UCSF

Research

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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.

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 - Acknowledgment of Funding Source(s). Please make sure to acknowledge the funding source(s) 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.

In your statement also include: a. the percentage and dollar amount of the total costs of the program or project funded with federal money; and b. the percentage and dollar amount of the total costs of the project or program funded by non-governmental source.

 

Project List

UCSF-Stanford CERSI has supported 68 collaborative research projects between UCSF/Stanford faculty and FDA scientists.  You can download a list of PDF iconUCSF-Stanford CERSI Research Projects.

Click on a category below to jump to those projects.

 

Biologics Research Projects
Research Project Title UCSF/Stanford Principal Investigator FDA Collaborators
Using the University of California Clinical Data Warehouse to Evaluate the Safety and Efficacy of Biologics, including Blood Transfusions, Vaccines, CAR-T cell Therapies, and other CBER Regulated Products Atul Butte, MD, PhD (UCSF)

Barbee Whitaker, PhD (CBER/FDA)
Steven Anderson, PhD, MPP (CBER/FDA)
Artur Belov, PhD (CBER/FDA)
Hui-Lee Wong, PhD (CBER/FDA)

Isolating Exosomes using a novel ExoTIC device from HIV-infected Patient Plasma and Saliva Utkan Demirci, PhD (Stanford) Indira Hewlett, PhD (CBER/FDA)
Mohan Haleyurgirisetty, PhD (CBER/FDA)
Jiangqin Zhao, PhD (CBER/FDA)
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)
Development of New and Innovative Methods for Automated Reporting for CBER-Regulated Biological Products Tina Hernandez-Boussard, PhD, MPH, MS (Stanford)

Barbee Whitaker, PhD (CBER/FDA)
Steven Anderson, PhD, MPP (CBER/FDA)
Artur Belov, PhD (CBER/FDA)
Hui-Lee Wong, PhD (CBER/FDA)

Improving Adverse Event Detection Related to Biologic Immunosuppressant Use – A Pilot Study of the BERT Deep Learning Model Adapted to Real-world Clinical Notes Vivek Rudrapatna, MD, PhD (UCSF)
Atul Butte, MD, PhD (UCSF)
Ludwig, Dana, MD (UCSF)
Samer El-Kamary, MD, MPH (CDER/FDA)
Jawahar Tiwari, PhD (CBER/FDA)
Tissue Chips for Multipotent Stromal Cell Manufacturing Ngan Huang, PhD (Stanford) Kyung Sung, PhD (CBER/FDA)
Development of New Machine Learning Algorithms to Quantify Treatment Effectiveness and Adverse Outcomes (Completed) James Zou, PhD (Stanford)

Steven Anderson, PhD, MPP (CBER/FDA)
Barbee Whitaker, PhD (CBER/FDA)
Alan Williams, PhD (CBER/FDA)
Gregory Pappas, MD, PhD (CBER/FDA)
Angela Moy (CBER/FDA)

Methods to Inactivate Pathogens in Blood (Completed)

Eric Kool, PhD (Stanford) Jaroslav Vostal, MD, PhD (CBER/FDA)
Chintamani Atreya,PhD (CBER/FDA)
Single Cell Mass Cytometry Based Assessment of MSCs (Completed) Sean Bendall, PhD (Stanford) Steven Bauer, PhD (CBER/FDA)

 

Drug Research Projects
Research Project Title UCSF/Stanford Principal Investigator FDA Collaborators
The Effect of Excipients on the Oral Absorption of Fexofenadine in Humans Kathy Giacomini, PhD (UCSF) Lei Zhang, PhD (CDER/FDA)
Eleftheria Tsakalozou, PhD (CDER/FDA)
OneSource Phase 2 Laura Esserman, MD, MBA (UCSF) Mitra Rocca, Dipl Inform Med (CDER/FDA)
Jacqueline Corrigan-Curay, JD, MD (CDER/FDA)
Dianne Paraoan (CDER/FDA)
Frank Weichold, MD, PhD (ORSI/FDA)
Paul Kluetz, MD (OCE/FDA)
Gideon (Scott) Gordon, PhD (CDER/FDA)
Identification and Validation of Biomarkers for Breast Cancer Resistance Protein (BCRP) Kathy Giacomini, PhD (UCSF) Shiew Mei Huang, PhD (CDER/FDA)
Qi Liu, PhD (CDER/FDA)
Lei Zhang, PhD (CDER/FDA)
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)
Effects of Excipients in Generic Drugs 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)
Chemoinformatic Tools to Predict the Effects of Excipients in Generic Drugs (Completed)

Excipient Browser (a 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)
OneSource: e-Course Checklist (Completed) Laura Esserman, MD, MBA (UCSF) Mitra Rocca, Dipl Inform Med (CDER/FDA)
Ronald Fitzmartin, PhD, MBA (CDER/FDA)
Fatima Frye (CDER/FDA)
MaryAnne Slack (CDER/FDA)
Developing an Operational Framework for Defining the Strength of Evidence in Therapeutic Development (Completed) Steve Goodman, MD, MHS, PhD (Stanford) Telba Irony, PhD (CBER/FDA)
Tom Permutt, PhD (CDER/FDA)
Estelle Russek-Cohen, PhD (CDER/FDA)
Gut Microbiome: Knowledge Synthesis (Completed) Peter Turnbaugh, PhD (UCSF) Roselie Bright, ScD, MS, PMP (OHI/FDA)
Elaine Johanson (OHI/FDA)
Healthy Citizen Hospital Pilot (Completed) Ida Sim, MD, PhD (UCSF) Elaine Johanson (OHI/FDA)
Ameeta Parekh, PhD (CDER/FDA)
Improving Efficiency and Rigor of Pharmacovigilance at FDA (Completed) 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)
Use of natural language processing/machine learning to analyze medication error reports and improve the quality of data submitted to the FDA Adverse Event Reporting System (FAERS) (Completed) 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)
Improving the Diagnostic Accuracy of ADR Signal Detection by Combining Signals from Spontaneous Reports and Electronic Health Records (Completed) 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)
Data Science Methods for Post-Marketing Surveillance of AI Diagnostic Tools and Algorithm-Based Therapeutics (Completed) Daniel Rubin, MD, MS (Stanford) Qi Liu, PhD, MStat, FCP (CDER/FDA)
Yaning Wang, PhD, Mstat (CDER/FDA)
Hao Zhu, PhD, Mstat (CDER/FDA)
M. Khair ElZarrad PHD, MPH (CDER/FDA)
Matthew Diamond, MD, PhD (CDRH/FDA)

 

Medical Device Research Projects
Research Project Title UCSF/Stanford Principal Investigator FDA Collaborators
Development of Thrombogenicity Testing Methods for Medical Devices with Large Blood-Contacting Surfaces Shuvo Roy, PhD (UCSF) Qijin Lu, PhD (CDRH/FDA)
Megan Jamiolkowski, PhD (CDRH/FDA)
Richard Malinauskas, PhD (CDRH/FDA)
Safe Algorithmic Change Protocols for Modifications to AI/ML-Based Software as a Medical Device Jean Feng, PhD (UCSF) Berkman Sahiner, PhD (CDRH/FDA)
Alexej Gossmann, PhD, CDRH/FDA)
Identification of Pacemaker and Implantable Cardioverter-Defibrillator Lead Failure Using Remote Monitoring Data Sanket Dhruva, MD, MHS (UCSF) Hetal Odobasic, MS (CDRH/FDA)
Li Wang, PhD, MBA, MS (CDRH/FDA)
Jacqueline M. Major, PhD (CDRH/FDA)
The Digital Variome: Understanding the Implications of Digital Tools on Health Andrew Auerbach, MD (UCSF)

Leeda Rashid, MD, MPH (CDRH/FDA)
Anindita Saha, (CDRH/FDA) 
Bakul Patel, MS, MBA (CDRH/FDA) 
Cathy Bahr (CDRH/FDA)
Vinay Pai, PhD (CDRH/FDA)
Arti Tandon, PhD (CDRH/FDA)
JiPing Chen, MD, PhD (CDRH/FDA) 
Charles Yongpravat (CDRH/FDA)
Aubrey Shick, MS (CDRH/FDA) 

Developing Frameworks and Tools for Integration of Digital Health Tools into Clinical Practice Andrew Auerbach, MD (UCSF)

Bakul Patel, MS, MBA (CDRH/FDA)
Vinay Pai, PhD (CDRH/FDA)

Post-Market Evaluation of Smartwatch Cardiovascular Notifications Mintu Turakhia, MD, MAS (Stanford) Anindita Saha (CDRH/FDA)
Bakul Patel, MS, MBA (CDRH/FDA) 
MiRa Jacobs, PhD (CDRH/FDA) 
Vinay Pai, PhD (CDRH/FDA) 
Aubrey Shick, MS (CDRH/FDA) 
Gloria Nyankima, PhD, (CDRH/FDA)
Jessica Paulsen (CDRH/FDA) 
Kan Fang, MD (CDRH/FDA)
Charlie Yongpravat (CDRH/FDA)
Advancing Computational Modeling in the Regulatory Evaluation of Spinal Fusion Cages (Completed) Jeffrey Lotz, PhD (UCSF) Anton Dmitriev, PhD (CDRH/FDA)
Andrew Baumann, PhD (CDRH/FDA)
Spinal Orthopedic Device Mechanics (Completed) Jeffrey Lotz, PhD (UCSF) Anton Dmitriev, PhD (CDRH/FDA)
Srinidhi Nagaraja, PhD (CDRH/FDA)
Jonathan Peck, MS (CDRH/FDA)
Development and Evaluation of Computational Test Methods Leveraging Real-world and Simulated Datasets for Predictive Medical Device Alarm Algorithms (Completed) Xiao Hu, PhD (UCSF) Christopher Scully, PhD (CDRH/FDA)

 

Patient Focused Research Projects
Research Project Title UCSF/Stanford Principal Investigator FDA Collaborators
Patient Reported Outcomes for Minimally Invasive Glaucoma Surgery Kuldev Singh, MD, MBA (Stanford) Malvina Eydelman, MD (CDRH/FDA)
Michelle Tarver, MD, PhD (CDRH/FDA)
Characterizing Risk-Benefit Tradeoff in Opioid-based Chronic Pain Treatment Sean Mackey, MD, PhD (Stanford)

Michelle Tarver, MD, PhD (CDRH/FDA)
Anindita Saha (CDRH/FDA)
David Gebben, PhD (CDRH/FDA)
Heather Benz, PhD (CDRH/FDA)

Adapting a Measure of Heart Failure to an Adolescent Population Christopher Almond, MD, MPH (Stanford) Fraser Bocell, PhD (CDRH/FDA)
Vasum Peiris, MD, MPH (CDRH/FDA)
Michelle Tarver, MD, PhD (CDRH/FDA)
Brittany Caldwell, PhD (CDRH/FDA)
Anindita Saha (CDRH/FDA)
Martin Ho, MSc (CDRH/FDA)
Assessment of Patient Tolerance for Risk Associated with High Intensity Focused Ultrasound (HIFU) for the Ablation of Prostate Tissue Geoffrey Sonn, MD (Stanford) Charles Viviano, MD, PhD (CDRH/FDA)
David Gebben, PhD (CDRH/FDA)
Olufemi Babalola, MSc, MHS (CDRH/FDA)
Development, Implementation, and Evaluation of an Open Source Software Program to Support Patient-based Estimation of Clinically Meaningful Levels and Change Scores for Patient Reported Outcome Measures Sean Mackey, MD, PhD
(Stanford)
Fraser Bocell, PhD (CDRH/OST/FDA)
Michelle Tarver, MD, PhD (CDRH/FDA)
Allen Chen, PhD (CDRH/FDA)
The Impact of Race and Ethnicity on Responses to Heart Failure Patient-Reported Outcome Measures (Completed) 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)
Annie Saha (CDRH/FDA)
Martin Ho, MSc (CDRH/FDA)
Comparing Qualitative and Quantitative Approaches for Eliciting Patient Preference on Upper Limb Prostheses (Completed) Leslie Wilson, PhD (UCSF) Eugene Civillico, PhD (CDRH/FDA)
Telba Irony, PhD (CBER/FDA)
Xuefeng Li, PhD (CDRH/FDA)
Anindita Saha (CDRH/FDA)
Mapping a Better Approach to Obtaining Pediatric Patient Preferences (Completed) Korey Hood, PhD (Stanford) Heather Benz, PhD (CDRH/FDA)
Martin Ho, MSc (CDRH/FDA)
Vasum Peiris, MD, MPH (CDRH/FDA)
Anindita Saha (CDRH/FDA)

 

Precision Medicine Research Projects

Research Project Title

UCSF/Stanford Principal Investigator

FDA Collaborators​

TOBIAS – A Clinical Decision Support tool to Personalize NGS Diagnostic Test Results based on Genetic Ancestry Snehit Prabhu, PhD (Stanford)

Elaine Johanson (OHI/FDA)
Zivana Tezak, PhD (CDRH/FDA)
Richardae Araojo, PharmD (OMHHE/FDA)
Christine Lee, PharmD, PhD (OMHHE/FDA)

HYDRA – A Federated Computational Infrastructure to Enable Inclusive, Large-scale Precision Medicine Studies Snehit Prabhu, PhD (Stanford)

Elaine Johanson (OHI/FDA)
Zivana Tezak, PhD (CDRH/FDA)
Richardae Araojo, PharmD (OMHHE/FDA)
Christine Lee, PharmD, PhD (OMHHE/FDA)

Identifying Genetic Mechanisms of Doxorubicin-Induced Cardiotoxicity Joseph Wu, MD, PhD (Stanford) Bridget Nugent, PhD (OWH/FDA)
Alexandre Ribeiro, PhD (CDER/DARS/FDA)
HIV Genomic Surveillance in Cameroon by Next-Generation Sequencing Charles Chiu, MD, PhD (UCSF) Indira Hewlett, PhD (CBER/FDA)
Assessing the Potential for Patient-Specific and Genome Edited Induced Pluripotent Cell-Based Models to Streamline Clinical Drug Development for Rare Diseases Joseph Wu, PhD (Stanford) David Strauss, MD, PhD (CDER/OTS/OCP/FDA)
Alexandre Ribeiro, PhD (CDER/FDA)
Rodney Rouse, DVM (CDER/OTS/OCP/FDA)
Kevin Ford, PhD (CDER/FDA)
Role of Ancestry in Genetic Diagnostics (Completed) 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)
Causes of Real-Life NGS Variability (Completed) Dmitri Petrov, PhD (Stanford) Elaine Johanson (OHI/FDA)
Network Integration for Precision Medicine Drug Models (Completed)

Russ Altman, MD, PhD (Stanford)

Michael Pacanowski, PharmD, MPH (CDER/FDA)
Anuradha Ramamoorthy, PhD (CDER/FDA)
Oluseyi Adeniyi, PhD (CDER/FDA)
Precision Medicine Initiative (Completed) Russ Altman, MD, PhD (Stanford) Elaine Johanson (OHI/FDA)
Next Generation Text Analytics for FDA-Relevant Text Mining (Completed) Russ Altman, MD, PhD (Stanford) Roselie Bright, ScD (OHI/FDA)
Larry Callahan, PhD (OHI/FDA)
Elaine Johanson (OHI/FDA)
Frank Switzer, PhD (OHI/FDA)
Evaluation of the impact of Genetic Variability on Drug Target Interactions using Structural Bioinformatics (Completed) Russ Altman, MD, PhD (Stanford)

Michael Pacanowski, PharmD, MPH (CDER/FDA)
Oluseyi Adeniyi, PhD (CDER/FDA)
Paula Hyland, PhD (CDER/FDA)
Ellis Christopher, PhD (CDER/FDA)
Rosane Charlab Orbach, PhD (CDER/FDA)
Robert Schuck, PhD (CDER/FDA)

 

Special Populations Research Projects

Research Project Title

UCSF/Stanford Principal Investigator

FDA Collaborators

Predicting Pediatric Dosing for Medical Countermeasures Kathy Giacomini, PhD (UCSF)

Shiew Mei Huang, PhD (CDER/FDA)
Lei Zhang, PhD (CDER/FDA)

Renal Impairment in New Drug Development: Phase II Timothy Meyer, MD (Stanford) Shiew Mei Huang, PhD (CDER/FDA)
Lei Zhang, PhD (CDER/FDA)
Qi Liu, PhD (CDER/FDA)
Characterizing Population-Specific Clinical Asthma Profiles Esteban Burchard, MD, MPH (UCSF) Richardae Araojo, PharmD (OMHHE/FDA)
Usability Testing of Virtual Reality for Opioid-Sparing Pain Management Among Diverse Patients Urmimala Sarkar, MD, MPH (UCSF)
Courtney Lyles, PhD (UCSF)
Richardae Araojo, PharmD, MS (OMHHE/FDA)
Christine Lee, PharmD, PhD (OMHHE/FDA)
Michelle Tarver, MD, PhD (CDRH/FDA)
Safer Labeling of Pediatric Medications: Reducing Literacy-related Health Disparities among Chronically Ill Adolescents Lee Sanders, MD (Stanford)
Bonnie Halpern-Felsher, PhD (Stanford)
Christine Lee, PharmD, PhD (OMHHE/FDA)
Richardae Araojo, PharmD, MS (OMHHE/FDA)
Shelly Harris, MPH (CDER/FDA)
Grace Jones, PharmD (CDER/FDA)
Martin Mendoza, PhD (OMHHE/FDA)
Amanda Pike-McCrudden, MAA (CDER/FDA)
Lee Zwanziger (OC/FDA)
Creating a Framework for a National Adaptive Platform Trial to Evaluate Pediatric Medical Devices Christopher Almond, MD, MPH (Stanford) Vasum Peiris, MD, MPH (CDRH/FDA)
Brittany Caldwell, PhD (CDRH/FDA)
The MUM study: MUltimorbidity and Medications: the unheard perspective of older adults Janice Schwartz, MD (UCSF) Qi Liu, PhD., M.Stat (CDER/OCP/FDA)
Shiew-Mei Huang, PhD (CDER/OCP/OTS/FDA)
Renal Impairment in New Drug Development (Completed)

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)
Comprehensive Assessment of Sex Differential Smoking related Effects in Publicly Available Gene Expression Data (Completed) Russ Altman, MD, PhD (Stanford) Bridget Nugent, PhD (OWH/FDA)
Patricia Bradfield (OWH/FDA)
Kaveeta Vasisht, MD, PharmD (OWH/FDA)
Ryan Conville (OWH/FDA)
Jonathan Kwan, MS (OTP/FDA)

 

COVID-19 Research Projects

Research Project Title

UCSF/Stanford Principal Investigator

FDA Collaborators

A Rapid Query Model to Address Prioritized COVID-19 Questions Using EHR Data Atul Butte, MD, PhD (UCSF) Amy Abernethy, MD, PhD (OC/FDA)
OneSource: SMART on FHIR for I-SPY COVID-19 Trial Laura Esserman, MD, MBA (UCSF) Mitra Rocca, Dipl. Inform. Med. (CDER/FDA)
Jacqueline Corrigan-Curay, JD, MD (CDER/FDA)
Dianne Paraoan (CDER/FDA)
Vishal Bhatnagar, MD (OCE/FDA)
Frank Weichold, MD, PhD (ORSI/FDA)
OneSource Phase III: Demonstration of EHR/eCRF Integration in the COVID-19 Critical Care Environment Laura Esserman, MD, MBA (UCSF) Mitra Rocca, Dipl. Inform. Med. (CDER/FDA)
Jacqueline Corrigan-Curay, JD, MD (CDER/FDA)
Dianne Paraoan (CDER/FDA)
Vishal Bhatnagar, MD (OCE/FDA)
Frank Weichold, MD, PhD (ORSI/FDA)
Learning Real-World Sex-Specific Clinical Factors Influencing the Susceptibility to Infection, Immune Response, Treatment Utilization and Outcomes Among Individuals Infected with SARS-CoV-2 Infection Rohit Vashisht, PhD
(UCSF)
Bridget Nugent, PhD (OWH/FDA)
Kaveeta Vasisht, MD, PharmD (OWH/FDA)
Susan Bersoff-Matcha, MD (OWH/FDA)
Osman Yogurtcu, PhD (CBER/FDA)
Yong Ma, PhD (CDER/FDA)
Andrew Giffin, PhD (CDER/FDA) 
Shuang (Sarah) Zhou, PhD (CDER/FDA)
Real-World Population Characteristics, Safety and Effectiveness of COVID-19 Vaccines Atul Butte, MD, PhD (UCSF) Barbee Whitaker, PhD (CBER/OBE/FDA)
Artur Belov, PhD (CBER/OBE/FDA)
Hussein Ezzeldin, PhD (CBER/OBE/FDA) 
Steve Anderson, PhD (CBER/OBE/FDA) 
Jane Mutanga, PhD (CBER/FDA) 

 

Publications

 

July 29, 2020

Scientific Considerations for Global Drug Development

Science Translational Medicine, Vol 12, Issue 554

Authors: Ling Zou, Jennifer L Wilson, Kit Wun Kathy Cheung, Lawrence Lin, Elizabeth A E Green, Analia I Porras, Ling Zou, David Mukanga, Paul A Akpa, Delese Mimi Darko, Rae Yuan, Sheng Ding, Wiltshire C N Johnson, Howard A Lee, Emer Cooke, Carl C Peck, Steven E Kern, Dan Hartman, Yoshikazu Hayashi, Peter W Marks, Russ B Altman, Murray M Lumpkin, Kathleen M Giacomini, Terrence F Blaschke

July 24, 2020

The Activities of Drug Inactive Ingredients on Biological Targets

Science, Vol. 369, Issue 6502, pp. 403-413

Authors: Joshua Pottel, Duncan Armstrong, Ling Zou, Alexander Fekete, Xi-Ping Huang, Hayarpi Torosyan, Dallas Bednarczyk, Steven Whitebread, Barun Bhhatarai, Guiqing Liang, Hong Jin, Nassir Ghaemi, Samuel Slocum, Katalin V. Lukacs, John J. Irwin, Ellen L. Berg, Kathleen M. Giacomini, Bryan L. Roth, Brian K. Shoichet, Laszlo Urban

July 7, 2020

Bacterial Metabolism Rescues the Inhibition of Intestinal Drug Absorption by Food and Drug Additives

PNAS , June 22, 2020

Authors: Ling Zou, Peter Spanogiannopoulos, Lindsey M Pieper, Huan-Chieh Chien, Wenlong Cai, Natalia Khuri, Joshua Pottel, Bianca Vora, Zhanglin Ni, Eleftheria Tsakalozou, Wenjun Zhang, Brian K Shoichet, Kathleen M Giacomini, Peter J Turnbaugh

July 3, 2020

Effects of Nicotine on the Translation of Stem Cell Therapy

Regenerative Medicine, Vol. 15, No. 5

Authors: Chan AH, Huang NF

May 27, 2020

Extracting Chemical Reactions from Text using Snorkel

BMC Bioinformatics 2020, Article number: 217, Vol. 21

Authors: Mallory EK, de Rochemonteix M, Ratner A, Acharya A, Re C, Bright RA, Altman RB

February 10, 2020

Interactions of Oral Molecular Excipients with Breast Cancer Resistance Protein, BCRP

Molecular Pharmaceutics 2020, 17, 3,  pp. 748-756

Authors: Zou L, Pottel J, Khuri N, Ngo HX, Ni Z, Tsakalozou E, Warren MS, Huang Y, Shoichet BK, Giacomini KM

January 2020

The Patient Perspective: Putting the Patient at the Center of the Translational Innovation Process

The Journal of Clinical Pharmacology, Vol.107, Number 1, pp. 82-84

Authors: Wilson L, Lin L, Singh K.

November 26, 2019

Patient-Reported Outcomes Measures and Patient Preferences for Minimally Invasive Glaucoma Surgical Devices

Eye, Volume 34, pp. 205-210, 2020

Authors: Tianjing Li, T. Le, Ronald D. Hays, Qi N. Cui, Malvina Eydelman, George Spaeth, Michelle E. Tarver & Kuldev Singh

September 10, 2019

Incorporating Ontogeny in Physiologically Based Pharmacokinetic Modeling to Improve Pediatric Drug Development: What We Know About Developmental Changes in Membrane Transporters

The Journal of Clinical Pharmacology, Vol 59, Number: S1 2019, pp. S56-S69

Authors: Cheung KWK, van Groen BD, Burckart GJ, Zhang L, de Wildt SN, Huang SM

June 1, 2019

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

Expert Review of Medical Devices, Vol. 16, 2019 - Issue 7

Authors: Sarode DN, Roy S

May 25, 2019

A Comprehensive Analysis of Ontogeny of Renal Drug Transporters: mRNA Analyses, Quantitative Proteomics, and Localization

Clinical Pharmacology & Therapeutics, Vol. 106, Number 5, November 2019

Authors: Cheung KWK, van Groen BD, Spaans E, van Borselen MD, de Bruijn ACJM, Simons-Oosterhuis Y, Tibboel D, Samsom JN, Verdijk RM, Smeets B, Zhang L, Huang SM, Giacomini KM, de Wildt SN

May 22, 2019

PathFXweb: A Web Application for Identifying Drug Safety and Efficacy Phenotypes

Bioinformatics, Vol. 35, Issue 21, 1 November 2019, pp. 4504–4506​

Authors: Jennifer L Wilson, Mike Wong, Ajinkya Chalke, Nicholas Stepanov, Dragutin Petkovic, Russ B Altman

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, Vol. 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, Vol. 23, Issue 8, pp. 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