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. 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.

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.

We especially encourage UCSF investigators working with clinical trials to utilize the UCSF Research Action Group for Equity (RAGE) program, which provides support and infrastructure for UCSF researchers to diversify their study populations. RAGE provides consultations on how to partner directly with special populations to remove barriers and increase research participation, and can also help with recruitment support.

 


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 Number U01 FD004979 / U01 FD005978 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 76 collaborative research projects between UCSF/Stanford faculty and FDA scientists.

Click on a category below to jump to those projects.

 

Plain Language Summaries for CERSI Projects can be found on the FDA CERSI Website.


Biologics Research Projects

Whole exome sequencing in patients on immune checkpoint inhibitors to risk stratify for treatment response and immune related adverse events

CERSI Principal Investigator: Elad Ziv, MD (UCSF)

FDA Collaborators: Marc Theoret (OCE/FDA), Julie Schneider (OCE/FDA), Wenming Xiao (CDER/FDA), Maitreyee Hazarika (CDER/FDA)

Project #75 [ACTIVE]

Improving Adverse Event Detection Related to Biologic Immunosuppressant Use – A Pilot Study of the BERT Deep Learning Model Adapted to Real-world Clinical Notes

CERSI Principal Investigators: Vivek Rudrapatna, MD, PhD (UCSF), Atul Butte, MD, PhD (UCSF), Ludwig, Dana, MD (UCSF)

FDA Collaborators: Samer El-Kamary, MD, MPH (CDER/FDA), Jawahar Tiwari, PhD (CBER/FDA)

Project #60 [ACTIVE]

Plain Language Summary

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

CERSI Principal Investigator: Atul Butte, MD, PhD (UCSF)

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

Project #41 [ACTIVE]

Plain Language Summary

Development of New and Innovative Methods for Automated Reporting for CBER-Regulated Biological Products

CERSI Principal Investigator: Tina Hernandez-Boussard, PhD, MPH, MS (Stanford)

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

Project #38 [ACTIVE]

Isolating Exosomes using a novel ExoTIC device from HIV-infected Patient Plasma and Saliva

CERSI Principal Investigator: Utkan Demirci, PhD (Stanford)

FDA Collaborators: Indira Hewlett, PhD (CBER/FDA), Mohan Haleyurgirisetty, PhD (CBER/FDA), Jiangqin Zhao, PhD (CBER/FDA)

Project #33 [ACTIVE]

Tissue Chips for Multipotent Stromal Cell Manufacturing

CERSI Principal Investigator: Ngan Huang, PhD (Stanford)

FDA Collaborators: Kyung Sung, PhD (CBER/FDA)

Project #32 [ACTIVE]

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

CERSI Principal Investigator: Matthew Porteus, MD, PhD (Stanford)

FDA Collaborators: Zhaohui Ye, PhD (CBER/FDA)

Project #27 [ACTIVE]

Development of New Machine Learning Algorithms to Quantify Treatment Effectiveness and Adverse Outcomes

CERSI Principal Investigator: James Zou, PhD (Stanford)

FDA Collaborators: 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)

Project #39 [COMPLETE]

Methods to Inactivate Pathogens in Blood

CERSI Principal Investigator: Eric Kool, PhD (Stanford)

FDA Collaborators: Jaroslav Vostal, MD, PhD (CBER/FDA), Chintamani Atreya,PhD (CBER/FDA)

Project #22 [COMPLETE]

Single Cell Mass Cytometry Based Assessment of MSCs

CERSI Principal Investigator: Sean Bendall, PhD (Stanford)

FDA Collaborators: Steven Bauer, PhD (CBER/FDA)

Project #7 [COMPLETE]


Drugs Research Projects

Effects of Antioxidants in Drugs Products on Intestinal Drug Transporters

CERSI Principal Investigators: Sook Wah Yee, PhD (UCSF), Deanna Kroetz, PhD (UCSF) (Co-PI)

FDA Collaborators: Liang Zhao, PhD (CDER/OGD/FDA), Lei Zhang, PhD (CDER/OGD/FDA), Khondoker Alam, PhD (CDER/OGD/FDA)

Project #69 [ACTIVE]

The Effect of Excipients on the Oral Absorption of Fexofenadine in Humans

CERSI Principal Investigator: Deanna Kroetz, PhD (UCSF)

FDA Collaborators: Lei Zhang, PhD (CDER/FDA), Eleftheria Tsakalozou, PhD (CDER/FDA)

Project #50 [ACTIVE]

Identification and Validation of Biomarkers for Breast Cancer Resistance Protein (BCRP)

CERSI Principal Investigator: Sook Wah Yee, PhD (UCSF)

FDA Collaborators: Shiew Mei Huang, PhD (CDER/FDA), Qi Liu, PhD (CDER/FDA), Lei Zhang, PhD (CDER/FDA)

Project #47 [ACTIVE]

OneSource Phase 2: Source Data Capture from Electronic Health Records using Standardized Clinical Research Data

CERSI Principal Investigator: Laura Esserman, MD, MBA (UCSF)

FDA Collaborators: 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)

Project #44 [ACTIVE]

Multi-organ Microphysiological Systems for Modeling Clinical Drug Effects

CERSI Principal Investigators: Kevin Healy, PhD (UC Berkeley), Edward Hsiao, MD, PhD (UCSF)

FDA Collaborators: Alexandre Ribeiro, PhD (CDER/FDA), David Strauss, MD, PhD (CDER/FDA)

Project #31 [ACTIVE]

Data Science Methods for Post-Marketing Surveillance of AI Diagnostic Tools and Algorithm-Based Therapeutics

CERSI Principal Investigator: Daniel Rubin, MD, MS (Stanford)

FDA Collaborators: 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)

Project #48 [COMPLETED]

Healthy Citizen Hospital Pilot

CERSI Principal Investigator: Ida Sim, MD, PhD (UCSF)

FDA Collaborators: Elaine Johanson (OHI/FDA), Ameeta Parekh, PhD (CDER/FDA)

Project #30 [COMPLETED]

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

CERSI Principal Investigator: Steve Goodman, MD, MHS, PhD (Stanford)

FDA Collaborators: Telba Irony, PhD (CBER/FDA), Tom Permutt, PhD (CDER/FDA), Estelle Russek-Cohen, PhD (CDER/FDA)

Project #21 [COMPLETED]

Gut Microbiome: Knowledge Synthesis

CERSI Principal Investigator: Peter Turnbaugh, PhD (UCSF)

FDA Collaborators: Roselie Bright, ScD, MS, PMP (OHI/FDA), Elaine Johanson (OHI/FDA)

Project #20 [COMPLETED]

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)

CERSI Principal Investigator: Russ Altman, MD, PhD (Stanford)

FDA Collaborators: 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)

Project #19 [COMPLETED]

Effects of Excipients in Generic Drugs on Intestinal Drug Transporters

CERSI Principal Investigator: Kathy Giacomini, PhD (UCSF)

FDA Collaborators: 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)

Project #15B [COMPLETED]

Plain Language Summary

Chemoinformatic Tools to Predict the Effects of Excipients in Generic Drugs
Excipient Browser (a research tool to help investigate and improve these important substances)
Usage Statistics of Excipient Browser

CERSI Principal Investigator: Brian Shoichet, PhD (UCSF)

FDA Collaborators: 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)

Project #15A [COMPLETED]

Plain Language Summary

OneSource Phase I: Source Data Capture from Electronic Health Records (EHRs) - Using Standardized Clinical Research Data

CERSI Principal Investigator: Laura Esserman, MD, MBA (UCSF)

FDA Collaborators: Mitra Rocca, Dipl Inform Med (CDER/FDA), Ronald Fitzmartin, PhD, MBA (CDER/FDA), Fatima Frye (CDER/FDA), MaryAnne Slack (CDER/FDA)

Project #10 [COMPLETED]

Plain Language Summary

Improving the Diagnostic Accuracy of ADR Signal Detection by Combining Signals from Spontaneous Reports and Electronic Health Records

CERSI Principal Investigator: Nigam Shah, MBBS, PhD (Stanford)

FDA Collaborators: 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)

Project #2 [COMPLETED]

Improving the Efficiency and Rigor of Pharmacovigilance at FDA

CERSI Principal Investigator: Russ Altman, MD, PhD (Stanford)

FDA Collaborators: 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)

Project #1 [COMPLETED]

Plain Language Summary


Medical Devices Research Projects

Prospective Clinical Study to Evaluate the Accuracy of Pulse Oximeters in Pediatric Patients with Increased Skin Pigmentation

CERSI Principal Investigator: Christopher Almond (Stanford), Chandra Ramamoorthy (Stanford)

FDA Collaborators: Nilsa Loyo-Berrios, PhD (CDRH/FDA), Malvina Eydelman, MD (CDRH/FDA), Rebecca Torguson, MPH (CDRH/FDA), Christine Merenda (OMHHE/FDA), Allison O'Neill, PhD (CDRH/FDA), Gene Pennello, PhD (CDRH/FDA), Rebecca Ward, PhD (CDRH/FDA), Vasum Peiris, MD, (CDRH/FDA), Michelle Tarver, MD, PhD (CDRH/FDA), Damia Jackson (CDRH/FDA)

Project #73 [ACTIVE]

Plain Language Summary

Prospective Clinical Study of Pulse Oximeter Errors in Hospitalized Patients

CERSI Principal Investigator: Philip Bickler, MD (UCSF), Michael Lipnick, MD (UCSF)

FDA Collaborators: Nilsa Loyo-Berrios, PhD (CDRH/OPEQ/OCEA/FDA), Malvina Eydelman, MD (CDRH/OPEQ/OHT1/FDA), Rebecca Torguson, MPH (CDRH/OPEQ/OHT1/FDA), Christine Merenda (OMHHE/FDA)

Project #70 [ACTIVE]

Plain Language Summary

Post-Market Evaluation of Smartwatch Cardiovascular Notifications

CERSI Principal Investigator:

FDA Collaborators: 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)

Project #66 [ACTIVE]

The Digital Variome: Understanding the Implications of Digital Tools on Health

CERSI Principal Investigator: Andrew Auerbach, MD (UCSF)

FDA Collaborators: 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)

Project #65 [ACTIVE]

Identification of Pacemaker and Implantable Cardioverter-Defibrillator Lead Failure Using Remote Monitoring Data

CERSI Principal Investigator: Sanket Dhruva, MD, MHS (UCSF)

FDA Collaborators: Hetal Odobasic, MS (CDRH/FDA), Li Wang, PhD, MBA, MS (CDRH/FDA), Jacqueline M. Major, PhD (CDRH/FDA)

Project #59 [ACTIVE]

Safe Algorithmic Change Protocols for Modifications to AI/ML-Based Software as a Medical Device

CERSI Principal Investigator: Jean Feng, PhD (UCSF)

FDA Collaborators: Berkman Sahiner, PhD (CDRH/FDA), Alexej Gossmann, PhD, CDRH/FDA)

Project #58 [ACTIVE]

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

CERSI Principal Investigator: Shuvo Roy, PhD (UCSF)

FDA Collaborators: Qijin Lu, PhD (CDRH/FDA), Megan Jamiolkowski, PhD (CDRH/FDA), Richard Malinauskas, PhD (CDRH/FDA)

Project #25 [ACTIVE]

Advancing Computational Modeling in the Regulatory Evaluation of Spinal Fusion Cages

CERSI Principal Investigator: Jeffrey Lotz, PhD (UCSF)

FDA Collaborators: Anton Dmitriev, PhD (CDRH/FDA), Andrew Baumann, PhD (CDRH/FDA)

Project #35 [COMPLETED]

Development and Evaluation of Computational Test Methods Leveraging Real-world and Simulated Datasets for Predictive Medical Device Alarm Algorithms

CERSI Principal Investigator: Xiao Hu, PhD (UCSF)

FDA Collaborators: Christopher Scully, PhD (CDRH/FDA)

Project #34 [COMPLETED]

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

CERSI Principal Investigator: Andrew Auerbach, MD (UCSF)

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

Project #26 [COMPLETED]

Spinal Orthopedic Device Mechanics

CERSI Principal Investigator: Jeffrey Lotz, PhD (UCSF)

FDA Collaborators: Anton Dmitriev, PhD (CDRH/FDA), Srinidhi Nagaraja, PhD (CDRH/FDA), Jonathan Peck, MS (CDRH/FDA)

Project #8 [COMPLETED]

Plain Language Summary


Patient-Focused Research Projects

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

CERSI Principal Investigator: Sean Mackey, MD, PhD (Stanford)

FDA Collaborators: Fraser Bocell, PhD (CDRH/OST/FDA), Michelle Tarver, MD, PhD (CDRH/FDA), Allen Chen, PhD (CDRH/FDA)

Project #63 [ACTIVE]

Characterizing Risk-Benefit Tradeoff in Opioid-based Chronic Pain Treatment

CERSI Principal Investigator: Sean Mackey, MD, PhD (Stanford)

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

Project #40 [ACTIVE]

Adapting a Measure of Heart Failure to an Adolescent Population

CERSI Principal Investigator: Christopher Almond, MD, MPH (Stanford)

FDA Collaborators: 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)

Project #29 [ACTIVE]

Patient Reported Outcomes for Minimally Invasive Glaucoma Surgery (MIGS)

CERSI Principal Investigator: Kuldev Singh, MD, MBA (Stanford)

FDA Collaborators: Malvina Eydelman, MD (CDRH/FDA) Michelle Tarver, MD, PhD (CDRH/FDA)

Project #14 [ACTIVE]

Plain Language Summary

Assessment of Patient Tolerance for Risk Associated with High Intensity Focused Ultrasound (HIFU) for the Ablation of Prostate Tissue

CERSI Principal Investigator: Geoffrey Sonn, MD (Stanford)

FDA Collaborators: Charles Viviano, MD, PhD (CDRH/FDA), David Gebben, PhD (CDRH/FDA), Olufemi Babalola, MSc, MHS (CDRH/FDA)

Project #51 [COMPLETED]

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

CERSI Principal Investigator: Courtney Lyles, PhD (UCSF), Urmimala Sarkar, MD, MPH (UCSF)

FDA Collaborators: 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)

Project #28 [COMPLETED]

Mapping a Better Approach to Obtaining Pediatric Patient Preferences

CERSI Principal Investigator: Korey Hood, PhD (Stanford)

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

Project #18 [COMPLETED]

Comparing Qualitative and Quantitative Approaches for Eliciting Patient Preference on Upper Limb Prostheses: A Case Study on Innovative Upper Limb Prostheses

CERSI Principal Investigator: Leslie Wilson, PhD (UCSF)

FDA Collaborators: Eugene Civillico, PhD (CDRH/FDA), Telba Irony, PhD (CBER/FDA), Xuefeng Li, PhD (CDRH/FDA), Anindita Saha (CDRH/FDA)

Project #17 [COMPLETED]

Plain Language Summary


Precision Medicine Research Projects

Role of Genomic Ancestry in Tyrosine Kinase Inhibitor-Induced Cardiotoxicity

CERSI Principal Investigator: Joseph Wu, MD, PhD (Stanford)

FDA Collaborators: Laleh Amiri-Kordestani (CDER/FDA), Kevin Ford (CDER/FDA), Margret Merino (CDER/FDA) , Julie Schneider (OCE/FDA)

Project #74 [ACTIVE]

Identify Genotype-Phenotype and Pharmacogenetic Association Using a Population-scale Cellular Platform

CERSI Principal Investigator: Joseph Wu, MD, PhD (Stanford)

FDA Collaborators: David Strauss (CDER/FDA), Kevin Ford (CDER/FDA), Dylan Bruckner (CDER/FDA)

Project #72 [ACTIVE]

Assessing the Potential for Patient-Specific and Genome Edited Induced Pluripotent Cell-Based Models to Streamline Clinical Drug Development for Rare Diseases

CERSI Principal Investigator: Joseph Wu, PhD (Stanford)

FDA Collaborators: 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)

Project #62 [ACTIVE]

Identifying Genetic Mechanisms of Doxorubicin-Induced Cardiotoxicity

CERSI Principal Investigator: Joseph Wu, MD, PhD (Stanford)

FDA Collaborators: Bridget Nugent, PhD (OWH/FDA), Alexandre Ribeiro, PhD (CDER/DARS/FDA)

Project #49 [ACTIVE]

HIV Genomic Surveillance in Cameroon by Next-Generation Sequencing

CERSI Principal Investigator: Charles Chiu, MD, PhD (UCSF)

FDA Collaborators: Indira Hewlett, PhD (CBER/FDA)

Project #45 [ACTIVE]

HYDRA – A Federated Computational Infrastructure to Enable Inclusive, Large-scale Precision Medicine Studies

CERSI Principal Investigator: Snehit Prabhu, PhD (Stanford)

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

Project #43 [ACTIVE]

TOBIAS – A Clinical Decision Support tool to Personalize NGS Diagnostic Test Results based on Genetic Ancestry

CERSI Principal Investigator: Snehit Prabhu, PhD (Stanford)

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

Project #42 [ACTIVE]

Evaluation of the impact of Genetic Variability on Drug Target Interactions using Structural Bioinformatics

CERSI Principal Investigator: Russ Altman, MD, PhD (Stanford)

FDA Collaborators: 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)

Project #36 [COMPLETED]

Network Integration for Precision Medicine Drug Models

CERSI Principal Investigator: Russ Altman, MD, PhD (Stanford)

FDA Collaborators: Michael Pacanowski, PharmD, MPH (CDER/FDA), Anuradha Ramamoorthy, PhD (CDER/FDA), Oluseyi Adeniyi, PhD (CDER/FDA)

Project #24 [COMPLETED]

Causes of Real-Life NGS Variability

CERSI Principal Investigator: Dmitri Petrov, PhD (Stanford)

FDA Collaborators: Elaine Johanson (OHI/FDA)

Project #16F [COMPLETED]

Role of Ancestry in Genetic Diagnostics

CERSI Principal Investigator: Snehit Prabhu, PhD (Stanford)

FDA Collaborators: 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)

Project #16E [COMPLETED]

Next Generation Text Analytics for FDA-Relevant Text Mining

CERSI Principal Investigator: Russ Altman, MD, PhD (Stanford)

FDA Collaborators: Roselie Bright, ScD (OHI/FDA), Larry Callahan, PhD (OHI/FDA), Elaine Johanson (OHI/FDA), Frank Switzer, PhD (OHI/FDA)

Project #16B [COMPLETED]

Plain Language Summary

CERSI Principal Investigator: Russ Altman, MD, PhD (Stanford)

FDA Collaborators: Elaine Johanson (OHI/FDA)

Project #16A [COMPLETED]

Plain Language Summary


Special Populations Research Projects

The Real-World Effectiveness of COVID-19 Vaccines in the Pediatric Population Across the University of California Health System

CERSI Principal Investigator: Atul Butte, MD, PhD (UCSF), Kendra Radtke, PharmD, PhD (UCSF)

FDA Collaborators: Steven Anderson (CBER/FDA), Yun Lu (CBER/FDA), Artur Belov (CBER/FDA), Barbee Whitaker (CBER/FDA), Richard Forshee (CBER/FDA), Angela Moy (CBER/FDA), Chartrina Andrell (CBER/FDA), 

Project #76 [ACTIVE]

The MUM-URMA1 study: Multimorbidity and Medications: The Unheard Perspective of Older Under-Represented Racial and Ethnic Minority Adults - Phase 1

CERSI Principal Investigator: Janice Schwartz, MD (UCSF)

FDA Collaborators: Christine Lee, PharmD, PhD (OMHHE/FDA), Qi Liu, PhD, MStat (CDER/OCP/FDA)

Project #71 [ACTIVE]

The MUM study: MUltimorbidity and Medications: The Unheard Perspective of Older Adults

CERSI Principal Investigator: Janice Schwartz, MD (UCSF)

FDA Collaborators: Qi Liu, PhD, MStat (CDER/OCP/FDA), Shiew-Mei Huang, PhD (CDER/OCP/OTS/FDA)

Project #64 [ACTIVE]

Renal Impairment in New Drug Development: Phase II

CERSI Principal Investigator: Timothy Meyer, MD (Stanford)

FDA Collaborators: Shiew Mei Huang, PhD (CDER/FDA), Lei Zhang, PhD (CDER/FDA), Qi Liu, PhD (CDER/FDA)

Project #57 [ACTIVE]

Creating a Framework for a National Adaptive Platform Trial to Evaluate Pediatric Medical Devices

CERSI Principal Investigator: Christopher Almond, MD, MPH (Stanford)

FDA Collaborators: Vasum Peiris, MD, MPH (CDRH/FDA), Brittany Caldwell, PhD (CDRH/FDA)

Project #54 [ACTIVE]

Usability Testing of Virtual Reality for Opioid-Sparing Pain Management Among Diverse Patients

CERSI Principal Investigator: Urmimala Sarkar, MD, MPH (UCSF), Courtney Lyles, PhD (UCSF)

FDA Collaborators: Richardae Araojo, PharmD, MS (OMHHE/FDA), Christine Lee, PharmD, PhD (OMHHE/FDA), Michelle Tarver, MD, PhD (CDRH/FDA)

Project #52 [ACTIVE]

Predicting Pediatric Dosing for Medical Countermeasures

CERSI Principal Investigator: Sook Wah Yee, PhD (UCSF)

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

Project #23 [ACTIVE]

Safer Labeling of Pediatric Medications: Reducing Literacy-related Health Disparities among Chronically Ill Adolescents

CERSI Principal Investigator: Lee Sanders, MD (Stanford), Bonnie Halpern-Felsher, PhD (Stanford)

FDA Collaborators: 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)

Project #13 [ACTIVE]

Characterizing Population-Specific Clinical Asthma Profiles

CERSI Principal Investigator: Esteban Burchard, MD, MPH (UCSF)

FDA Collaborators: Richardae Araojo, PharmD (OMHHE/FDA)

Project #46 [COMPLETE]

Comprehensive Assessment of Sex Differential Smoking-related Effects in Publicly Available Gene Expression Data

CERSI Principal Investigator: Russ Altman, MD, PhD (Stanford)

FDA Collaborators: Bridget Nugent, PhD (OWH/FDA), Susan Bersoff-Matcha, MD (OWH/FDA), Patricia Bradfield (OWH/FDA), Kaveeta Vasisht, MD, PharmD (OWH/FDA), Ryan Conville (OWH/FDA), Jonathan Kwan, MS (OTP/FDA)

Project #37 [COMPLETED]

Plain Language Summary

Renal Impairment in New Drug Development

CERSI Principal Investigator: Kathy Giacomini, PhD (UCSF), Timothy Meyer, MD (Stanford)

FDA Collaborators: 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)

Project #3 [COMPLETED]

Plain Language Summary


COVID-19 Research Projects

Real-World Population Characteristics, Safety and Effectiveness of COVID-19 Vaccines

CERSI Principal Investigator: Atul Butte, MD, PhD (UCSF)

FDA Collaborators: 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)

Project #68 [ACTIVE]

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

CERSI Principal Investigator: Rohit Vashisht, PhD (UCSF)

FDA Collaborators: 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)

Project #61 [ACTIVE]

Plain Language Summary

OneSource Phase III: Demonstration of EHR/eCRF Integration in the COVID-19 Critical Care Environment

CERSI Principal Investigator: Laura Esserman, MD, MBA (UCSF)

FDA Collaborators: 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)

Project #56 [ACTIVE]

OneSource: SMART on FHIR for I-SPY COVID-19 Trial

CERSI Principal Investigator: Laura Esserman, MD, MBA (UCSF)

FDA Collaborators: 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)

Project #55 [ACTIVE]

A Rapid Query Model to Address Prioritized COVID-19 Questions Using EHR Data

CERSI Principal Investigator: Atul Butte, MD, PhD (UCSF)

FDA Collaborators: Amy Abernethy, MD, PhD (OC/FDA)

Project #53 [COMPLETED]

Publications

2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015

 

2022 August 4

Technical Applications of Microelectrode Array and Patch Clamp Recordings on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Journal of Visualized Experiments

Authors: Zhao SR, Mondéjar-Parreño G, Li D, Shen M, Wu JC

PMID 35993757

(Project #62)

2022 April 19

Analyzing real world data of blood transfusion adverse events: Opportunities and challenges

Transfusion

Authors: Jhaveri P, Bozkurt S, Moyal A, Belov A, Anderson S, Shan H, Whitaker B, Hernandez-Boussard T

PMID 35437749

(Project #38)

2022 March 1

Preventive drugs for Huntington's disease: A choice-based conjoint survey of patient preferences

Journal of Clinical and Translational Science

Authors: Parrish MC, Hanson-Kahn A, Srinivasan V, Grimes KV

PMID 35433035

2022 January 28

High Throughput Screening of a Prescription Drug Library for Inhibitors of Organic Cation Transporter 3, OCT3

Pharmaceutical Research (Online ahead of print)

Authors: Chen EC, Matsson P, Azimi M, Zhou X, Handin N, Yee SW, Artursson P, Giacomini KM

PMID 35089508

(Project #23)

2022 January 25

Tisagenlecleucel outcomes in relapsed/refractory extramedullary ALL: a Pediatric Real World CAR Consortium Report

Blood Advances, Volume 6, Issue 2, pp. 600-610

Authors: Fabrizio VA, Phillips CL, Lane A, Baggott C, Prabhu S, Egeler E, Mavroukakis S, Pacenta H, Rossoff J, Stefanski HE, Talano JA, Moskop A, Margossian SP, Verneris MR, Myers GD, Karras NA, Brown PA, Qayed M, Hermiston M, Satwani P, Krupski C, Keating AK, Wilcox R, Rabik CA, Chinnabhandar V, Kunicki M, Goksenin AY, Curran KJ, Mackall CL, Laetsch TW, Schultz LM

PMID 34794180

(Project #43)

2022 January 15

Do patient-reported outcome measures measure up? A qualitative study to examine perceptions and experiences with heart failure proms among diverse, low-income patients

Journal of Patient-Reported Outcomes, Volume 6, Issue 1, Article 6 (pp. 1-12)

Authors: Davis J, Olazo K, Sierra M, Tarver ME, Caldwell B, Saha A, Lisker S, Lyles C, Sarkar U

PMID 35032226

(Project #28)

2022 January 11

Bayesian logistic regression for online recalibration and revision of risk prediction models with performance guarantees

Journal of the American Medical Informatics Association (Online ahead of print)

Authors: Feng J, Gossmann A, Sahiner B, Pirracchio R

PMID 35022756

(Project #58)

2021 December 09

Disease Burden Affects Outcomes in Pediatric and Young Adult B-Cell Lymphoblastic Leukemia After Commercial Tisagenlecleucel: A Pediatric Real-World Chimeric Antigen Receptor Consortium Report

Journal of Clinical Oncology (Online ahead of print)

Authors: Schultz LM, Baggott C, Prabhu S, Pacenta HL, Phillips CL, Rossoff J, Stefanski HE, Talano JA, Moskop A, Margossian SP, Verneris MR, Myers GD, Karras NA, Brown PA, Qayed M, Hermiston M, Satwani P, Krupski C, Keating AK, Wilcox R, Rabik CA, Fabrizio VA, Rouce RH, Chinnabhandar V, Kunicki M, Barsan VV, Goksenin AY, Li Y, Mavroukakis S, Egeler E, Curran KJ, Mackall CL, Laetsch TW

PMID 34882493

(Project #43)

2021 November 25

Out-of-specification tisagenlecleucel does not compromise safety or efficacy in pediatric acute lymphoblastic leukemia

Blood, Volume 138, Issue 21, pp. 2138-2142

Authors: Rossoff J, Baggott C, Prabhu S, Pacenta H, Phillips CL, Stefanski H, Talano JA, Moskop A, Margossian SP, Verneris MR, Myers GD, Karras N, Brown PA, Qayed M, Hermiston M, Satwani P, Krupski C, Keating AK, Wilcox R, Rabik CA, Fabrizio VA, Kunicki M, Chinnabhandar V, Goksenin AY, Curran KJ, Mackall CL, Laetsch TW, Schultz LM

PMID 34499715

(Project #43)

2021 November 17

Optimal fludarabine lymphodepletion is associated with improved outcomes following CAR T-cell Therapy

Blood Advances (Online ahead of print)

Authors: Fabrizio VA, Boelens JJ, Mauguen A, Baggott C, Prabhu S, Egeler E, Mavroukakis S, Pacenta HL, Phillips CL, Rossoff J, Stefanski H, Talano JA, Moskop A, Margossian SP, Verneris MR, Myers GD, Karras NA, Brown PA, Qayed M, Hermiston ML, Satwani P, Krupski C, Keating AK, Wilcox R, Rabik CA, Chinnabhandar V, Kunicki M, Goksenin AY, Mackall CL, Laetsch TW, Schultz LM, Curran KJ

PMID 34788386

(Project #43)

2021 September 22

Barriers and Facilitators to the Implementation of Virtual Reality as a Pain Management Modality in Academic, Community, and Safety-Net Settings: Qualitative Analysis

Journal of Medical Internet Research, Volume 23, Issue 9, Article 26623 (pp. 1-9)

Authors: Sarkar U, Lee JE, Nguyen KH, Lisker S, Lyles CR

PMID 34550074

(Project #52)

2021 September 21

U.S. Food and Drug Administration Reasoning in Approval Decisions When Efficacy Evidence Is Borderline, 2013-2018

Annals of Internal Medicine, Volume 174, Issue 11, pp. 1603-1611

Authors: Janiaud P, Irony T, Russek-Cohen E, Goodman SN

PMID 34543584

(Project #21)

2021 September 16

Racial/ethnic differences in eligibility for asthma biologics among pediatric populations

Journal of Allergy and Clinical Immunology, Volume 148, Issue 5, pp. 1324-1331.e12 

Authors: Wohlford EM, Huang PF, Elhawary JR, Millette LA, Contreras MG, Witonsky J, Holweg CTJ, Oh SS, Lee C, Merenda C, Rabin RL, Araojo R, Mak ACY, Eng CS, Hu D, Huntsman S, LeNoir MA, Rodríguez-Santana JR, Borrell LN, Burchard EG

PMID 34536416

(Project #46)

2021 September 15

Interaction of Commonly Used Oral Molecular Excipients with P-glycoprotein

American Association of Pharmaceutical Scientists (AAPS) Journal, Volume 23, Issue 5, Article 106 (pp. 1-12)

Authors: Bajaj R, Chong LB, Zou L, Tsakalozou E, Ni Z, Giacomini KM, Kroetz DL

PMID 34528148

(Project #15B)

2021 July 24

ACVR1 R206H extends inflammatory responses in human induced pluripotent stem cell-derived macrophages

Bone, Volume 153, Article 116129 (pp. 1-15)

Authors: Matsuo K, Lepinski A, Chavez RD, Barruet E, Pereira A, Moody TA, Ton AN, Sharma A, Hellman J, Tomoda K, Nakamura MC, Hsiao EC

PMID 34311122

(Project #31)

2021 July 18

Genomewide Association Studies in Pharmacogenomics

Clinical Pharmacology & Therapeutics, Volume 110, Issue 3, pp. 637-648

Authors: McInnes G, Yee SW, Pershad Y, Altman RB

PMID 34185318

(Project #36)

2021 June 17

Technical considerations for evaluating clinical prediction indices: a case study for predicting code blue events with MEWS

Physiological Measurement, Volume 42, Issue 5, Article 055005 (pp. 1-17)

Authors: Gadhoumi K, Beltran A, Scully CG, Xiao R, Nahmias DO, Hu X

PMID 33902012

(Project #34)

2021 May 03

Drugs in COVID-19 Clinical Trials: Predicting Transporter-Mediated Drug-Drug Interactions Using In Vitro Assays and Real-World Data

Clinical Pharmacology & Therapeutics, Volume 110, Issue 1, pp. 108-122

Authors: Yee SW, Vora B, Oskotsky T, Zou L, Jakobsen S, Enogieru OJ, Koleske ML, Kosti I, Rödin M, Sirota M, Giacomini KM

PMID 33759449

2021 April 30

Engineering Hydrogel-Based Biomedical Photonics: Design, Fabrication, and Applications

Advanced Materials, Volume 33, Issue 23, Article 2006582 (pp. 1-25)

Authors: Guimarães CF, Ahmed R, Marques AP, Reis RL, Demirci U

PMID 33929771

(Project #33)

2021 April 20

Engineering Cardiovascular Tissue Chips for Disease Modeling and Drug Screening Applications

Frontiers in Bioengineering and Biotechnology

Authors: Chan AHP, Huang NF

PMID 33959600

(Project #32)

2021 April 11

Vision-Targeted Health-Related Quality-of-Life Survey for Evaluating Minimally Invasive Glaucoma Surgery

American Journal of Ophthalmology, Volume 229, pp. 145-151

Authors: Cui QN, Hays RD, Tarver ME, Spaeth GL, Paz SH, Weidmer B, Fellman RL, Vold SD, Eydelman M, Singh K

PMID 33852908

(Project #14)

2021 April

How medical AI devices are evaluated: limitations and recommendations from an analysis of FDA approvals

Nature Medicine, Volume 27, Issue 4, pp. 582-584

Authors: Wu E, Wu K, Daneshjou R, Ouyang D, Ho DE, Zou J

PMID 33820998

(Project #39)

2021 February 28

A New Era in Pharmacovigilance: Toward Real-World Data and Digital Monitoring

Journal of the American Medical Informatics Association, Volume 109, Issue 5, 1197-1202

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

PMID 33492663

(Project #1)

2020 September 07

Drug Metabolites Potently Inhibit Renal Organic Anion Transporters, OAT1 and OAT3

Journal of Pharmaceutical Sciences, Volume 110, Issue 1, pp. 347-353

Authors: Zou L, Matsson P, Stecula A, Ngo HX, Zur AA, Giacomini KM

PMID 32910949

(Project #3)

2020 July 29

Scientific Considerations for Global Drug Development

Science Translational Medicine, Vol 12, Issue 554, Article eaax2550 (pp. 1-5)

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

PMID 32727913

2020 July 24

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

PMID 32703874

(Project #15A)

2020 July 03

Effects of Nicotine on the Translation of Stem Cell Therapy

Regenerative Medicine, Volume 15, Issue 5, pp. 1679-1688

Authors: Chan AH, Huang NF

PMID 32618492

(Project #32)

2020 June 22

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

Proceedings of the National Academy of Sciences, Volume 117, Issue 27, pp. 16009-16018

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

PMID 32571913

(Project #15B)

2020 May 27

Extracting Chemical Reactions from Text using Snorkel

BMC (BioMed Central) Bioinformatics 2020, Volume 21, Issue 1, Article 217 (pp. 1-15)

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

PMID 32460703

(Project #16B)

2020 February 10

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

Molecular Pharmaceutics, Volume 17, Issue 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

PMID 31990564

(Project #15B)

2019 December

Advancing the Use of Patient Preference Information as Scientific Evidence in Medical Product Evaluation: A Summary Report of the Patient Preference Workshop

Patient, Volume 12, Issue 6, pp. 553-557

Authors: Benz HL, Lee TJ, Tsai JH, Bridges JFP, Eggers S, Moncur M, Shaya FT, Shoulson I, Spatz ES, Wilson L, Saha A

PMID 31696436

(Project #17)

2019 November 26

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

Eye, Volume 34, Issue 1, pp. 205-210

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

PMID 31772384

(Project #14)

2019 November 23

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

Clinical Pharmacology & Therapeutics, Volume 107, Issue 1, pp. 82-84

Authors: Wilson L, Lin L, Singh K.

PMID 31758800

(Project #14, 17)

2019 November 01

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

Bioinformatics, Volume 35, Issue 21, pp. 4504–4506​

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

PMID 31114840

(Project #24)

2019 September

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, Volume 59, Issue S1, pp. S56-S69

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

PMID 31502692

(Project #23)

2019 July 03

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

Clinical Pharmacology & Therapeutics, Volume 106, Issue 5, pp. 1083-1092

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

PMID 31127606

(Project #23)

2019 June 20

An Overview of Genomic Biomarker Use in Cardiovascular Disease Clinical Trials

Clinical Pharmacology & Therapeutics, Volume 106, Issue 4, pp. 841-846

Authors: Adeniyi O, Ramamoorthy A, Schuck R, Sun J, Wilson J, Zineh I, Pacanowski M

PMID 31002380

(Project #24)

2019 June 10

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

Expert Review of Medical Devices, Volume 16, Issue 7, pp. 603-616

Authors: Sarode DN, Roy S

PMID 31154869

(Project #25)

2019 February 17

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

Clinical Pharmacology & Therapeutics, Volume 105, Issue 4, pp. 815-818

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

PMID 30773618

2019 January 20

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

Clinical Pharmacology & Therapeutics, Volume 105, Issue 2, pp. 323-325

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

PMID 30663035

(Project #15B)

2018 December 07

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

PLOS (Public Library of Science) Computational Biology, Volume 14, Issue 12, Article e1006614 (pp. 1-27)

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

PMID 30532240

(Project #24)

2018 September 27

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

BMC (BioMed Central) Cancer, Volume 18, Issue 1, Article 933 (pp. 1-10)

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

PMID 30261931

(Project #16E)

2018 September 12

Surviving in the Valley of Death: Opportunities and Challenges in Translating Academic Drug Discoveries

Annual Review of Pharmacology and Toxicology, Volume 59, pp. 405-421

Authors: Parrish MC, Tan YJ, Grimes KV, Mochly-Rosen D

PMID 30208282

2018 August 06

Network Enhancement as a General Method to Denoise Weighted Biological Networks

Nature Communications, Volume 9, Issue 1, Article 3108 (pp. 1-8)

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

PMID 30082777

(Project #16E)

2018 May 08

Machine Learning in Chemoinformatics and Drug Discovery

Drug Discovery Today, Volume 23, Issue 8, pp. 1538-1546

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

PMID 29750902

2018 May 01

Pharmacogenomics and big genomic data: from lab to clinic and back again

Human Molecular Genetics, Volume 27, Issue R1, pp. R72-R78

Authors: Lavertu A, McInnes G, Daneshjou R, Whirl-Carrillo M, Klein TE, Altman RB

PMID 29635477

2018 January 27

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

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

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

PMID 29218869

(Project #16B, 20)

2017 December 03

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

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

Authors: Wilson JL, Altman RB

PMID 29199461

(Project #24)

2017 November 01

Toward Multimodal Signal Detection of Adverse Drug Reactions

Journal of Biomedical Informatics, Volume 76, pp. 41-49

Authors: Harpaz R, DuMouchel W, Schuemie M, Bodenreider O, Friedman C, Horvitz E, Ripple A, Sorbello A, White RW, Winnenburg R, Shah NH

PMID 29081385

(Project #2)

2017 September 01

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

Journal of the American Medical Informatics Association, Volume 25, Issue 5, pp. 913-920

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

PMID 28371826

(Project #1)

2017 June 15

Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1

Journal of Chemical Information and Modeling, Volume 57, Issue 6, pp. 1402-1413

Authors: Khuri N, Zur AA, Wittwer MB, Lin L, Yee SW, Sali A, Giacomini KM

PMID 28562037

(Project #3)

2017 May 05

The Effect of Uremic Solutes on the Organic Cation Transporter 2

Journal of Pharmaceutical Sciences, Volume 106, Issue 9, pp. 2551-2557

Authors: Cheung KWK, Hsueh CH, Zhao P, Meyer TW, Zhang L, Huang SM, Giacomini KM

PMID 28483424

(Project #3)

2017 February 01

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

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

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

PMID 28256243

(Project #8)

2016 September 20

Metabolomic and Genome-wide Association Studies Reveal Potential Endogenous Biomarkers for OATP1B1

Clinical Pharmacology & Therapeutics, Volume 100, Issue 5, pp. 524-536

Authors: Yee SW, Giacomini MM, Hsueh CH, Weitz D, Liang X, Goswami S, Kinchen JM, Coelho A, Zur AA, Mertsch K, Brian W, Kroetz DL, Giacomini KM

PMID 27447836

(Project #3)

2016 October 27

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

American Journal of Ophthalmology, Volume 172, pp. xii-xiv

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

PMID 28327295

(Project #14)

2016 September 28

A Molecular Basis for Innovation in Drug Excipients

Clinical Pharmacology & Therapeutics, Volume101, 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

PMID 27557422

(Project #15A, 15B)

2016 August 09

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

Molecular Pharmaceutics, Volume 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

PMID 27467266

(Project #3)

2016 June 14

Pharmacometabolomic Assessment of Metformin in Non-diabetic, African Americans

Frontiers in Pharmacology, Volume 7, Article 135 (pp. 1-12)

Authors: Rotroff DM, Oki NO, Liang X, Yee SW, Stocker SL, Corum DG, Meisner M, Fiehn O, Motsinger-Reif AA, Giacomini KM, Kaddurah-Daouk R

PMID 27378919

(Project #)

2016 June 14

The Effect of Famotidine, a MATE1-Selective Inhibitor, on the Pharmacokinetics and Pharmacodynamics of Metformin

Clinical Pharmacokinetics, Volume 55, Issue 6, pp. 711-21

Authors: Hibma JE, Zur AA, Castro RA, Wittwer MB, Keizer RJ, Yee SW, Goswami S, Stocker SL, Zhang X, Huang Y, Brett CM, Savic RM, Giacomini KM

PMID 26597253

(Project #)

2016 April 20

A Research Roadmap for Next Generation Sequencing Informatics

Science Translational Medicine, Volume 8, Issue 335, Article 335ps10 (pp. 1-4)

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

PMID 27099173

(Project #16A)

2015 November 25

Unmet Needs: Research Helps Regulators do their Jobs

Science Translational Medicine, Volume 7, Issue 315, Article 315ps22 (pp. 1-7)

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

PMID 26606966

2015 November 16

Metformin Is a Substrate and Inhibitor of the Human Thiamine Transporter, THTR-2 (SLC19A3)

Molecular Pharmaceutics, Volume 12, Issue 12, pp. 4301-10

Authors: Liang X, Chien HC, Yee SW, Giacomini MM, Chen EC, Piao M, Hao J, Twelves J, Lepist EI, Ray AS, Giacomini KM

PMID 26528626

(Project #)

2015 July 31

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

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

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

PMID 26232442

(Project #2)