Ploetz, E., Ambrose, B., Barth, A., Börner, R., Erichson, F., Kapanidis, A. N., Kim, H. D., Levitus, M., Lohman, T. M., Mazumder, A., Rueda, D. S., Steffen, F. D., Cordes, T., Magennis, S. W., & Lerner, E. (2023). A new twist on PIFE: Photoisomerisation-related fluorescence enhancement. Methods and Applications in Fluorescence.
Karsai, A., Cassidy, G. J., Rajanala, A. P., Yang, L., Kerimoglu, D., Gumbart, J. C., Kim, H. D., & Goldman, D. I. (2023). Toward a 3D physical model of diffusive polymer chains. Frontiers in Physics.
Hart, D. J., Jeong, J., Gumbart, J. C., & Kim, H. D. (2023). Weak tension accelerates hybridization and dehybridization of short oligonucleotides. Nucleic Acids Research.
Moon, Y., Moon, H., Chang, J., Kim, H. D., Lee, J. H., & Lee, J. (2022). Development of a highly sensitive lateral flow strip device for nucleic acid detection using molecular beacons. Frontiers in Sensors.
Gravina, N. M., Gumbart, J. C., & Kim, H. D. (2021). Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding. The Journal of Physical Chemistry B.
Broadwater, D. W. B., Cook, A. W., & Kim, H. D. (2021). First passage time study of DNA strand displacement. Biophysical Journal.
("New and Notable")
Lerner, E., et al. (2021). FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. ELife.
Garcia, P. D., et al. (2020). Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nature Communications.
Jeong, J., & Kim, H. D. (2020). Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Research.
Jeong, J., & Kim, H. D. (2019). Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking. Physical Review Letters.
Broadwater, D. W. B., Altman, R. B., Blanchard, S. C., & Kim, H. D. (2019). ERASE: A novel surface reconditioning strategy for single-molecule experiments. Nucleic Acids Research.
Wadsworth, G. M., Parikh, R. Y., Choy, J. S., & Kim, H. D. (2017). mRNA detection in budding yeast with single fluorophores. Nucleic Acids Research.
Waters, J. T., Lu, X.-J., Galindo-Murillo, R., Gumbart, J. C., Kim, H. D., Cheatham, T. E., & Harvey, S. C. (2016). Transitions of Double-Stranded DNA Between the A- and B-Forms. The Journal of Physical Chemistry B.
Waters, J. T., Kim, H. D., Gumbart, J. C., Lu, X.-J., & Harvey, S. C. (2016). DNA Scrunching in the Packaging of Viral Genomes. The Journal of Physical Chemistry B.
Waters, J. T., & Kim, H. D. (2016). Force distribution in a semiflexible loop. Physical Review E.
Jeong, J., Le, T. T., & Kim, H. D. (2016). Single-molecule fluorescence studies on DNA looping. Methods.
Broadwater, D. W. B., & Kim, H. D. (2016). The Effect of Basepair Mismatch on DNA Strand Displacement. Biophysical Journal.
Waters, J. T., & Kim, H. D. (2015). Calculation of a fluctuating entropic force by phase space sampling. Physical Review E.
Chang, Y.-W., Fragkopoulos, A. A., Marquez, S. M., Kim, H. D., Angelini, T. E., & Fernandez-Nieves, A. (2015). Biofilm formation in geometries with different surface curvature and oxygen availability. New Journal of Physics.
Le, T. T., & Kim, H. D. (2014). Probing the elastic limit of DNA bending. Nucleic Acids Research.
Lee, T. J., Parikh, R. Y., Weitz, J. S., & Kim, H. D. (2014). Suppression of Expression Between Adjacent Genes Within Heterologous Modules in Yeast. G3: Genes, Genomes, Genetics.
Le, T. T., & Kim, H. D. (2014). Studying DNA Looping by Single-Molecule FRET. JoVE (Journal of Visualized Experiments).
Waters, J. T., & Kim, H. D. (2013). Equilibrium Statistics of a Surface-Pinned Semiflexible Polymer. Macromolecules.
Parikh, R. Y., & Kim, H. D. (2013). The Effect of an Intervening Promoter Nucleosome on Gene Expression. PLOS ONE.
Le, T. T., & Kim, H. D. (2013). Measuring Shape-Dependent Looping Probability of DNA. Biophysical Journal.
Select publications before Kim lab
Kim, H. D., & O'Shea, E. K. (2008). A Quantitative Model of Transcription Factor-Activated Gene Expression. Nature Structural & Molecular Biology.
Kim, H. D., Puglisi, J. D., & Chu, S. (2007). Fluctuations of Transfer RNAs between Classical and Hybrid States. Biophysical Journal.
Kim, H. D., Nienhaus, G. U., Ha, T., Orr, J. W., Williamson, J. R., & Chu, S. (2002). Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proceedings of the National Academy of Sciences.