Deborah Dean, MD, MPH

Professor in Residence

Professor Dean’s research involves in vitro and bioinformatic approaches along with studies of human populations to address host-pathogen interactions, including bacterial genomics, host immune responses and microbiota/microbiome/metabolome associations with disease protection and pathogenesis related to the obligate intracellular bacterium Chlamydia trachomatis. Her group was the first to identify genomic recombination in this human pathogen. The Dean lab also studies the evolution of zoonotic chlamydial species. Professor Dean’s international research focusses on 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. She has a track record of 33 years of uninterrupted 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 has also 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. Professor Dean remains an advocate for ocular and reproductive health among vulnerable and neglected populations worldwide.


Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae.

New microbes and new infections

Greub G, Pillonel T, Bavoil PM, Borel N, Campbell LA, Dean D, Hefty S, Horn M, Morré SA, Ouellette SP, Pannekoek Y, Puolakkainen M, Timms P, Valdivia R, Vanrompay D

Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis.

bioRxiv : the preprint server for biology

Joseph SJ, Bommana S, Ziklo N, Kama M, Dean D, Read TD

Multiplex recombinase polymerase amplification for high-risk and low-risk type HPV detection, as potential local use in single tube.

Scientific reports

Wongsamart R, Bhattarakasol P, Chaiwongkot A, Wongsawaeng D, Okada PA, Palaga T, Leelahavanichkul A, Khovidhunkit W, Dean D, Somboonna N

Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants.

Frontiers in Microbiology

Marti H, Bommana S, Read TD, Pesch T, Prähauser B, Dean D, Borel N

Development and Evaluation of a Point-of-Care Test in a Low-Resource Setting with High Rates of Chlamydia trachomatis Urogenital Infections in Fiji.

Journal of clinical microbiology

Dean D, Swaminathan S, Kama M, Goemans S, Faktaufon D, Alnabelseya N, Spelke D, Kahrizi K, Black M, Mitra D

Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs.


Bowden KE, Joseph SJ, Cartee JC, Ziklo N, Danavall D, Raphael BH, Read TD, Dean D

Fluorometric Paper-Based, Loop-Mediated Isothermal Amplification Devices for Quantitative Point-of-Care Detection of Methicillin-Resistant Staphylococcus aureus (MRSA).

ACS sensors

Choopara I, Suea-Ngam A, Teethaisong Y, Howes PD, Schmelcher M, Leelahavanichkul A, Thunyaharn S, Wongsawaeng D, deMello AJ, Dean D, Somboonna N

Chlamydia trachomatis L2c Infection in a Porcine Model Produced Urogenital Pathology and Failed to Induce Protective Immune Responses Against Re-Infection.

Frontiers in immunology

De Clercq E, Van Gils M, Schautteet K, Devriendt B, Kiekens C, Chiers K, Van Den Broeck W, Cox E, Dean D, Vanrompay D

Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products.

Scientific reports

Srimongkol G, Ditmangklo B, Choopara I, Thaniyavarn J, Dean D, Kokpol S, Vilaivan T, Somboonna N

Hyperendemic Chlamydia trachomatis sexually transmitted infections among females represent a high burden of asymptomatic disease and health disparity among Pacific Islanders in Fiji.

PLoS neglected tropical diseases

Svigals V, Blair A, Muller S, Sahu Khan A, Faktaufon D, Kama M, Tamani T, Esfandiari L, O'Brien M, Dean D

Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo".


Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T

The utility of serology for elimination surveillance of trachoma.

Nature communications

Pinsent A, Solomon AW, Bailey RL, Bid R, Cama A, Dean D, Goodhew B, Gwyn SE, Jack KR, Kandel RP, Kama M, Massae P, Macleod C, Mabey DCW, Migchelsen S, Müller A, Sandi F, Sokana O, Taoaba R, Tekeraoi R, Martin DL, White MT

Rapid and sensitive detection of Chlamydia trachomatis sexually transmitted infections in resource-constrained settings in Thailand at the point-of-care.

PLoS neglected tropical diseases

Somboonna N, Choopara I, Arunrut N, Sukhonpan K, Sayasathid J, Dean D, Kiatpathomchai W

Evaluating the Antibiotic Susceptibility of Chlamydia - New Approaches for in Vitro Assays.

Frontiers in Microbiology

Marti H, Borel N, Dean D, Leonard CA

Prevalence of Chlamydia trachomatis-Specific Antibodies before and after Mass Drug Administration for Trachoma in Community-Wide Surveys of Four Communities in Nepal.

The American journal of tropical medicine and hygiene

Gwyn SE, Xiang L, Kandel RP, Dean D, Gambhir M, Martin DL

Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides.

Frontiers in Microbiology

Smelov V, Vrbanac A, van Ess EF, Noz MP, Wan R, Eklund C, Morgan T, Shrier LA, Sanders B, Dillner J, de Vries HJC, Morre SA, Dean D

Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay.

PloS one

Turingan RS, Kaplun L, Krautz-Peterson G, Norsworthy S, Zolotova A, Joseph SJ, Read TD, Dean D, Tan E, Selden RF

Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.

PloS one

Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM

Dynamics of genome change among Legionella species.

Scientific reports

Joseph SJ, Cox D, Wolff B, Morrison SS, Kozak-Muiznieks NA, Frace M, Didelot X, Castillo-Ramirez S, Winchell J, Read TD, Dean D

Lateral flow-based antibody testing for Chlamydia trachomatis.

Journal of immunological methods

Gwyn S, Mitchell A, Dean D, Mkocha H, Handali S, Martin DL

Chlamydia trachomatis growth and development requires the activity of host Long-chain Acyl-CoA Synthetases (ACSLs).

Scientific reports

Recuero-Checa MA, Sharma M, Lau C, Watkins PA, Gaydos CA, Dean D

A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells.

Cell reports

Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding M, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Sharma M, Dean D, Cohen AR, Gelfand VI

Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans.

Genome biology and evolution

Joseph SJ, Marti H, Didelot X, Castillo-Ramirez S, Read TD, Dean D

Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance.


Ezewudo MN, Joseph SJ, Castillo-Ramirez S, Dean D, Del Rio C, Didelot X, Dillon JA, Selden RF, Shafer WM, Turingan RS, Unemo M, Read TD

Novel Chlamydia trachomatis strains in heterosexual sex partners, Indianapolis, Indiana, USA.

Emerging infectious diseases

Batteiger BE, Wan R, Williams JA, He L, Ma A, Fortenberry JD, Dean D

TRAIL-R1 is a negative regulator of pro-inflammatory responses and modulates long-term sequelae resulting from Chlamydia trachomatis infections in humans.

PloS one

Al-Kuhlani M, Rothschild J, Rothchild J, Pal S, de la Maza LM, Ouburg S, Morré SA, Dean D, Ojcius DM

Zoonotic Chlamydiaceae species associated with trachoma, Nepal.

Emerging infectious diseases

Dean D, Rothschild J, Ruettger A, Kandel RP, Sachse K

Analyzing microsatellites using the QIAxcel system.

Methods in molecular biology (Clifton, N.J.)

Dean DA, Wadl PA, Hadziabdic D, Wang X, Trigiano RN

Transcription factor complex AP-1 mediates inflammation initiated by Chlamydia pneumoniae infection.

Cellular microbiology

Wang A, Al-Kuhlani M, Johnston SC, Ojcius DM, Chou J, Dean D

A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis.

PloS one

Dean D, Turingan RS, Thomann HU, Zolotova A, Rothschild J, Joseph SJ, Read TD, Tan E, Selden RF

Population genomics of Chlamydia trachomatis: insights on drift, selection, recombination, and population structure.

Molecular biology and evolution

Joseph SJ, Didelot X, Rothschild J, de Vries HJ, Morré SA, Read TD, Dean D

Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina.


Trigiano RN, Wadl PA, Dean D, Hadziabdic D, Scheffler BE, Runge F, Telle S, Thines M, Ristaino J, Spring O

Interplay of recombination and selection in the genomes of Chlamydia trachomatis.

Biology direct

Joseph SJ, Didelot X, Gandhi K, Dean D, Read TD

Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2)) and D lineages.


Somboonna N, Wan R, Ojcius DM, Pettengill MA, Joseph SJ, Chang A, Hsu R, Read TD, Dean D

Characterization of humoral immune responses to chlamydial HSP60, CPAF, and CT795 in inflammatory and severe trachoma.

Investigative ophthalmology & visual science

Skwor T, Kandel RP, Basravi S, Khan A, Sharma B, Dean D

A systemic network for Chlamydia pneumoniae entry into human cells.

Journal of bacteriology

Wang A, Johnston SC, Chou J, Dean D

Predicting phenotype and emerging strains among Chlamydia trachomatis infections.

Emerging infectious diseases

Dean D, Bruno WJ, Wan R, Gomes JP, Devignot S, Mehari T, de Vries HJ, Morré SA, Myers G, Read TD, Spratt BG

Chlamydia trachomatis-infected patients display variable antibody profiles against the nine-member polymorphic membrane protein family.

Infection and immunity

Tan C, Hsia RC, Shou H, Haggerty CL, Ness RB, Gaydos CA, Dean D, Scurlock AM, Wilson DP, Bavoil PM

Identification of novel single nucleotide polymorphisms in inflammatory genes as risk factors associated with trachomatous trichiasis.

PloS one

Atik B, Skwor TA, Kandel RP, Sharma B, Adhikari HK, Steiner L, Erlich H, Dean D

Role of secreted conjunctival mucosal cytokine and chemokine proteins in different stages of trachomatous disease.

PLoS neglected tropical diseases

Skwor TA, Atik B, Kandel RP, Adhikari HK, Sharma B, Dean D

Comparative expression profiling of the Chlamydia trachomatis pmp gene family for clinical and reference strains.

PloS one

Nunes A, Gomes JP, Mead S, Florindo C, Correia H, Borrego MJ, Dean D

Evaluating the "A" component of the SAFE strategy.

The Lancet. Infectious diseases

Dean D, Atik B, Ton TK, Vu QL, Lagree S

Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae.

Journal of bacteriology

Liu Z, Rank R, Kaltenboeck B, Magnino S, Dean D, Burall L, Plaut RD, Read TD, Myers G, Bavoil PM

Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots.

Genome research

Gomes JP, Bruno WJ, Nunes A, Santos N, Florindo C, Borrego MJ, Dean D

Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes.

Microbes and infection

Millman K, Black CM, Stamm WE, Jones RB, Hook EW, Martin DH, Bolan G, Tavaré S, Dean D

Chlamydia pneumoniae burden in carotid arteries is associated with upregulation of plaque interleukin-6 and elevated C-reactive protein in serum.

Arteriosclerosis, thrombosis, and vascular biology

Johnston SC, Zhang H, Messina LM, Lawton MT, Dean D

Correlating Chlamydia trachomatis infectious load with urogenital ecological success and disease pathogenesis.

Microbes and infection

Gomes JP, Borrego MJ, Atik B, Santo I, Azevedo J, Brito de Sá A, Nogueira P, Dean D

Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States.

Journal of bacteriology

Millman K, Black CM, Johnson RE, Stamm WE, Jones RB, Hook EW, Martin DH, Bolan G, Tavaré S, Dean D

Risk factors for recurrence of postoperative trichiasis: implications for trachoma blindness prevention.

Archives of ophthalmology (Chicago, Ill. : 1960)

Zhang H, Kandel RP, Sharma B, Dean D

Limitations of screening tests for the detection of Chlamydia trachomatis in asymptomatic adolescent and young adult women.

American journal of obstetrics and gynecology

Shrier LA, Dean D, Klein E, Harter K, Rice PA

Chlamydia pneumoniae and acute chest syndrome in patients with sickle cell disease.

Journal of pediatric hematology/oncology

Dean D, Neumayr L, Kelly DM, Ballas SK, Kleman K, Robertson S, Iyer RV, Ware RE, Koshy M, Rackoff WR, Pegelow CH, Waldron P, Benjamin L, Vichinsky E, Acute Chest Syndrome Study Group