Proctor Foundation
The Doan Lab
A metagenomic epidemiology laboratory at the UCSF Proctor Foundation. Samples reach us from clinics, hospitals, and field research centers around the world — from Niger and Burkina Faso to India, Nepal, Thailand, Vietnam, Vanuatu, Chile, and across the United States. We study how the human microbiome responds to change, and we use sequencing to name the cause of an eye infection when conventional testing cannot.
Opens doanlab.ucsf.edu, the lab's own UCSF site.
Principal Investigator
Thuy Doan, MD, PhD
Associate Professor
Dr. Doan leads the lab's work on ocular infection and inflammation, microbiomes, and antimicrobial resistance. Her research asks why mass antibiotic distribution improves child survival in sub-Saharan Africa, and what that treatment costs in resistance, so that the answer can inform public health policy rather than sit in a journal.
Alongside that population work, she applies the same sequencing tools one patient at a time, identifying the organisms behind uveitis, conjunctivitis, corneal ulcers, and scleritis.
Our Work
What the lab does
Three lines of work, one method. Samples are collected inside randomized trials and clinics rather than generated in the laboratory, then sequenced without assuming in advance what they contain.
Mechanism
Why mass treatment saves children
Distributing azithromycin to preschool children in sub-Saharan Africa lowers childhood mortality. We look at the gut, ocular, and upper respiratory microbiomes to work out how.
Surveillance
Tracking antimicrobial resistance
Any benefit from mass treatment has to be weighed against resistance. We track it in the same communities over time, so policy rests on measurement rather than assumption.
Diagnosis
Naming the cause of an eye infection
Unbiased sequencing identifies pathogens in uveitis, conjunctivitis, corneal ulcers, and scleritis, including cases where culture and targeted testing return nothing.
Explore
More from the lab
The lab keeps its own site, where each of these is maintained in full.
Research
Current projects
Four active studies, spanning corneal pathogens, uveitis tissue, mass drug distribution, and a global look at conjunctivitis epidemics.
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capriCORN
Comprehensive Analysis of Pathogens, Resistomes, and Inflammatory-markers in the CORNea.
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LOTUS
Leveraging Ocular Tissues in Uveitis Study — working with partners at home and abroad on how ocular inflammatory disease arises, and on better classification, diagnosis, and biomarkers.
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MORDOR / AVENIR
Large randomized trials testing whether mass drug distribution improves childhood survival in Niger and Burkina Faso.
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SCORPIO
An international, multi-site study of conjunctivitis epidemics: which pathogens drive them, how their genomes shift across time and place, and how the immune system answers.
People
Lab members
The scientists, students, and coordinators who run the sequencing, the pipelines, and the field collections.
Output
Publications
Peer-reviewed work from the lab and its collaborators, kept current on the lab site.
Get in touch
Work with the lab
Sending a sample, joining as a trainee, or starting a collaboration — the lab site lists who to contact and what to include.
Where Samples Come From
Collecting sites around the world
Specimens reach San Francisco from clinics, hospitals, and field research centers on six continents. Each site collects under a shared protocol so that samples arriving from Niamey and from Indianapolis can be compared directly.
Africa
3 sites
- Health Research Center in Nouna Nouna, Burkina Faso
- Programme National de Santé Oculaire Niamey, Niger
- Blantyre Institute for Community Outreach Blantyre, Malawi
Asia
9 sites
- Rabin Medical Center Petah Tikva, Israel
- Aravind Eye Hospital Madurai, India
- B. P. Koirala Lion's Center for Ophthalmic Studies Kathmandu, Nepal
- Chulalongkorn University Bangkok, Thailand
- Phramongkutklao Hospital Bangkok, Thailand
- Srinagarind Hospital Khon Kaen, Thailand
- Hai Yen Vision Institute Ho Chi Minh City, Vietnam
- Singapore National Eye Centre Singapore
- National Yang Ming Chiao Tung University Taipei, Taiwan
Europe
2 sites
- Saarland University Medical Center Homburg, Germany
- Pallas Kliniken Olten, Switzerland
North America
10 sites
- EyeSight Hawaii Honolulu, HI
- Pacific Vision Institute of Hawaii Honolulu, HI
- OHSU Casey Eye Institute Portland, OR
- University of California, Berkeley Berkeley, CA
- UCLA Stein Eye Institute Los Angeles, CA
- UC San Diego Shiley Eye Institute La Jolla, CA
- Cornea Associates of Texas Dallas, TX
- Price Vision Group Indianapolis, IN
- Edward S. Harkness Eye Institute, Columbia New York, NY
- Visualiza Guatemala City, Guatemala
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