Deborah Dean, MD, MPH
Professor
Pediatrics
School of Medicine

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.

• Chlamydial and gonorrheal neglected sexually transmitted diseases among Pacific Islanders of the Western Pacific Region-A narrative review and call to action.
  PLoS neglected tropical diseases 2023 Auchus IC, Kama M, Bhuiyan RA, Brown J, Dean 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 2023 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 2023 Wongsamart R, Bhattarakasol P, Chaiwongkot A, Wongsawaeng D, Okada PA, Palaga T, Leelahavanichkul A, Khovidhunkit W, Dean D, Somboonna N
• Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Function across Anatomic Sites: a Pilot Study.
  Microbiology spectrum 2022 Bommana S, Richards G, Kama M, Kodimerla R, Jijakli K, Read TD, Dean D
• Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants.
  Frontiers in microbiology 2021 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 2021 Dean D, Swaminathan S, Kama M, Goemans S, Faktaufon D, Alnabelseya N, Spelke D, Kahrizi K, Black M, Mitra D
• Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function.
  mBio 2021 Bommana S, Somboonna N, Richards G, Tarazkar M, Dean D
• Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs.
  mSphere 2021 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 2021 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 2020 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 2020 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 2020 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".
  mBio 2019 Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T
• Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional αββα Tetramer of the Tryptophan Synthase Operon.
  mBio 2019 Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D
• Stromal Fibroblasts Drive Host Inflammatory Responses That Are Dependent on Chlamydia trachomatis Strain Type and Likely Influence Disease Outcomes.
  mBio 2019 Jolly AL, Rau S, Chadha AK, Abdulraheem EA, Dean D
• The utility of serology for elimination surveillance of trachoma.
  Nature communications 2018 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…
• 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 2018 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 2018 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 2018 Gwyn SE, Xiang L, Kandel RP, Dean D, Gambhir M, Martin DL
• Chlamydia trachomatis regulates growth and development in response to host cell fatty acid availability in the absence of lipid droplets.
  Cellular microbiology 2017 Sharma M, Recuero-Checa MA, Fan FY, Dean D
• Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides.
  Frontiers in microbiology 2017 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
• Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.
  PloS one 2017 Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM
• Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay.
  PloS one 2017 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 2017 Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM
• Tet(C) Gene Transfer between Chlamydia suis Strains Occurs by Homologous Recombination after Co-infection: Implications for Spread of Tetracycline-Resistance among Chlamydiaceae.
  Frontiers in microbiology 2017 Marti H, Kim H, Joseph SJ, Dojiri S, Read TD, Dean D
• Dynamics of genome change among Legionella species.
  Scientific reports 2016 Joseph SJ, Cox D, Wolff B, Morrison SS, Kozak-Muiznieks NA, Frace M, Didelot X, Castillo-Ramirez S, Winchell J, Read TD, Dean D
• Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia suis: A Recently Identified Zoonotic Pathogen.
  Genome biology and evolution 2016 Joseph SJ, Marti H, Didelot X, Read TD, Dean D
• Lateral flow-based antibody testing for Chlamydia trachomatis.
  Journal of immunological methods 2016 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 2016 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 2016 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 2015 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.
  PeerJ 2015 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 2014 Batteiger BE, Wan R, Williams JA, He L, Ma A, Fortenberry JD, Dean D
• Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.
  PloS one 2014 Joseph SJ, Li B, Ghonasgi T, Haase CP, Qin ZS, Dean D, Read TD
• TRAIL-R1 is a negative regulator of pro-inflammatory responses and modulates long-term sequelae resulting from Chlamydia trachomatis infections in humans.
  PloS one 2014 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 2013 Dean D, Rothschild J, Ruettger A, Kandel RP, Sachse K
• Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range.
  mBio 2013 Read TD, Joseph SJ, Didelot X, Liang B, Patel L, Dean D
• Analyzing microsatellites using the QIAxcel system.
  Methods in molecular biology (Clifton, N.J.) 2013 Dean DA, Wadl PA, Hadziabdic D, Wang X, Trigiano RN
• Transcription factor complex AP-1 mediates inflammation initiated by Chlamydia pneumoniae infection.
  Cellular microbiology 2012 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 2012 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 2012 Joseph SJ, Didelot X, Rothschild J, de Vries HJ, Morré SA, Read TD, Dean D
• Eukaryotic protein recruitment into the Chlamydia inclusion: implications for survival and growth.
  PloS one 2012 Soupene E, Rothschild J, Kuypers FA, Dean D
• Engineered phage-based therapeutic materials inhibit Chlamydia trachomatis intracellular infection.
  Biomaterials 2012 Bhattarai SR, Yoo SY, Lee SW, Dean D
• Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina.
  Mycologia 2012 Trigiano RN, Wadl PA, Dean D, Hadziabdic D, Scheffler BE, Runge F, Telle S, Thines M, Ristaino J, Spring O
• In vitro recombinants of antibiotic-resistant Chlamydia trachomatis strains have statistically more breakpoints than clinical recombinants for the same sequenced loci and exhibit selection at unexpected loci.
  Journal of bacteriology 2011 Srinivasan T, Bruno WJ, Wan R, Yen A, Duong J, Dean D
• Interplay of recombination and selection in the genomes of Chlamydia trachomatis.
  Biology direct 2011 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.
  mBio 2011 Somboonna N, Wan R, Ojcius DM, Pettengill MA, Joseph SJ, Chang A, Hsu R, Read TD, Dean D
• Association of carotid plaque Lp-PLA(2) with macrophages and Chlamydia pneumoniae infection among patients at risk for stroke.
  PloS one 2010 Atik B, Johnston SC, Dean D
• Characterization of humoral immune responses to chlamydial HSP60, CPAF, and CT795 in inflammatory and severe trachoma.
  Investigative ophthalmology & visual science 2010 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 2010 Wang A, Johnston SC, Chou J, Dean D
• Predicting phenotype and emerging strains among Chlamydia trachomatis infections.
  Emerging infectious diseases 2009 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 2009 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 2008 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 2008 Skwor TA, Atik B, Kandel RP, Adhikari HK, Sharma B, Dean D
• Discovering and differentiating new and emerging clonal populations of Chlamydia trachomatis with a novel shotgun cell culture harvest assay.
  Emerging infectious diseases 2008 Somboonna N, Mead S, Liu J, Dean D
• Multiple Chlamydiaceae species in trachoma: implications for disease pathogenesis and control.
  PLoS medicine 2008 Dean D, Kandel RP, Adhikari HK, Hessel T
• Comparative expression profiling of the Chlamydia trachomatis pmp gene family for clinical and reference strains.
  PloS one 2007 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 2007 Dean D, Atik B, Ton TK, Vu QL, Lagree S
• Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae.
  Journal of bacteriology 2006 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 2006 Gomes JP, Bruno WJ, Nunes A, Santos N, Florindo C, Borrego MJ, Dean D
• Impact of annual targeted treatment on infectious trachoma and susceptibility to reinfection.
  JAMA 2006 Atik B, Thanh TT, Luong VQ, Lagree S, Dean D
• Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes.
  Microbes and infection 2006 Millman K, Black CM, Stamm WE, Jones RB, Hook EW, Martin DH, Bolan G, Tavaré S, Dean D
• Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars: evidence for serovar Da recombination and correlation with tissue tropism.
  Journal of bacteriology 2006 Gomes JP, Nunes A, Bruno WJ, Borrego MJ, Florindo C, 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 2005 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 2005 Gomes JP, Borrego MJ, Atik B, Santo I, Azevedo J, Brito de Sá A, Nogueira P, Dean D
• Immunoreactivity and differential developmental expression of known and putative Chlamydia trachomatis membrane proteins for biologically variant serovars representing distinct disease groups.
  Microbes and infection 2005 Gomes JP, Hsia RC, Mead S, Borrego MJ, Dean D
• Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer.
  Journal of bacteriology 2004 Gomes JP, Bruno WJ, Borrego MJ, Dean D
• Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States.
  Journal of bacteriology 2004 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) 2004 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 2004 Shrier LA, Dean D, Klein E, Harter K, Rice PA
• Modeling the economic net benefit of a potential vaccination program against ocular infection with Chlamydia trachomatis.
  Vaccine 2004 Frick KD, Colchero MA, Dean D
• Chlamydia pneumoniae and acute chest syndrome in patients with sickle cell disease.
  Journal of pediatric hematology/oncology 2003 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