Publications

1

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 breat cancer cells", under review.

2

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.T. Petty, I.J. Finkelstein and H.-C. Yeh, "Massively parallel selection of NanoCluster Beacons", under review. 

3

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, "Deep learning improves complex lifetime estimation in fluorescence lifetime imaging microscopy", under review.

4

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.

5

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, 2021.

6

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.

7

C.-K. Chiou, 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.

8

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, A.K. Dunn and H.-C. Yeh* (co-corresponding authors), "Development of three-dimensional two-color dual-particle tracking microscope and its applications in monitoring DNA conformational changes and antibody-conjugated nanoparticle landings on the plasma membrane", ACS Nano 14, 7927-7939, 2020.

9

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.

10

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.

11

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.

12

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.

13

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.

14

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.

15

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.

16

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.

17

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.

18

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.

19

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.

20

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.

21

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.

22

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.

23

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.

24

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.

25

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.

26

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.

27

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.

28

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.

30

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.

31

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.

32

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.

33

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.

34

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.

35

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.

36

J.M. Obliosca, C. Liu, and H.-C. Yeh, "Fluorescent silver nanoclusters as DNA probes," Nanoscale 5: 8443-8461, 2013.

37

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.

38

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.

39

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.

40

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.

41

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.

42

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.

43

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.

44

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.

45

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.

46

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.

47

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.

48

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.

49

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.

51

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.

52

C. Puleo, H.-C. Yeh, and T.-H. Wang, "Applications of MEMS technologies in tissue engineering," Tissue Engineering 13(12): 2839-2854, 2007.

53

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.

54

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.

55

C. Zhang, H.-C. Yeh, M. Kuroki, and T.-H. Wang, "Single-quantum-dot-based DNA nanosensor," Nature Materials 4(11): 826-831, 2005.

56

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.

57

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.