Connect with us


Thomas Chi

United States

Associate Professor

UCSF Department of Urology


EDUCATION/TRAINING (Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)



(if applicable)



Stanford University



Human Biology

Stanford University




Stanford University




University of California, San Francisco





A. Personal Statement

As Associate Professor in Urology at UCSF, my clinical and translational research efforts have been focused on improving our understanding of urinary stone disease. As Associate Director of our NIH-funded P20 stone research center, I developed a Drosophila model to study how stones form. These studies demonstrated that metals play an important role in stone formation. We were successfully awarded funding for competitive renewal of the P20 center to translate our work into metallome and metabolome studies in human and vertebrate samples. In addition, I was actively involved in a multi-institutional clinical randomized controlled trial examining the use of CT versus ultrasound in the emergency department setting for the treatment of flank pain. This study involved 16 sites and over 2700 prospectively enrolled patients, providing me with several years of experience in developing and effectively managing prospective multi-institutional clinical research studies. Extending on skills gained serving in these two capacities, I invested in developing infrastructure for a robust prospective clinical registry in urinary stone disease, called ReSKU (Registry for Stones of the Kidney and Ureter), primed for automated data collection from clinical encounters. In developing this clinical registry, I have garnered expertise in clinical database development and management, creating opportunities for high quality prospective clinical and translational research. Using ReSKU as a foundation, we were successfully awarded an NIH R01 grant to performed a randomized control trial for a new drug intervention as a treatment for cystinuria on which I am a co-PI. Our proof of concept is that using our automated registry, we can more efficiently and successfully complete prospective clinical studies, which we have now done in the study of ureteroscopy and ultrasound- guided percutaneous nephrolithotomy by layering data instruments on top of the registry data already being collected. This concept has supported my successful award for both NIH R21 and P20 grants implementing novel applications of ReSKU for clinical and translational research. My full time academic appointment is comprised of 50% dedicated effort for research with the remaining time dedicated to clinical care for patients with urologic diseases, specializing in urinary stone patients. With my clinical research infrastructure and proven track record in leading NIH-supported clinical-translational research teams, my vision is to transform the care of nephrolithiasis patients with continued innovations in research and clinical care.

B. Positions and Honors Positions

2018-prsentAssociate Chair for Clinical Affairs, Dept of Urology, University of California, San Francisco 2018-presentAmbulatory Executive Medical Director, UCSF Health

2018-presentKutzmann Endowed Professor for Clinical Urology

2017-presentAssociate Professor, Department of Urology, University of California, San Francisco 2013-2017Assistant Professor, Department of Urology, University of California, San Francisco

2010-presentPeer Reviewer for Advances in Urology, Journal of Urology, Urology, Journal of Endourology, Journal Clinical Nephrology and Urology Science

2013-presentAssociate Editor, Translational Andrology Urology


2011-2013Fellow in Endourology and Laparoscopy, Department of Urology, UCSF

2006-2011Resident in Urology, Department of Urology, University of California, San Francisco 2005-2006Intern and Resident II training in General Surgery, University of California, San Francisco Honors

2018 Peter R. Carroll Mentoring Award: award recipient selected by urology resident body at UCSF

2018 WSAUA Joseph F. McCarthy Essay Contest: awarded second place for essay entitled "Fatty acid binding protein 4 is an essential molecule for the development of kidney stones: A new understanding of why obesity and nephrolithiasis go hand in hand"

2018 Second Place Prize in the AUA Research Forum Early-Career Investigators Showcase for "A novel urinary Kidney Injury Test (KIT) differentiates nephrolithiasis from immune-mediated renal disease"

2017 World Congress of Endourology: awarded best paper for project entitled “Optimizing RNA extraction of renal papilla biopsy tissue in kidney stone formers: a new methodology for genomic study”

2017 WSAUA Joseph F. McCarthy Essay Contest: awarded second place for essay entitled “Optimizing RNA extraction of renal papilla biopsy tissue in kidney stone formers: a new methodology for genomic study” 2016 UCSF Exceptional Physician Award: selected by university to receive award for exceptional demonstration of Professionalism, Respect, Integrity, Diversity and Excellence (PRIDE)

2016 WSAUA Joseph F. McCarthy Essay Contest: awarded first place for essay entitled “Feasibility of contrast-enhanced ultrasound nephrostograms”

2015 William Smart UCSF Urology Teaching Award: selected by residents to receive faculty teaching award 2013 WSAUA Joseph F. McCarthy Essay Contest: awarded first place for essay entitled “A Drosophila melanogaster model identifies a critical role for zinc in initiating urinary stones”

2012 WSAUA regional meeting: awarded 3rd place best poster in session for “Novel Genetic Loci for Kidney Stone in Diverse Ancestry Samples: the Women’s Health Initiative study”

2012 AUA Foundation Research Scholar Award: awarded $80,000 research scholarship for 2012-2013 2010 WSAUA Miley B. Wesson Essay Contest and AUA national meeting: awarded first place essay and best poster in session for project entitled “A Novel Animal Model for Studying Urinary Stone Formation Using Drosophila Melanogaster

2010 Northern California Urologic Resident Seminar: awarded 3rd place for research presentation in basic science category

2008 California Urology Foundation: Received $6000 grant to pursue development of animal stone model utilizing fruit flies

2002 Dean’s Research Fund: $1000 competitive grant awarded to conduct research on out-of-hospital- cardiac arrest survival.

1999 Undergraduate Research Opportunity Grant: $2500 competitive research grant given for continued study of Complementary Medicine users.

1996 President’s Scholar: $1500 research grant selectively given to top 10% of incoming freshman at Stanford University.





2005-present  American Urologic Association

2005-present Western Section of the American Urologic Association 2005-present American College of Surgeons

C. Selected peer-review publications

1. NIH P20 Center Director and Lead investigator for ReSKU

My current translational efforts have been establishing a robust infrastructure for clinical research based on a prospective registry called ReSKU, the Registry for Stones of the Kidney and Ureter. High quality registry data in urinary stone disease is an area of paucity within nephrolithiasis research, and as a result, many fundamental questions regarding the natural history of the disease remain unanswered. For example, we know very little about how the asymptomatic, incidentally discovered lower pole renal stone behaves. To answer questions like this, I established a secure, web portal based clinical registry using REDCap to collect clinical information on all urinary stone patients, integrated with patient urine, blood, renal biopsy, and stone specimen collection. I obtained CHR approval to enroll all patients with urinary stone disease into this registry at UCSF and data collection is ongoing. Early efforts from this registry work facilitated new imaging, structural, and elemental analysis studies of human stone samples demonstrating the potential relevance and significance of heavy metals in the mineralization process. Clinical patient data is automatically uploaded from the electronic medical record into the registry. This novel approach facilitates easy, high quality implementation of clinical trials and is the backbone on which future clinical and translational studies will be built. I was awarded an NIH P20 grant to support expansion of ReSKU to multiple institutions to build a foundation for future, multi-institutional high quality clinical studies.

1. Rationale and Design of the Registry for Stones of the Kidney and Ureter (ReSKU): A Prospective, Observational Registry to Study the Natural History of Urolithiasis Patients. Chang HC, Tzou DT, Usawachintachit M, Duty BD, Hsi RS, Harper JD, Sorensen MD, Stoller ML, Sur RL, Chi T. J Endourol, 2016 Dec;30(12):1332-1338. Epub 2016 Nov 1. PMID: 27758162.

2. Variation in Radiologic and Urologic Computed Tomography Interpretation of Urinary Tract Stone Burden: Results From ReSKU. Tzou DT, Isaacson D, Usawachintachit M, Wang ZJ, Taguchi K, Hills NK, Hsi RS, Sherer BA, Reliford-Titus S, Duty B, Harper J, Sorensen M, Sur RL, Stoller ML, Chi T. Urology. 2017 Oct 12. pii: S0090-4295(17)31073-7. doi: 10.1016/j.urology.2017.10.002. PMID: 29032235

3. Strontium Substitution for Calcium in Lithogenesis. Blaschko SD, Chi T, Miller J, Flechner L, Fakra S, Kahn A, Kapahi P, Stoller ML J Urol. 2013 Feb; 189(2): 735-9. PMID: 23260568. PMCID: PMC4124908. NIHMSID # 497975

4. Changes in urinary stone risk factors in hypocitraturic calcium oxalate stone formers treated with dietary sodium supplementation. Stoller ML, Chi T, Eisner BH, Shami G, Gentle DL. J Urol. 2009 Mar; 181(3): 1140-4. PMID: 19152919. PMCID in process

2. Associate director of NIH funded cross-disciplinary team studying the etiology of kidney stones and investigating novel therapeutics

The etiology of kidney stones is not well understood and few translational animal models exist for this study. My basic science research has focused on developing a novel animal model for the study of urinary stone disease. I dedicated my residency research year from 2009-2010 and fellowship years from 2011-2013 establishing the foundation for this work. This project represents the first time a genetically-based invertebrate model has been developed for translational research in urinary stone disease. I performed primary Drosophila experiments for this study, drafted our manuscript detailing these initial findings, and led data analyses for this purpose. Collaborative efforts within the context of this team also led to publication of a review article detailing the power of Drosophila as a new model organism for stone disease and two advanced analysis studies highlighting novel ultrastructural analyses of kidney stones. I was a primary author for an NIH R21 supporting this work as well as the programmatic P20 grant now funded for which I am Associate Director of the research program. A novel approach to understanding this disease process, these efforts led to developing a mouse model for cystinuria which led to an NIH/FDA-funded randomized control clinical trial examining a novel therapy for treating cystine stone disease. I serve as the co-PI and lead investigator for this RCT. The nature of our work is cross-disciplinary and our group is unique in that our collaborations extend from the field of urinary stone disease to metabolism and aging, biomineralization, veterinary medicine, drug modeling, and dentistry. My responsibilities include fostering new collaborations between various fields and across different sites and coordinating projects extending across disciplines. In our P20 program, I lead a team that brings together metabolomics, advanced elemental analysis and imaging to apply animal models to understanding stone formation and translating this to the bedside.

1. A Drosophila model identifies a critical role for zinc in mineralization for kidney stone disease. Chi T, Kim MS, Lang S, Bose N, Kahn A, Flechner L, Blaschko SD, Zee T, Muteliefu G, Bond N, Kolipinski M, Fakra SC, Mandel N, Miller J, Ramanathan A, Killilea DW, Brückner K, Kapahi P, Stoller ML. PLoS One. 2015 May 13;10(5):e0124150. doi: 10.1371/journal.pone.0124150. eCollection 2015.PMID: 25970330. PMCID: PMC4430225

2. Drosophila Melanogaster as an Emerging Translational Model of Human Nephrolithiasis. Miller J, Chi T, Kapahi P, Kahn AK, Kim MS, Hirata T, Romero MF, Dow JAT, Stoller ML. J Urol. 2013. doi:10.1016/j.juro.2013.03.010. PMID: 23500641. PMCID: PMC3842186

3. α-Lipoic acid treatment prevents cystine urolithiasis in a mouse model of cystinuria. Zee T, Bose N, Zee J, Beck JN, Yang S, Parihar J, Yang M, Damodar S, Hall D, O'Leary MN, Ramanathan A, Gerona RR, Killilea DW, Chi T, Tischfield J, Sahota A, Kahn A, Stoller ML, Kapahi P. Nat Med. 2017 Mar;23(3):288-290. doi: 10.1038/nm.4280. Epub 2017 Feb 6. PMID: 28165480

4. Elemental Content of Calcium Oxalate Stones from a Canine Model of Urinary Stone Disease. Killilea DW, Westropp JL, Shiraki R, Mellema M, Larsen J, Kahn AJ, Kapahi P, Chi T, Stoller ML. PLoS One. 2015 Jun 11;10(6):e0128374. doi: 10.1371/journal.pone.0128374. eCollection 2015. PMID: 26066810. PMCID: 4466234

3. Internationally-recognized expert in ultrasound-guided percutaneous nephrolithotomy

At UCSF, one of my clinical specialties is percutaneous renal stone surgery. Traditionally, fluoroscopic imaging is used to guide all steps of this procedure. In 2014, I initiated an innovative program in establishing ultrasound imaging to guide percutaneous renal access and stone removal, an approach not utilized in the United States. Our research demonstrates that by applying intraoperative ultrasound to these procedures, radiation exposure to the patient and intraoperative staff is significantly decreased. I have also established a new training program in the clinical use of intraoperative ultrasound amongst UCSF residents and regional urologists. In May 2015, I organized an inaugural UCSF Urinary Stones Course, focused on providing an update on surgical management of urinary stones and the novel use of ultrasound for percutaneous stone surgery. This educational course was held at UCSF and attended by trainees and attendings from around the country. I have been invited to speak at the national American Urological Association meeting on this topic and to provide skills workshops for attendees to learn how to apply ultrasound for gaining percutaneous renal access. I have also been awarded an NIH R21 grant to examine novel ways to apply ultrasound to reducing radiation exposure for nephrolithiasis patients. This ultrasound research has been a platform in which to demonstrate that the tools built for ReSKU can be applied to clinical studies in a rapid and relatively easy fashion.

1. Contrast Enhanced Ultrasound as a Radiation Free Alternative to Fluoroscopic Nephrostogram for Evaluating Ureteral Patency. Chi T, Usawachintachit M, Weinstein S, Kohi MP, Taylor A, Tzou DT, Chang HC, Stoller M, Mongan J. J Urol. 2017 Jul 23. pii: S0022-5347(17)77191-1. doi: 10.1016/j.juro.2017.07.074. PMID: 28743528

2. Feasibility of Antegrade Contrast-enhanced US Nephrostograms to Evaluate Ureteral Patency. Chi T, Usawachintachit M, Mongan J, Kohi MP, Taylor A, Jha P, Chang HC, Stoller M, Goldstein R, Weinstein S. Radiology. 2017 Apr;283(1):273-279. doi: 0.1148/radiol.2016160959. Epub 2016 Oct 19. PMID: 28234551

3. Ultrasound Guidance for Renal Tract Access and Dilation Reduces Radiation Exposure during Percutaneous Nephrolithotomy. Chi T, Masic S, Li J, Usawachintachit M. Adv Urol. 2016;2016:3840697. doi: 10.1155/2016/3840697. Epub 2016 Mar 2. PMID: 27042176

4. Ultrasound Guidance to Assist Percutaneous Nephrolithotomy Reduces Radiation Exposure in Obese Patients. Usawachintachit M, Masic S, Chang HC, Allen IE, Chi T. Urology. 2016 Apr 22. pii: S0090-4295(16)30107-8. doi: 10.1016/j.urology.2016.04.012. PMID: 27112513

4. Founder and lead investigator for the WEstern STone (WEST) Consortium

In 2013, I began leading an effort to establish a multi-institutional consortium of high volume urinary stone treatment centers to drive high quality clinical research in urinary stone disease. This consortium includes the University of California, San Francisco, San Francisco General Hospital, University of Washington, Oregon Health Sciences University, Puget Veteran’s Medical Center, University of British Columbia, and University of California, San Diego. I organize monthly conference calls to discuss new research ideas and collaborative efforts. I was a primary author for a grant successfully funded through the Boston Scientific Foundation to support a multi-institutional study on durability of reusable flexible ureteroscopes. For this study, I coordinated data collection across 6 clinical sites into a centralized REDCap database to examine factors that influence scope durability and cost. The study closed in April 2015 and we have presented our findings at the national American Urological Association meeting. In this role, I have garnered experience in establishing prospective clinical trials looking at clinical outcomes. Within this consortium, we have collaborated to publish several clinical outcomes papers looking at various aspects within urinary stone disease. Few multi-institutional urinary stone consortia exist to provide high quality prospective data on the natural history of stone disease, and a primary goal of our consortium is to fill this gap in urology research needs. With WEST, our vision is to heighten the quality of level of prospective multi-institutional nephrolithiasis research.

1. Defining the Costs of Reusable Flexible Ureteroscope Reprocessing Using Time-Driven Activity- Based Costing. Isaacson D, Ahmad T, Metzler I, Tzou DT, Taguchi K, Usawachintachit M, Zetumer S, Sherer B, Stoller M, Chi T. J Endourol. 2017 Sep 20. doi: 10.1089/end.2017.0463. PMID: 28830223


2. Dyslipidemia is associated with an increased risk of nephrolithiasis. Masterson JH, Woo JR, Chang DC, Chi T, L'Esperance JO, Stoller ML, Sur RL. Urolithiasis. 2015 Feb;43(1):49-53. doi: 10.1007/s00240-014-0719-3. Epub 2014 Sep 6. PMID: 25193087. PMCID: PMC4527684

3. Dietary Intake of Fiber, Fruit, and Vegetables Decrease the Risk of Incident Kidney Stones in Women: A Women’s Health Initiative (WHI) Report. Sorensen MD, Hsi RS, Chi T, Shara N, Wactawski-Wende J, Kahn AJ, Wang H, Hou L, Stoller ML. J Urol. (2014). doi: 10.1016/j.juro.2014.05.086. PMID: 24859445. PMCID: PMC4241174. NIHMSID # 619886

4. Activity, Energy Intake, Obesity, and the Risk of Incident Kidney Stones in Postmenopausal Women: A Report from the Women's Health Initiative. Sorensen MD, Chi T, Shara NM, Wang H, Hsi RS, Orchard T, Kahn AJ, Jackson RD, Miller J, Reiner AP, Stoller ML. J Am Soc Nephrol. 2014 Feb;25(2):362-9. doi: 10.1681/ASN.2013050548. PMID: 24335976. PMCID: PMC3904570


D. Research Support. 


NIH/NIDDK – R21-DK-109433 (Chi)6/1/2016-5/31/2018

Can contrast enhanced ultrasound nephrostogram replace fluoroscopic nephrostogram?

A silent, under-recognized danger for patients with kidney stones is repetitive exposure to ionizing radiation. We propose to validate a novel ultrasound approach to replace fluoroscopic nephrostogram for evaluating antegrade urine flow, laying the groundwork to introduce a new way of imaging the kidney and ureter.

NIH/NIDDK – P20-DK-116193 (Chi)12/01/2017-11/30/2019

Validating an automated nephrolithiasis registry as a community research tool

We propose a Resource Development Project that supports a mission of cross-discipline, multi-institutional discovery whose aim is to establish and validate an automated clinical registry called ReSKU that integrates with the electronic medical record (EMR) system, provides high quality clinical data for research purposes, and does not require an excessive time or cost commitment from providers to participate.

NIH/FDA – R01-FD-005716(Stoller/Chi)4/01/2017-03/31/2021

Phase 2: Impact of Lipoic Acid on Cystine Nephrolithiasis; IND129545

The goal of this project is to access the impact of lipoic acid in cystinuric urinary stone patients in hopes of minimizing recurrent stones and need for surgical intervention. Using metabolomics and metallomic analyses, predictive biomarkers for stone formation will also be investigated in these patients.


NIH/NIDDK –K12DK083021 (Baskin)Role: Scholar9/30/2008-7/31/2016

UCSF KURe Career Development Program

Goals: The major goal of this proposal is to recruit a superb and diverse group of health science scholars early in their academic careers to facilitate their long-term retention for significant contributions as researchers and leaders with a focus in the research of benign urologic diseases.

NIH/NIDDK – P20 DK100863-01 (Stoller)12/2013-11/2017


Goal: This program project seeks to take an integrative approach to understand how metals influence the formation of urinary stones in a Drosophila model. As associate director, I have led a translational science team effectively for 4 years. We have successfully undergone competitive renewal.

Role: Co-Investigator and Associate Director

NIH/NIDDK – R21DK091727 (Kapahi/Stoller)Role: Key Personnel 7/1/2012-6/30/2014


Goal: This R21 provided funding to support continued development of the Drosophila animal model for urinary stone formation. I took a lead role to write the grant and transition this work to a successful P20 application.

American Urological Association Foundation (Chi)7/1/2012-6/30/2013

AUA Foundation Research Scholars Program

Goal: The AUA Foundation Research Scholars Program provides an opportunity for young scientists to begin a career in urologic research at a time when many urology departments across the country are faced with budget challenges that limit research opportunities. This scholarship was geared toward supporting continued development of the Drosophila animal model for urinary stone formation.

Corresponding parameter set not found, please add it in property template of background
Previous article
Next article