Deborah Dean, MD, MPH ~ Professor in Residence ~ [email protected]
Deborah is an infectious disease physician-scientist in the Departments of Medicine and Pediatrics, Division of Infectious Diseases and Global Health. Her undergraduate degree is from the University of California Berkeley, and MD from Albert Einstein College of Medicine. She completed a residency in Internal Medicine at UCSF, an MPH in Epidemiology and Biostatistics from UC Berkeley, and postdoctoral fellowship in Microbial Pathogenesis at Stanford University School of Medicine, Department of Microbiology and Immunology, with Stan Falkow, PhD. During her postdoc, she also completed an Infectious Disease Fellowship. She is also:
Core Faculty - UC Berkeley - UCSF Joint Program in Bioengineering
Member - UCSF Bixby Center for Global Reproductive Health
Member - UCSF Benioff Center for Microbiome Medicine (BCMM)
Affiliate Faculty - UCSF Institute for Global Health Sciences
Summary
The Dean Lab research involves in vitro and integrated bioinformatic approaches along with studies of human populations to address host-pathogen interactions, including bacterial genomics, host immune responses, antimicrobial resistance and multi-omics analyses of microbiomes. Disease protection and pathogenesis related to the obligate intracellular bacterium Chlamydia trachomatis are a key focus. The Dean lab also studies the evolution of zoonotic chlamydial species. The Lab’s international research involves the epidemiology and molecular epidemiology of and risk factors for trachoma and sexually transmitted disease populations in Nepal, India, Ecuador, Thailand, Vietnam and Fiji. In addition, her group collaborates with Bay Area biotech start-ups to develop vaccines and rapid inexpensive point-of-care diagnostics for C. trachomatis and Neisseria gonorrhoeae for global deployment. Professor Dean has a track record of over 34 years of uninterrupted R01 funding from the National Institutes of Health in addition to grants from the U.S. Centers for Disease Control, World Health Organization and the National Science Foundation. She is a Fellow of the American Academy of Microbiology and has mentored over 170 national and international undergraduate, graduate and medical students, and postdoctoral fellows who have gone on to university professorships and positions at institutes of health and centers for disease control throughout the world. In 2018, she was awarded the Influential Alumni Award for Significant Contributions in the Field of Public Health by the UC Berkeley School of Public Health and, in 2021, became a UCSF Diversity, Equity and Inclusion Champion. She remains an advocate for ocular and reproductive health among vulnerable and neglected populations worldwide.
Olusola (Shola) Olagoke, PhD
Postdoctoral Fellow
Shola is a microbiologist with expertise in microbial genomics, host–pathogen interactions, and multi-omics data analysis. He has an MSc in animal and veterinary sciences and a PhD in Microbiology. His research is focused on applying and creating integrative bioinformatics tools to explore the molecular mechanisms of chlamydial pathogenesis and host-pathogen interactions related to sexually transmitted infections and trachoma — the leading infectious cause of blindness in the world today.
Augusta Uwamanzu-nna, BS
MD/PhD student
Augusta has a BS in Engineering Sciences with a focus in Bioengineering from Harvard University and is currently a UCSF MD/PhD student in the lab. Her research focuses on understanding ocular microbiomes in trachoma populations in the Global South through defining community state types using various clustering algorithms. She also aims to develop predictive models for infection risk and trachomatous disease.
Neeraja Sripada, BA
Post Bac Researcher
Neeraja graduated May 2025 from UC Berkeley with a BA with Honors in Molecular and Cell Biology and a minor in Bioengineering. She completed her Honor’s Thesis in the lab and is the recipient of the MCB Departmental Spencer W. Brown Award in Genetics, Genomics, Evolution, and Development. Her research focus has been to characterize the host immune response to rectal C. trachomatis infections among females residing in Fiji and the role that C. trachomatis genomic strain types have on immunity and persistent infections, integrating comparative and functional genomics into the analyses.
Swongwon Chung, dual BAs
Post Bac Researcher
Seongwon graduated May 2025 from UC Berkeley with a BA with Honors in Molecular and Cell Biology and a BA in Public Health. He completed his Honor’s Thesis in the lab and is the recipient of the MCB Departmental Award for Academic Excellence in Immunology. His research focuses on defining the host immune response among trachoma populations and the role that the microbial composition of the microbiome might play in enhancing disease pathogenesis.
Lucile Zhu, dual BSs
Post Bac Researcher
Lucile graduated May 2025 from UC Berkeley with a BS with Honors in Bioengineering and a BS in Electrical Engineering and Computer Science. The focus of her research in the lab has been on genome assembly. annotation and comparative genomics of C. trachomatis ocular strains on a global level to interrogate single nucleotide polymorphisms (SNPs) in virulence and other genes as part of evaluating the evolutionary dynamics of these genomes.
Charlotte Shi
Undergraduate Researcher
Charlotte is majoring in Microbial Biology at UC Berkeley. Her research focus is on applying bioinformatic tools to understand community state types within ocular microbiomes and characterizing the host-immune response in trachoma populations.
Sarah Risoen
Undergraduate Researcher
Sarah is majoring in Molecular and Cell Biology at UC Berkeley with a minor in Global Poverty and Practice. The focus of her research is on defining the host immune response to male urethral and rectal C. trachomatis infections among an at-risk populations in Fiji.
Natalia Toledo
Undergraduate Researcher
Natalia is majoring in Molecular and Cell Biology and Data Science at UC Berkeley. Her research focuses on interrogating C. trachomatis plasmids associated with ocular genomes and their pathogenic potential.
Brianna Titiheruw
Undergraduate Researcher
Brianna is majoring in Molecular and Cell Biology and Data Science at UC Berkeley. She will focus on characterizing the host-immune response in trachoma populations.
Anish Krishnan
Undergraduate Researcher
Anish is majoring in Molecular and Cell Biology and Data Science at UC Berkeley. His research focuses on understanding the comparative and functional genomics of C. trachomatis ocular strains from around the world.
Sreyas Yallapragada
Undergraduate Researcher
Sreyas is majoring in Bioengineering and a BS in Electrical Engineering and Computer Science. He will focus on a constellation of bioinformatic tools to interrogate multi-omics approaches to metagenomic shotgun sequencing analyses.
Sam Miloslavsky
Undergraduate Researcher
Sam is majoring in Bioengineering. His research focuses on exploring microbiome profiles in the male urethra, specifically the effects of C. trachomatis infection and treatment on metabolomics and the resistome.
Marley Michel
Undergraduate Researcher
Marley is majoring in Integrative Biology with a minor in Spanish. She is focusing on analyses of female urogenital and rectal microbiomes including characterization of the resistome and metabolome.
Mila Yosiff Reyes
Undergraduate Researcher
Mila is majoring in Neuroscience. Her research focus is on functional genomics related to C. trachomatis genomic strains in endocervical and rectal sites.