Lingyan Shi

Title(s)Associate Professor, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
ORCID ORCID Icon0000-0003-1373-3206 Additional info
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    Collapse Biography 
    Collapse awards and honors
    SPIE2025Optics Notebook--Woman in Optics
    Med-X of Spinger Nature2025Med-X Young Investigator Award by Springer Nature
    WACBE2025WACBE Young Investigator Award
    NAI2025Senior member of National Academy of Inventors (NAI)
    Spectroscopy2025Emerging Leader in Molecular Spectroscopy Award
    Davos Summit iCANx Conference2024  - 2024Davos Summit iCANx Young Scientist Award
    IUPS2024International Union of Physiological Sciences IUPS Young Faculty Award
    BMES-CMBE Cellular Molecular Bioengineering Society2024Cellular Molecular Bioengineering Rising Star Young Faculty Award 2024
    ICBME2024ICBME Rising Star Award
    The Alfred P. Sloan Foundation 2023  - 2025Sloan Research Fellowship
    Kern Lipid Conference2023  - 2023David L. Williams Lectureship Award
    RCSA and the Chan Zuckerberg Initiative2021  - 2023Advancing Bioimaging Scialog Fellow
    Society of Hellman Fellows2021  - 2023Hellman Fellow Award
    Nature Light: Science & Applications2021  - 2022Rising Star Award
    NYAS and the Blavatnik Family Foundation2018  - 2020the Blavatnik Regional Award for Young Scientist

    Collapse Research 
    Collapse research activities and funding
    Lympnoids tissue senescence and multimodal imaging using REDCAT
    NIH R01AG086548Feb 1, 2026 - Jan 31, 2031
    Role: Principal Investigator
    Shear stress Regulation of Endothelial Glycolysis via METTL3-mediated RNA m6A Modification
    NIH R01HL170107Jul 1, 2024 - Jun 30, 2028
    Role: Co-Investigator
    Sugar Probed SRS Volumetric imaging of Metabolic Activities
    NIH R01GM149976Sep 21, 2023 - Aug 31, 2028
    Role: Principal Investigator
    Novel Optical Imaging Approach to Study Neurovascular Coupling System
    NIH R21NS125395Sep 21, 2022 - Aug 31, 2024
    Role: Principal Investigator
    Kidney single cell and spatial molecular atlas project - KIDSSMAP
    NIH U54DK134301Sep 15, 2022 - Jun 30, 2026
    Role: Co-Investigator
    The Human Lung BioMolecular Multi-Scale Atlas Program (HuBMAP-Lung)
    NIH U54HL165443Sep 1, 2022 - Aug 31, 2026
    Role: Co-Investigator

    Collapse Featured Content 

    Collapse Bibliographic 
    Collapse publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details 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. Illuminating aging with multimodal optical metabolic imaging. Sci Adv. 2026 Jul 03; 12(27):eaed9156. Li Y, Alvarado E, Li Z, Shrestha R, Villazon J, Shi L. PMID: 42384794; PMCID: PMC13322256.
      View in: PubMed   Mentions:
    2. 3D multi-omics tumour atlases: from technology to biology and clinical translation. Nat Rev Cancer. 2026 Jun 15. Liu M, Villazon J, Forjaz A, Tian X, Fan R, Wang S, Shi L, Wirtz D, Kiemen AL. PMID: 42298141.
      View in: PubMed   Mentions:
    3. Regional and Systemic Metabolic Remodeling Promotes Longevity by Bioengineered Yeast-Derived Lipids. bioRxiv. 2026 Apr 13. Li Y, Bai Z, Li Y, Gao F, Qin S, Ran J, Villazon J, Wang A, Jang H, Li Z, Sankaran S, Liu Y, Skowronska-Krawczyk D, Hao N, Fan R, Shi L. PMID: 42039507; PMCID: PMC13104885.
      View in: PubMed   Mentions:
    4. A label-free optical analysis for molecular nephrology. Nat Rev Nephrol. 2026 Jan; 22(1):6-7. Fung AA, Shi L. PMID: 41219522.
      View in: PubMed   Mentions: 1     Fields:    
    5. Consensus guidelines for cellular label-free optical metabolic imaging: ensuring accuracy and reproducibility in metabolic profiling. J Biomed Opt. 2025 Feb; 30(Suppl 2):S23901. Georgakoudi I, Skala MC, Quinn KP, Stringari C, Sorrells JE, Heikal AA, Li LZ, Xu HN, You S, Walsh AJ, Datta R, Samimi K, Gillette AA, Eliceiri KW, Balu M, Boppart SA, Digman MA, Dunning KR, Evans CL, Garcia AA, Houston JP, Hwang W, Lindley MM, Li X, Liu Z, Marcu L, Murugkar S, Nichols MG, Niesner R, Parekh SH, Rajaram N, Ranjit S, Shen K, Shi L, Torrado B, Vallmitjana A, Wang-Evers M, Zemp R. PMID: 41230436; PMCID: PMC12604823.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    6. Imaging Cellular Metabolic Rewiring with SuMMIT-SRS. bioRxiv. 2025 Oct 13. Li Y, Li Z, Li Y, Rhine K, Ranamukhaarachchi S, Qin S, Jang H, Villazon J, Bai Z, Fraley SI, Yeo GW, Fan R, Shi L. PMID: 41279865; PMCID: PMC12632847.
      View in: PubMed   Mentions:
    7. Light and metabolism: label-free optical imaging of metabolic activities in biological systems [Invited]. Biomed Opt Express. 2025 Sep 01; 16(9):3770-3796. Menozzi L, Li Z, Choi S, Vu T, Shi L, Yao J. PMID: 41368095; PMCID: PMC12684064.
      View in: PubMed   Mentions:
    8. LYVAC/PDZD8 is a lysosomal vacuolator. Science. 2025 Aug 21; 389(6762):eadz0972. Yang H, Xun J, Li Y, Mondal A, Lv B, Watkins SC, Shi L, Tan JX. PMID: 40839735; PMCID: PMC12897110.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    9. A multimodal imaging approach for imaging the metabolic changes resulting from bronchopulmonary dysplasia. bioRxiv. 2025 Jun 22. Gorman BL, Li Z, Deutsch G, Huyck HL, Beishembieva N, Olson H, Villazon J, Yu P, Pryhuber GS, Clair G, Shi L, Anderton CR. PMID: 40667045; PMCID: PMC12262683.
      View in: PubMed   Mentions:
    10. The APSES transcription factor Swi6B upregulates CATALASE 1 transcription to enhance oxidative stress tolerance of Ganoderma lucidum. Appl Environ Microbiol. 2025 07 23; 91(7):e0067925. Wang L, Shi L, Zhang S, Ma J, Zhang C, Chen H, Zhao M. PMID: 40530877; PMCID: PMC12285235.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    11. Multimodal Optical Imaging Platform for Studying Cellular Metabolism. J Vis Exp. 2025 06 06; (220). Villazon J, Li Z, Fan A, Shi L. PMID: 40549710; PMCID: PMC12626104.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    12. Optical imaging of metabolic dynamics in ALS under methionine regulation. J Biomed Opt. 2025 02; 30(Suppl 2):S23906. Hoang K, Prayotamornkul S, Kuo CY, Jang H, Shi L. PMID: 40417702; PMCID: PMC12102500.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    13. Label-free multimodal optical biopsy reveals biomolecular and morphological features of diabetic kidney tissue in 2D and 3D. Nat Commun. 2025 May 15; 16(1):4509. Fung AA, Li Z, Boote C, Markov P, Gaut JP, Jain S, Shi L. PMID: 40374604; PMCID: PMC12081717.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimals
    14. Illuminating life processes by vibrational probes. Nat Methods. 2025 May; 22(5):928-944. Qian N, Zhao Z, El Khoury E, Gao X, Canela C, Shen Y, Shi L, Shi L, Hu F, Wei L, Min W. PMID: 40360917; PMCID: PMC12626105.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimals
    15. METTL3 mediates atheroprone flow-induced glycolysis in endothelial cells. Proc Natl Acad Sci U S A. 2025 May 13; 122(19):e2424796122. Zhao GJ, Han SY, Li Y, Yuan D, Qin S, Li Y, Jang H, Chen LJ, Wei TW, He M, Li YS, Bouman Chen Z, Shi L, Chien S, Shyy JY. PMID: 40327688; PMCID: PMC12088407.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    16. General control nonderepressible 4 activates the transcription of trehalose phosphorylase to improve trehalose production and abiotic stress tolerance in Ganoderma lucidum. Int J Biol Macromol. 2025 Jun; 311(Pt 3):143840. Shi L, Lian L, Wang L, Zhang S, Han Q, Shi L, Chen H, Zhao M. PMID: 40318725.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    17. Far-red chemigenetic kinase biosensors enable multiplexed and super-resolved imaging of signaling networks. Nat Biotechnol. 2026 Mar; 44(3):444-453. Frei MS, Sanchez SA, He X, Liu L, Schneider F, Wang Z, Hakozaki H, Li Y, Lyons AC, Rohm TV, Olefsky JM, Shi L, Schöneberg J, Fraser SE, Mehta S, Wang Y, Zhang J. PMID: 40258957; PMCID: PMC13193679.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    18. Single-Frame Vignetting Correction for Post-Stitched-Tile Imaging Using VISTAmap. Nanomaterials (Basel). 2025 Apr 07; 15(7). Fung AA, Fung AH, Li Z, Shi L. PMID: 40214608; PMCID: PMC11990085.
      View in: PubMed   Mentions: 2  
    19. Cancer Cell Line Classification Using Raman Spectroscopy of Cancer-Derived Exosomes and Machine Learning. Anal Chem. 2025 Apr 08; 97(13):7289-7298. Villazon J, Dela Cruz N, Shi L. PMID: 40145503; PMCID: PMC11983372.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    20. The GCN4-Swi6B module mediates low nitrogen-induced cell wall remodeling in Ganoderma lucidum. Appl Environ Microbiol. 2025 04 23; 91(4):e0016425. Shi L, Wang L, Liu R, Zhu J, Shi L, Ren A, Chen H, Zhao M. PMID: 40145759; PMCID: PMC12016525.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    21. Innovations in aging biology: highlights from the ARDD emerging science & technologies workshop. NPJ Aging. 2025 Feb 18; 11(1):8. Unfried M, Schmauck-Medina T, Amin ND, Boyden ES, Fuellen G, Han JJ, Hanna JH, Heckenbach I, Khodosevich K, Melton L, Moeendarbary E, Moon TS, Peleg S, Sandberg A, Shi L, Bakula D, Zhavoronkov A, Scheibye-Knudsen M. PMID: 39966395; PMCID: PMC11836439.
      View in: PubMed   Mentions: 1  
    22. UTE MRI technical developments and applications in osteoporosis: a review. Front Endocrinol (Lausanne). 2025; 16:1510010. Shin SH, Chae HD, Suprana A, Jerban S, Chang EY, Shi L, Sah RL, Pettus JH, Woods GN, Du J. PMID: 39980853; PMCID: PMC11839439.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    23. Spermidine enhances the heat tolerance of Ganoderma lucidum by promoting mitochondrial respiration driven by fatty acid β-oxidation. Appl Environ Microbiol. 2025 02 19; 91(2):e0097924. Han X, Wang Z, Shi L, Wei Z, Shangguan J, Shi L, Zhao M. PMID: 39878489; PMCID: PMC11837530.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    24. Metabolic nanoscopy enhanced by experimental and computational approaches. Npj Imaging. 2024; 2(1):55. Jang H, Wu S, Li Y, Li Z, Shi L. PMID: 39677560; PMCID: PMC11638068.
      View in: PubMed   Mentions: 1  
    25. Multimodal Imaging Unveils the Impact of Nanotopography on Cellular Metabolic Activities. Chem Biomed Imaging. 2024 Dec 23; 2(12):825-834. Li Z, Sarikhani E, Prayotamornkul S, Meganathan DP, Jahed Z, Shi L. PMID: 39735831; PMCID: PMC11672213.
      View in: PubMed   Mentions: 5  
    26. Label-Free Optical Biopsy Reveals Biomolecular and Morphological Features of Diabetic Kidney Tissue in 2D and 3D. bioRxiv. 2024 Oct 29. Fung AA, Li Z, Boote C, Markov P, Jain S, Shi L. PMID: 39553929; PMCID: PMC11565847.
      View in: PubMed   Mentions:
    27. Engineered Nanotopographies Induce Transient Openings in the Nuclear Membrane. Adv Funct Mater. 2025 Feb 05; 35(6). Sarikhani E, Patel V, Li Z, Meganathan DP, Rahmani K, Sadr L, Hosseini R, Visda D, Shukla S, Naghsh-Nilchi H, Balaji A, McMahon G, Chen S, Schöneberg J, McHugh CA, Shi L, Jahed Z. PMID: 40657484; PMCID: PMC12246998.
      View in: PubMed   Mentions: 5  
    28. Divergent iron regulatory states contribute to heterogeneity in breast cancer aggressiveness. iScience. 2024 Sep 20; 27(9):110661. Leineweber WD, Rowell MZ, Ranamukhaarachchi SK, Walker A, Li Y, Villazon J, Mestre-Farrera A, Hu Z, Yang J, Shi L, Fraley SI. PMID: 39262774; PMCID: PMC11387597.
      View in: PubMed   Mentions: 4  
    29. Virtual-point-based deconvolution for optical-resolution photoacoustic microscopy. J Biophotonics. 2024 08; 17(8):e202400078. Yao R, DiSpirito A, Jang H, McGarraugh CT, Nguyen VT, Shi L, Yao J. PMID: 38934081; PMCID: PMC11330737.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    30. Microglial lipid droplet accumulation in tauopathy brain is regulated by neuronal AMPK. Cell Metab. 2024 Jun 04; 36(6):1351-1370.e8. Li Y, Munoz-Mayorga D, Nie Y, Kang N, Tao Y, Lagerwall J, Pernaci C, Curtin G, Coufal NG, Mertens J, Shi L, Chen X. PMID: 38657612; PMCID: PMC11153007.
      View in: PubMed   Mentions: 66     Fields:    Translation:HumansAnimalsCells
    31. Multi-molecular hyperspectral PRM-SRS microscopy. Nat Commun. 2024 02 21; 15(1):1599. 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. PMID: 38383552; PMCID: PMC10881988.
      View in: PubMed   Mentions: 30     Fields:    Translation:HumansAnimals
    32. Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness. bioRxiv. 2024 Feb 13. Leineweber WD, Rowell MZ, Ranamukhaarachchi S, Walker A, Li Y, Villazon J, Farrera AM, Hu Z, Yang J, Shi L, Fraley SI. PMID: 37425829; PMCID: PMC10327122.
      View in: PubMed   Mentions:
    33. Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging. bioRxiv. 2024 Feb 11. Frei MS, Sanchez SA, Liu L, Schneider F, Wang Z, Hakozaki H, Li Y, Lyons AC, Rohm TV, Olefsky JM, Shi L, Schöneberg J, Fraser SE, Mehta S, Wang Y, Zhang J. PMID: 38370804; PMCID: PMC10871310.
      View in: PubMed   Mentions:
    34. Super-Resolution Stimulated Raman Scattering Microscopy with Graphical User Interface-Supported A-PoD. Curr Protoc. 2024 Jan; 4(1):e970. Jang H, Li Y, Wu S, Shi L. PMID: 38270527; PMCID: PMC10832363.
      View in: PubMed   Mentions: 3     Fields:    
    35. Femtosecond optical Kerr effect in normal and grades of cancerous breast tissues as a new optical biopsy method. J Biophotonics. 2024 02; 17(2):e202300344. Meyer HJ, Mamani S, Li Z, Shi L, Alfano RR. PMID: 38010367.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    36. Self-Assembled Homopolymeric Spherulites from Small Molecules in Solution. J Am Chem Soc. 2023 11 29; 145(47):25664-25672. Song Q, Li Y, Jin Z, Liu H, Creyer MN, Yim W, Huang Y, Hu X, He T, Li Y, Kelley SO, Shi L, Zhou J, Jokerst JV. PMID: 37921495.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    37. Multimodal imaging of metabolic activities for distinguishing subtypes of breast cancer. Biomed Opt Express. 2023 Nov 01; 14(11):5764-5780. Li Z, Nguyen C, Jang H, Hoang D, Min S, Ackerstaff E, Koutcher JA, Shi L. PMID: 38021123; PMCID: PMC10659775.
      View in: PubMed   Mentions: 10  
    38. Correction to "Goldilocks Energy Minimum: Peptide-Based Reversible Aggregation and Biosensing". ACS Appl Mater Interfaces. 2023 Oct 18; 15(41):48838. Yim W, Retout M, Chen AA, Ling C, Amer L, Jin Z, Chang YC, Chavez S, Barrios K, Lam B, Li Z, Zhou J, Shi L, Pascal TA, Jokerst JV. PMID: 37787714.
      View in: PubMed   Mentions:    Fields:    
    39. Early cancer detection by SERS spectroscopy and machine learning. Light Sci Appl. 2023 Sep 15; 12(1):234. Shi L, Li Y, Li Z. PMID: 37714845; PMCID: PMC10504315.
      View in: PubMed   Mentions: 24  
    40. Goldilocks Energy Minimum: Peptide-Based Reversible Aggregation and Biosensing. ACS Appl Mater Interfaces. 2023 Sep 13; 15(36):42293-42303. Yim W, Retout M, Chen AA, Ling C, Amer L, Jin Z, Chang YC, Chavez S, Barrios K, Lam B, Li Z, Zhou J, Shi L, Pascal TA, Jokerst JV. PMID: 37651748; PMCID: PMC10619458.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    41. Perspectives on SRS Imaging of Nanoparticles. Acc Mater Res. 2023 Sep 22; 4(9):726-728. Shi L, Jang H. PMID: 37766942; PMCID: PMC10521017.
      View in: PubMed   Mentions: 1  
    42. Bioorthogonal Stimulated Raman Scattering Imaging Uncovers Lipid Metabolic Dynamics in Drosophila Brain During Aging. GEN Biotechnol. 2023 Jun 01; 2(3):247-261. Li Y, Chang P, Sankaran S, Jang H, Nie Y, Zeng A, Hussain S, Wu JY, Chen X, Shi L. PMID: 37363411; PMCID: PMC10286263.
      View in: PubMed   Mentions: 11  
    43. Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids. J Vis Exp. 2023 05 12; (195). Bagheri P, Hoang K, Kuo CY, Trivedi H, Jang H, Shi L. PMID: 37246865; PMCID: PMC10725321.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    44. Femtosecond Optical Kerr Gates in Cancerous Breast Tissue for a New Optical Biopsy Method. Res Sq. 2023 May 10. Meyer H, Mamani S, Li Z, Shi L, Alfano R. PMID: 37214848; PMCID: PMC10197745.
      View in: PubMed   Mentions:
    45. Super-resolution SRS microscopy with A-PoD. Nat Methods. 2023 03; 20(3):448-458. Jang H, Li Y, Fung AA, Bagheri P, Hoang K, Skowronska-Krawczyk D, Chen X, Wu JY, Bintu B, Shi L. PMID: 36797410; PMCID: PMC10246886.
      View in: PubMed   Mentions: 35     Fields:    
    46. Alzheimer's-Associated Upregulation of Mitochondria-Associated ER Membranes After Traumatic Brain Injury. Cell Mol Neurobiol. 2023 Jul; 43(5):2219-2241. Agrawal RR, Larrea D, Xu Y, Shi L, Zirpoli H, Cummins LG, Emmanuele V, Song D, Yun TD, Macaluso FP, Min W, Kernie SG, Deckelbaum RJ, Area-Gomez E. PMID: 36571634; PMCID: PMC10287820.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    47. Towards Mapping Mouse Metabolic Tissue Atlas by Mid-Infrared Imaging with Heavy Water Labeling. Adv Sci (Weinh). 2022 05; 9(15):e2105437. Liu X, Shi L, Shi L, Wei M, Zhao Z, Min W. PMID: 35319171; PMCID: PMC9131428.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    48. Imaging Sub-Cellular Methionine and Insulin Interplay in Triple Negative Breast Cancer Lipid Droplet Metabolism. Front Oncol. 2022; 12:858017. Fung AA, Hoang K, Zha H, Chen D, Zhang W, Shi L. PMID: 35359364; PMCID: PMC8960266.
      View in: PubMed   Mentions: 16  
    49. DO-SRS imaging of diet regulated metabolic activities in Drosophila during aging processes. Aging Cell. 2022; (e13586). Yajuan Li, Wenxu Zhang, Anthony A. Fung, Lingyan Shi. . View Publication.
    50. DO-SRS imaging of diet regulated metabolic activities in Drosophila during aging processes. Aging Cell. 2022 04; 21(4):e13586. Li Y, Zhang W, Fung AA, Shi L. PMID: 35257470; PMCID: PMC9009230.
      View in: PubMed   Mentions: 18     Fields:    Translation:Animals
    51. A high-throughput technique to map cell images to cell positions using a 3D imaging flow cytometer. Proc Natl Acad Sci U S A. 2022 02 22; 119(8). Zhang Z, Tang R, Chen X, Waller L, Kau A, Fung AA, Gutierrez B, An C, Cho SH, Shi L, Lo YH. PMID: 35173045; PMCID: PMC8872737.
      View in: PubMed   Mentions: 13     Fields:    Translation:Humans
    52. Direct Imaging of Lipid Metabolic Changes in Drosophila Ovary During Aging Using DO-SRS Microscopy. Front Aging. 2021; 2:819903. Li Y, Bagheri P, Chang P, Zeng A, Hao J, Fung A, Wu JY, Shi L. PMID: 35822015; PMCID: PMC9261447.
      View in: PubMed   Mentions: 16  
    53. Fano resonance line shapes in the Raman spectra of tubulin and microtubules reveal quantum effects. Biophys Rep (N Y). 2022 Mar 09; 2(1):100043. Zhang W, Craddock TJA, Li Y, Swartzlander M, Alfano RR, Shi L. PMID: 36425084; PMCID: PMC9680776.
      View in: PubMed   Mentions: 4     Fields:    
    54. Visualizing Cancer Cell Metabolic Dynamics Regulated With Aromatic Amino Acids Using DO-SRS and 2PEF Microscopy. Front Mol Biosci. 2021; 8:779702. Bagheri P, Hoang K, Fung AA, Hussain S, Shi L. PMID: 34977157; PMCID: PMC8714916.
      View in: PubMed   Mentions: 8  
    55. DO-SRS imaging of metabolic dynamics in aging Drosophila. Analyst. 2021 Dec 06; 146(24):7510-7519. Li Y, Zhang W, Fung AA, Shi L. PMID: 34781326; PMCID: PMC10870347.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    56. Highly-multiplexed volumetric mapping with Raman dye imaging and tissue clearing. Nat Biotechnol. 2022 03; 40(3):364-373. Shi L, Wei M, Miao Y, Qian N, Shi L, Singer RA, Benninger RKP, Min W. PMID: 34608326; PMCID: PMC8930416.
      View in: PubMed   Mentions: 45     Fields:    
    57. 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 Jul 18; 11(7). Chang D, Brown Q, Tsui G, He Y, Liu J, Shi L, Rodríguez-Contreras A. PMID: 34356178; PMCID: PMC8304335.
      View in: PubMed   Mentions: 4  
    58. Advances in stimulated Raman scattering imaging for tissues and animals. Quant Imaging Med Surg. 2021 Mar; 11(3):1078-1101. Shi L, Fung AA, Zhou A. PMID: 33654679; PMCID: PMC7829158.
      View in: PubMed   Mentions: 22  
    59. Enhanced stimulated raman scattering of solvent due to anharmonic energy transfer from resonance raman solute molecules. Opt Express. 2020 Jul 20; 28(15):21792-21804. Shi L, Gayen T, Budansky Y, Yoo K, Secor J, Harvey T, Harvey G, Shumyatsky P, Nolan D, Alfano R. PMID: 32752451; PMCID: PMC7470682.
      View in: PubMed   Mentions: 1     Fields:    
    60. Mammalian cell and tissue imaging using Raman and coherent Raman microscopy. Wiley Interdiscip Rev Syst Biol Med. 2020 11; 12(6):e1501. Fung AA, Shi L. PMID: 32686297; PMCID: PMC7554227.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimals
    61. Mid-infrared metabolic imaging with vibrational probes. Nat Methods. 2020 08; 17(8):844-851. Shi L, Liu X, Shi L, Stinson HT, Rowlette J, Kahl LJ, Evans CR, Zheng C, Dietrich LEP, Min W. PMID: 32601425; PMCID: PMC7396315.
      View in: PubMed   Mentions: 61     Fields:    Translation:Animals
    62. Explanation of the competition between O- and E-wave induced stimulated Raman and supercontinuum in calcite under ultrafast laser excitation. Appl Opt. 2020 Jun 10; 59(17):5252-5257. Mazhar SFB, Meyer HJ, Samuels T, Sharonov M, Shi L, Alfano RR. PMID: 32543546.
      View in: PubMed   Mentions: 1     Fields:    
    63. Background-free imaging of chemical bonds by a simple and robust frequency-modulated stimulated Raman scattering microscopy. Opt Express. 2020 May 11; 28(10):15663-15677. Xiong H, Qian N, Zhao Z, Shi L, Miao Y, Min W. PMID: 32403589; PMCID: PMC7340375.
      View in: PubMed   Mentions: 10     Fields:    
    64. Distinguishing metastatic triple-negative breast cancer from nonmetastatic breast cancer using second harmonic generation imaging and resonance Raman spectroscopy. J Biophotonics. 2020 07; 13(7):e202000005. Bendau E, Smith J, Zhang L, Ackerstaff E, Kruchevsky N, Wu B, Koutcher JA, Alfano R, Shi L. PMID: 32219996; PMCID: PMC7433748.
      View in: PubMed   Mentions: 14     Fields:    Translation:Humans
    65. Comparison of continuous wave versus picosecond SRS and the resonance SRS effect. Appl Opt. 2020 Jan 20; 59(3):622-627. Shumyatsky P, Shi L, Sordillo LA, Budansky Y, Alfano RR. PMID: 32225186.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    66. Optical biopsy identification and grading of gliomas using label-free visible resonance Raman spectroscopy. J Biomed Opt. 2019 09; 24(9):1-12. Zhou Y, Liu CH, Wu B, Yu X, Cheng G, Zhu K, Wang K, Zhang C, Zhao M, Zong R, Zhang L, Shi L, Alfano RR. PMID: 31512439; PMCID: PMC6997631.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    67. Majorana vortex photons a form of entangled photons propagation through brain tissue. J Biophotonics. 2019 10; 12(10):e201900036. Mamani S, Shi L, Nolan D, Alfano R. PMID: 31162813.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    68. Spectral tracing of deuterium for imaging glucose metabolism. Nat Biomed Eng. 2019 05; 3(5):402-413. Zhang L, Shi L, Shen Y, Miao Y, Wei M, Qian N, Liu Y, Min W. PMID: 31036888; PMCID: PMC6599680.
      View in: PubMed   Mentions: 93     Fields:    Translation:HumansAnimalsCells
    69. Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy. Proc Natl Acad Sci U S A. 2019 04 02; 116(14):6608-6617. Wei M, Shi L, Shen Y, Zhao Z, Guzman A, Kaufman LJ, Wei L, Min W. PMID: 30872474; PMCID: PMC6452712.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansAnimalsCells
    70. Transmission of classically entangled beams through mouse brain tissue. J Biophotonics. 2018 12; 11(12):e201800096. Mamani S, Shi L, Ahmed T, Karnik R, Rodríguez-Contreras A, Nolan D, Alfano R. PMID: 30027681.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    71. Optical imaging of metabolic dynamics in animals. Nat Commun. 2018 08 06; 9(1):2995. Shi L, Zheng C, Shen Y, Chen Z, Silveira ES, Zhang L, Wei M, Liu C, de Sena-Tomas C, Targoff K, Min W. PMID: 30082908; PMCID: PMC6079036.
      View in: PubMed   Mentions: 122     Fields:    Translation:HumansAnimalsCells
    72. Visualizing protein synthesis in mice with in vivo labeling of deuterated amino acids using vibrational imaging. APL Photonics. 2018; 3(9):092401-1-10. Shi L, Shen Y, Min W. View Publication.
    73. Resonance Raman scattering of β-carotene solution excited by visible laser beams into second singlet state. J Photochem Photobiol B. 2018 Feb; 179:18-22. Lu L, Shi L, Secor J, Alfano R. PMID: 29306722.
      View in: PubMed   Mentions: 13     Fields:    
    74. Two-color vibrational imaging of glucose metabolism using stimulated Raman scattering. Chem Commun (Camb). 2018 Jan 07; 54(2):152-155. Long R, Zhang L, Shi L, Shen Y, Hu F, Zeng C, Min W. PMID: 29218356; PMCID: PMC5764084.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    75. Metabolic activity induces membrane phase separation in endoplasmic reticulum. Proc Natl Acad Sci U S A. 2017 12 19; 114(51):13394-13399. Shen Y, Zhao Z, Zhang L, Shi L, Shahriar S, Chan RB, Di Paolo G, Min W. PMID: 29196526; PMCID: PMC5754785.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansAnimalsCells
    76. Propagation of Gaussian and Laguerre-Gaussian vortex beams through mouse brain tissue. J Biophotonics. 2017 Dec; 10(12):1756-1760. Shi L, Lindwasser L, Wang W, Alfano R, Rodríguez-Contreras A. PMID: 28635151; PMCID: PMC5862546.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    77. Label-Free Fluorescence Spectroscopy for Detecting Key Biomolecules in Brain Tissue from a Mouse Model of Alzheimer's Disease. Sci Rep. 2017 06 01; 7(1):2599. Shi L, Lu L, Harvey G, Harvey T, Rodríguez-Contreras A, Alfano RR. PMID: 28572632; PMCID: PMC5454017.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimals
    78. Alzheimer mouse brain tissue measured by time resolved fluorescence spectroscopy using single- and multi-photon excitation of label free native molecules. J Biophotonics. 2018 01; 11(1). Das B, Shi L, Budansky Y, Rodriguez-Contreras A, Alfano R. PMID: 28464457; PMCID: PMC5668196.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    79. Short wavelength infrared optical windows for evaluation of benign and malignant tissues. J Biomed Opt. 2017 04 01; 22(4):45002. Sordillo DC, Sordillo LA, Sordillo PP, Shi L, Alfano RR. PMID: 28384701.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimals
    80. Photon Entanglement Through Brain Tissue. Sci Rep. 2016 12 20; 6:37714. Shi L, Galvez EJ, Alfano RR. PMID: 27995952; PMCID: PMC5171785.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    81. Vulnerable atherosclerotic plaque detection by resonance Raman spectroscopy. J Biomed Opt. 2016 12 01; 21(12):127006. Liu CH, Boydston-White S, Weisberg A, Wang W, Sordillo LA, Perotte A, Tomaselli VP, Sordillo PP, Pei Z, Shi L, Alfano RR. PMID: 27999865; PMCID: PMC5174785.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    82. Deep transmission of Laguerre-Gaussian vortex beams through turbid scattering media. Opt Lett. 2016 May 01; 41(9):2069-72. Wang WB, Gozali R, Shi L, Lindwasser L, Alfano RR. PMID: 27128076.
      View in: PubMed   Mentions: 11     Fields:    
    83. Terahertz spectroscopy of brain tissue from a mouse model of Alzheimer's disease. J Biomed Opt. 2016 Jan; 21(1):15014. Shi L, Shumyatsky P, Rodríguez-Contreras A, Alfano R. PMID: 26818714; PMCID: PMC4728211.
      View in: PubMed   Mentions: 10     Fields:    Translation:Animals
    84. Transmission in near-infrared optical windows for deep brain imaging. J Biophotonics. 2016 Jan; 9(1-2):38-43. Shi L, Sordillo LA, Rodríguez-Contreras A, Alfano R. PMID: 26556561; PMCID: PMC4827444.
      View in: PubMed   Mentions: 71     Fields:    Translation:Animals
    85. Gaussian beam in two-photon fluorescence imaging of rat brain microvessel. J Biomed Opt. 2014 Dec; 19(12):126006. Shi L, Rodríguez-Contreras A, Alfano RR. PMID: 25490048; PMCID: PMC4260768.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    86. Quantification of transient increase of the blood-brain barrier permeability to macromolecules by optimized focused ultrasound combined with microbubbles. Int J Nanomedicine. 2014; 9:4437-48. Shi L, Palacio-Mancheno P, Badami J, Shin DW, Zeng M, Cardoso L, Tu R, Fu BM. PMID: 25258533; PMCID: PMC4173757.
      View in: PubMed   Mentions: 14     Fields:    Translation:Animals
    87. Temporal effects of vascular endothelial growth factor and 3,5-cyclic monophosphate on blood-brain barrier solute permeability in vivo. J Neurosci Res. 2014 Dec; 92(12):1678-89. Shi L, Zeng M, Fu BM. PMID: 25066133; PMCID: PMC4692382.
      View in: PubMed   Mentions: 13     Fields:    Translation:Animals
    88. Deep two-photon microscopic imaging through brain tissue using the second singlet state from fluorescent agent chlorophyll α in spinach leaf. J Biomed Opt. 2014 Jun; 19(6):066009. Shi L, Rodríguez-Contreras A, Budansky Y, Pu Y, Nguyen TA, Alfano RR. PMID: 24967915; PMCID: PMC4071303.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    89. A method to make a craniotomy on the ventral skull of neonate rodents. J Vis Exp. 2014 May 22; (87). Rodríguez-Contreras A, Shi L, Fu BM. PMID: 24894439; PMCID: PMC4122667.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    90. Quantification of blood-brain barrier solute permeability and brain transport by multiphoton microscopy. J Biomech Eng. 2014 Mar; 136(3):031005. Shi L, Zeng M, Sun Y, Fu BM. PMID: 24193698.
      View in: PubMed   Mentions: 54     Fields:    Translation:Animals
    91. Time-resolved photoluminescence of Zn(OH)2 and its composites with graphite oxides. Opt Lett. 2013 Jul 01; 38(13):2227-9. Islam SZ, Gayen T, Das BB, Shi L, Seredych M, Moussawi A, Bandosz TJ, Alfano R. PMID: 23811885.
      View in: PubMed   Mentions:    Fields:    
    92. Structural and optical characterization of Zn(OH)2 and its composites with graphite oxides. Opt Lett. 2013 Mar 15; 38(6):962-4. Islam SM, Gayen T, Moussawi A, Shi L, Seredych M, Bandosz TJ, Alfano R. PMID: 23503274.
      View in: PubMed   Mentions: 1     Fields:    
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