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Harold D. Kim, Ph.D. - Publications

Affiliations: 
2010- Physics Georgia Institute of Technology, Atlanta, GA 
Area:
Biological physics, DNA packaging, Gene regulation
Website:
https://haroldkimlab.gatech.edu/
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Wadsworth GM, Kim HD. FISHing on a Budget. Methods in Molecular Biology (Clifton, N.J.). 2349: 81-90. PMID 34718992 DOI: 10.1007/978-1-0716-1585-0_5  0.785
2021 Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Jung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, ... ... Kim HD, et al. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife. 10. PMID 33779550 DOI: 10.7554/eLife.60416  0.533
2020 Garcia PD, Leach RW, Wadsworth GM, Choudhary K, Li H, Aviran S, Kim HD, Zakian VA. Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nature Communications. 11: 2173. PMID 32358529 DOI: 10.1038/S41467-020-15875-9  0.749
2020 Jeong J, Kim HD. Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Research. PMID 32282905 DOI: 10.1093/Nar/Gkaa207  0.395
2019 Jeong J, Kim HD. Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking. Physical Review Letters. 122: 218101. PMID 31283336 DOI: 10.1103/Physrevlett.122.218101  0.401
2019 Cook AW, Broadwater B, Kim H. Kinetics of DNA Strand Displacement Biophysical Journal. 116: 499a. DOI: 10.1016/J.Bpj.2018.11.2691  0.336
2019 Wadsworth GM, Kim HD. RNA Isoform Identification via Sequential Hybridization and Strand Displacement Based Amplication in the Caenorhabditis Elegans Germline Biophysical Journal. 116: 209a. DOI: 10.1016/J.Bpj.2018.11.1153  0.364
2018 Wadsworth GM, Parikh RY, Kim HD. Single-probe RNA FISH in Yeast. Bio-Protocol. 8: e2868. PMID 34285982 DOI: 10.21769/BioProtoc.2868  0.786
2018 Wadsworth GM, Parikh RY, Kim HD. Dual-probe RNA FRET-FISH in Yeast. Bio-Protocol. 8: e2867. PMID 34285981 DOI: 10.21769/BioProtoc.2867  0.781
2018 Broadwater DWB, Altman RB, Blanchard SC, Kim HD. ERASE: a novel surface reconditioning strategy for single-molecule experiments. Nucleic Acids Research. PMID 30462308 DOI: 10.1093/Nar/Gky1168  0.338
2018 Wadsworth GM, Kim HD. Highly Specific Circular RNA Quantification in Single Yeast Cells Biophysical Journal. 114: 247a. DOI: 10.1016/J.Bpj.2017.11.1378  0.361
2017 Wadsworth GM, Parikh RY, Choy JS, Kim HD. mRNA detection in budding yeast with single fluorophores. Nucleic Acids Research. PMID 28666354 DOI: 10.1093/Nar/Gkx568  0.774
2017 Broadwater DB, Kim HD. Is DNA Branch Migration a One-Dimensional Random Walk? Biophysical Journal. 112: 215a. DOI: 10.1016/J.Bpj.2016.11.1187  0.381
2017 Jeong J, Kim HD. Observation of Flexibility Reversal in DNA Bending Biophysical Journal. 112: 213a. DOI: 10.1016/J.Bpj.2016.11.1177  0.368
2017 Wadsworth GM, Kim HD. mRNA Transcript Quantification in Yeast with Single-Molecule FRET Biophysical Journal. 112: 211a. DOI: 10.1016/J.Bpj.2016.11.1165  0.441
2016 Waters JT, Kim HD, Gumbart JC, Lu XJ, Harvey SC. DNA Scrunching in the Packaging of Viral Genomes. The Journal of Physical Chemistry. B. PMID 27214211 DOI: 10.1021/Acs.Jpcb.6B02149  0.351
2016 Waters JT, Lu XJ, Galindo-Murillo R, Gumbart JC, Kim HD, Cheatham TE, Harvey SC. Transitions of Double-Stranded DNA Between the A- and B-Forms. The Journal of Physical Chemistry. B. PMID 27135262 DOI: 10.1021/Acs.Jpcb.6B02155  0.341
2016 Broadwater DW, Kim HD. The Effect of Basepair Mismatch on DNA Strand Displacement. Biophysical Journal. 110: 1476-84. PMID 27074674 DOI: 10.1016/J.Bpj.2016.02.027  0.379
2016 Jeong J, Le TT, Kim HD. Single-molecule fluorescence studies on DNA looping. Methods (San Diego, Calif.). PMID 27064000 DOI: 10.1016/J.Ymeth.2016.04.005  0.693
2016 Jeong J, Kim HD. The Effect of Local Melting of DNA on DNA Loop Formation Biophysical Journal. 110: 564a. DOI: 10.1016/J.Bpj.2015.11.3020  0.414
2016 Broadwater DB, Kim HD. Measuring and Modeling the Effect of Single Mismatch on DNA Strand Displacement Biophysical Journal. 110: 563a. DOI: 10.1016/J.Bpj.2015.11.3011  0.377
2016 Wadsworth GM, Kim H. Single-Probe Fluorescence in Situ Hybridization (FISH) in Budding Yeast Biophysical Journal. 110: 21a. DOI: 10.1016/J.Bpj.2015.11.171  0.451
2015 Choi JY, Park EJ, Kim HD, Park SH, Song JY, Lee DI, Shim J, Kim YH. Ethanol Infusion in the Vein of Marshall in a Patient with Persistent Atrial Fibrillation. Korean Circulation Journal. 45: 424-7. PMID 26413111 DOI: 10.4070/kcj.2015.45.5.424  0.356
2014 Le TT, Kim HD. Probing the elastic limit of DNA bending. Nucleic Acids Research. 42: 10786-94. PMID 25122748 DOI: 10.1093/Nar/Gku735  0.685
2014 Le TT, Kim HD. Studying DNA looping by single-molecule FRET. Journal of Visualized Experiments : Jove. e51667. PMID 24998459 DOI: 10.3791/51667  0.698
2014 Le TT, Kim HD. Measuring Energetics of Sharp DNA Bending from Breakage Kinetics of Small DNA Loops Biophysical Journal. 106: 276a. DOI: 10.1016/J.Bpj.2013.11.1619  0.68
2013 Parikh RY, Kim HD. The effect of an intervening promoter nucleosome on gene expression. Plos One. 8: e63072. PMID 23700413 DOI: 10.1371/Journal.Pone.0063072  0.305
2013 Le TT, Kim HD. Measuring shape-dependent looping probability of DNA. Biophysical Journal. 104: 2068-76. PMID 23663850 DOI: 10.1016/J.Bpj.2013.03.029  0.681
2013 Parikh RY, Kim HD. The Non-Monotonic Effect of Nucleosome Occupancy on Gene Expression Biophysical Journal. 104: 580a. DOI: 10.1016/J.Bpj.2012.11.3223  0.313
2013 Le TT, Kim HD. Catch-Slip Transition in DNA Duplex Biophysical Journal. 104: 422a. DOI: 10.1016/J.Bpj.2012.11.2351  0.685
2013 Kim H. Understanding How Chromatin Structure and Dynamics affect Transcription In Vivo Biophysical Journal. 104: 385a. DOI: 10.1016/J.Bpj.2012.11.2147  0.342
2012 Le T, Kim H. Measuring Sequence-Dependent DNA Looping Kinetics Biophysical Journal. 102: 276a. DOI: 10.1016/J.Bpj.2011.11.1522  0.683
2009 Kim HD, Shay T, O'Shea EK, Regev A. Transcriptional regulatory circuits: predicting numbers from alphabets. Science (New York, N.Y.). 325: 429-32. PMID 19628860 DOI: 10.1126/Science.1171347  0.606
2008 Kim HD, O'Shea EK. A quantitative model of transcription factor-activated gene expression. Nature Structural & Molecular Biology. 15: 1192-8. PMID 18849996 DOI: 10.1038/Nsmb.1500  0.588
2007 Lee TH, Blanchard SC, Kim HD, Puglisi JD, Chu S. The role of fluctuations in tRNA selection by the ribosome. Proceedings of the National Academy of Sciences of the United States of America. 104: 13661-5. PMID 17699629 DOI: 10.1073/Pnas.0705988104  0.602
2007 Kim HD, Puglisi JD, Chu S. Fluctuations of transfer RNAs between classical and hybrid states. Biophysical Journal. 93: 3575-82. PMID 17693476 DOI: 10.1529/Biophysj.107.109884  0.506
2007 Uemura S, Dorywalska M, Lee TH, Kim HD, Puglisi JD, Chu S. Peptide bond formation destabilizes Shine-Dalgarno interaction on the ribosome. Nature. 446: 454-7. PMID 17377584 DOI: 10.1038/Nature05625  0.595
2006 Uemura S, Dorywalska M, Lee T, Kim H, Puglisi J, Chu S. 1P557 Peptide bond formation induces the breakage of Shine-Dalgarno interaction on the ribosome(26. Single molecule biophysics,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) Seibutsu Butsuri. 46: S286. DOI: 10.2142/Biophys.46.S286_1  0.559
2005 Mohanty U, Spasic A, Kim HD, Chu S. Ion atmosphere of three-way junction nucleic acid. The Journal of Physical Chemistry. B. 109: 21369-74. PMID 16853772 DOI: 10.1021/Jp050005O  0.441
2005 Dorywalska M, Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD. Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Research. 33: 182-9. PMID 15647501 DOI: 10.1093/Nar/Gki151  0.557
2004 Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD. tRNA selection and kinetic proofreading in translation. Nature Structural & Molecular Biology. 11: 1008-14. PMID 15448679 DOI: 10.1038/Nsmb831  0.51
2004 Blanchard SC, Kim HD, Gonzalez RL, Puglisi JD, Chu S. tRNA dynamics on the ribosome during translation. Proceedings of the National Academy of Sciences of the United States of America. 101: 12893-8. PMID 15317937 DOI: 10.1073/Pnas.0403884101  0.544
2002 Zhuang X, Kim H, Pereira MJ, Babcock HP, Walter NG, Chu S. Correlating structural dynamics and function in single ribozyme molecules. Science (New York, N.Y.). 296: 1473-6. PMID 12029135 DOI: 10.1126/Science.1069013  0.743
2002 Kim HD, Nienhaus GU, Ha T, Orr JW, Williamson JR, Chu S. Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. Proceedings of the National Academy of Sciences of the United States of America. 99: 4284-9. PMID 11929999 DOI: 10.1073/Pnas.032077799  0.628
2000 Zhuang X, Ha T, Kim HD, Centner T, Labeit S, Chu S. Fluorescence quenching: A tool for single-molecule protein-folding study. Proceedings of the National Academy of Sciences of the United States of America. 97: 14241-4. PMID 11121030 DOI: 10.1073/Pnas.97.26.14241  0.674
1999 Ha T, Zhuang X, Kim HD, Orr JW, Williamson JR, Chu S. Ligand-induced conformational changes observed in single RNA molecules. Proceedings of the National Academy of Sciences of the United States of America. 96: 9077-82. PMID 10430898 DOI: 10.1073/Pnas.96.16.9077  0.691
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