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
    The Alfred P. Sloan Foundation 2023  - 2025Sloan Research Fellowship
    BMES-CMBE Cellular Molecular Bioengineering Society2024Cellular Molecular Bioengineering Rising Star Young Faculty Award 2024
    NYAS and the Blavatnik Family Foundation2018  - 2020the Blavatnik Regional Award for Young Scientist
    RCSA and the Chan Zuckerberg Initiative2021  - 2023Advancing Bioimaging Scialog Fellow
    Society of Hellman Fellows2021  - 2023Hellman Fellow Award
    Kern Lipid Conference2023  - 2023David L. Williams Lectureship Award
    Nature Light: Science & Applications2021  - 2022Rising Star Award

    Collapse Overview 

    Collapse Research 
    Collapse research activities and funding
    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 ORNG Applications 
    Collapse Featured Publications

    Collapse Bibliographic 
    Collapse selected 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. Multi-molecular hyperspectral PRM-SRS microscopy. Nat Commun. 2024 Feb 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: 6     Fields:    
    2. 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:
    3. 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:    
    4. 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
    5. 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
    6. 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: 3  
    7. 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: 8  
    8. 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: 2     Fields:    Translation:Humans
    9. 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  
    10. 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: 5  
    11. 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: 2     Fields:    Translation:HumansCells
    12. 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:
    13. 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: 14     Fields:    
    14. 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: 4     Fields:    Translation:AnimalsCells
    15. 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: 5     Fields:    Translation:Animals
    16. 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: 8  
    17. 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.
    18. 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: 10     Fields:    Translation:Animals
    19. 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: 6     Fields:    Translation:Humans
    20. 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: 8  
    21. 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  
    22. 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: 5  
    23. 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: 6     Fields:    Translation:AnimalsCells
    24. 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: 26     Fields:    
    25. 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: 2  
    26. 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: 12  
    27. 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:    
    28. 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: 13     Fields:    Translation:HumansAnimals
    29. 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: 42     Fields:    Translation:Animals
    30. 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:    
    31. 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: 8     Fields:    
    32. 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: 13     Fields:    Translation:Humans
    33. 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
    34. 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: 20     Fields:    Translation:HumansCells
    35. 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: 3     Fields:    Translation:Humans
    36. 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: 66     Fields:    Translation:HumansAnimalsCells
    37. 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: 44     Fields:    Translation:HumansAnimalsCells
    38. 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: 5     Fields:    Translation:Animals
    39. 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: 93     Fields:    Translation:HumansAnimalsCells
    40. 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.
    41. 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: 7     Fields:    
    42. 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: 24     Fields:    Translation:HumansAnimalsCells
    43. 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: 55     Fields:    Translation:HumansAnimalsCells
    44. 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
    45. 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
    46. 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: 7     Fields:    Translation:AnimalsCells
    47. 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: 23     Fields:    Translation:HumansAnimals
    48. 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: 3     Fields:    Translation:Animals
    49. 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
    50. 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: 8     Fields:    
    51. 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
    52. 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: 64     Fields:    Translation:Animals
    53. 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
    54. 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
    55. 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: 10     Fields:    Translation:Animals
    56. 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
    57. 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
    58. 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: 43     Fields:    Translation:Animals
    59. 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:    
    60. 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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