[1] H.D. Kim*, T. Shay*, E.K. O'Shea, and A. Regev, “Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets,” Science, vol. 325, 2009, p. 429.  
[2] H.D. Kim and E.K. O’Shea, “A quantitative model of transcription factor–activated gene expression,” Nature Structural & Molecular Biology, vol. 15, 2008, p. 1192.  
[3] S. Uemura, M. Dorywalska, T.H. Lee, H.D. Kim, J.D. Puglisi, and S. Chu, “Peptide bond formation destabilizes Shine–Dalgarno interaction on the ribosome,” Nature, vol. 446, 2007, p. 454.  
[4] T.H. Lee, S.C. Blanchard, H.D. Kim, J.D. Puglisi, and S. Chu, “The role of fluctuations in tRNA selection by the ribosome,” Proceedings of the National Academy of Sciences, vol. 104, 2007, p. 13661.  
[5] H.D. Kim, J.D. Puglisi, and S. Chu, “Fluctuations of transfer RNAs between classical and hybrid states,” Biophysical Journal, vol. 93, 2007, pp. 3575–3582.  
[6] U. Mohanty, A. Spasic, H.D. Kim, and S. Chu, “Ion Atmosphere of Three-Way Junction Nucleic Acid” J. Phys. Chem. B, vol. 109, 2005, pp. 21369–21374.  
[7] M. Dorywalska, S.C. Blanchard, R.L. Gonzalez, H.D. Kim, S. Chu, and J.D. Puglisi, “Site-specific labeling of the ribosome for single-molecule spectroscopy,” Nucleic Acids Research, vol. 33, 2005, p. 182.  
[8] S.C. Blanchard*, H.D. Kim*, R.L. Gonzalez*, J.D. Puglisi, and S. Chu, “tRNA dynamics on the ribosome during translation,” Proceedings of the National Academy of Sciences, vol. 101, 2004, p. 12893.  
[9] S.C. Blanchard, R.L. Gonzalez*, H.D. Kim*, S. Chu, and J.D. Puglisi, “tRNA selection and kinetic proofreading in translation,” Nature structural & molecular biology, vol. 11, 2004, pp. 1008–1014.  
[10] X. Zhuang, H. Kim, M.J. Pereira, H.P. Babcock, N.G. Walter, and S. Chu, “Correlating structural dynamics and function in single ribozyme molecules,” Science, vol. 296, 2002, p. 1473.  
[11] H.D. Kim, G.U. Nienhaus, T. Ha, J.W. Orr, J.R. Williamson, and S. Chu, “Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules,” Proceedings of the National Academy of Sciences, vol. 99, 2002, p. 4284.  
[12] X. Zhuang, T. Ha, H.D. Kim, T. Centner, S. Labeit, and S. Chu, “Fluorescence quenching: A tool for single-molecule protein-folding study,” Proceedings of the National Academy of Sciences, vol. 97, 2000, p. 14241.  
[13] T. Ha, X. Zhuang, H.D. Kim, J.W. Orr, J.R. Williamson, and S. Chu, “Ligand-induced conformational changes observed in single RNA molecules,” Proceedings of the National Academy of Sciences of the United States, vol. 96, 1999, p. 9077.