Journal Publications



69.Li Z, Nguyen C, Jang H, Hoang D, Min S, Ackerstaff E, Koutcher J, Shi L** "Multimodal Imaging of Metabolic Activities for Distinguishing Subtypes of Breast Cancer", Biomedical Optics Express, in press, 2023

68. Yim W, Retout M, Chen A, Ling C, Amer L, Jin Z, Chang Y, Chavez S, Barrios K, Lam B, Li Z, Zhou J, Shi L, Pascal T, and Jokerst J**, "Goldilocks Energy Minimum: Peptide-Based Reversible Aggregation and Biosensing", ACS Appl. Mater. Interfaces 2023, 15, 36, 42293–42303,, 2023

67. Shi L**, Li Y, Li Z, "Early cancer detection by SERS spectroscopy and machine learning", Light: Science & Applications news & views, , 2023

66.  Li Y, Chang P, Sankaran S, Jang H, Nie Y, Zeng A, Hussain S, Wu JY, Chen X, Shi L**, "Bioorthogonal SRS Imaging Uncovers Lipid Metabolic Dynamics in Brain During Aging" GEN Biotechnology, , 2023

65. Shi L**, Jang H, "Perspectives on SRS Imaging of Nanoparticles", Accounts of Materials Research,2023, 4, 9, 726–728 , 2023  (Journal Cover)

64. Bagheri, P., Hoang, K., Kuo, C. y., Trivedi, H., Jang, H. , Shi L.**, "Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids", J. Vis. Exp., e65121, doi: (2023)

63. Jang H, Li Y,  Fung AA, Bagheri P, Hoang K,  Skowronska-Krawczyk D, Chen X, Wu JY,  Bintu B,  Shi L**, "Super-resolution stimulated Raman Scattering microscopy with A-PoD", Nature Methods 2023,

62. Jang H, Shi L**, "A deconvolution algorithm to achieve super-resolution stimulated Raman scattering imaging". Nat Methods (2023).


61. E. J. Galvez, B. Sharma, F. K. Williams, C.-J. You, B. Khajavi, J. Castrillon, L. Shi, S. Mamani, L. A. Sordillo, L. Zhang, and R. R. Alfano, "Decoherence of photon entanglement by transmission through brain tissue with Alzheimer’s disease," Biomed. Opt. Express 13, 6621-6630 (2022),

60. Zhang W, Li Y,  Fung AA, Li Z, Jang H, Zha H, Chen X, Gao F,  Wu JY,  Sheng H,  Yao J,  Skowronska-Krawczyk D,  Jain S,  Shi L**, "Multi-Molecular Hyperspectral PRM-SRS Imaging", biorxiv, 2022, 

59. Preprint (Biorxiv): Shi L**, Rodriguez-Contreras A, "The general anesthetic isoflurane inhibits calcium activity in cerebrovascular endothelial cells and disrupts vascular tone", doi:, 2022

58. Mamani S, Shintre S, Li Z, Rodríguez-Contreras A, Shi L**,  Alfano R**, "OAM transmission of polarized multipole laser beams in rat cerebellum tissue", Optics Communications 532, 129241, 2023,

57. Liu X, Shi L, Shi L, Wei M, Zhao Z, Min W,  "Towards Mapping Mouse Metabolic Tissue Atlas by Mid-Infrared Imaging with Heavy Water Labeling"  Advanced Science, Mar 2022

56. Li Y., Zhang W., Fung A.A., Shi L.**,  "DO-SRS Imaging of Diet Regulated Metabolic Activities in Drosophila During Aging Processes", Aging Cell. 2022;00:e13586., 2022

55. Li Z., Mazhar S.F.B.,Alfano R., Shi L.**,  "The 1086 cm-1 Phonon Decay Routes in the O- and E-directions in Calcite from Raman Scattering", Optik,, 2022

54. Agrawal R., Larrea D., Xu Y., Shi L., Zirpoli H., Cummins L., Emmanuele V., Song D.,Yun T., Macaluso F., Min W., Kernie G., Deckelbaum R., Area-Gomez E., “Alzheimer’s-associated upregulation of mitochondria-associated ER membranes after traumatic brain injury”,, Cellular & Molecular Neurobiology 2022. 

53. Fung A.A., Hoang K., Zha H., Chen D., Zhang W., and Shi L.**  "Imaging Sub-Cellular Methionine and Insulin Interplay in Triple Negative Breast Cancer Lipid Droplet Metabolism", Frontier Oncology, Cancer Metabolism , 2022,

52. Zhang Z, Tang R, Chen X, Waller L, Kau A, Fung A.A., Gutierrez B, An C, Cho S, Shi L, Lo Y. "A high-throughput technique to map cell images to cell positions using a 3D imaging flow cytometer", PNAS, Feb 2022, 119 (8) e2118068119; 

51. Zhang W*, Craddock T**, Li Y, Swartzlander M, Alfano R, Shi L**  "Fano Resonance in Raman Spectra of Tubulin and Microtubules Reveals Active Quantum Effects", Biophysical Reports (Cellpress publisher), Volume 2, Issue 1, 100043, 2022,  

(** corresponding author; * equal contribution author)


50.  Li Y., Bagheri P, Chang P, Zeng A, Hao J, Fung A.A., Wu J and Shi L**,Direct Imaging of Lipid Metabolic Changes in Drosophila Ovary during Aging using DO-SRS Microscopy”,  Frontiers in Aging-Aging, Metabolism and Redox Biology, 2021.

49.  Bagheri P*., Hoang K*., Fung A.A., Hussain S., Shi L.**, "Visualizing Cancer Cell Metabolic Dynamics Regulated with Aromatic Amino Acids using DO-SRS and 2PEF microscopy", Front. Mol. Biosci. |, 2021

48.  Li Y, Zhang W, Fung AA., Shi L.**, "DO-SRS Imaging of Metabolic Dynamics in Aging Drosophila", Analyst. , 2021

47. Alfano R,  Mazhar SFB, Sharonov M, L Shi, "Ultra-supercontinuum generation with high intense femtosecond pulses ", Optik, 168208, 2021

46. Alfano R, Mazhar SFB, Shi L, "Higher harmonic and supercontinuum generation arising from electronic self-phase modulation under ultrafast laser pulses for various states of matter", Optik, 167872, 2021

45. Shi L, Wei M, Miao Y, Qian N, Shi L, Singer R, Benninger R, Min W., “One-shot highly-multiplexed volumetric mapping with Raman dye imaging and tissue clearing”, Nature Biotechnology., 2021

44. Chang, D.; Brown, Q.; Tsui, G.; He, Y.; Liu, J.; Shi, L.**; Rodríguez-Contreras, A**. Distinct Cellular Profiles of Hif1a and Vegf mRNA Localization in Microglia, Astrocytes and Neurons during a Period of Vascular Maturation in the Auditory Brainstem of Neonate Rats. Brain Sci. 2021, 11, 944. 2020  (co-corresponding)

43. Shi L.**, Fung A.A. Andy Zhou. “Advances of Stimulated Raman Scattering Imaging in Tissues and Animals”, Quantitative Imaging in Medicine and Surgery. Vol 11, No 3, 2021


42.  Fung A. A., Shi L**. “Mammalian cell and tissue imaging using Raman and coherent Raman microscopy”. WIREs Systems Biology and Medicine. 2020;e1501. , 2020.

41.  Shi L.**, Gayen T., Budansky Y., Yoo K., Secor J., Harvey T., Harvey G., Shumyatsky P., Nolan D., and Alfano R. "Enhanced stimulated raman scattering of solvent due to anharmonic energy transfer from resonance raman solute molecules". Opt. Express 28, 21792-21804, 2020.

40.  Shi L., Liu X.*, Shi L.*, Stinson H., Rowlette J., Kahl L., Evans C., Zheng C., Dietrich L., Min W. "Mid-infrared metabolic imaging with vibrational probes". Nature Methods 17, 844-851, 2020.

39. Mazhar SFB., Meyer H.J., Samuels T., Sharonov M., Shi L, Alfano R.R. “Explanation of the competition between O-and E-wave induced stimulated Raman and supercontinuum in calcite under ultrafast laser excitation”. Applied Optics 59 (17), 5252-5257, 2020.

38.  Xiong H., Qian N., Zhao L., Shi L, Miao Y, Min W. “Background-free imaging of chemical bonds by a simple and robust frequency-modulated stimulated Raman scattering microscopy”. Optics Express 28 (10), 15663-15677, 2020.

37.  Bendau E., Smith J., Zhang L., Ackerstaff E., Kruchevsky N., Wu B., Koutcher J. A., Alfano R. R. and Shi L.** Distinguishing Metastatic Triple Negative Breast Cancer from Non‐Metastatic Breast Cancer using SHG Imaging and Resonance Raman Spectroscopy". J. Biophotonics, 2020;e202000005, 2020 (**corresponding author) 

36.  Mamani S., Nolan D. A., Shi L., Alfano R. R. “Special classes of optical vector vortex beams are Majorana-like photons”. Optics Communications, 464, 125425, 2020. 

35.  Shumyatsky P., Shi L., Sordillo L. A., Budansky Y., Alfano R. R. “Comparison of continuous wave versus picosecond SRS and the resonance SRS effect”. Applied Optics 59 (3), 622-627, 2020.

Before UCSD:


34.  Zhang L*, Shi L*, Shen Y*, Miao Y, Wei M, Qian N, Liu Y, Min W. “Spectral tracing of deuterium for imaging glucose metabolism”. Nature Biomedical Engineering 3(5):402-413, 2019. (co-first author)

33.  Wei M*, Shi L*, Shen Y, Zhao Z, Guzman A, Kaufman L, Wei L, Min W. “Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy”. PNAS 116 (14): 6608-6617, 2019. (co-first author)

32.  Zhou Y., Liu C., Wu B.,Yu X., Cheng G., Zhu K., Wang K., Zhang C., Zhao M., Zong R., Zhang L., Shi L., Alfano R. R. Optical biopsy identification and grading of gliomas using label-free visible resonance Raman spectroscopy, J. of Biomedical Optics, 24(9), 095001, 2019.

31.  Liu C., Wu B., Sordillo L., Boydston-White S., Sriramoju V., Zhang C., Beckman H., Zhang L., Pei Z., Shi L., Alfano R. R. "A pilot study for distinguishing basal cell carcinoma from normal human skin tissues using visible resonance Raman spectroscopy". J Cancer Metastasis Treat; 5:4, 2019.


30.  Zhou Y, Liu C, Wu B, Zhang C, Yu X, Cheng G, Chen H, Li S, Liang Q, Zhang M, Zhu K, Shi L, and Alfano R. R. "Molecular biomarkers characterization for human brain glioma grading using visible resonance Raman spectroscopy". APL Photonics 3, 120802, 2018.

29.  Shi L*, Zheng C*, Shen Y, Chen Z, Silveira E, Zhang L, Wei M, Liu C, De Sena-Tomas C, Targoff K, Min W. “Optical imaging of metabolic dynamics in animals”. Nature Communications, 9, 2995, 2018.

28.  Shi L, Shen Y, and Min W. “Visualizing protein synthesis in mice with in vivo labeling of deuterated amino acids using vibrational imaging”. APL Photonics 3, 092401, 2018.

27.  Long R, Zhang L, Shi L, Shen Y, Hu F, Zeng C. and Min W. “Two-color vibrational imaging of glucose metabolism by stimulated Raman scattering”. Chemical Communications 152-155, 2018.

26.  Mamani S, Shi L, Ahmed T, Karnik R, Rodríguez‐Contreras A, Nolan D. and Alfano R. R.  “Transmission of classically entangled beams through mouse brain tissue”. J. Biophotonics. 11(12):e201800096, 2018.

25.  Lu L, Shi L, Secor J, Alfano R. R. "Resonance Raman scattering of β-carotene solution excited by visible laser beams into second singlet state". J. Photochem. Photobiol. B 179:18-22, 2018.


24.  Shen Y, Zhao Z, Zhang L, Shi L, Shahriar S, Chan R, Paolo G, Min W. “Metabolic activity induces membrane phase separation in endoplasmic reticulum”. PNAS 114(51):13394-13399, 2017.

23.  Sordillo DC, Sordillo LA, Sordillo PP, Shi L, Alfano RR. "Short wavelength infrared optical windows for evaluation of benign and malignant tissues". J. Biomed. Opt. 22(4):45002, 2017.

22.  Shi L**, Lindwasser L, Wang W, Rodríguez-Contreras A, and Alfano RR. “Propagation of Gaussian and Laguerre Gaussian vortex beams through mouse brain tissue”. J. Biophotonics 10(12): 1756-1760, 2017.

21.  Shi L, Lu L, Harvey G, Harvey T, Rodríguez-Contreras A, and Alfano RR. “Label-free fluorescence spectroscopy for detecting key biomolecules in brain tissue from a mouse model of Alzheimer’s disease”. Scientific Reports 7:2599, 2017.

20.  Das B*, Shi L*, Budansky Y, Rodríguez-Contreras A, and Alfano RR. “Alzheimer mouse brain tissue measured by time resolved fluorescence spectroscopy using single- and multi-photon excitation of label free native molecules”. J. Biophotonics 11(1), 2017. (co-first author).


19.  Shi L, Galvez E, and Alfano R. R. “Photon entanglement through brain tissue”. Scientific Reports 6:37714, 2016.

18.  Liu C, Boydston-White S, Weisberg A, Wang W, Sordillo L, Perotte A, Tomaselli V, Sordillo P, Pei Z, Shi L, and Alfano RR. “Vulnerable atherosclerotic plaque detection by resonance Raman spectroscopy”, J. Biomed. Opt. 21 (12):127006, 2016.

17.  Alfano RR, Milione G, Galvez E. J., Shi L. “Optical sources: A laser for complex spatial modes”. Nature Photonics 10 (5): 286-288, 2016.

16.  Wang W, Gozali R, Shi L, and Alfano R. R. “Deep transmission of Laguerre-Gaussian vortex beams through turbid scattering media”. Opt. Lett. 41(9): 2069-72, 2016.

15.  Shi L**, Shumyatsky P, Rodríguez-Contreras A, Alfano R. R. “Terahertz spectra ofbrain tissue from a mouse model of Alzheimer disease”. J. Biomed. Opt. 21(1):015014-1, 2016.

14.  Shi L**, Sordillo LA, Rodríguez-Contreras A, Alfano R. R. “Transmission in near-infrared optical windows for deep brain imaging”. J. Biophotonics 9(1–2):38–43, 2016.


13.  Shi L**, Rodriguez-Contreras A, Alfano R. R. “Gaussian beam in two photon fluorescence imaging of rat brain microvessel”. J. Biomed. Opt. 19(12):126006, 2014.

12.  Shi L, Palacio P, Badami J, Shin D, Zeng M, Cardoso L, Tu R, Fu B. M. “Quantification of transient increase of the blood-brain barrier permeability to macromolecules by optimized focused ultrasound combined with microbubbles”. Int. J. Nanomedicine. 9(1): 4437-48, 2014.

11.  Shi L, Zeng M, Fu BM. “Temporal effects of vascular endothelial growth factor and 3,5-cyclic monophosphate on blood–brain barrier solute permeability in vivo”. J. Neurosci. Res. 92(12):1678-89, 2014.

10.  Shi L, Rodriguez-Contreras A, Budansky Y, Pu Y, Nguyen T, Alfano R. R. “Deep two-photon microscopic imaging through brain tissue using the second singlet state from fluorescent agent chlorophyll α in spinach leaf”. J. Biomed. Opt. 19(6):066009, 2014.

9.   Shi L. Book review of “Diagnostic Endoscopy”. J. Biomed. Opt. 19(4):049902-1. 2014.

8.   Shi L, Zeng M, Sun Y, Fu B. M. “Quantification of blood-brain barrier solute permeability and brain transport by multiphoton microscopy”. J. Biomech. Eng. 136: 031005, 2014.

7.   Rodríguez-Contreras A, Shi L, Fu B. M. “A method to make a craniotomy on the ventral skull of neonate rodents”. J. Vis. Exp. (87), e51350, 2014.

6.   Islam SMZ, Gayen T, Tint N, Shi L, Seredych M, Bandosz T. J., and Alfano R. R. “The effects of fabrication temperature on current-voltage characteristics and energy efficiencies of quantum dot sensitized ZnOH-GO hybrid solar cells”. J. Appl. Phys. 116, 173102, 2014.

5.   Islam SMZ, Gayen T, Tint N, Shi L, Seredych M, Bandosz T. J., Alfano R. R. “Hybrid solar cells of micro/meso-porous Zn(OH)2 and its graphite composites sensitized by CdSe quantum dots”. J. Photon. Energy. 4 (1):043098, 2014.


4.   Pu Y, Shi L, Pratavieira S, Alfano R. R. “Two-Photon excitation microscopy using the second singlet state of fluorescent agents within the tissue optical window”. J. Appl. Phys. 114(15):153102-4, 2013.

3.   Islam SMZ, Gayen T, Seredych M, Mabayoye O, Shi L, Bandosz TJ, and Alfano R. R. “Band gap energies of solar micro/meso-porous composites of zinc (hydr)oxide with graphite oxides”. J. Appl. Phys. 114 (4): 043522 - 6, 2013.

2.   Islam SMZ, Gayen T, Das B, Shi L, Seredych M, Moussawi A, Bandosz TJ, Alfano R. R. “Time resolved fluorescence of Zn(OH)2 and it composite with graphite Oxide”. Opt. Lett. 38(13): 2227- 2229, 2013.

1.   Islam SMZ, Gayen T, Moussawi A, Shi L, Seredych M, Bandosz TJ, Alfano R. R. “Structural and optical characterization of Zn(OH)2 and its composites with graphite oxides”. Opt. Lett. 38(6): 962- 964, 2013.

Books and book chapters


5) A Rodríguez-Contreras, L Shi, RR Alfano, Effects of tryptophan metabolism on the brain: From early development to Alzheimer's disease. Biophotonics, Tryptophan and Disease, 107-114

4) Wei W., Wang X., Li Y. , Cheng Y. , Fung A.A. Yang X., Wu J.Y., Shi L.**, Optical Imaging of Drug Delivery Across the Blood Brain Barrier, Progress in Optics, Elsevier, 2021 (chapter)

3) Li Y., Shi L.**, “Isotope-Probed SRS Imaging of Metabolic Dynamics in Living Organisms” , Ji-Xin Cheng, Wei Min, Yasuyuki Ozeki, Dario Polli (co-editors), Stimulated Raman Scattering Microscopy, Elsevier, 2021 (chapter)

Before UCSD:

2) Alfano R. R., Shi L. (Editors) “Neurophotonics and Biomedical Spectroscopy” (1st Ed.). Elsevier Publishing, 2018. ISBN-13: 978-0323480673. (Book)

1) Shi L, Alfano R. R. (Editors) “Deep Imaging in Tissue and biomedical materials using Linear and Non-linear Optics” (1st Ed.). Pan Stanford Publishing, 2017. ISBN 9789814745888. (Book)


12. Shi L., Jang H., “Super-Resolution Stimulated Raman Scattering Microscopy with A-POD”, U.S. Provisional Application Serial No. _63/379,226_ filed on October, 2022 

11. Shi L., Zhang W., “Multi-Molecular Hyperspectral PRM-SRS Imaging”, Application No. 63/379,210 10/12/2022 03:40:40 PM ET Docket No: 24978-0756, Provisional Application, 2022

10. Shi L., Min W. “System, method and computer-accessible medium for use of heavy water as a probe for imaging metabolic activities”. U.S. Patent Docket No.: 300440.US.01 – 32883-280915 PATENT APPLICATION 

9. Alfano RR, Mamani S., Shi L.,  "Method for imaging biological tissue using polarized majorana vector and complex vortex photons from laser and supercontinuum light sources", US11614398 B2, USA, 03 28 2023.

8. Alfano RR, Shi L, Wu B, “Compact optical virus detection analyzer of nano-and micro-size bio particles using light scattering and fluorescence”, US Patent App. 17/503,086 2.      

7. Alfano RR, Mazhar SFB, Sharonov M, Shi L, “Table-top utra supercontinuum and higher harmonic generation source for microscopy”, US Patent App. 17/532,834

6. Alfano R.R., Shi L. “Supercontinuum microscope for resonance and non-resonance enhanced linear and nonlinear time resolved microscope for tissue and materials”. U.S. Patent NO. US10962751B2, 3/30/2021

5. Alfano R.R., Shi L. “Resonant Stimulated Raman Scattering Microscope”. U.S. Patent NO. 10281331 , May 7 2019

4. Alfano R.R., Yang P., Shi L., Pratavieira S.  “Method of deep tissue imaging using multi-photon excitation of a fluorophore”. Awarded patent number 10420471. 09/04/2019

3. Alfano R.R., Shi L., Budansky Y. “Continuous Diode Laser Stimulated Raman Gain/Loss Vibrational Microscope”. Awarded patent number 10433731, 10/08/2019

2. Alfano R.R., Yang P., Shi L., Pratavieira S. “Method of deep tissue imaging using multi-photon excitation of a fluorophore”. Patent Number: US10420471B2 9/24/2019

1. Alfano R.R., Laura Sordillo, Yang Pu, Shi L. “Deep optical imaging of tissue with less scattering in the second, third and fourth NIR spectral windows using supercontinuum and other laser coherent light sources” Awarded patent Number: 10123705 Grant Date: 11/13/2018