomics, vol. 10, p. 268, 2009.
K. H. Link, Guo, L., Ames, T. D., Yen, L., Mulligan, R. C., and Breaker, R. R., “Engineering high-speed allosteric hammerhead ribozymes.”, Biol Chem, vol. 388, no. 8, pp. 779-86, 2007.