Yan Li, PhD

Associate Professor
Assoc Professor In Residence
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Biography

Dr. Yan Li is an Associate Professor in the Department of Radiology and Biomedical Imaging. Her research focuses on developing methods for obtaining reliable metabolic information from the brain to characterize spatial and temporal heterogeneity and the biological behavior during disease time for brain tumors, psychiatric and neurologic diseases. This includes the development of new methods for obtaining whole-brain metabolites and tools for generating metrics of brain neurotransmitters using 3T and 7T MR scanners, implementation of statistical methods to relate metabolic metrics to clinical outcomes or measures, and integration of steady-state 1H metabolic imaging with PET, hyperpolarized 13C and advanced MR imaging parameters in order to elucidate the underlying normal and abnormal biological process.

Education

2021 - Diversity, Equity, and Inclusion Champion Training, University of California
Ph.D., 2008 - Bioengineering, University of California, Berkeley & San Francisco
MS, 2004 - Biochemistry, McGill University
Bachelor of Medicine, 2002 - Clinical Medicine, Shanghai Jiao Tong University

Honors and Awards

RAP Shared Technology Award, UCSF, 2024
RAP Pilot Award for Early Career Investigators, UCSF, 2023
Developmental Research Program Award, UCSF Brain Tumor SPORE, 2021-2022
The National Comprehensive Cancer Network (NCCN) Foundation Young Investigator Award, UCSF nominee, UCSF, 2020
RAP Pilot Award in Precision Imaging of Cancer and Therapy, UCSF, 2017-2018
RAP Pilot for Junior Investigators in Basic and Clinical/Translational Sciences, UCSF, 2015-2016
T32 training award in translational brain tumor research, UCSF Brain Tumor Center, 2012-2013
Margaret Heart Surbeck Scholar Award, UCSF, 2008
Krevans Graduate Research Fellowship, UCSF, 2007-2008

Publications

Ellison J, Caliva F, Damasceno P, Luks TL, LaFontaine M, Cluceru J, Kemisetti A, Li Y, Molinaro AM, Pedoia V, Villanueva-Meyer JE, Lupo JM. Improving the Generalizability of Deep Learning for T2-Lesion Segmentation of Gliomas in the Post-Treatment Setting. Bioengineering (Basel). 2024 May 16; 11(5).
Autry AW, Vaziri S, Gordon JW, Chen HY, Kim Y, Dang D, LaFontaine M, Noeske R, Bok R, Villanueva-Meyer JE, Clarke JL, Oberheim Bush NA, Chang SM, Xu D, Lupo JM, Larson PEZ, Vigneron DB, Li Y. Advanced Hyperpolarized 13C Metabolic Imaging Protocol for Patients with Gliomas: A Comprehensive Multimodal MRI Approach. Cancers (Basel). 2024 Jan 13; 16(2).
Coury SM, López V, Bajwa Z, Garcia JM, Teresi GI, Kuhlman KR, Li Y, Cole S, Miklowitz DJ, Pappas I, Ho TC. Protocol for teen inflammation glutamate emotion research (TIGER): Toward predictors of treatment response and clinical course in depressed adolescents. Brain Behav Immun Health. 2024 Feb; 35:100718.
Hu JY, Vaziri S, Bøgh N, Kim Y, Autry AW, Bok RA, Li Y, Laustsen C, Xu D, Larson PEZ, Chang S, Vigneron DB, Gordon JW. Investigating cerebral perfusion with high resolution hyperpolarized [1-13 C]pyruvate MRI. Magn Reson Med. 2023 12; 90(6):2233-2241.
Sana Vaziri, Huawei Liu, Emily Xie, Hélène Ratiney, Michaël Sdika, Janine M. Lupo, Duan Xu, Yan Li. Evaluation of deep learning models for quality control of MR spectra. Frontiers in Neuroscience. 2023 Aug 29; 17:1219343.
Chung BT, Kim Y, Gordon JW, Chen HY, Autry AW, Lee PM, Hu JY, Tan CT, Suszczynski C, Chang SM, Villanueva-Meyer JE, Bok RA, Larson PEZ, Xu D, Li Y, Vigneron DB. Hyperpolarized [2-13C]pyruvate MR molecular imaging with whole brain coverage. Neuroimage. 2023 10 15; 280:120350.
Huawei Liu, Adam W. Autry, Peder E. Z. Larson, Duan Xu, Yan Li. Atlas-Based Adaptive Hadamard-Encoded MR Spectroscopic Imaging at 3T. Tomography. 2023 Aug 23; 9(5):1592-1602.
Autry AW, Vaziri S, LaFontaine M, Gordon JW, Chen HY, Kim Y, Villanueva-Meyer JE, Molinaro A, Clarke JL, Oberheim Bush NA, Xu D, Lupo JM, Larson PEZ, Vigneron DB, Chang SM, Li Y. Multi-parametric hyperpolarized 13C/1H imaging reveals Warburg-related metabolic dysfunction and associated regional heterogeneity in high-grade human gliomas. Neuroimage Clin. 2023; 39:103501.
Jakary A, Lupo JM, Mackin S, Yin A, Murray D, Yang T, Mukherjee P, Larson P, Xu D, Eisendrath S, Luks T, Li Y. Evaluation of major depressive disorder using 7 Tesla phase sensitive neuroimaging before and after mindfulness-based cognitive therapy. J Affect Disord. 2023 08 15; 335:383-391.
Avalos LN, Luks TL, Gleason T, Damasceno P, Li Y, Lupo JM, Phillips J, Oberheim Bush NA, Taylor JW, Chang SM, Villanueva-Meyer JE. Longitudinal MR spectroscopy to detect progression in patients with lower-grade glioma in the surveillance phase. Neurooncol Adv. 2022 Jan-Dec; 4(1):vdac175.
Vaziri S, Autry AW, Lafontaine M, Kim Y, Gordon JW, Chen HY, Hu JY, Lupo JM, Chang SM, Clarke JL, Villanueva-Meyer JE, Bush NAO, Xu D, Larson PEZ, Vigneron DB, Li Y. Assessment of higher-order singular value decomposition denoising methods on dynamic hyperpolarized [1-13C]pyruvate MRI data from patients with glioma. Neuroimage Clin. 2022; 36:103155.
Hu JY, Kim Y, Autry AW, Frost MM, Bok RA, Villanueva-Meyer JE, Xu D, Li Y, Larson PEZ, Vigneron DB, Gordon JW. Kinetic analysis of multi-resolution hyperpolarized 13 C human brain MRI to study cerebral metabolism. Magn Reson Med. 2022 11; 88(5):2190-2197.
Autry AW, Lafontaine M, Jalbert L, Phillips E, Phillips JJ, Villanueva-Meyer J, Berger MS, Chang SM, Li Y. Spectroscopic imaging of D-2-hydroxyglutarate and other metabolites in pre-surgical patients with IDH-mutant lower-grade gliomas. J Neurooncol. 2022 Aug; 159(1):43-52.
Li Y, Vigneron DB, Xu D. Current human brain applications and challenges of dynamic hyperpolarized carbon-13 labeled pyruvate MR metabolic imaging. Eur J Nucl Med Mol Imaging. 2021 12; 48(13):4225-4235.
Kim Y, Chen HY, Autry AW, Villanueva-Meyer J, Chang SM, Li Y, Larson PEZ, Brender JR, Krishna MC, Xu D, Vigneron DB, Gordon JW. Denoising of hyperpolarized 13 C MR images of the human brain using patch-based higher-order singular value decomposition. Magn Reson Med. 2021 11; 86(5):2497-2511.
Wiggins CJ, Choi C, Li Y, Lin AP, Thakur SB, Ratai EM. Shimming-the forgotten child of in-vivo MR? MAGMA. 2021 04; 34(2):179-181.
Autry AW, Park I, Kline C, Chen HY, Gordon JW, Raber S, Hoffman C, Kim Y, Okamoto K, Vigneron DB, Lupo JM, Prados M, Li Y, Xu D, Mueller S. Pilot Study of Hyperpolarized 13C Metabolic Imaging in Pediatric Patients with Diffuse Intrinsic Pontine Glioma and Other CNS Cancers. AJNR Am J Neuroradiol. 2021 01; 42(1):178-184.
Gordon JW, Autry AW, Tang S, Graham JY, Bok RA, Zhu X, Villanueva-Meyer JE, Li Y, Ohilger MA, Abraham MR, Xu D, Vigneron DB, Larson PEZ. A variable resolution approach for improved acquisition of hyperpolarized 13 C metabolic MRI. Magn Reson Med. 2020 12; 84(6):2943-2952.
Autry AW, Gordon JW, Chen HY, LaFontaine M, Bok R, Van Criekinge M, Slater JB, Carvajal L, Villanueva-Meyer JE, Chang SM, Clarke JL, Lupo JM, Xu D, Larson PEZ, Vigneron DB, Li Y. Characterization of serial hyperpolarized 13C metabolic imaging in patients with glioma. Neuroimage Clin. 2020; 27:102323.
Chen HY, Autry AW, Brender JR, Kishimoto S, Krishna MC, Vareth M, Bok RA, Reed GD, Carvajal L, Gordon JW, van Criekinge M, Korenchan DE, Chen AP, Xu D, Li Y, Chang SM, Kurhanewicz J, Larson PEZ, Vigneron DB. Tensor image enhancement and optimal multichannel receiver combination analyses for human hyperpolarized 13 C MRSI. Magn Reson Med. 2020 12; 84(6):3351-3365.
Crane JC, Gordon JW, Chen HY, Autry AW, Li Y, Olson MP, Kurhanewicz J, Vigneron DB, Larson PEZ, Xu D. Hyperpolarized 13 C MRI data acquisition and analysis in prostate and brain at University of California, San Francisco. NMR Biomed. 2021 05; 34(5):e4280.
Pavithra Viswanath, Yan Li, Sabrina M. Ronen. C-13 Hyperpolarized MR Spectroscopy for Metabolic Imaging of Brain Tumors. . 2020 Jan 1; 191-209.
Chung BT, Chen HY, Gordon J, Mammoli D, Sriram R, Autry AW, Le Page LM, Chaumeil MM, Shin P, Slater J, Tan CT, Suszczynski C, Chang S, Li Y, Bok RA, Ronen SM, Larson PEZ, Kurhanewicz J, Vigneron DB. First hyperpolarized [2-13C]pyruvate MR studies of human brain metabolism. J Magn Reson. 2019 12; 309:106617.
Mammoli D, Gordon J, Autry A, Larson PEZ, Li Y, Chen HY, Chung B, Shin P, Van Criekinge M, Carvajal L, Slater JB, Bok R, Crane J, Xu D, Chang S, Vigneron DB. Kinetic Modeling of Hyperpolarized Carbon-13 Pyruvate Metabolism in the Human Brain. IEEE Trans Med Imaging. 2020 02; 39(2):320-327.
Autry AW, Gordon JW, Carvajal L, Mareyam A, Chen HY, Park I, Mammoli D, Vareth M, Chang SM, Wald LL, Xu D, Vigneron DB, Nelson SJ, Li Y. Comparison between 8- and 32-channel phased-array receive coils for in vivo hyperpolarized 13 C imaging of the human brain. Magn Reson Med. 2019 08; 82(2):833-841.
Zhu Z, Zhu X, Ohliger MA, Tang S, Cao P, Carvajal L, Autry AW, Li Y, Kurhanewicz J, Chang S, Aggarwal R, Munster P, Xu D, Larson PEZ, Vigneron DB, Gordon JW. Coil combination methods for multi-channel hyperpolarized 13C imaging data from human studies. J Magn Reson. 2019 04; 301:73-79.
Behr SC, Villanueva-Meyer JE, Li Y, Wang YH, Wei J, Moroz A, Lee JK, Hsiao JC, Gao KT, Ma W, Cha S, Wilson DM, Seo Y, Nelson SJ, Chang SM, Evans MJ. Targeting iron metabolism in high-grade glioma with 68Ga-citrate PET/MR. JCI Insight. 2018 11 02; 3(21).
Gordon JW, Chen HY, Autry A, Park I, Van Criekinge M, Mammoli D, Milshteyn E, Bok R, Xu D, Li Y, Aggarwal R, Chang S, Slater JB, Ferrone M, Nelson S, Kurhanewicz J, Larson PEZ, Vigneron DB. Translation of Carbon-13 EPI for hyperpolarized MR molecular imaging of prostate and brain cancer patients. Magn Reson Med. 2019 04; 81(4):2702-2709.
Yan Li and Sarah J. Nelson. Quantitative MRI of the Brain: Principles of Physical Measurement (by Mara Cercignani, Nicholas G. Dowell, Paul S. Tofts). Chapter 12: 1H Spectroscopy of the Brain. 2018.
Li Y, Bian W, Larson P, Crane JC, Parvathaneni P, Nagarajan S, Nelson SJ. Reliable and Reproducible GABA Measurements Using Automated Spectral Prescription at Ultra-High Field. Front Hum Neurosci. 2017; 11:506.
Li Y, Lafontaine M, Chang S, Nelson SJ. Comparison between Short and Long Echo Time Magnetic Resonance Spectroscopic Imaging at 3T and 7T for Evaluating Brain Metabolites in Patients with Glioma. ACS Chem Neurosci. 2018 01 17; 9(1):130-137.
Bian W, Li Y, Crane JC, Nelson SJ. Fully automated atlas-based method for prescribing 3D PRESS MR spectroscopic imaging: Toward robust and reproducible metabolite measurements in human brain. Magn Reson Med. 2018 02; 79(2):636-642.
Nelson SJ, Kadambi AK, Park I, Li Y, Crane J, Olson M, Molinaro A, Roy R, Butowski N, Cha S, Chang S. Association of early changes in 1H MRSI parameters with survival for patients with newly diagnosed glioblastoma receiving a multimodality treatment regimen. Neuro Oncol. 2017 03 01; 19(3):430-439.
Yan Li, Tracy Luks, Jason Crane, Sarah Nelson, Tracy McKnight. NIMG-32. 3D SHORT AND LONG ECHO TIME 1H MRSI IN PATIENTS WITH NON-ENHANCING GLIOMAS. Neuro-Oncology. 2016 Nov 1; 18(suppl_6):vi131-vi131.
Yan Li, Janine Lupo, Susan Chang, Sarah Nelson. NIMG-65. IN VIVO DETECTION OF 2-HYDROXYGLUTARATE IN LOW-GRADE IDH-MUTANT GLIOMAS WITH STABLE DISEASE. Neuro-Oncology. 2016 Nov 1; 18(suppl_6):vi138-vi139.
Nelson SJ, Li Y, Lupo JM, Olson M, Crane JC, Molinaro A, Roy R, Clarke J, Butowski N, Prados M, Cha S, Chang SM. Serial analysis of 3D H-1 MRSI for patients with newly diagnosed GBM treated with combination therapy that includes bevacizumab. J Neurooncol. 2016 10; 130(1):171-179.
Li Y, Jakary A, Gillung E, Eisendrath S, Nelson SJ, Mukherjee P, Luks T. Evaluating metabolites in patients with major depressive disorder who received mindfulness-based cognitive therapy and healthy controls using short echo MRSI at 7 Tesla. MAGMA. 2016 Jun; 29(3):523-33.
Wen Q, Jalilian L, Lupo JM, Li Y, Roy R, Molinaro AM, Chang SM, Prados M, Butowski N, Clarke J, Nelson SJ. Association of Diffusion and Anatomic Imaging Parameters with Survival for Patients with Newly Diagnosed Glioblastoma Participating in Two Different Clinical Trials. Transl Oncol. 2015 Dec; 8(6):446-55.
Li Y, Park I, Nelson SJ. Imaging tumor metabolism using in vivo magnetic resonance spectroscopy. Cancer J. 2015 Mar-Apr; 21(2):123-8.
Li Y, Larson P, Chen AP, Lupo JM, Ozhinsky E, Kelley D, Chang SM, Nelson SJ. Short-echo three-dimensional H-1 MR spectroscopic imaging of patients with glioma at 7 Tesla for characterization of differences in metabolite levels. J Magn Reson Imaging. 2015 May; 41(5):1332-41.
Nelson SJ, Ozhinsky E, Li Y, Park Iw, Crane J. Strategies for rapid in vivo 1H and hyperpolarized 13C MR spectroscopic imaging. J Magn Reson. 2013 Apr; 229:187-97.
Li Y, Lupo JM, Parvataneni R, Lamborn KR, Cha S, Chang SM, Nelson SJ. Survival analysis in patients with newly diagnosed glioblastoma using pre- and postradiotherapy MR spectroscopic imaging. Neuro Oncol. 2013 May; 15(5):607-17.
Lupo JM, Li Y, Hess CP, Nelson SJ. Advances in ultra-high field MRI for the clinical management of patients with brain tumors. Curr Opin Neurol. 2011 Dec; 24(6):605-15.
Li Y, Lupo JM, Polley MY, Crane JC, Bian W, Cha S, Chang S, Nelson SJ. Serial analysis of imaging parameters in patients with newly diagnosed glioblastoma multiforme. Neuro Oncol. 2011 May; 13(5):546-57.
Li Y, Srinivasan R, Ratiney H, Lu Y, Chang SM, Nelson SJ. Comparison of T(1) and T(2) metabolite relaxation times in glioma and normal brain at 3T. J Magn Reson Imaging. 2008 Aug; 28(2):342-50.
Xu D, Cunningham CH, Chen AP, Li Y, Kelley DA, Mukherjee P, Pauly JM, Nelson SJ, Vigneron DB. Phased array 3D MR spectroscopic imaging of the brain at 7 T. Magn Reson Imaging. 2008 Nov; 26(9):1201-6.
Li Y, Chen AP, Crane JC, Chang SM, Vigneron DB, Nelson SJ. Three-dimensional J-resolved H-1 magnetic resonance spectroscopic imaging of volunteers and patients with brain tumors at 3T. Magn Reson Med. 2007 Nov; 58(5):886-92.
Li Y, Osorio JA, Ozturk-Isik E, Chen AP, Xu D, Crane JC, Cha S, Chang S, Berger MS, Vigneron DB, Nelson SJ. Considerations in applying 3D PRESS H-1 brain MRSI with an eight-channel phased-array coil at 3 T. Magn Reson Imaging. 2006 Dec; 24(10):1295-302.