Lupo Lab

Janine Lupo, PhD

Associate Professor
Department of Radiology and Biomedical Imaging

Lupo Pubmed Search


Our group is focused on developing novel methods for acquisition, reconstruction, post-processing, and quantitative analysis of Magnetic Resonance (MR) brain images. Using a combination of multiparametric structural, physiological, and metabolic MRI techniques, our goal is to quantitatively characterize heterogeneity within malignant brain tumors, monitor response to novel treatment regimens, and investigate the long-term effects of therapy on healthy brain tissue structure and cognitive function. As part of the Surbeck Laboratory for Advanced Imaging, we are based in Byers Hall at the UCSF Mission Bay campus and have access to state-of-the-art 3T and 7T human research scanners.  Many of the methodologies we develop initially to evaluate patients with brain tumors are also being applied to other neurological diseases.


Adegbite Oluwaseun
[email protected]

Jacob EllisonJacob Ellison
PhD Candidate
Email: [email protected]

Jacob Ellison completed his MS in Biomedical Imaging at UCSF, and is currently pursuing a PhD in the UCSF - UC Berkeley joint graduate program in Bioengineering. His current research in the Lupo Lab is focused on developing and applying quantitative methods for improving diagnosis, monitoring, and treatment of brain tumors using multi-parametric MRI.

Ozan GencOzan Genc
Assistant Specialist
Email:  [email protected]

Ozan is interested in applying both classical machine learning and deep learning techniques to medical image data. In his previous research, he focused on dimensionality reduction techniques to find possible MRI biomarkers identifying Mild Cognitive Impairment in Parkinson’s disease. Currently in the Lupo lab, he works on synthesizing MR images using deep convolutional neural networks. Ozan has completed his MSc in Biomedical Engineering at Bogazici University, Istanbul after getting his BSc degree in Electrical & Electronics Engineering.  

Angela Jakary, BA
Staff Research Associate III
Email: [email protected]

Angela enjoys acquiring, processing, and analyzing high-field 3T and 7T MRI data for a variety of brain research studies. She also analyzes multi-modal MRI data to provide neurosurgeons with research tissue targets during surgery to elucidate the relationship between brain tumor pathology and neuroimaging measures and performs neurocognitive testing to relate to imaging metrics. She likes the people she works with and hopes our combined efforts will have a positive impact on the world.

Bo LiuBo Liu
PhD student
Email: [email protected]

Bo Liu is a graduate student in the UC Berkeley - UCSF Bioengineering PhD program. His research interest focuses on the transferring of deep learning algorithm onto multi-modality medical data to help the diagnose and treatment of cancer. Bo likes landscape photography and road trip.

Brendan MitchellBrendan Mitchell
Rotation Student
Email: [email protected]

Brendan Mitchell graduated with honors from the University of California, Riverside in June 2020 with a B.S. in Neuroscience. He worked in Dr. Xiaoping Hu's lab for four years, focusing on Schizophrenia classification using deep convolutional neural networks based on multi-modal MRI. In August 2020, he joined the National Institute on Aging as a Post-Bac Fellow under the supervision of Drs. Qu Tian and Luigi Ferrucci. For two years, his research focused on examining age-related changes in plasma biomarkers and mitochondrial bioenergetics. Now as a first year Bioengineering PhD student in the joint UC Berkeley-UCSF graduate program, he is rotating in the Lupo Lab to study the progression of Huntington's disease using multi-modal MRI.

Devika Nair
Clinical Research Coordinator
Email: [email protected]

Devika oversees the image-guided tissue studies for patients with recurrent and newly diagnosed primary brain tumors (i.e., gliomas). In addition to ensuring proper collection of targets during surgery and maintaining clinical study records, she enjoys retrieving anatomic and physiologic imaging parameters to better understand the molecular characteristics of these tumors.

Paul Rowley
Clinical Research Coordinator
Email: [email protected]

Born in San Francisco and raised in Madison, Wisconsin, Paul joined the Lupo Lab in 2017 while studying medicine at the University of Wisconsin School of Medicine and Public Health (class of 2022). His research interests include applying diffusion tensor imaging (DTI) and quantitive susceptibility mapping (QSM) to study Huntington’s disease; developing and comparing QSM reconstruction methodologies; and using multiparametric imaging to improve radiotherapy planning for patients with glioblastoma multiforme. Paul loves to play jazz guitar, take runs in nature, and visit his extended family in the Bay Area whenever possible.

Nate Tran, Lupo LabNate Tran
PhD Candidate
Email: [email protected]

Nate Tran is a Ph.D. student in the UC Berkeley-UCSF Graduate Program in Bioengineering. He is currently working on the application of artificial intelligence and multi-parametric MRI in predicting brain tumor pathology and tumor progression trajectory in newly diagnosed glioblastoma patients. Outside of the lab, Nate enjoys backpacking, snowboarding, climbing, and football.

Jingwen Yao, PhDJingwen Yao, PhD
Postdoctoral Scholar
Email: [email protected] 

Jingwen’s research interest focuses on the development and application of advanced MRI techniques in brain diseases. She is currently working on developing myelin imaging technique using ultrashort echo (UTE) relaxometry MRI with Dr. Peder Larson and multi-modal characterization of Huntington’s disease (HD) at 7T with Dr. Janine Lupo. Jingwen received her PhD in Bioengineering in March 2021 from University of California Los Angeles, under the mentorship of Dr. Benjamin Ellingson. Her dissertation involved developing and validating pH-sensitive chemical exchange saturation transfer (CEST) MRI in adult glioma patients. Outside the lab, she loves origami and hiking.


Past Group Members/Alumni

  • Melanie Morrison, PhD, focused on the use of ultra-high field MRI (7T) to better understand the long-term effects of radiotherapy on the developing brain. She used different MRI techniques, image processing and statistical methods to evaluiate the relationship between at radiotherapy-induced vascular changes, brain connectivity, and neurocognitive function.
  • Julia Cluceru, PhD, worked on using multi-parametric approaches to understand differences between glioma recurrence and pseudoprogression & treatment necrosis.
  • Sivakami Avadiappan, worked on acquisition, processing and interpretation of vascular MR images from brain tumor survivors post radiation therapy. 
  • Maryam Vareth designed and developed techniques for acquisition, reconstruction, post-processing and quantitative analysis of multi-channel, phased array detectors for high field Magnetic Resonance Spectroscopy imaging (MRSI) with the goal of improving the sensitivity and specificity of the data obtained for characterizing human disease.
  • James Golden, PhD, interests include both the application and theory of deep learning. James built deep networks for the detection of cerebral microbleeds and symptom onset in Huntington's disease. 
  • Yicheng (Eason) Chen, former PhD candidate. Eason focused on applying quantitative susceptibility mapping (QSM) to dieases related to brain iron deposition. He was also interested in incorporating deep learning techniques into medical imaging.
  • Guanzhong Su was a graduate student in the Master of Science in Biomedical Imaging (MSBI) program at UCSF.  His research was focused on developing a pipeline for integration of metabolic and physiology imaging into clinical workflow for radiation treatment planning for glioblastoma (GBM) patients. 
  • Justin P. Yuan was an Assistant Specialist at UCSF Radiology & Biomedical Imaging. His research interests were in the usage of MRI to characterize adolescent brain changes and the reliability of such measures.
  • Xiaowei Zou, PhD, Former Post doctoral Scholar: Dr. Xiaowei Zou worked with Dr. Lupo from 2014-2016 on image acquisition, reconstruction, and post-processing algorithms for the detection and quantification of cerebral microbleeds.
  • Prasanna Parvathaneni, MSc, worked on incorporating distortion correction of EPI images into our perfusion image processing pipeline, implementing a faster tool for NODDI modeling of diffusion imaging data and relating derived metrics to histopathology. Her interests lay in integrating software to facilitate the processing and visualization of more advanced MRI imaging modalities for research.
  • Shauna O’Donnell was the previous Clinical Research Coordinator.


Essock-Burns E, Lupo JM, Cha S, Polley MY, Butowski NA, Chang SM, Nelson SJ. Assessment of perfusion MRI-derived parameters in evaluating and predicting response to antiangiogenic therapy in patients with newly diagnosed glioblastoma.  Neuro Oncol. 2011 Jan;13(1):119-31. Epub 2010 Oct 29. (pdf)

Tropp J, Lupo JM, Chen AP, Calderon P, Grafendorfer T, McCune D, Robb F, Yen Y, Larson PE, Bok R, Hu S, Schulte R, Vigneron DB, Hurd R, Nelson SJ. Multi-Channel Metabolic Imaging, with SENSE reconstruction, of  Hyperpolarized [1-13C] Pyruvate in a Live Rat at 3.0 tesla on a Clinical MR Scanner.  J Magn Reson. 2010 Oct 14. [Epub ahead of print] (pdf)

Lupo JM, Chen AP, Cunningham CH, Bok R, Kurhanewicz J, Vigneron DB, and Nelson SJ.   Hyperpolarized dynamic 13C lactate imaging of disease progression in a Transgenic Mouse Model of Prostate Cancer. Magn Reson Imaging. 2010 Feb;28(2):153-62. Epub 2009 Aug 18. (pdf)

Bian W, Khayal IS, Lupo JM, Cloyd C, Vandenberg V, Lamborn KR, Chang SM, Cha S, Nelson SJ. Multiparametric characterization of grade 2 glioma subtypes using magnetic resonance spectroscopic, perfusion, and diffusion imaging. Transl Oncol. 2009 Dec;2(4):271-80. (pdf)

Lupo JM, Banerjee S, Hammond KE, Kelley DAC, Xu D, Chang SM, Vigneron DB, Majumdar S, Nelson SJ. GRAPPA-based Susceptibility-Weighted Imaging of Normal Volunteers and Brain Tumor Patients at 7T. Magn Reson Imaging. 2009 May;27(4):480-8. Epub 2008 Sep 26. (pdf)

Cunningham CH, Chen AP, Lustig M, Hargreaves BA, Lupo J, Xu D, Kurhanewicz J, Hurd RE, Pauly JM, Nelson SJ, Vigneron DB. Pulse sequence for dynamic volumetric imaging of hyperpolarized metabolic products. J Magn Reson. 2008 Jul;193(1):139-46. Epub 2008 Mar 23. (pdf)

Hammond KE, Lupo JM, Xu D, Metcalf M, Kelley DA, Pelletier D, Chang SM, Mukherjee P, Vigneron DB, Nelson SJ. Development of a robust method for generating 7.0 T multichannel phase images of the brain with application to normal volunteers and patients with neurological diseases.  Neuroimage. 2008 Feb 15;39(4):1682-92. Epub 2007 Nov 7. (pdf)