Allen Ye, MD, PhD

Title(s)Assistant Professor, Radiology
SchoolSchool of Medicine
Address185 Berry Street Bldg B, #001
San Francisco CA 94158
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    Dr. Ye obtained his MD and his PhD in bioengineering in 2017 at the University of Illinois Chicago in the Medical Scientist Training Program. After his internship at St. Francis Hospital in Evanston, Illinois, he completed his diagnostic radiology residency at the University of California San Francisco in 2022. During that time, he was selected as an NIH T32 research fellow and remained at UCSF to complete a neuroradiology fellowship in 2023. He has received multiple honors for his work including the Dr. Edward P. Cohen Medical Scientist Training Award, the UCSF Resident Research Fund Award, and the UCSF Radiology Outstanding Fellow/Instructor Teaching Award. Dr. Ye has served as director of the Resident Informatics Team and as a representative on the AIIMS (PACS) Steering Committee.

    Dr. Ye’s research focuses on utilization and application of advanced magnetic resonance imaging techniques such as anomalous diffusion, elastography, and connectomics in the clinical setting. He has translated these techniques for better characterization of vascular, neurodegenerative, and psychiatric diseases. Dr. Ye also has a strong interest in trauma research and has performed retrospective studies that categorize cervical spine trauma with respect to established trauma classifications and to evaluate the utility of MRI in the setting of isolated prevertebral edema.

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    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. Diffusion Imaging of the Spinal Cord: Clinical Applications. Radiol Clin North Am. 2024 Mar; 62(2):273-285. Talbott JF, Shah V, Ye AQ. PMID: 38272620.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    2. Utilizing a Digital Swarm Intelligence Platform to Improve Consensus Among Radiologists and Exploring Its Applications. J Digit Imaging. 2023 04; 36(2):401-413. Shah R, Astuto Arouche Nunes B, Gleason T, Fletcher W, Banaga J, Sweetwood K, Ye A, Patel R, McGill K, Link T, Crane J, Pedoia V, Majumdar S. PMID: 36414832; PMCID: PMC10039189.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    3. Boba sign with a twist - A variant presentation of a mature cystic teratoma complicated by torsion and rupture. Clin Imaging. 2022 Mar; 83:28-32. Ye AQ, Reyes MF, Lester F, Ye J, Umetsu S, Poder L, Shum DJ, Choi HH. PMID: 34952488; PMCID: PMC9254327.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    4. Detection of axonal degeneration in a mouse model of Huntington's disease: comparison between diffusion tensor imaging and anomalous diffusion metrics. MAGMA. 2019 Aug; 32(4):461-471. Gatto RG, Ye AQ, Colon-Perez L, Mareci TH, Lysakowski A, Price SD, Brady ST, Karaman M, Morfini G, Magin RL. PMID: 30771034; PMCID: PMC7837609.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    5. Scattering and Diffraction of Elastodynamic Waves in a Concentric Cylindrical Phantom for MR Elastography. IEEE Trans Biomed Eng. 2016 11; 63(11):2308-2316. Schwartz BL, Yin Z, Yasar TK, Liu Y, Khan AA, Ye AQ, Royston TJ, Magin RL. PMID: 26886963; PMCID: PMC5097039.
      View in: PubMed   Mentions: 2     Fields:    
    6. The intrinsic geometry of the human brain connectome. Brain Inform. 2015 Dec; 2(4):197-210. Ye AQ, Ajilore OA, Conte G, GadElkarim J, Thomas-Ramos G, Zhan L, Yang S, Kumar A, Magin RL, G Forbes A, Leow AD. PMID: 27747562; PMCID: PMC4737666.
      View in: PubMed   Mentions: 6  
    7. The intrinsic geometry of the human brain connectome. Brain Inform. 2015; 2:197-210. Ye AQ, Ajilore OA, Conte G, GadElkarim J, Thomas-Ramos G, Zhan L, Yang S, Kumar A, Magin RL, G Forbes A, Leow AD. PMID: 26870631.
      View in: PubMed   Mentions:
    8. Biological and MRI characterization of biomimetic ECM scaffolds for cartilage tissue regeneration. Biomaterials. 2015 Dec; 71:58-70. Ravindran S, Kotecha M, Huang CC, Ye A, Pothirajan P, Yin Z, Magin R, George A. PMID: 26318817; PMCID: PMC4572912.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    9. Analysis of YFP(J16)-R6/2 reporter mice and postmortem brains reveals early pathology and increased vulnerability of callosal axons in Huntington's disease. Hum Mol Genet. 2015 Sep 15; 24(18):5285-98. Gatto RG, Chu Y, Ye AQ, Price SD, Tavassoli E, Buenaventura A, Brady ST, Magin RL, Kordower JH, Morfini GA. PMID: 26123489; PMCID: PMC4550824.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    10. Measuring embeddedness: Hierarchical scale-dependent information exchange efficiency of the human brain connectome. Hum Brain Mapp. 2015 Sep; 36(9):3653-65. Ye AQ, Zhan L, Conrin S, GadElKarim J, Zhang A, Yang S, Feusner JD, Kumar A, Ajilore O, Leow A. PMID: 26096223; PMCID: PMC4898972.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    11. Anisotropic fractional diffusion tensor imaging. J Vib Control. 2016 May; 22(9):2211-2221. Meerschaert MM, Magin RL, Ye AQ. PMID: 27499605; PMCID: PMC4973862.
      View in: PubMed   Mentions: 4  
    12. Diffusion tensor MRI phantom exhibits anomalous diffusion. Annu Int Conf IEEE Eng Med Biol Soc. 2014; 2014:746-9. Ye AQ, Hubbard Cristinacce PL, Zhou FL, Yin Z, Parker GJ, Magin RL. PMID: 25570066; PMCID: PMC4605561.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    13. In vivo assessment of oxygen consumption via Deuterium Magnetic Resonance. Adv Exp Med Biol. 2011; 701:193-9. Mateescu GD, Ye A, Flask CA, Erokwu B, Duerk JL. PMID: 21445787.
      View in: PubMed   Mentions: 9     Fields:    Translation:Animals
    14. Ex vivo diffusion tensor MRI reflects microscopic structural remodeling associated with aging and disease progression in normal and cardiomyopathic Syrian hamsters. NMR Biomed. 2009 Oct; 22(8):819-25. Li W, Lu M, Banerjee S, Zhong J, Ye A, Molter J, Yu X. PMID: 19434665; PMCID: PMC2849973.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimals
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