Lemos, T., & Kim, H. D. (2025). Visualizing Poloidal Orientation in DNA Minicircles. Preprint.
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.