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.

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 Number U01FD004979/U01FD005978from 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."

 

Pilot Research Projects

 

Pilot 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. Next Generation Text Analytics for FDA-Relevant Text Mining

Russ Altman, MD, PhD (Stanford)

Roselie Bright, ScD, MS, PMP, OHI/FDA

Larry Callahan, PhD, JD, OHI/FDA

Elaine Johanson, OHI/FDA

Frank Switzer, PhD, OHI/FDA

4. 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

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

Laszio Urban, MD, PhD, Novartis (in kind)

6. 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

7. 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

8. Patient Reported Outcomes for Minimally Invasive Glaucoma Surgery

Kuldev Singh, MD (Stanford)

Tianjing Li, MD, PhD (JHU)

Kay Dickerson, PhD (JHU)

Malvina Eydelman, MD, CDRH/FDA

Michelle Tarver, MD, PhD, CDRH/FDA

Leslie Wilson, PhD (UCSF)

Heather Benz, PhD, CDRH/FDA

Eugene Civilico, PhD, CDRH/FDA

Martin Ho, MSc, CDRH/FDA

Telba Irony, PhD, CBER/FDA

Xuefeng Li, PhD, CDRH/FDA

Anindita Saha, CDRH/FDA

10. 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

11. Use of NLP/Machine Learning to Analyze Medication Error Reports

Russ Altman, MD, PhD (Stanford)

Sonja Brajovic, MD, CDER/FDA

Todd Bridges, RPh, CDER/FDA

Carol Pamer, RPh, MPH, CDER/FDA

Jim Schlick, RPh, MBA, CDER/FDA

Jo Wyeth, PharmD, CDER/FDA

12. Knowledge Synthesis - Gut Microbiome

Peter Turnbaugh, PhD (UCSF)

Roselie Bright, ScD, MS, PMP, OHI/FDA

Elaine Johanson, OHI/FDA

13. 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

14. Predicting Pediatric Dosing for Medical Countermeasures

Kathy Giacomini, PhD (UCSF)

Kathy Cheung, PharmD (UCSF)

Shiew Mei Huang, PhD, CDER/FDA

15. 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

16. Methods to Inactivate Pathogens in Blood

Eric Kool, PhD (Stanford)

Jaroslav Vostal, MD, PhD, CBER/FDA

Chintamani Atreya, PhD, CBER/FDA

17. 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

18. Catalyzing the FDA Pre-Certification Program: The Accelerated Digital Clinical Ecosystem (ADviCE)

Andrew Auerbach, MD (UCSF)

Bakul Patel, MS, MBA, CDRH/FDA

Marisa Cruz, MD, CDRH/FDA

19. 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

20. 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

Brittany Caldwell, PhD, CDRH/FDA

Martin Ho, CDRH/FDA

Annie Saha, CDRH/FDA

Michelle Tarver, MD PhD, CDRH/FDA

21. 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

Brittany Caldwell, PhD, CDRH/FDA

Martin Ho, CDRH/FDA

Vasum Peiris, MD, MPH, CDRH/FDA

Annie Saha, CDRH/FDA

Michelle Tarver, MD, PhD, CDRH/FDA

22. Health Citizen Hospital Pilot

Ida Sim, PhD (UCSF)

Anne Hammer, CDRH/FDA

Elaine Johanson, OHI/FDA

Mimi Nguyen, CDRH/FDA

Annie Saha, CDRH/FDA

Michelle Tarver, MD PhD, CDRH/FDA

23. 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

Research Pilot Projects (Completed)

Research pilot project name                                                                                                              
Lead scientist at UCSF & Stanford University                       

FDA collaborators​/​non-federal entities collaboratorS

Russ Altman, MD, PhD (Stanford)

Steve Anderson, PhD, MPP, CBER/FDA

Robert Ball, MD, MPH, CDER/FDA

Ruth Barratt, PhD, DVM, CDER/FDA

Carol Pamer, RPh, MPH, CDER/FDA

Scott Proestel, MD, CDER/FDA

Mitra Rocca, Dipl. Inform. Med., CDER/FDA

25Precision Medicine Initiative

Russ Altman, MD, PhD (Stanford)

Elaine Johanson, OHI/FDA

26Renal Impairment in New Drug Development

Kathy Giacomini, PhD (UCSF)

Timothy Meyer, MD (Stanford)

Ruth Barratt, PhD, DVM, CDER/FDA

Shiew Mei Huang, PhD, CDER/FDA

Ming-Liang Tan, PhD, CDER/FDA

Lei Zhang, PhD, CDER/FDA

Issam Zineh, PharmD, MPH, CDER/FDA

27. Improving the Diagnostic Accuracy of ADR Signal Detection

Nigam Shah, MBBS, PhD (Stanford)

Robert Ball, MD, MPH, CDER/FDA

Ruth Barratt, PhD, DVM, CDER/FDA

Isaac Chang, MD, PhD, CDRH/FDA

Henry Francis, MD, CDER/FDA

Mitra Rocca, Dipl. Inform. Med., CDER/FDA

Ana Szarfman, MD, PhD, CDER/FDA

Joseph Tonning, MD, CDER/FDA

28. Single Cell Mass Cytometry Based Assessment of MSCs

Sean Bendall, PhD (Stanford)

Steven Bauer, PhD, CBER/FDA
29. Spinal Orthopedic Device Mechanics Jeff Lotz, PhD (UCSF)

Anton Dmitriev, PhD, CDRH/FDA

Srinidhi Nagaraja, PhD, CDRH/FDA

Jonathan Peck, MS, CDRH/FDA

 

Publications

 

February 2, 2018
Experimental Biology Medicine, Vol. 243, Issue 3, pp. 313-322
Authors: Wilson JL, Altman RB
 
January 17, 2018
Proceedings of the 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

Journal of the American Medical Informatics Association

Authors: Han L, Ball R, Pamer CA, Altman RB, Proestel S
 
March 21, 2017
Journal of Biomechanics, Vol. 54, pp. 26-32
Authors: Peck JH, Sing DC, Nagaraja S, Peck DG, Lotz JC, Dmitriev AE
 
October 27, 2016
American Journal of Ophthalmology, Vol. 172, pp. 12-14
Authors: Qui N. Cui, Kuldev Singh, George L. Spaeth
 
August 24, 2016
Clinical Pharmacology and 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
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
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
Science Translational Medicine, Vol. 7, Issue 315, pp. 22
Authors: Altman RB, Khuri N, Salit M, Giacomini KM
 
July 31, 2015
Journal of the American Medical Informatics Association, Vol. 22, Issue 6, pp. 1196-204
Authors: Wang G, Jung K, Winnenberg R, Shah NIH