Selected Publications

Zhang, Z.; Fan, H.; Richardson, W.; Gao, B. Z.; Ye, T. Management of Autofluorescence in Formaldehyde-Fixed Myocardium: Choosing the Right Treatment. European Journal of Histochemistry 2023, 67 (4). | Link to journal website

Zhang, Z.; Neff, L.; Bradshaw, A. D.; Fan, H.; Ye, E.; Richardson, W.; Gao, B. Z.; Ye, T. Multimodal Microscopy Imaging of Cardiac Collagen Network: Are We Looking at the Same Structures? In Diagnostic and Therapeutic Applications of Light in Cardiology 2023; SPIE, 2023; Vol. 12355, pp 52–56. | Link to journal website

Chernyatinskiy, C.; Fan, H.; Le, M.; Zhang, Z.; Ye, E.; Hsu, J.; Lutas, M.; Gao, B.; Ye, T. Assessment of the Microstructural Differences of the Articular Cartilage Surface in a Porcine Tibiofemoral Joint Using Nonlinear Optical Microscopy. In Multiphoton Microscopy in the Biomedical Sciences XXIII; SPIE, 2023; Vol. 12384, pp 107–115. | Link to journal website

Chen, X.; Li, Y.; Chen, P.; Yao, H.; Ye, T. High Speed Two-Photon Laser Scanning Stereomicroscopy for Three-Dimension Tracking Multiple Particles Simultaneously in Three-Dimension. Frontiers in Photonics 2022, 3. | Link to journal website

Fan, H.; Xu, P.; Le, M.; Hsu, J.; Chen, X.; Li, Y.; Zhang, Z.; Gao, B.; Woolf, S.; Ye, T. Automated Chondrocyte Viability Analysis of Articular Cartilage Based on Deep Learning Segmentation and Classification of Two-Photon Microscopic Images. In Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXIX; SPIE, 2022; Vol. 11966, pp 65–73. | Link to journal website

Zhang, Z.; Baker, A.; Fan, H.; Richardson, W.; Borg, T. K.; Gao, B. Z.; Ye, T. Integrating SHG and Two-Color STED Microscopy for Super-Resolved Imaging of Cell-Matrix Interactions in Myocardium. In Single Molecule Spectroscopy and Superresolution Imaging XV; SPIE, 2022; Vol. 11967, pp 55–63. | Link to journal website

Kwapisz, A.; Bowman, M.; Walters, J.; Cosh, H.; Burnikel, B.; Tokish, J.; Ye, T.; Mercuri, J. Human Adipose- and Amnion-Derived Mesenchymal Stromal Cells Similarly Mitigate Osteoarthritis Progression in the Dunkin Hartley Guinea Pig. The American Journal of Sports Medicine, 2022, 50 (14), 3963–3973. | Link to journal website

Fan, H.; Lucia, G. S.; Ritter, A.; Snyder, A.; Plante, J.; Sloger, A.; Rose, C.; Gannon, S.; Li, Y.; Revelo, H.; Strat, N.; Colwell, C.; Roberts, A.; Valdebran, M.; Ye, T. Effects of Timolol in Skin Tissue Repair: A Longitudinal and Multimodal in Vivo Imaging Study with Two-Photon Excitation Fluorescence and Second Harmonic Generation Microscopy. In Photonics in Dermatology and Plastic Surgery 2021; International Society for Optics and Photonics, 2021; Vol. 11618, 116180I. | Link to journal website

Chen, X.; Li, Y.; Wyman, N.; Zhang, Z.; Fan, H.; Le, M.; Gannon, S.; Rose, C.; Zhang, Z.; Mercuri, J.; Yao, H.; Gao, B.; Woolf, S.; Pécot, T.; Ye, T. Deep Learning Provides High Accuracy in Automated Chondrocyte Viability Assessment in Articular Cartilage Using Nonlinear Optical Microscopy. Biomedical Optics Express, 2021, 12 (5), 2759–2772. | Link to journal website

Chen, P.; Chen, X.; Hepfer, R. G.; Damon, B. J.; Shi, C.; Yao, J. J.; Coombs, M. C.; Kern, M. J.; Ye, T.; Yao, H. A Noninvasive Fluorescence Imaging-Based Platform Measures 3D Anisotropic Extracellular Diffusion. Nature Communications, 2021, 12 (1), 1913. | Link to journal website

Yuan, C.; Zhao, X.; Wang, Z.; Borg, T. K.; Ye, T.; Khalpey, Z. I.; Runyan, R. B.; Shao, Y.; Gao, B. Z. Study of the Expression Transition of Cardiac Myosin Using Polarization-Dependent SHG Microscopy. Biophysical Journal 2020, 118 (5), 1058–1066. | Link to journal website

Wei, A.; Wang, Z.; Yang, Z.; Tan, S.; Ye, T.; Shao, Y.; Borg, T. K.; Gao, B. Z. Study of the Sarcomeric Addition Process in a Tissue-like Cell Construct under Mechanical Overload via TPEF-SHG Imaging System. In Multiphoton Microscopy in the Biomedical Sciences XX; International Society for Optics and Photonics, 2020; Vol. 11244, p 112442E. | Link to journal website

Schmidt, L.; Wang, Z.; Yang, X.; Ye, T.; Borg, T. K.; Shao, Y.; Gao, B. Z. Multiple Beam Laser Guidance for Patterning Irregularly Shaped Cells. Frontiers in Physics 2020, 8, 495. | Link to journal website

Richards, D. J.; Li, Y.; Kerr, C. M.; Yao, J.; Beeson, G. C.; Coyle, R. C.; Chen, X.; Jia, J.; Damon, B.; Wilson, R.; Starr Hazard, E.; Hardiman, G.; Menick, D. R.; Beeson, C. C.; Yao, H.; Ye, T.; Mei, Y. Human Cardiac Organoids for the Modelling of Myocardial Infarction and Drug Cardiotoxicity. Nature Biomedical Engineering, ; 2020, 4 (4), 446–462. | Link to journal website

Li, Y.; Chen, X.; Watkins, B.; Saini, N.; Gannon, S.; Nadeau, E.; Reeves, R.; Gao, B.; Pelligrini, V.; Yao, H.; Mercuri, J.; Ye, T.; Nonlabeling and Quantitative Assessment of Chondrocyte Viability in Articular Cartilage with Intrinsic Nonlinear Optical Signatures. Experimental Biology and Medicine 2020, 245 (4), 348–359. | Link to journal website

Chen, X.; Wyman, N.; Li, Y.; Zhang, Z.; Gannon, S.; Rose, C.; Lutas, M.; Gao, B.; Ye, T. Deep Learning Cell Segmentation in Chondrocyte Viability Assessment Using Nonlinear Optical Microscopy. In Label-free Biomedical Imaging and Sensing (LBIS) 2020; International Society for Optics and Photonics, 2020; Vol. 11251, p 112512K. | Link to journal website

Yuan, C.; Wang, Z.; Borg, T. K.; Ye, T.; Baicu, C.; Bradshaw, A.; Zile, M.; Runyan, R. B.; Shao, Y.; Shao, Y.; Gao, B. Z. Changes in the Crystallographic Structures of Cardiac Myosin Filaments Detected by Polarization-Dependent Second Harmonic Generation Microscopy. Biomedical Optics Express, 2019, 10 (7), 3183–3195. | Link to journal website

Wang, L.-W.; Chen, Y.; Yan, W.; Weng, X.-Y.; Yang, Z.-G.; Ye, T. ; Qu, J.-L. Increasing Fluorescence Lifetime for Resolution Improvement in Stimulated Emission Depletion Nanoscopy. Journal of Biophotonics 2019, 12 (5), e201800315. | Link to journal website

Li, Y.; Watkins, B.; Nadeau, E.; Reeves, R.; Basunia, R.; Saini, N.; Chen, X.; Gannon, S.; Pellegrini, V.; Yao, H.; Ye, T. Nondestructive Method for Chondrocyte Viability Assessment in Articular Cartilage Tissues with Nonlinear Optical Microscopy. In Multiphoton Microscopy in the Biomedical Sciences XIX ; International Society for Optics and Photonics, 2019; Vol. 10882, p 108822L. | Link to journal website

Li, R.; Peng, T.; Zhou, M.; Yu, X.; Gao, P.; Min, J.; Yang, Y.; Lei, M.; Yao, B.; Zhang, C.; Ye, T. Rapid Wide-Field Imaging through Scattering Media by Digital Holographic Wavefront Correction. Applied Optics, 2019, 58 (11), 2845–2853. | Link to journal website

Wang, L.; Yan, W.; Li, R.; Weng, X.; Zhang, J.; Yang, Z.; Liu, L.; Ye, T. ; Qu, J. Aberration Correction for Improving the Image Quality in STED Microscopy Using the Genetic Algorithm. Nanophotonics 2018, 7 (12), 1971–1980. | Link to journal website

Reno, A.; Hunter, A. W.; Li, Y.; Ye, T. ; Foley, A. C. Quantification of Cardiomyocyte Beating Frequency Using Fourier Transform Analysis. Photonics 2018, 5 (4), 39. | Link to journal website

Ye, T.; Chen, P.; Li, Y.; Chen, X. Imaging Fibrillar Collagen with Optical Microscopy. In Mechanobiology Handbook; CRC Press, 2018. | Link to journal website

Li, R.; Yu, X.; Peng, T.; Yang, Y.; Yao, B.; Zhang, C.; Ye, T. Shaping the On-Axis Intensity Profile of Generalized Bessel Beams by Iterative Optimization Methods. Journal of Optics 2018, 20 (8), 085603. | Link to journal website

Yan, W.; Yang, Y.; Tan, Y.; Chen, X.; Li, Y.; Qu, J.;Ye, T. Coherent Optical Adaptive Technique Improves the Spatial Resolution of STED Microscopy in Thick Samples. Photonics Research, 2017, 5 (3), 176–181. | Link to journal website

Yang, Y.; Yao, B.; Lei, M.; Dan, D.; Li, R.; Horn, M. V.; Chen, X.; Li, Y.; Ye, T. Two-Photon Laser Scanning Stereomicroscopy for Fast Volumetric Imaging. PLOS ONE 2016, 11 (12). | Link to journal website

Yan, W.; Yang, Y.; Li, Y.; Peng, X.; Lin, D.; Qu, J.; Ye, T. Aberration Correction for Stimulated Emission Depletion Microscopy with Coherent Optical Adaptive Technique. In Adaptive Optics and Wavefront Control for Biological Systems II; International Society for Optics and Photonics, 2016; Vol. 9717, p 97170K. | Link to journal website

Zhou, X.; Lei, M.; Dan, D.; Yao, B.; Qian, J.; Yan, S.; Yang, Y.; Min, J.; Peng, T.; Ye, T. ; Chen, G. Double-Exposure Optical Sectioning Structured Illumination Microscopy Based on Hilbert Transform Reconstruction. PLOS ONE 2015, 10 (3), e0120892. | Link to journal website

Yang, Y.; Zhou, X.; Li, R.; Horn, M. V.; Peng, T.; Lei, M.; Wu, D.; Chen, X.; Yao, B.; Ye, T. Laser Scanning Stereomicroscopy for Fast Volumetric Imaging with Two-Photon Excitation and Scanned Bessel Beams. In Multiphoton Microscopy in the Biomedical Sciences XV; International Society for Optics and Photonics, 2015; Vol. 9329, p 93292W. | Link to journal website

Yan, W.; Peng, X.; Lin, D.; Wang, Q.; Gao, J.; Luo, T.; Zhou, J.; Ye, T.; Qu, J.; Niu, H. Fluorescence Microendoscopy Imaging Based on GRIN Lenses with One- and Two-Photon Excitation Modes. Front. Optoelectron. 2015, 8 (2), 177–182. | Link to journal website

Wu, D.; Zhou, X.; Yao, B.; Li, R.; Yang, Y.; Peng, T.; Lei, M.; Dan, D.; Ye, T. Fast Frame Scanning Camera System for Light-Sheet Microscopy. Applied Optics 2015, 54 (29), 8632–8636. | Link to journal website

Zheng, J.; Gao, P.; Yao, B.;Ye, T. ; Lei, M.; Min, J.; Dan, D.; Yang, Y.; Yan, S. Digital Holographic Microscopy with Phase-Shift-Free Structured Illumination. Photonics Research , 2014, 2 (3), 87–91. | Link to journal website

Yu, X.; Yao, B.; Lei, M.; Hampp, N.; Liang, Y.; Dan, D.; Yang, Y.; Yan, S.; Gao, P.; Ye, T. Polarization-Sensitive Diffractive Optical Elements Fabricated in BR Films with Femtosecond Laser. Applied Physics B 2014, 115 (3), 365–369. | Link to journal website

Qi, Y.; Lei, M.; Yang, Y.; Yao, B.; Dan, D.; Yu, X.; Yan, S.;Ye, T. Remote-Focusing Microscopy with Long Working Distance Objective Lenses. Applied Optics, 2014, 53 (16), 3473–3478. | Link to journal website

Li, R.; Zhou, X.; Wu, D.; Peng, T.; Yang, Y.; Lei, M.; Yu, X.; Yao, B.; Ye, T. Selective Plane Illumination Microscopy with Structured Illumination Based on Spatial Light Modulators. In Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXI; International Society for Optics and Photonics, 2014; Vol. 8949, p 89491S. | Link to journal website

Karki, S.; Surolia, R.; Hock, T. D.; Guroji, P.; Zolak, J. S.; Duggal, R.; Ye, T. ; Thannickal, V. J.; Antony, V. B. Wilms’ Tumor 1 (Wt1) Regulates Pleural Mesothelial Cell Plasticity and Transition into Myofibroblasts in Idiopathic Pulmonary Fibrosis. The FASEB Journal 2014, 28 (3), 1122–1131. | Link to journal website

Zheng, J.; Yao, B.; Yang, Y.; Lei, M.; Gao, P.; Li, R.; Yan, S.; Dan, D.; Ye, T. Investigation of Bessel Beam Propagation in Scattering Media with Scalar Diffraction Method. Chinese Optics Letters, 2013, 11 (11), 112601. | Link to journal website

Yang, Y.; Lei, M.; Zheng, J.; Li, R.; Yan, S.; Yao, B.; Ye, T. Two-Photon Fluorescence Stereomicroscopy with Bessel Beams. In Multiphoton Microscopy in the Biomedical Sciences XIII; International Society for Optics and Photonics, 2013; Vol. 8588, p 85882K. | Link to journal website

Guo, R.; Yao, B.; Gao, P.; Min, J.; Zhou, M.; Han, J.; Yu, X.; Yu, X.; Lei, M.; Yan, S.; Yang, Y.; Dan, D.; Ye, T. Off-Axis Digital Holographic Microscopy with LED Illumination Based on Polarization Filtering. Applied Optics, 2013, 52 (34), 8233–8238. | Link to journal website

Fraser, K. B.; Moehle, M. S.; Daher, J. P. L.; Webber, P. J.; Williams, J. Y.; Stewart, C. A.; Yacoubian, T. A.; Cowell, R. M.; Dokland, T.; Ye, T. ; Chen, D.; Siegal, G. P.; Galemmo, R. A.; Tsika, E.; Moore, D. J.; Standaert, D. G.; Kojima, K.; Mobley, J. A.; West, A. B. LRRK2 Secretion in Exosomes Is Regulated by 14-3-3. Human Molecular Genetics 2013, 22 (24), 4988–5000. | Link to journal website

Dan, D.; Lei, M.; Yao, B.; Wang, W.; Winterhalder, M.; Zumbusch, A.; Qi, Y.; Xia, L.; Yan, S.; Yang, Y.; Gao, P.; Ye, T. ; Zhao, W. DMD-Based LED-Illumination Super-Resolution and Optical Sectioning Microscopy. Scientific Reports 2013, 3 (1), 1116. | Link to journal website

Chen, B. J.; Jiao, Y.; Zhang, P.; Sun, A. Y.; Pitt, G. S.; Deoliveira, D.; Drago, N.; Ye, T. ; Liu, C.; Chao, N. J. Long-Term In Vivo Imaging of Multiple Organs at the Single Cell Level. PLOS ONE 2013, 8 (1), e52087. | Link to journal website

Zheng, J.; Yao, B.; Rupp, R. A.; Ye, T. ; Gao, P.; Min, J.; Guo, R. Dual-Channel Phase-Shifting Interferometry for Microscopy with Second Wavelength Assistance. Chinese Optics Letters, 2012, 10 (1), 010901.

Zheng, J.; Yao, B.; Gao, P.; Ye, T. Phase Contrast Microscopy with Fringe Contrast Adjustable by Using Grating-Based Phase-Shifter. Optics Express, 2012, 20 (14), 16077–16082. | Link to journal website

Zheng, J.; Yang, Y.; Lei, M.; Yao, B.; Gao, P.; Ye, T. Fluorescence Volume Imaging with an Axicon: Simulation Study Based on Scalar Diffraction Method. Applied Optics, 2012, 51 (30), 7236–7245. | Link to journal website

Ye, T.; Zhang, Y.; Ai, X.; Pozzo-Miller, L.; Keyser, K. Stimulated Emission Depletion Microscopy with a Single Ultrafast Laser. In Biomedical Optics; Optical Society of America, 2012; pp BSu3A-39. | Link to journal website

Min, J.; Yao, B.; Gao, P.; Guo, R.; Ma, B.; Zheng, J.; Lei, M.; Yan, S.; Dan, D.; Duan, T.; Yang, Y.; Ye, T. Dual-Wavelength Slightly off-Axis Digital Holographic Microscopy. Applied Optics, 2012, 51 (2), 191–196. | Link to journal website

Gao, P.; Yao, B.; Rupp, R.; Min, J.; Guo, R.; Ma, B.; Zheng, J.; Lei, M.; Yan, S.; Dan, D.; Ye, T. Autofocusing Based on Wavelength Dependence of Diffraction in Two-Wavelength Digital Holographic Microscopy. Optics Letters, 2012, 37 (7), 1172–1174. | Link to journal website

Shao, Y.; Liu, H.; Ye, T.; Borg, T.; Qu, J.; Peng, X.; Niu, H.; Gao, B. 3D Myofibril Imaging in Live Cardiomyocytes via Hybrid SHG-TPEF Microscopy. In Multiphoton Microscopy in the Biomedical Sciences XI; International Society for Optics and Photonics, 2011; Vol. 7903, p 79030F. | Link to journal website

Ma, B.; Yao, B.; Li, Z.; Ye, T. Improvement of the Performance of the Twisted-Nematic Liquid- Crystal Display as a Phase Modulator. Applied Optics, 2011, 50 (17), 2588–2593. | Link to journal website

Lu, R.-W.; Li, Y.-C.; Ye, T.; Strang, C.; Keyser, K.; Curcio, C. A.; Yao, X.-C. Two-Photon Excited Autofluorescence Imaging of Freshly Isolated Frog Retinas. Biomedical Optics Express, 2011, 2 (6), 1494–1503. | Link to journal website

Liu, H.; Qin, W.; Ma, Z.; Gao, B. Z.; Shao, Y.; Ye, T.; Borg, T. K. Myofibrillogenesis in Live Neonatal Cardiomyocytes Observed with Hybrid Two-Photon Excitation Fluorescence-Second Harmonic Generation Microscopy. Journal of Biomedical Optics, 2011, 16 (12), 126012. | Link to journal website

Guo, R.; Yao, B.; Gao, P.; Min, J.; Zheng, J.; Ye, T. Reflective Point-Dif Fraction Microscopic Interferometer with Long-Term Stability (Invited Paper).Chinese Optics Letters, 2011, 9 (12), 120002. |

Gao, P.; Yao, B.; Min, J.; Guo, R.; Zheng, J.; Ye, T.; Harder, I.; Nercissian, V.; Mantel, K. Parallel Two-Step Phase-Shifting Point-Diffraction Interferometry for Microscopy Based on a Pair of Cube Beamsplitters. Optics Express, 2011, 19 (3), 1930–1935. | Link to journal website

Gao, P.; Yao, B.; Min, J.; Guo, R.; Zheng, J.; Ye, T. Parallel Two-Step Phase-Shifting Microscopic Interferometry Based on a Cube Beamsplitter. Optics Communications 2011, 284 (18), 4136–4140. | Link to journal website

Gao, P.; Yao, B.; Harder, I.; Min, J.; Guo, R.; Zheng, J.; Ye, T. Parallel Two-Step Phase-Shifting Digital Holograph Microscopy Based on a Grating Pair. Journal of the Optical Society of America A, JOSAA 2011, 28 (3), 434–440. | Link to journal website

Min, J.; Yao, B.; Gao, P.; Guo, R.; Zheng, J.; Ye, T. Parallel Phase-Shifting Interferometry Based on Michelson-like Architecture. Applied Optics, 2010, 49 (34), 6612–6616. | Link to journal website

Ma, B.; Yao, B.; Yan, S.; Peng, F.; Min, J.; Lei, M.; Ye, T. Simulation and Optimization of Spatial Light Modulation of Twisted-Nematic Liquid Crystal Display. Chinese Optics Letters, 2010, 8 (10), 960–963. |

Ye, T.; Fu, D.; Warren, W. S. Nonlinear Absorption Microscopy. Photochemistry and Photobiology 2009, 85 (3), 631–645. | Link to journal website

Fu, D.; Ye, T.; Matthews, T. E.; Grichnik, J.; Hong, L.; Simon, J. D.; Warren, W. S. Probing Skin Pigmentation Changes with Transient Absorption Imaging of Eumelanin and Pheomelanin. Journal of Biomedical Optics 2008, 13 (5), 054036-054036–054037. | Link to journal website

Fu, D.; Matthews, T. E.; Ye, T.; Piletic, I. R.; Warren, W. S. Label-Free in Vivo Optical Imaging of Microvasculature and Oxygenation Level. Journal of Biomedical Optics 2008, 13 (4), 040503-040503–3. | Link to journal website

Fu, D.; Ye, T.; Matthews, T. E.; Yurtsever, G.; Warren, W. S. Two-Color, Two-Photon, and Excited-State Absorption Microscopy. Journal of Biomedical Optics 2007, 12 (5), 054004- 054004–054008. | Link to journal website

Fu, D.; Ye, T.; Matthews, T. E.; Yurtsever, G.; Hong, L.; Simon, J. D.; Warren, W. S. Two-Color Excited-State Absorption Imaging of Melanins. In Photonic Therapeutics and Diagnostics III; International Society for Optics and Photonics, 2007; Vol. 6424, p 642402. | Link to journal website

Fu, D.; Ye, T.; Matthews, T. E.; Chen, B. J.; Yurtserver, G.; Warren, W. S. High-Resolution in Vivo Imaging of Blood Vessels without Labeling. Optics Letters, OL 2007, 32 (18), 2641–2643. | Link to journal website

Ye, T.; Yurtsever, G.; Fischer, M.; Simon, J. D.; Warren, W. S. Imaging Melanin by Two- Photon Absorption Microscopy. In Multiphoton Microscopy in the Biomedical Sciences VI; International Society for Optics and Photonics, 2006; Vol. 6089, p 60891X. | Link to journal website

Ye, T.; Hong, L.; Garguilo, J.; Pawlak, A.; Edwards, G. S.; Nemanich, R. J.; Sarna, T.; Simon, J. D. Photoionization Thresholds of Melanins Obtained from Free Electron Laser-Photoelectron Emission Microscopy, Femtosecond Transient Absorption Spectroscopy and Electron Paramagnetic Resonance Measurements of Oxygen Photoconsumption. Photochemistry and Photobiology 2006, 82 (3), 733–737. | Link to journal website

Warren, W. S.; Ye, T.; Fischer, M.; Yurtsever, G.; Li, C.; Liu, H.; Fu, D. Deep Tissue Imaging with Shaped Femtosecond Laser Pulses. In 15th International Conference on Ultrafast Phenomena (2006), paper ThC1; Optical Society of America, 2006; p ThC1. | Link to journal website

Simon, J. D.; Goldsmith, M. R.; Hong, L.; Kempf, V. R.; McGuckin, L. E. L.; Ye, T.; Zuber, G. Spectroscopy and Photoreactivity of Trichochromes: Molecular Components of Pheomelanins†. Photochemistry and Photobiology 2006, 82 (1), 318–323. | Link to journal website

Warren, W. S.; Miller, A.; Wagner, W.; Ye, T.; Fischer, M.; Yurtsever, G. Two-Photon Absorption Imaging with Shaped Femtosecond Laser Pulses. In Ultrafast Phenomena XIV; Kobayashi, T., Okada, T., Kobayashi, T., Nelson, K. A., De Silvestri, S., Eds.; Springer Series in Chemical Physics; Springer: Berlin, Heidelberg, 2005; pp 867–869. | Link to journal website

Fischer, M. C.; Ye, T.; Yurtsever, G.; Miller, A.; Ciocca, M.; Wagner, W.; Warren, W. S. Two-Photon Absorption and Self-Phase Modulation Measurements with Shaped Femtosecond Laser Pulses. Optics Letters, OL 2005, 30 (12), 1551–1553. | Link to journal website

Ye, T.; Wagner, W.; Tian, P.; Yurtsever, G.; Fischer, M.; Warren, W. S. Deep Tissue Imaging Approaches by Direct Capture of Two-Photon Absorption. In 2004 2nd IEEE International Symposium on Biomedical Imaging: Nano to Macro (IEEE Cat No. 04EX821); 2004; pp 668-671 Vol. 1. | Link to journal website

Ye, T.; Simon, J. D.; Sarna, T. Ultrafast Energy Transfer from Bound Tetra(4-N,N,N,N-Trimethylanilinium)Porphyrin to Synthetic Dopa and Cysteinyldopa Melanins¶. Photochemistry and Photobiology 2003, 77 (1), 1–4. | Link to journal website

Ye, T.; Simon, J. D. The Action Spectrum for Generation of the Primary Intermediate Revealed by Ultrafast Absorption Spectroscopy Studies of Pheomelanin¶. Photochemistry and Photobiology 2003, 77 (1), 41–45. | Link to journal website

Ye, T.; Simon, J. D. Comparison of the Ultrafast Absorption Dynamics of Eumelanin and Pheomelanin. The Journal of Physical Chemistry B 2003, 107 (40), 11240–11244. | Link to journal website

Ye, T.; Lamb, L. E.; Wakamatsu, K.; Ito, S.; Simon, J. D. Ultrafast Absorption and Photothermal Studies of Decarboxytrichochrome C in Solution. Photochemical & Photobiological Sciences 2003, 2 (7), 821–823. | Link to journal website

Warren, W. S.; Wagner, W.; Ye, T. The Prospects for High Resolution Optical Brain Imaging: The Magnetic Resonance Perspective. Magnetic Resonance Imaging 2003, 21 (10), 1225–1233. | Link to journal website

Gu, T.; Ye, T.; Simon, J. D.; Whitesell, J. K.; Fox, M. A. Subpicosecond Transient Dynamics in Gold Nanoparticles Encapsulated by a Fluorophore-Terminated Monolayer. The Journal of Physical Chemistry B 2003, 107 (8), 1765–1771. | Link to journal website

Haralampus-Grynaviski, N.; Ransom, C.; Ye, T.; Rôżanowska, M.; Wrona, M.; Sarna, T.; Simon, J. D. Photogeneration and Quenching of Reactive Oxygen Species by Urocanic Acid. Journal of the American Chemical Society, 2002, 124 (13), 3461–3468. | Link to journal website

Ye, T.; Hou, B.; Gershgoren, E.; Ottolenghi, M.; Friedman, N.; Sheves, M.; Ruhman, S. Resolving the Primary Dynamics of Bacteriorhodopsin, and Locked Analogs in the Reactive Excited State. In Ultrafast Phenomena XII; Elsaesser, T., Mukamel, S., Murnane, M. M., Scherer, N. F., Eds.; Springer Series in Chemical Physics; Springer: Berlin, Heidelberg, 2001; pp 683–685. | Link to journal website

Lamb, L. E.; Ye, T.; Haralampus-Grynaviski, N. M.; Williams, T. R.; Pawlak, A.; Sarna, T.; Simon, J. D. Primary Photophysical Properties of A2E in Solution. The Journal of Physical Chemistry B 2001, 105 (46), 11507–11512. | Link to journal website

Floyd, J. S.; Haralampus-Grynaviski, N.; Ye, T.; Zheng, B.; Simon, J. D.; Edington, M. D. Time-Resolved Spectroscopic Studies of Radiationless Decay Processes in Photoexcited Hemocyanins. The Journal of Physical Chemistry B 2001, 105 (7), 1478–1483. | Link to journal website

Edington, M. D.; Floyd, J. S.; Haralampus-Grynaviski, N. M.; Ye, T.; Zheng, B.; Simon, J. D. Femtosecond Pump-Probe Studies of Radiationless Decay Dynamics in Arthropod and Mollusc Hemocyanins. In Ultrafast Phenomena XII; Elsaesser, T., Mukamel, S., Murnane, M. M., Scherer, N. F., Eds.; Springer Series in Chemical Physics; Springer: Berlin, Heidelberg, 2001; pp 692–694. | Link to journal website

Ye, T.; Friedman, N.; Gat, Y.; Atkinson, G. H.; Sheves, M.; Ottolenghi, M.; Ruhman, S. On the Nature of the Primary Light-Induced Events in Bacteriorhodopsin:  Ultrafast Spectroscopy of Native and C13=C14 Locked Pigments. The Journal of Physical Chemistry B 1999, 103 (24), 5122–5130. | Link to journal website