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Jing Yong Ye

TitleAssociate Professor
InstitutionUniversity of Texas at San Antonio
DepartmentBiomedical Engineering
AddressOne UTSA Circle
San Antonio TX 78249
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    Dr. Ye’s research covers a wide range of areas in biomedical optics and nanobiotechnology, with special emphasis on the development of cutting-edge ultrasensitive and ultrafast laser-based detection techniques and methodologies to address critical issues at the frontier of biomedical research and applications. He has led multiple exciting research programs including the development of a novel optoacoustic sensor for high-frequency photoacoustic imaging, biomolecular assays with photonic-crystal based label-free sensors, in vivo fiber-optic biosensing and imaging of a multifunctional nano-device for targeted cancer drug delivery, ultrafast laser interaction with nanoparticle-targeted cancer cells, in vivo two-photon flow cytometry, adaptive optical aberration correction in multiphoton scanning microscopy, and single-molecule fluorescence imaging and spectroscopy. He has published 86 refereed articles, 150 conference papers, and two book chapters, and holds 12 patents. He serves as a reviewer for funding agencies including NIH, NSF, Petroleum Research Fund, United States-Israel Binational Science Foundation, the James & Esther King Biomedical Research Program and the Bankhead-Coley Cancer Research Program. Dr. Ye was elected as the president of Ann Arbor Section of Optical Society of American in 2008-2009. He also serves as a guest editor for three high-impact journals, as an advisory board member for a biotech company, as a professional consultant for five companies, as a reviewer for over 30 journals, and on technical program committee for conferences.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Trabucco L, Heath S, Shaw J, McFadden S, Wang X, Ye JY. Characterizing Conformational Change of a Thermoresponsive Polymeric Nanoparticle with Raman Spectroscopy. Sensors (Basel). 2023 Jun 19; 23(12). PMID: 37420877.
      Citations:    Fields:    
    2. Shrestha B, Stojkova K, Yi R, Anastasio MA, Ye JY, Brey EM. Gold nanorods enable noninvasive longitudinal monitoring of hydrogels in vivo with photoacoustic tomography. Acta Biomater. 2020 11; 117:374-383. PMID: 33010515.
      Citations: 4     Fields:    Translation:Animals
    3. Christenson C, Baryeh K, Ahadian S, Nasiri R, Dokmeci MR, Goudie M, Khademhosseini A, Ye JY. Enhancement of label-free biosensing of cardiac troponin I. Proc SPIE Int Soc Opt Eng. 2020 Feb; 11251. PMID: 32528214.
      Citations:    
    4. Cadena M, DeLuna F, Baryeh K, Sun LZ, Ye JY. Prostate Cancer Epithelial Mesenchymal Transition by TGF-?1 exposure monitored with a Photonic Crystal Biosensor. Proc SPIE Int Soc Opt Eng. 2020 Feb; 11251. PMID: 32632340.
      Citations:    
    5. Attia M, McMahon N, Li H, Lin RB, DeLuna F, Shi Y, Chen B, Ye JY. Novel route to size-controlled synthesis of MnFe2O4@MOF core-shell nanoparticles. J Solid State Chem. 2020 Mar; 283. PMID: 32095025.
      Citations:    
    6. DeLuna F, Cadena M, Wang B, Sun LZ, Ye JY. Cellular Refractive Index Comparison of Various Prostate Cancer and Noncancerous Cell Lines via Photonic-Crystal Biosensor. Proc SPIE Int Soc Opt Eng. 2019 Feb; 10881. PMID: 32313355.
      Citations:    
    7. DeLuna F, Ding X, Sagredo I, Bustamante G, Sun LZ, Ye JY. Label-free in vitro prostate cancer cell detection via photonic-crystal biosensor. Proc SPIE Int Soc Opt Eng. 2018 Jan-Feb; 10504. PMID: 32528210.
      Citations:    
    8. Scudder J, Ye JY. Limulus amoebocyte lysate test via an open-microcavity optical biosensor. J Biomed Opt. 2018 02; 23(2):1-6. PMID: 29411562.
      Citations: 3     Fields:    
    9. Nawn CD, Souhan BE, Carter R, Kneapler C, Fell N, Ye JY. Distinguishing tracheal and esophageal tissues with hyperspectral imaging and fiber-optic sensing. J Biomed Opt. 2016 11 01; 21(11):117004. PMID: 27893090.
      Citations: 5     Fields:    Translation:Animals
    10. Zhang B, Wang B, Morales AW, Scudder J, Bhattacharyya MK, Ye JY. Study of the Interactions of Fusarium virguliforme Toxin FvTox1 with Synthetic Peptides by Molecular Simulations and a Label-Free Biosensor. Anal Chem. 2016 Mar 15; 88(6):3024-30. PMID: 26859241.
      Citations: 2     Fields:    Translation:Animals
    11. Huang H, Bustamante G, Peterson R, Ye JY. An adaptive filtered back-projection for photoacoustic image reconstruction. Med Phys. 2015 May; 42(5):2169-78. PMID: 25979011.
      Citations: 10     Fields:    
    12. Zhang B, Morales AW, Peterson R, Tang L, Ye JY. Label-free detection of cardiac troponin I with a photonic crystal biosensor. Biosens Bioelectron. 2014 Aug 15; 58:107-13. PMID: 24632136.
      Citations: 14     Fields:    Translation:Cells
    13. Peterson R, Solis S, Zhang B, Huang H, Ye JY. Sensitivity enhancement of an open-cavity-based optoacoustic sensor. Opt Lett. 2013 Aug 01; 38(15):2739-41. PMID: 23903128.
      Citations: 2     Fields:    
    14. Zhang B, Tamez-Vela JM, Solis S, Bustamante G, Peterson R, Rahman S, Morales A, Tang L, Ye JY. Detection of Myoglobin with an Open-Cavity-Based Label-Free Photonic Crystal Biosensor. J Med Eng. 2013; 2013:808056. PMID: 27006922.
      Citations:    
    15. Zhang B, Fang CY, Chang CC, Peterson R, Maswadi S, Glickman RD, Chang HC, Ye JY. Photoacoustic emission from fluorescent nanodiamonds enhanced with gold nanoparticles. Biomed Opt Express. 2012 Jul 01; 3(7):1662-29. PMID: 22808436.
      Citations:    
    16. Dallo SF, Zhang B, Denno J, Hong S, Tsai A, Haskins W, Ye JY, Weitao T. Association of Acinetobacter baumannii EF-Tu with cell surface, outer membrane vesicles, and fibronectin. ScientificWorldJournal. 2012; 2012:128705. PMID: 22666090.
      Citations: 38     Fields:    Translation:Cells
    17. Zhang B, Dallo S, Peterson R, Hussain S, Weitao T, Ye JY. Detection of anthrax lef with DNA-based photonic crystal sensors. J Biomed Opt. 2011 Dec; 16(12):127006. PMID: 22191936.
      Citations: 14     Fields:    Translation:Cells
    18. Zhou Y, Yang K, Cui J, Ye JY, Deng CX. Controlled permeation of cell membrane by single bubble acoustic cavitation. J Control Release. 2012 Jan 10; 157(1):103-11. PMID: 21945682.
      Citations: 57     Fields:    Translation:AnimalsCells
    19. Thomas TP, Chang YC, Ye JY, Kotlyar A, Cao Z, Shukla R, Qin S, Norris TB, Baker JR. Optical fiber-based in vivo quantification of growth factor receptors. Cancer. 2012 Apr 15; 118(8):2148-56. PMID: 22488668.
      Citations: 1     Fields:    Translation:AnimalsCells
    20. Chow CM, Zhou Y, Guo Y, Norris TB, Wang X, Deng CX, Ye JY. Broadband optical ultrasound sensor with a unique open-cavity structure. J Biomed Opt. 2011 Jan-Feb; 16(1):017001. PMID: 21280922.
      Citations: 10     Fields:    
    21. Tse C, Zohdy MJ, Ye JY, O'Donnell M, Lesniak W, Balogh L. Enhanced optical breakdown in KB cells labeled with folate-targeted silver-dendrimer composite nanodevices. Nanomedicine. 2011 Feb; 7(1):97-106. PMID: 20883823.
      Citations: 4     Fields:    Translation:HumansCells
    22. Chang YC, Ye JY, Thomas TP, Cao Z, Kotlyar A, Tkaczyk ER, Baker JR, Norris TB. Fiber-optic multiphoton flow cytometry in whole blood and in vivo. J Biomed Opt. 2010 Jul-Aug; 15(4):047004. PMID: 20799835.
      Citations: 14     Fields:    Translation:HumansAnimalsCells
    23. Guo Y, Ye JY, Divin C, Huang B, Thomas TP, Baker JR, Norris TB. Real-time biomolecular binding detection using a sensitive photonic crystal biosensor. Anal Chem. 2010 Jun 15; 82(12):5211-8. PMID: 20486666.
      Citations: 26     Fields:    Translation:Cells
    24. Tkaczyk ER, Tkaczyk AH, Mauring K, Ye JY, Baker JR, Norris TB. Quantitative differentiation of dyes with overlapping one-photon spectra by femtosecond pulse shaping. J Lumin. 2010 Jan 01; 130(1):29-34. PMID: 20160886.
      Citations:    
    25. Yang K, Zhou Y, Ren Q, Ye JY, Deng CX. Dynamics of microbubble generation and trapping by self-focused femtosecond laser pulses. Appl Phys Lett. 2009 Aug 03; 95(5):051107. PMID: 24958933.
      Citations:    
    26. Tkaczyk ER, Tkaczyk AH, Mauring K, Ye JY, Baker JR, Norris TB. Control of two-photon fluorescence of common dyes and conjugated dyes. J Fluoresc. 2009 May; 19(3):517-32. PMID: 19082694.
      Citations: 3     Fields:    
    27. Tkaczyk ER, Mauring K, Tkaczyk AH, Krasnenko V, Ye JY, Baker JR, Norris TB. Control of the blue fluorescent protein with advanced evolutionary pulse shaping. Biochem Biophys Res Commun. 2008 Nov 28; 376(4):733-7. PMID: 18817751.
      Citations: 3     Fields:    Translation:Cells
    28. Chang YC, Ye JY, Thomas T, Chen Y, Baker JR, Norris TB. Two-photon fluorescence correlation spectroscopy through a dual-clad optical fiber. Opt Express. 2008 Aug 18; 16(17):12640-9. PMID: 18711501.
      Citations: 12     Fields:    
    29. Guo Y, Divin C, Myc A, Terry FL, Baker JR, Norris TB, Ye JY. Sensitive molecular binding assay using a photonic crystal structure in total internal reflection. Opt Express. 2008 Aug 04; 16(16):11741-9. PMID: 18679444.
      Citations: 19     Fields:    Translation:Cells
    30. Ye JY, Ishikawa M. Enhancing fluorescence detection with a photonic crystal structure in a total-internal-reflection configuration. Opt Lett. 2008 Aug 01; 33(15):1729-31. PMID: 18670518.
      Citations: 9     Fields:    
    31. Tkaczyk ER, Tkaczyk AH, Katnik S, Ye JY, Luker KE, Luker GD, Myc A, Baker JR, Norris TB. Extended cavity laser enhanced two-photon flow cytometry. J Biomed Opt. 2008 Jul-Aug; 13(4):041319. PMID: 19021327.
      Citations: 5     Fields:    
    32. Zhong CF, Tkaczyk ER, Thomas T, Ye JY, Myc A, Bielinska AU, Cao Z, Majoros I, Keszler B, Baker JR, Norris TB. Quantitative two-photon flow cytometry--in vitro and in vivo. J Biomed Opt. 2008 May-Jun; 13(3):034008. PMID: 18601553.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    33. Tkaczyk ER, Zhong CF, Ye JY, Myc A, Thomas T, Cao Z, Duran-Struuck R, Luker KE, Luker GD, Norris TB, Baker JR. In Vivo Monitoring of Multiple Circulating Cell Populations Using Two-photon Flow Cytometry. Opt Commun. 2008 Feb 15; 281(4):888-894. PMID: 19221581.
      Citations:    
    34. Thomas TP, Shukla R, Kotlyar A, Liang B, Ye JY, Norris TB, Baker JR. Dendrimer-epidermal growth factor conjugate displays superagonist activity. Biomacromolecules. 2008 Feb; 9(2):603-9. PMID: 18193839.
      Citations: 33     Fields:    Translation:HumansAnimalsCells
    35. Thomas TP, Ye JY, Chang YC, Kotlyar A, Cao Z, Majoros IJ, Norris TB, Baker JR. Investigation of tumor cell targeting of a dendrimer nanoparticle using a double-clad optical fiber probe. J Biomed Opt. 2008 Jan-Feb; 13(1):014024. PMID: 18315382.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    36. Ye JY, Divin CJ, Baker JR, Norris TB. Whole spectrum fluorescence detection with ultrafast white light excitation. Opt Express. 2007 Aug 06; 15(16):10439-45. PMID: 19547396.
      Citations: 1     Fields:    
    37. Zohdy MJ, Tse C, Ye JY, O'Donnell M. Acoustic estimation of thermal distribution in the vicinity of femtosecond laser-induced optical breakdown. IEEE Trans Biomed Eng. 2006 Nov; 53(11):2347-55. PMID: 17073341.
      Citations: 5     Fields:    
    38. Zohdy MJ, Tse C, Ye JY, O'Donnell M. Optical and acoustic detection of laser-generated microbubbles in single cells. IEEE Trans Ultrason Ferroelectr Freq Control. 2006 Jan; 53(1):117-25. PMID: 16471438.
      Citations: 8     Fields:    Translation:AnimalsCells
    39. Tse C, Zohdy MJ, Ye JY, Norris TB, Balogh LP, Hollman KW, O'Donnell M. Acoustic detection of controlled laser-induced microbubble creation in gelatin. IEEE Trans Ultrason Ferroelectr Freq Control. 2005 Nov; 52(11):1962-9. PMID: 16422408.
      Citations: 5     Fields:    
    40. Thomas TP, Patri AK, Myc A, Myaing MT, Ye JY, Norris TB, Baker JR. In vitro targeting of synthesized antibody-conjugated dendrimer nanoparticles. Biomacromolecules. 2004 Nov-Dec; 5(6):2269-74. PMID: 15530041.
      Citations: 25     Fields:    Translation:HumansCells
    41. Ye JY, Chang G, Norris TB, Tse C, Zohdy MJ, Hollman KW, O'Donnell M, Baker JR. Trapping cavitation bubbles with a self-focused laser beam. Opt Lett. 2004 Sep 15; 29(18):2136-8. PMID: 15460881.
      Citations: 4     Fields:    
    42. Thomas TP, Myaing MT, Ye JY, Candido K, Kotlyar A, Beals J, Cao P, Keszler B, Patri AK, Norris TB, Baker JR. Detection and analysis of tumor fluorescence using a two-photon optical fiber probe. Biophys J. 2004 Jun; 86(6):3959-65. PMID: 15189892.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    43. Myaing MT, Ye JY, Norris TB, Thomas T, Baker JR, Wadsworth WJ, Bouwmans G, Knight JC, Russell PS. Enhanced two-photon biosensing with double-clad photonic crystal fibers. Opt Lett. 2003 Jul 15; 28(14):1224-6. PMID: 12885028.
      Citations: 13     Fields:    
    44. Ishikawa M, Maruyama Y, Ye JY, Futamata M. Single-molecule imaging and spectroscopy using fluorescence and surface-enhanced Raman scattering. J Biol Phys. 2002 Dec; 28(4):573-85. PMID: 23345799.
      Citations: 1     Fields:    
    45. Ye JY, Myaing MT, Norris TB, Thomas T, Baker J. Biosensing based on two-photon fluorescence measurements through optical fibers. Opt Lett. 2002 Aug 15; 27(16):1412-4. PMID: 18026463.
      Citations: 7     Fields:    
    46. Sherman L, Ye JY, Albert O, Norris TB. Adaptive correction of depth-induced aberrations in multiphoton scanning microscopy using a deformable mirror. J Microsc. 2002 Apr; 206(Pt 1):65-71. PMID: 12000564.
      Citations: 29     Fields:    
    47. Yogi O, Kawakami T, Yamauchi M, Ye JY, Ishikawa M. On-demand droplet spotter for preparing pico- to femtoliter droplets on surfaces. Anal Chem. 2001 Apr 15; 73(8):1896-902. PMID: 11338608.
      Citations: 9     Fields:    
    48. Ye JY, Umemura K, Ishikawa M, Kuroda R. Atomic force microscopy of DNA molecules stretched by spin-coating technique. Anal Biochem. 2000 May 15; 281(1):21-5. PMID: 10847606.
      Citations: 3     Fields:    Translation:Cells
    49. Ye JY, Hattori T, Inouye H, Ueta H, Nakatsuka H, Maruyama Y, Ishikawa M. Glass transition of associated solvents studied by fluorescence measurement of doped chromophores. Phys Rev B Condens Matter. 1996 Apr 01; 53(13):8349-8353. PMID: 9982335.
      Citations:    
    50. Ye JY, Zhan MS, Zhou SK. Gain due to level-dependent collisions. Phys Rev A. 1993 Sep; 48(3):2256-2260. PMID: 9909848.
      Citations:    
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