UCSF

Research

Overview

The research unit of the UCSF-Stanford CERSI stimulates innovative and collaborative research in regulatory science among FDA scientists, academic scientists, and scientists in the biotechnology and pharmaceutical industries. Particular attention is paid to research involving computational methods to integrate vast and multiple data sets in the evaluation of therapies that will lead to better quality and safer medical products for the health of the public. A complete list of all collaborative research projects can be found here: PDF iconResearch Projects

Funding for collaborative science

The UCSF-Stanford CERSI will fund collaborative research projects that focus on “unmet needs” in regulatory science. A broad net will be cast to define the most critical problems in regulatory science that can be solved through collaborative research efforts; the center will fund research that addresses the most critical problems. Complementing the research program funded by the FDA is an Innovation in Regulatory Sciences Award from the Burroughs Wellcome Fund. This award is focused on using systems pharmacology approaches to identify the targets and mechanisms for drug-induced obesity, a major adverse event for many drugs including many neuropsychiatric agents. A copy of our Procedures for Initiating Collaborative Research Projects can be found here: PDF iconResearch Guidelines

Research environment of UCSF and Stanford

The center’s collaborative research unit engages top-tier researchers at UCSF and Stanford University to apply modern methods to problems in regulatory science.

Historically, UCSF has been the premier institution in quantitative pharmacology as it relates to drug discovery and development. UCSF pioneered pharmacokinetics and pharmacodynamics and computational drug discovery, which are used commonly in regulatory science. UCSF has continued to lead the pharmacological sciences with internationally renowned faculty members in pharmacogenomics, chemoinformatics, disease modeling, imaging and high throughput methodologies, and by forging strong research programs relevant to the discovery and development of therapeutics. The California Institute for Quantitative Biosciences-UCSF (QB3-UCSF) provides a home and resources for the recruitment of exceptional new faculty with quantitative skills.

Stanford University features a world-class Stanford Center for Biomedical Informatics Research, which recently pioneered the use of internet query logs, population health databases (e.g., FDA AERS Database), and electronic medical records from hospitals to identify adverse drug events and drug interactions.

Collaborations among Stanford University and UCSF scientists and the FDA are already under way for using new informatics methods for data fusion to construct safety profiles of drugs and for developing quantitative models to predict drug levels in the central nervous system. The collaborative research projects include a pilot project funding mechanism.


For Current Awardees: Please make sure to acknowledge the funding source for your project by including the following statement:

This publication/poster was made possible by Grant NumberU01FD004979/U01FD005978 from the FDA, which supports the UCSF-Stanford Center of Excellence in Regulatory Sciences and Innovation. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the HHS or FDA.

Listing of Research Projects

Jump below to: Not Yet Completed or Completed.

Research Projects: Not Yet Completed

Research Project Title

Lead scientist at UCSF & Stanford University

FDA Collaborators​/​Non-federal entities collaborators

1. Role of Ancestry in Genetic Diagnostics

Snehit Prabhu, PhD (Stanford)

Adam Berger, PhD, CDRH/FDA
Roselie Bright, ScD, Ms, PMP, OHI/FDA
Elaine Johanson, OHI/FDA
Samir Lababidi, PhD, OHI/FDA
David Litwack, PhD, CDRH/FDA
Zivana Tezak, PhD, CDRH/FDA

2. Causes of Real-Life NGS Variability

Dmitri Petrov, PhD (Stanford)

Elaine Johanson, OHI/FDA

3. Effects of Excipients in Generic Drugs Products on Intestinal Drug Transporters

Kathy Giacomini, PhD (UCSF)

Andrew Babiskin, PhD, CDER/FDA
Sruthi King, PhD, CDER/FDA
Zhanglin Ni, PhD, CDER/FDA
Eleftheria Tsakalozou, PhD, CDER/FDA
Liang Zhao, PhD, CDER/FDA
Susan Zuk, MS, CDER/FDA

4. Chemoinformatic Tools to Predict the Effects of Excipients in Generic Drugs

Excipient Browser (a new research tool to help investigate and improve these important substances)

Usage Statistics of Excipient Browser

Brian Shoichet, PhD (UCSF)

Andrew Babiskin, PhD, CDER/FDA
Robert Dorsam, PhD, CDER/FDA
Victoria Keck, MHA, CDER/FDA
Zhanglin Ni, PhD, CDER/FDA
Eleftheria Tsakalozou, PhD, CDER/FDA
Liang Zhao, PhD, CDER/FDA
Susan Zuk, MS, CDER/FDA
Bryan Roth, MD, PhD, University of North Carolina, Chapel Hill (in kind)
Laszio Urban, MD, PhD, Novartis (in kind)

5. OneSource

Laura Esserman, MD, MBA (UCSF)

Ronald Fitzmartin, PhD, MBA, CDER/FDA
Fatima Frye, CDER/FDA
Mitra Rocca, Dipl. Inform. Med., CDER/FDA
MaryAnne Slack, CDER/FDA

6. Safer Labeling of Pediatric Medications

Lee Sanders, MD (Stanford)
Bonnie Halpern-Felsher, PhD (Stanford)
Shelly Harris, MPH, CDER/FDA
Grace Jones, PharmD, CDER/FDA
Martin Mendoza, PhD, OMH/FDA
Amanda Pike-McCrudden, MAA, CDER/FDA
Lee Zwanziger, OC/FDA

7. Patient Reported Outcomes for Minimally Invasive Glaucoma Surgery

Kuldev Singh, MD, MBA (Stanford)
Tianjing Li, MD, PhD (JHU)
Kay Dickerson, PhD (JHU)
Malvina Eydelman, MD, CDRH/FDA
Michelle Tarver, MD, PhD, CDRH/FDA

8. Comparing Qualitative and Quantitative Approaches to Eliciting Patient Preferences on Upper Limb Prostheses

Leslie Wilson, PhD (UCSF)

Heather Benz, PhD, CDRH/FDA
Eugene Civillico, PhD, CDRH/FDA
Martin Ho, MSc, CDRH/FDA
Telba Irony, PhD, CBER/FDA
Xuefeng Li, PhD, CDRH/FDA
Anindita Saha, CDRH/FDA

9. Mapping a Better Approach to Obtaining Pediatric Patient Preferences

Korey Hood, PhD (Stanford)

Heather Benz, PhD, CDRH/FDA
Martin Ho, MSc, CDRH/FDA
Vasum Peiris, MD, MPH, CDRH/FDA
Anindita Saha, CDRH/FDA

10. Developing an Operational Framework for Defining the Strength of Evidence in Therapeutic Development

Steve Goodman, MD, MHS, PhD (Stanford)

Telba Irony, PhD, CBER/FDA
Tom Permutt, PhD, CDER/FDA
Estelle Russek-Cohen, PhD, CDER/FDA

11. Predicting Pediatric Dosing for Medical Countermeasures

Kathy Giacomini, PhD (UCSF)
Kathy Cheung, PharmD (UCSF)

Shiew Mei Huang, PhD, CDER/FDA

12. Network Integration for Precision Medicine Drug Models

Russ Altman, MD, PhD (Stanford)
Jennifer Wilson, PhD (Stanford)
Michael Pacanowski, PharmD, MPH, CDER/FDA
Anuradha Ramamoorthy, PhD, CDER/FDA
Oluseyi Adeniyi, PhD, CDER/FDA

13. Development of Thrombogenicity Testing Methods for Medical Devices with Large Blood-Contacting Surfaces

Shuvo Roy, PhD (UCSF)

Megan Jamiolkowski, PhD, CDRH/FDA
Richard Malinauskas, PhD, CDRH/FDA

14. Developing Frameworks and Tools for Integration of Digital Health Tools into Clinical Practice

Andrew Auerbach, MD (UCSF)

Bakul Patel, MS, MBA, CDRH/FDA
Marisa Cruz, MD, CDRH/FDA

15. An Unbiased Analysis of Identification and Assessment of Cas9/gRNA Potential Off-Target Sites in Clinical Development of Ex Vivo Manufactured Genome Edited Cell Products

Matthew Porteus, MD, PhD (Stanford)

Zhaohui Ye, PhD, CBER/FDA

16. The Impact of Race and Ethnicity on Responses to Heart Failure Patient-Reported Outcome Measures

Courtney Lyles, PhD (UCSF)
Urmimala Sarkar, MD, MPH (UCSF)
Fraser Bocell, PhD, CDRH/FDA
Michelle Tarver, MD PhD, CDRH/FDA
Brittany Caldwell, PhD, CDRH/FDA
Fraser Bocell, PhD, CDRH/FDA
Annie Saha, CDRH/FDA
Martin Ho, CDRH/FDA

17. Adapting a Measure of Heart Failure to an Adolescent Population

Christopher Almond, MD, MPH (Stanford)
Jonathan Johnson, MD (Mayo Clinic)
Fraser Bocell, PhD, CDRH/FDA
Vasum Peiris, MD, MPH, CDRH/FDA
Michelle Tarver, MD, PhD, CDRH/FDA
Brittany Caldwell, PhD, CDRH/FDA
Annie Saha, CDRH/FDA
Martin Ho, CDRH/FDA

18. Healthy Citizen Hospital Pilot

Ida Sim, PhD (UCSF)

Elaine Johanson, OHI/FDA
Ameeta Parekh, PhD, CDER/FDA

19. Multi-organ Microphysiological Systems for Modeling Clinical Drug Effects

Kevin Healy, PhD (UC Berkeley)
Edward Hsiao, MD, PhD (UCSF)
Alexandre Ribeiro, PhD, CDER/FDA
David Strauss, MD, PhD, CDER/FDA
20. Tissue Chips for Multipotent Stromal Cell Manufacturing
Ngan Huang, PhD (Stanford)
Kyung Sung, PhD, CBER/FDA
21. Isolating Exosomes using a novel ExoTIC device from HIV-infected patient plasma and saliva
Utkan Demirci, PhD (Stanford)
Indira Hewlett, PhD, CBER
Mohan Haleyurgirisetty, PhD, CBER
Jiangqin Zhao, PhD, CBER
22. Development and Evaluation of Computational Test Methods Leveraging Real-world and Simulated Datasets for Predictive Medical Device Alarm Algorithms
Xiao Hu, PhD (UCSF)
Christopher Scully, PhD, CDRH
23. Advancing Computational Modeling in the Regulatory Evaluation of Spinal Fusion Cages
Jeffrey Lotz, PhD (UCSF)
Anton Dmitriev, PhD, CDRH
Andrew Baumann, PhD, CDRH

Research Projects: Completed

Research project name

Lead scientist at UCSF & Stanford University

FDA collaborators​/​non-federal entities collaboratorS

24. Improving Efficiency and Rigor of Pharmacovigilance at FDA

Russ Altman, MD, PhD (Stanford)

Steve Anderson, PhD, MPP, CBER/FDA
Robert Ball, MD, MPH, CDER/FDA
Ruth Barratt, PhD, DVM, CDER/FDA
Mitra Rocca, Dipl. Inform. Med., CDER/FDA
Carol Pamer, RPh, MPH, CDER/FDA
Scott Proestel, MD, CDER/FDA

25. Precision Medicine Initiative

Russ Altman, MD, PhD (Stanford)

Elaine Johanson, OHI/FDA

26. Next Generation Text Analytics for FDA-Relevant Text Mining Russ Altman, MD, PhD (Stanford)
Roselie Bright, ScD, OHI/FDA
Larry Callahan, PhD, OHI/FDA
Elaine Johanson, OHI/FDA
Frank Switzer, PhD, OHI/FDA
27. Use of NLP/Machine Learning to Analyze Medication Error Reports Russ Altman, MD, PhD (Stanford)
Sonja Brajovic, MD, OSE/RSS/CDER/FDA
Todd Bridges, RPh, OSE/DMEPA/CDER/FDA
Carol Pamer, RPh, MPH, CDER/FDA
Jim Schlick, RPh, MBA, OSE/DMEPA/CDER/FDA
Jo Wyeth, PharmD, OSE/DMEPA/CDER/FDA

28. Renal Impairment in New Drug Development

Kathy Giacomini, PhD (UCSF)

Timothy Meyer, MD (Stanford)

Ruth Barratt, PhD, DVM, CDER/FDA
Lei Zhang, PhD, CDER/FDA
Shiew Mei Huang, PhD, CDER/FDA
Issam Zineh, PharmD, MPH, CDER/FDA
Ming-Liang Tan, PhD, CDER/FDA

29. Improving the Diagnostic Accuracy of ADR Signal Detection

Nigam Shah, MBBS, PhD (Stanford)

Ruth Barratt, PhD, DVM, CDER/FDA
Henry Francis, MD, CDER/FDA
Ana Szarfman, MD, PhD, CDER/FDA
Isaac Chang, MD, PhD, CDRH/FDA
Joseph Tonning, MD, CDER/FDA
Robert Ball, MD, MPH, CDER/FDA
Mitra Rocca, Dipl. Inform. Med., CDER/FDA

30. Single Cell Mass Cytometry Based Assessment of MSCs

Sean Bendall, PhD (Stanford)

Steven Bauer, PhD, CBER/FDA

31. Spinal Orthopedic Device Mechanics

Jeff Lotz, PhD (UCSF)

Anton Dmitriev, PhD, CDRH/FDA
Srinidhi Nagaraja, PhD, CDRH/FDA
Jonathan Peck, MS, CDRH/FDA

32. Methods to Inactivate Pathogens in Blood

Eric Kool, PhD (Stanford)

Jaroslav Vostal, MD, PhD, CBER/FDA
Chintamani Atreya,PhD, CBER/FDA
33. 10. Knowledge Synthesis - Gut Microbiome Peter Turnbaugh, PhD (UCSF)
Roselie Bright, ScD, MS, PMP, OHI/FDA
Elaine Johanson, OHI/FDA

Publications

 

June 1, 2019

In Vitro Models for Thrombogenicity Testing of Blood-Recirculating Medical Devices

Expert Review of Medical Devices

Authors: Sarode DN, Roy S

 

February 17, 2019

Research Projects Supported by the University of California, San Francisco-Stanford Center of Excellence in Regulatory Science and Innovation

Clinical Pharmacology & Therapeutics, Volume 105, Number 4, pp. 815-818, April 2019

Authors: Kathleen M. Giacomini, Lawrence Lin, Russ B. Altman

 

January 20, 2019

Impact of Pharmaceutical Excipients on Oral Drug Absorption: A Focus on Intestinal Drug Transporters

Clinical Pharmacology & Therapeutics, Vol. 105, Number 2, pp. 323-325, February 2019

Authors: Ling Zou, Zhanglin Ni, Eleftheria Tsakalozou, Kathleen M. Giacomini

 

December 7, 2018

PathFX Provides Mechanistic Insights into Drug Efficacy and Safety for Regulatory Review and Therapeutic Development

PLOS Computational Biology, Vol. 14, Issue 12: e.1006614

Authors: Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ Altman

 

September 27, 2018

Data mining of digitized health records in a resource-constrained setting reveals that timely immunophenotyping is associated with improved breast cancer outcomes

BMC Cancer, 2018 18:933

Authors: López-Pineda A, Rodríguez-Moran MF, Álvarez-Aguilar C, Fuentes Valle SM, Acosta-Rosales R, Bhatt AS, Sheth SN, Bustamante CD

 

August 6, 2018

Network Enhancement as a General Method to Denoise Weighted Biological Networks

Nature Communications 9, Article number: 3108 (2018)

Authors: Wang B, Pourshafeie A, Zitnik M, Zhu J, Bustamante CD, Batzoglou S, Leskovec J

 

August, 2018

Machine Learning in Chemoinformatics and Drug Discovery

Drug Dicovery Today, Volume 23, Issue 8, Pages 1538-1546, August 2018

Authors: Lo YC, Rensi SE, Torng W, Altman RB

 

February 2, 2018

Biomarkers: Delivering on the Expectation of Molecularly Driven, Quantitative Health

Experimental Biology Medicine, Vol. 243, Issue 3, pp. 313-322

Authors: Wilson JL, Altman RB

 

January 17, 2018

Chemical Reaction Vector Embeddings: Towards Predicting Drug Metabolism in the Human Gut Microbiome

Pacific Symposium of Biocomputing, Vol. 23, pp. 56-67

Authors: Mallory EK, Acharya A, Rensi SE, Turnbaugh PJ, Bright RA, Altman RB

 

March 21, 2017

Development of an Automated Assessment Tool for MedWatch Reports in the FDA Adverse Event Reporting System

Journal of the American Medical Informatics Association

Authors: Han L, Ball R, Pamer CA, Altman RB, Proestel S

 

March 21, 2017

Mechanical Performance of Cervical Intervertebral Body Fusion Devices: A Systematic Analysis of Data Submitted to the Food and Drug Administration

Journal of Biomechanics, Vol. 54, pp. 26-32

Authors: Peck JH, Sing DC, Nagaraja S, Peck DG, Lotz JC, Dmitriev AE

 

October 27, 2016

From the Patient's Point of View, How Should Minimally Invasive Glaucoma Surgeries be Evaluated?

American Journal of Ophthalmology, Vol. 172, pp. 12-14

Authors: Qui N. Cui, Kuldev Singh, George L. Spaeth

 

August 24, 2016

A Molecular Basis for Innovation in Drug Excipients

Clinical Pharmacology & Therapeutics, Vol. 101, Issue 3, pp. 320-323

Authors: John J. Irwin, Joshua Pottel, Ling Zou, Hong Wen, Susan Zuk, Xinyuan Zhang, Teague Sterling, Brian K., Shoichet, Robert Lionberger, Kathleen M. Giacomini

 

July 28, 2016

Identification and Quantitative Assessment of Uremic Solutes as Inhibitors of Renal Organic Anion Transporters, OAT1 and OAT3

Molecular Pharmaceutics, Vol. 12, Issue 9, pp. 3130-40

Authors: Chia-Hsiang Hsueh, Kenta Yoshida, Ping Zhao, Timothy W Meyer, Lei Zhang, Shiew-Mei Huang, Kathleen M Giacomini

 

April 20, 2016

A Research Roadmap for Next Generation Sequencing Informatics

Science Translational Medicine, Vol. 8, Issue 335, pp. 10

Authors: Altman RB, Prabhu S, Sidow A, Zook JM, Goldfeder R, Litwack D, Ashley E, Asimenos G, Bustamante DC, Donigan K, Giacomini KM, Johansen E, Khuri N, Lee E, Liang XS, Salit M, Serang O, Tezak Z, Wall DP, Mansfield E, Kass-Hout T

 

November 25, 2015

Unmet Needs: Research Helps Regulators do their Jobs

Science Translational Medicine, Vol. 7, Issue 315, pp. 22

Authors: Altman RB, Khuri N, Salit M, Giacomini KM

 

July 31, 2015

A Method for Systematic Discovery of Adverse Drug Events from Clinical Notes

Journal of the American Medical Informatics Association, Vol. 22, Issue 6, pp. 1196-204

Authors: Wang G, Jung K, Winnenberg R, Shah NIH