72. Y.-A. Kuo, Y.-I. Chen, Y. Wang, Z. Korkmaz, S. Yonas, Y. He, T.D. Nguyen, S. Hong, A.-T. Nguyen, S. Kim, S. Seifi, P.-H. Fan, Y. Wu, Z. Yang, H.-W. Liu, Y. Lu, P. Ren and H.-C. Yeh, “Fluorogenic aptamer optimizations on a massively parallel sequencing platform”, under review.
71. Y. Wu, W. Kong, J.V. Stappen, L. Kong, Z. Huang, Z. Yang, Y.-A. Kuo, Y.-I. Chen, Y. He, H.-C. Yeh, T. Lu, Y. Lu, “Genetically encoded fluorogenic DNA aptamers for imaging metabolite in living cells”, under review.
70. M. Kamra, Y.-I. Chen, P.C. Delgado, E. Seeley, S.K. Seidlits, H.-C. Yeh, A. Brock and S. Parekh, “Ketomimetic nutrients trigger a dual metabolic defense in breast cancer cells”, under review.
69. H.-C. Kuo, Y.-A. Kuo, H.-C. Yeh and I. Finkelstein, “CHAMP: Profiling protein-nucleic acid interactions on repurposed next-generation sequencer chips”, under review at Nature Protocols.
68. M.R. Pickett, Y.-I. Chen, M. Kamra, S. Kumar, N. Kalkunte, G.P. Sugerman, K. Varodom, M.K. Rausch, J. Zoldan, H.-C. Yeh and S.H. Parekh, “Assessing the impact of extracellular matrix fiber orientation on breast cancer cellular metabolism“, Cancer Cell International, 24, 199, 2024.
67. S. Hong, J. Walker, A.T. Luong, J. Mathews, S. Shields, Y.-A. Kuo, Y.-I. Chen, T.D. Nguyen, Y. He, A.-T. Nguyen, M. Ghimire, M.J. Kim, J.S. Brodbelt and H.-C. Yeh, “A non-FRET DNA probe that changes fluorescence color upon nuclease digestion“, Nature Nanotechnology, 19, 810-817, 2024.
66. T.D. Nguyen, Y.-I. Chen, A.-T. Nguyen, S. Yonas, M.P. Sripati, Y.-A. Kuo, S. Hong, M. Litvinlov, Y. He, H.-C, Yeh and H.G. Rylander, “Two-photon autofluorescence lifetime assay of rabbit photoreceptors and retinal pigment epithelium during light-dark visual cycles in rabbit retina“, Biomedical Optics Express, 15 (5), 3094-3111, 2024.
65. Y.-J. Chang, Y.-I. Chen, H.-C. Yeh and S.R. Santacruz, “Neurobiologically realistic neural network enables multi-scale modeling of neural dynamics,” Scientific Reports, 14, 5145, 2024.
64. T.D. Nguyen, Y.-I. Chen, A.-T. Nguyen, L.H. Chen, S. Yonas, M. Litvinlov, Y. He, Y.-A. Kuo, S. Hong, H.G. Rylander and H.-C, Yeh, “Multiplexed imaging in live cells using pulsed interleaved excitation spectral FLIM“, Optics Express, 32, 3, 3290-3307, 2024.
63. M. Hedayati, Y.-I. Chen, J.R. Houser, Y. Wang, S. Norouzi, H.-C. Yeh and S.H. Parekh, “Visualizing molecular deformation in fibrin networks under tensile loading via FRET-FLIM“, Chemical Communications, 59, 14575-14578, 2023.
62. J. Karam, B.J. Singer, H. Miwa, L. Chen, K. Maran, M. Hasani, S. Garza, B. Onyekwere, H.-C. Yeh, S. Li, D.D. Carlo and S.K. Seidlits, “Molecular weight of hyaluronic acid crosslinked into biomaterial scaffolds affects angiogenic potential,” Acta Biomaterialia, 169, 228-242, 2023.
61. Y.-I. Chen, Y.-J. Chang, Y.S. Sun, S.-C. Liao, S.R. Santacruz and H.-C. Yeh, “Spatial resolution enhancement in photon-starved STED imaging using deep learning-based fluorescence lifetime analysis,” Nanoscale, 15, 9449-9456, 2023.
60. T.D. Nguyen, Y.-I. Chen, L. Chen and H.-C. Yeh, “Recent advances in single-molecule tracking and imaging techniques,” Annual Review of Analytical Chemistry, 16, 253-284, 2023.
59. Y.S. Sun, T.D. Nguyen, Y.-I. Chen, U.C. Coskun, S.-C. Liao and H.-C. Yeh, “Characterization of a time-resolved spectral detector for spectral fluorescence lifetime imaging with the parallel 16-channel FastFLIM and the phasor analysis,” SPIE Proceedings, 12384-21, 2023.
58. X. Yang, C. Liu, Y.-A. Kuo, H.-C. Yeh and P. Ren, “Computational study on the binding of mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA“, Frontiers in Molecular Biosciences, 9, 946708, 2022.
57. Y.-A. Kuo, C. Jung, Y.-A. Chen, H.-C. Kuo, O.S. Zhao, T.D. Nguyen, J.R. Rybarski, S. Hong, Y.-I. Chen, D.C. Wylie, J.A. Hawkins, J.N. Walker, S.W. Shields, J.S. Brodbelt, J.T. Petty, I.J. Finkelstein and H.-C. Yeh, “Massively parallel selection of NanoCluster Beacons“, Advanced Materials, 2204957, 2022.
56. Y.-I. Chen, Y.-J. Chang, S.-C. Liao, T.D. Nguyen, J. Yang, Y.-A. Kuo, S. Hong, H.-C. Li, Y.-L. Liu, H.G. Rylander III, S.R. Santacruz, T.E. Yankeelov, and H.-C. Yeh, “Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells“, Communications Biology, 5, 18, 2022.
55. M. Kim, S. Hong, T.E. Yankeelov, H.-C. Yeh* and Y.-L. Liu* (co-corresponding authors), “Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics“, Bioinformatics, 38, 1, 243-249, 2022.
54. J. Yang, T. Davis, A.S. Kazerouni, Y.-I. Chen, M.J. Bloom, H.-C. Yeh, T.E. Yankeelov and J. Virostko, “Longitudinal FRET imaging of glucose and lactate dynamics and response to therapy in breast cancer cells“, Molecular Imaging and Biology, 24, 144-155, 2021.
53. I.C. Santos, S. Hong, H.-C. Yeh and J.S. Brodbelt, “Electron photodetachment mass spectrometry to study interactions of silver nanoclusters with DNA monomers and dimers“, under review.
52. Y.-I. Chen, M.P. Sripati, T.D. Nguyen, Y.-J. Chang, Y.-A. Kuo, S. Hong and H.-C. Yeh, “Recent developments in the characterization of nucleic acids hybridization kinetics“, Current Opinion in Biomedical Engineering, 19, 100305, 2021.
51. C.-K. Chou, Y.-L. Liu, P.-J. Huang, P.-H. Tsou, C.-T Chen, H.-H. Lee, Y.-N. Wang, J.L. Hsu, J.-F. Lee, T.E. Yankeelov, J. Kameoka*, H.-C. Yeh*, and M.-C. Hung*, “Digital receptor occupancy assay in quantifying on- and off-target binding affinities of therapeutic antibodies“, ACS Sensors, 5, 296-302, 2020.
50. Y.-L. Liu*, E.P. Perillo, P. Ang, M. Kim, D.T. Nguyen, K. Blocher, Y.-A. Chen, C. Liu, A.M. Hassan, H.T. Vu, Y.-I. Chen, A.K. Dunn and H.-C. Yeh* (co-corresponding authors), “Three-dimensional two-color dual-particle tracking microscope for monitoring DNA conformational changes and nanoparticle landings on live cells“, ACS Nano, 14, 7927-7939, 2020.
49. M.S. Blevins, D. Kim, C.M. Crittenden, S. Hong, H.-C. Yeh, J.T. Petty and J.S. Brodbelt, “Footprints of nanoscale DNA-silver cluster chromophores via activated-electron photodetachment mass spectrometry“, ACS Nano, 13, 14070-14079, 2019.
48. X. Peng, X. Liu, Y.-L. Liu, J.Y. Kim, Y.-I. Chen, P. Ang, A. Nguyen, J. Leal, H.-C. Yeh and D. Ghosh, “Brain-penetrating peptide shuttles through the blood-brain barrier and extracellular-like space“, ChemRxiv, 2019.
47. Y.-I. Chen, Y.-J. Chang, T.D. Nguyen, C. Liu, S. Phillion, Y.-A. Kuo, H.T. Vu, A. Liu, Y.-L. Liu, S. Hong, P. Ren, T.E. Yankeelov and H.-C. Yeh, “Measuring DNA hybridization kinetics in live cells using a time-resolved 3D single-molecule tracking method“, Journal of the American Chemical Society, 141(40): 15747-15750, 2019.
46. Y.-L. Liu, A.M. Horning, B. Lieberman, C.-K. Lin, C.-N. Hung, C.-W. Chou, C.-M. Wang, M.A. Liss, M. Kim, R. Vasisht, E.P. Perillo, K. Blocher, H. Horng, A.K. Dunn, T. H.-M. Huang, H.-C. Yeh* and C.-L. Chen*, “Spatial EGFR dynamics and metastatic phenotypes modulated by upregulated EPHB2 and SRC pathways predicting poor prognosis“, Cancer, 11(12), 1910, 2019.
45. Y.-L. Liu, C.-K. Chou; M. Kim, R. Vasisht, Y.-A. Kuo, C. Liu, E.P. Perillo, Y.-A. Chen, K. Blocher, H. Horng, Y.-I Chen, D.T. Nguyen, T. Yankeelov, M.-C. Hung, A. Dunn, and H.-C. Yeh, “Assessing metastatic potential of breast cancer cells based on EGFR dynamics“, Scientific Reports, 9, 3395, 2019.
44. A.M. Hassan, X. Wu, J.W. Jarrett, S. Xu, J. Yu, D.R. Miller, E.P. Perillo, Y.-L. Liu, D.T. Chiu, H.-C. Yeh*, and A.K. Dunn* (co-corresponding authors) “Polymer dots enable deep in vivo multiphoton fluorescence imaging of microvasculature,” Biomedical Optics Express, 10(2): 584-599, 2019.
43. H.T. Vu, S. Hong and H.-C. Yeh, “Fluorescence Biosensors,” in Advances in Biosensing Technology for Medical Diagnosis, edited by H.-S. Chuang and Y.-P. Ho, Bentham Science, 2019.
42. Y.-A. Chen, H.T. Vu, Y.-L. Liu, Y.-I Chen, T.D. Nguyen, Y.-A. Kuo, S. Hong, Y.-A. Chen, S. Carnahan, J.T. Petty and H.-C. Yeh, “Improving NanoCluster Beacon performance by blocking the unlabeled NC probes,” Chemical Communications, 55, 462-465, 2019.
41. C.-K. Chou, P.-J. Huang, P.-H. Tsou, Y. Wei, H.-H. Lee, Y.-N. Wang, Y.-L. Liu, C. Shi, H.-C. Yeh, J. Kameoka, and M.-C. Hung, “A flow-proteometric platform for analyzing protein concentration (FAP): Proof of concept for quantification of PD-L1 protein in cells and tissues“, Bioelectronics and Biosensors, 117, 97-103, 2018.
40. V. Le, J. Lee, S. Chaterji, A. Spencer, Y.-L. Liu, P. Kim, H.-C. Yeh, D.-H. Kim and A.B. Baker, “Syndecan-1 in mechanosensing of nanotopological cues in engineered materials,” Biomaterials, 155, 13-24, 2018.
39. A.M. Hassan, X. Wu, J.W. Jarrett, S. Xu, D.R. Miller, J. Yu, E.P. Perillo, Y.-L. Liu, D.T. Chiu, H.-C. Yeh*, and A.K. Dunn* (co-corresponding authors) “Polymer dots enable deep in vivo multiphoton fluorescence imaging of cerebrovascular architecture,” SPIE Proceedings, 104982Y, 2018.
38. C.-W. Li, S.-O. Lim, E.M. Chung, Y.-S. Kim, A.H. Park, J.-H. Cha, W. Xia, L.-C. Chan, T. Kim, S.-S. Chang, H.-H. Lee, C.-K. Chou, Y.-L. Liu, H.-C. Yeh, E.P. Perillo, A.K. Dunn, C.-W. Kuo, K.-H. Khoo, J.L. Hsu, Y. Wu, J.-M. Hsu, H. Yamaguchi, J. Yao, A.A. Sahin, G.N. Hortobagyi, S.S. Yoo and M.-C. Hung, “Eradication of Triple-Negative Breast Cancer Cells by Targeting Glycosylated PD-L1,” Cancer Cell, 33(2): 187-201, 2018.
37. E.P. Perillo, J.W. Jarrett, Y.-L. Liu, A. Hassan, D.C. Fernée, J.R. Goldak, A. Bonteanu, D.J. Spence, H.-C. Yeh and A.K. Dunn, “Two-color multiphoton in vivo imaging with a femtosecond diamond Raman laser,” Light: Sciences & Applications, 6, e17095, 2017.
36. J.M. Obliosca, S.Y. Cheng, Y.-A. Chen, M.F. Llanos, Y.-L. Liu, D.M. Imphean, D. Bell, J.T. Petty, P. Ren and H.-C. Yeh, “LNA thymidine monomer enables differentiation of the four single-nucleotide variants by melting temperature,” Journal of the American Chemical Society, 139(20): 7110-7116, 2017.
35. C. Liu, A. Rastogi and H.-C. Yeh, “Quantification of rare single-molecule species based on fluorescence lifetime,” Analytical Chemistry, 89(9): 4772-4775, 2017.
34. C. Liu, J.M. Obliosca, Y.-L. Liu, Y.-A. Chen, N. Jiang and H.-C. Yeh, “3D single-molecule tracking enables direct hybridization kinetics measurement in solution,” Nanoscale, 9: 5664-5670, 2017.
33. Y.-L. Liu, E.P. Perillo, C. Liu, P. Yu, C.-K. Chou, M.-C. Hung, A.K. Dunn and H.-C. Yeh, “Segmentation of 3D trajectories acquired by TSUNAMI microscope: an application to EGFR trafficking,” Biophysical Journal, 111(10): 2214-2227, 2016.
32. C. Liu, Y.-L. Liu, E.P. Perillo, A.K. Dunn and H.-C. Yeh, “Single-molecule tracking and its application in biomolecular detection,” IEEE Journal of Selected Topics in Quantum Electronics, 22(4): 6804013, 2016.
31. E.P. Perillo, J.E. McCracken, D.C. Fernée, J.R. Goldak, F.A. Medina, D.R. Miller, H.-C. Yeh, and A.K. Dunn, “Deep in vivo two-photon microscopy with a low cost custom built mode-locked 1060 nm fiber laser,” Biomedical Optics Express, 7(2): 324-334, 2016.
30. C. Liu*, Y.-L. Liu* (equal contribution), E.P. Perillo, N. Jiang, A.K. Dunn and H.-C. Yeh, “Improving z-tracking accuracy in the two-photon single-particle tracking microscope,” Applied Physics Letters, 107, 153701, 2015.
29. Y.-A. Chen*, J.M. Obliosca* (equal contribution), Y.-L. Liu, C. Liu, M.L. Gwozdz, and H.-C. Yeh, “NanoCluster Beacons enable detection of a single N6-methyladenine,” Journal of the American Chemical Society, 137(33): 10476-10479, 2015.
28. E. P. Perillo, Y.-L. Liu, K. Huynh, C. Liu, C.-K. Chou, M.-C. Hung, H.-C. Yeh*, and A. Dunn* (co-corresponding authors) “Deep and high-resolution three-dimensional tracking of single particles using nonlinear and multiplexed illumination,” Nature Communications, 6, 7874, 2015.
27. S. Juul*, J.M. Obliosca* (equal contribution), C. Liu, Y.-L. Liu, Y.-A. Chen, D.M. Imphean, B. R. Knudsen, Y.-P. Ho, K.W. Leong, and H.-C. Yeh, “NanoCluster Beacons as reporter probes in rolling circle enhanced enzyme activity detection,” Nanoscale, 7, 8332-8337, 2015.
26. E. Perillo, Y.-L. Liu, C. Liu, H.-C. Yeh, and A.K. Dunn, “Single particle tracking through highly scattering media with multiplexed two-photon excitation,” SPIE Proceedings, 933107, 2015.
25. J.M. Obliosca, M.C. Babin, C. Liu, Y.-L. Liu, Y.-A. Chen, R.A. Batson, M. Ganguly, J.T. Petty, and H.-C. Yeh, “A complementary palette of NanoCluster Beacons,” ACS Nano, 8(10): 10150-10160, 2014.
24. C. Liu, E.P. Perillo, Q. Zhuang, K.T. Huynh, A.K. Dunn, and H.-C. Yeh, “3D single-molecule tracking using one- and two-photon excitation microscopy,” SPIE Proceedings, 89501C, 2014.
23. E.P. Perillo, L. De Haro, M.E. Phipps, J.S. Martinez, H.-C. Yeh, A.K. Dunn, D.P. Shepherd, and J.H. Werner, “Enhanced 3D localization of individual RNA transcripts via astigmatic imaging,” SPIE Proceedings, 895003, 2014.
22. J.M. Obliosca, C. Liu, and H.-C. Yeh, “Fluorescent silver nanoclusters as DNA probes,” Nanoscale, 5: 8443-8461, 2013.
21. J.M. Obliosca, C. Liu, R.A. Batson, M.C. Babin, J.H. Werner, and H.-C. Yeh, “DNA/RNA detection using DNA-templated few-atom silver nanoclusters,” Biosensors, 3(2): 185-200, 2013.
20. H.-C. Yeh, J. Sharma, I.-M. Shih, D.M. Vu, J.S. Martinez, and J.H. Werner, “A fluorescence light-up Ag nanocluster probe that discriminates single-nucleotide variants by emission color,” Journal of the American Chemical Society, 134(28): 11550-11558, 2012.
19. S.H. Yau, N. Abeyasinghe, M. Orr, L. Upton, O. Varnavski, J.H. Werner, H.-C. Yeh, J. Sharma, A.P. Shreve, J.S. Martinez, and T. Goodson III, “Bright two-photon emission and ultra-fast relaxation dynamics in a DNA-templated nanocluster investigated by ultra-fast spectroscopy,” Nanoscale, 4: 4247-4254, 2012.
18. J. Sharma, R.C. Rocha, M.L. Phipps, H.-C. Yeh, K.A. Balatsky, D.M. Vu, A.P. Shreve, J.H. Werner, and J.S. Martinez, “A DNA-templated fluorescent silver nanocluster with enhanced stability,” Nanoscale, 4: 4107-4110, 2012.
17. M.L. Neidig, J. Sharma, H.-C. Yeh, J.S. Martinez, S.D. Conradson, and A.P. Shreve, “Ag K-edge EXAFS of DNA-templated fluorescent silver nanoclusters: insight into the structural origins of emission tuning by DNA sequence variation,” Journal of the American Chemical Society, 133(31): 11837-11839, 2011.
16. J. Sharma, H.-C. Yeh, H. Yoo, J.H. Werner, and J.S. Martinez, “Silver nanocluster aptamers: in situ generation of intrinsically fluorescent recognition ligands for protein detection,” Chemical Communications, 47(8): 2294-2296, 2011.
15. H.-C. Yeh, J. Sharma, J.J. Han, J.S. Martinez, and J.H. Werner, “A beacon of light: a new molecular probe for homogeneous detection of nucleic acid targets,” IEEE Nanotechnology Magazine, 5(2): 28-33, 2011.
14. H.-C. Yeh, J. Sharma, J.J. Han, J.S. Martinez, and J.H. Werner, “A DNA-silver nanocluster probe that fluoresces upon hybridization,” Nano Letters, 10(8): 3106-3110, 2010.
13. J. Sharma*, H.-C. Yeh* (*equal contribution), H. Yoo, J.H. Werner, and J.S. Martinez, “A complementary palette of fluorescent silver nanoclusters,” Chemical Communications, 46(19): 3280-3282, 2010.
12. H. Yoo, J. Sharma, H.-C. Yeh, and J.S. Martinez, “Solution-phase synthesis of Au fibers using rod-shaped micelles as shape directing agents,” Chemical Communications, 46(36): 6813-6815, 2010.
11. H.-C. Yeh, J. Sharma, H. Yoo, J.S. Martinez, and J.H. Werner, “Photophysical characterization of fluorescent metal nanoclusters synthesized using oligonucleotides, proteins and small molecule ligands,” SPIE Proceedings, 7576, 75760N, 2010.
10. Y. Bao, H.-C. Yeh, C. Zhong, S.A. Ivanov, J. Sharma, M.L. Neidig, D.M. Vu, A.P. Shreve, R.B. Dyer, J.H. Werner, and J.S. Martinez, “Formation and stabilization of fluorescent gold nanoclusters using small molecules,” Journal of Physical Chemistry C, 114(38): 1587915882, 2010.
9. H.-C. Yeh, C. Puleo, Y.-P. Ho, V. Bailey, T.C. Lim, K. Liu, and T.-H. Wang, “Tunable blinking kinetics of Cy5 for precise DNA quantification and single-nucleotide difference detection,” Biophysical Journal, 95(2): 729-737, 2008.
8. C. Puleo, H.-C. Yeh, K. Liu, and T.-H. Wang, “Coupling confocal fluorescence detection and recirculating microfluidic control for single particle analysis in discrete nanoliter volumes,” Lab on a Chip, 8: 822-825, 2008.
7. Y. Joo, H.-C. Yeh, K. Dieu, and C.-J Kim, “Air cooling of a microelectronic chip with diverging metal microchannels monolithically processed using a single mask,” Journal of Micromechanics and Microengineering, 18(11): 115022, 2008.
6. C. Puleo, H.-C. Yeh, and T.-H. Wang, “Applications of MEMS technologies in tissue engineering,” Tissue Engineering, 13(12): 2839-2854, 2007.
5. H.-C. Yeh, C. Puleo, T.C. Lim, Y.-P. Ho, P. Giza, R.-C. Huang, and T.-H. Wang. “A microfluidic-FCS platform for investigation on the dissociation of Sp1-DNA complex by doxorubicin,” Nucleic Acids Research, 34(21): e144, 2006.
4. H.-C. Yeh, Y.-P. Ho, I.-M. Shih, and T.-H. Wang, “Homogeneous point mutation detection by quantum dot-mediated two-color fluorescence coincidence analysis,” Nucleic Acids Research, 34(5): e35, 2006.
3. C. Zhang, H.-C. Yeh, M. Kuroki, and T.-H. Wang, “Single-quantum-dot-based DNA nanosensor,” Nature Materials, 4(11): 826-831, 2005.
2. H.-C. Yeh, S.-Y. Chao, Y.-P. Ho, and T.-H. Wang, “Single-molecule detection and probe strategies for rapid and ultrasensitive genomic detection,” Current Pharmaceutical Biotechnology, 6(6): 453-461, 2005.
1. H.-C. Yeh, Y.-P. Ho, and T.-H. Wang, “Quantum dot-mediated biosensing assays for specific nucleic acid detection,” Nanomedicine: Nanotechnology, Biology and Medicine, 1(2): 115-121, 2005.