Education and Training

Postdoctoral Fellow, 1991 Microbial Pathogenesis, Stanford University School of Medicine
Clinical Fellow, 1989 Infectious Diseases, Stanford University School of Medicine
MPH, 1986 Epidemiology & Biostatistics, University of California Berkeley School of Public Health
Internship & Residency, 1983 Straight Internal Medicine, University of California San Francisco School of Medicine
MD, 1982 Medicine, Albert Einstein College of Medicine
B.S./B.A., 1977 Environmental Sciences/Philosophy, University of California Berkeley


Bommana S, Somboonna N, Richards G, Tarazkar M, Dean D. Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. mBio. 2021 May 11; 12(3).
Dean D, Swaminathan S, Kama M, Goemans S, Faktaufon D, Alnabelseya N, Spelke D, Kahrizi K, Black M, Mitra D. Development and evaluation of a Point-of-Care Test (POCT) in a low resource setting with high rates of Chlamydia trachomatis urogenital infections in Fiji. J Clin Microbiol. 2021 Apr 28.
Bowden KE, Joseph SJ, Cartee JC, Ziklo N, Danavall D, Raphael BH, Read TD, Dean D. Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs. mSphere. 2021 Mar 03; 6(2).
Choopara I, Suea-Ngam A, Teethaisong Y, Howes PD, Schmelcher M, Leelahavanichkul A, Thunyaharn S, Wongsawaeng D, deMello AJ, Dean D, Somboonna N. Fluorometric Paper-Based, Loop-Mediated Isothermal Amplification Devices for Quantitative Point-of-Care Detection of Methicillin-Resistant Staphylococcus aureus (MRSA). ACS Sens. 2021 Jan 13.
De Clercq E, Van Gils M, Schautteet K, Devriendt B, Kiekens C, Chiers K, Van Den Broeck W, Cox E, Dean D, Vanrompay D. Chlamydia trachomatis L2c Infection in a Porcine Model Produced Urogenital Pathology and Failed to Induce Protective Immune Responses Against Re-Infection. Front Immunol. 2020; 11:555305.
Srimongkol G, Ditmangklo B, Choopara I, Thaniyavarn J, Dean D, Kokpol S, Vilaivan T, Somboonna N. Rapid colorimetric loop-mediated isothermal amplification for hypersensitive point-of-care Staphylococcus aureus enterotoxin A gene detection in milk and pork products. Sci Rep. 2020 05 08; 10(1):7768.
Svigals V, Blair A, Muller S, Sahu Khan A, Faktaufon D, Kama M, Tamani T, Esfandiari L, O'Brien M, Dean D. Hyperendemic Chlamydia trachomatis sexually transmitted infections among females represent a high burden of asymptomatic disease and health disparity among Pacific Islanders in Fiji. PLoS Negl Trop Dis. 2020 01; 14(1):e0008022.
Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T. Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo". mBio. 2019 12 17; 10(6).
Somboonna N, Ziklo N, Ferrin TE, Hyuk Suh J, Dean D. Clinical Persistence of Chlamydia trachomatis Sexually Transmitted Strains Involves Novel Mutations in the Functional aßßa Tetramer of the Tryptophan Synthase Operon. mBio. 2019 07 16; 10(4).
Jolly AL, Rau S, Chadha AK, Abdulraheem EA, Dean D. Stromal Fibroblasts Drive Host Inflammatory Responses That Are Dependent on Chlamydia trachomatis Strain Type and Likely Influence Disease Outcomes. mBio. 2019 03 19; 10(2).
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. The utility of serology for elimination surveillance of trachoma. Nat Commun. 2018 12 21; 9(1):5444.
Somboonna N, Choopara I, Arunrut N, Sukhonpan K, Sayasathid J, Dean D, Kiatpathomchai W. Rapid and sensitive detection of Chlamydia trachomatis sexually transmitted infections in resource-constrained settings in Thailand at the point-of-care. PLoS Negl Trop Dis. 2018 12; 12(12):e0006900.
Marti H, Borel N, Dean D, Leonard CA. Evaluating the Antibiotic Susceptibility of Chlamydia - New Approaches for in Vitro Assays. Front Microbiol. 2018; 9:1414.
Gwyn SE, Xiang L, Kandel RP, Dean D, Gambhir M, Martin DL. Prevalence of Chlamydia trachomatis-Specific Antibodies before and after Mass Drug Administration for Trachoma in Community-Wide Surveys of Four Communities in Nepal. Am J Trop Med Hyg. 2018 01; 98(1):216-220.
Sharma M, Recuero-Checa MA, Fan FY, Dean D. Chlamydia trachomatis regulates growth and development in response to host cell fatty acid availability in the absence of lipid droplets. Cell Microbiol. 2018 02; 20(2).
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. Chlamydia trachomatis Strain Types Have Diversified Regionally and Globally with Evidence for Recombination across Geographic Divides. Front Microbiol. 2017; 8:2195.
Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM. Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PLoS One. 2017; 12(10):e0186030.
Turingan RS, Kaplun L, Krautz-Peterson G, Norsworthy S, Zolotova A, Joseph SJ, Read TD, Dean D, Tan E, Selden RF. Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay. PLoS One. 2017; 12(5):e0178653.
Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM. Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PLoS One. 2017; 12(4):e0174701.
Marti H, Kim H, Joseph SJ, Dojiri S, Read TD, Dean D. Tet(C) Gene Transfer between Chlamydia suis Strains Occurs by Homologous Recombination after Co-infection: Implications for Spread of Tetracycline-Resistance among Chlamydiaceae. Front Microbiol. 2017; 8:156.
Joseph SJ, Cox D, Wolff B, Morrison SS, Kozak-Muiznieks NA, Frace M, Didelot X, Castillo-Ramirez S, Winchell J, Read TD, Dean D. Dynamics of genome change among Legionella species. Sci Rep. 2016 09 16; 6:33442.
Joseph SJ, Marti H, Didelot X, Read TD, Dean D. Tetracycline Selective Pressure and Homologous Recombination Shape the Evolution of Chlamydia suis: A Recently Identified Zoonotic Pathogen. Genome Biol Evol. 2016 09 02; 8(8):2613-23.
Gwyn S, Mitchell A, Dean D, Mkocha H, Handali S, Martin DL. Lateral flow-based antibody testing for Chlamydia trachomatis. J Immunol Methods. 2016 08; 435:27-31.
Recuero-Checa MA, Sharma M, Lau C, Watkins PA, Gaydos CA, Dean D. Chlamydia trachomatis growth and development requires the activity of host Long-chain Acyl-CoA Synthetases (ACSLs). Sci Rep. 2016 Mar 18; 6:23148.
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. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell Rep. 2016 Jan 26; 14(3):611-620.
Joseph SJ, Marti H, Didelot X, Castillo-Ramirez S, Read TD, Dean D. Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans. Genome Biol Evol. 2015 Oct 27; 7(11):3070-84.
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. Population structure of Neisseria gonorrhoeae based on whole genome data and its relationship with antibiotic resistance. PeerJ. 2015; 3:e806.
Batteiger BE, Wan R, Williams JA, He L, Ma A, Fortenberry JD, Dean D. Novel Chlamydia trachomatis strains in heterosexual sex partners, Indianapolis, Indiana, USA. Emerg Infect Dis. 2014 Nov; 20(11):1841-7.
Joseph SJ, Li B, Ghonasgi T, Haase CP, Qin ZS, Dean D, Read TD. Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples. PLoS One. 2014; 9(6):e99290.
Al-Kuhlani M, Rothschild J, Rothchild J, Pal S, de la Maza LM, Ouburg S, Morré SA, Dean D, Ojcius DM. 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; 9(4):e93939.
Dean D, Rothschild J, Ruettger A, Kandel RP, Sachse K. Zoonotic Chlamydiaceae species associated with trachoma, Nepal. Emerg Infect Dis. 2013 Dec; 19(12):1948-55.
Read TD, Joseph SJ, Didelot X, Liang B, Patel L, Dean D. Comparative analysis of Chlamydia psittaci genomes reveals the recent emergence of a pathogenic lineage with a broad host range. mBio. 2013 Mar 26; 4(2).
Dean DA, Wadl PA, Hadziabdic D, Wang X, Trigiano RN. Analyzing microsatellites using the QIAxcel system. Methods Mol Biol. 2013; 1006:223-43.
Wang A, Al-Kuhlani M, Johnston SC, Ojcius DM, Chou J, Dean D. Transcription factor complex AP-1 mediates inflammation initiated by Chlamydia pneumoniae infection. Cell Microbiol. 2013 May; 15(5):779-94.
Dean D, Turingan RS, Thomann HU, Zolotova A, Rothschild J, Joseph SJ, Read TD, Tan E, Selden RF. A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis. PLoS One. 2012; 7(12):e51685.
Joseph SJ, Didelot X, Rothschild J, de Vries HJ, Morré SA, Read TD, Dean D. Population genomics of Chlamydia trachomatis: insights on drift, selection, recombination, and population structure. Mol Biol Evol. 2012 Dec; 29(12):3933-46.
Soupene E, Rothschild J, Kuypers FA, Dean D. Eukaryotic protein recruitment into the Chlamydia inclusion: implications for survival and growth. PLoS One. 2012; 7(5):e36843.
Bhattarai SR, Yoo SY, Lee SW, Dean D. Engineered phage-based therapeutic materials inhibit Chlamydia trachomatis intracellular infection. Biomaterials. 2012 Jul; 33(20):5166-74.
Trigiano RN, Wadl PA, Dean D, Hadziabdic D, Scheffler BE, Runge F, Telle S, Thines M, Ristaino J, Spring O. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. Mycologia. 2012 May-Jun; 104(3):633-40.
Srinivasan T, Bruno WJ, Wan R, Yen A, Duong J, Dean D. 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. J Bacteriol. 2012 Feb; 194(3):617-26.
Joseph SJ, Didelot X, Gandhi K, Dean D, Read TD. Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biol Direct. 2011 May 26; 6:28.
Somboonna N, Wan R, Ojcius DM, Pettengill MA, Joseph SJ, Chang A, Hsu R, Read TD, Dean D. Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L(2)) and D lineages. mBio. 2011; 2(3):e00045-11.
Atik B, Johnston SC, Dean D. Association of carotid plaque Lp-PLA(2) with macrophages and Chlamydia pneumoniae infection among patients at risk for stroke. PLoS One. 2010 Jun 09; 5(6):e11026.
Skwor T, Kandel RP, Basravi S, Khan A, Sharma B, Dean D. Characterization of humoral immune responses to chlamydial HSP60, CPAF, and CT795 in inflammatory and severe trachoma. Invest Ophthalmol Vis Sci. 2010 Oct; 51(10):5128-36.
Wang A, Johnston SC, Chou J, Dean D. A systemic network for Chlamydia pneumoniae entry into human cells. J Bacteriol. 2010 Jun; 192(11):2809-15.
Dean D, Bruno WJ, Wan R, Gomes JP, Devignot S, Mehari T, de Vries HJ, Morré SA, Myers G, Read TD, Spratt BG. Predicting phenotype and emerging strains among Chlamydia trachomatis infections. Emerg Infect Dis. 2009 Sep; 15(9):1385-94.
Tan C, Hsia RC, Shou H, Haggerty CL, Ness RB, Gaydos CA, Dean D, Scurlock AM, Wilson DP, Bavoil PM. Chlamydia trachomatis-infected patients display variable antibody profiles against the nine-member polymorphic membrane protein family. Infect Immun. 2009 Aug; 77(8):3218-26.
Atik B, Skwor TA, Kandel RP, Sharma B, Adhikari HK, Steiner L, Erlich H, Dean D. Identification of novel single nucleotide polymorphisms in inflammatory genes as risk factors associated with trachomatous trichiasis. PLoS One. 2008; 3(10):e3600.
Skwor TA, Atik B, Kandel RP, Adhikari HK, Sharma B, Dean D. Role of secreted conjunctival mucosal cytokine and chemokine proteins in different stages of trachomatous disease. PLoS Negl Trop Dis. 2008 Jul 16; 2(7):e264.
Somboonna N, Mead S, Liu J, Dean D. Discovering and differentiating new and emerging clonal populations of Chlamydia trachomatis with a novel shotgun cell culture harvest assay. Emerg Infect Dis. 2008 Mar; 14(3):445-53.
Dean D, Kandel RP, Adhikari HK, Hessel T. Multiple Chlamydiaceae species in trachoma: implications for disease pathogenesis and control. PLoS Med. 2008 Jan 03; 5(1):e14.
Nunes A, Gomes JP, Mead S, Florindo C, Correia H, Borrego MJ, Dean D. Comparative expression profiling of the Chlamydia trachomatis pmp gene family for clinical and reference strains. PLoS One. 2007 Sep 12; 2(9):e878.
Dean D, Atik B, Ton TK, Vu QL, Lagree S. Evaluating the "A" component of the SAFE strategy. Lancet Infect Dis. 2007 Jan; 7(1):2-3.
Liu Z, Rank R, Kaltenboeck B, Magnino S, Dean D, Burall L, Plaut RD, Read TD, Myers G, Bavoil PM. Genomic plasticity of the rrn-nqrF intergenic segment in the Chlamydiaceae. J Bacteriol. 2007 Mar; 189(5):2128-32.
Gomes JP, Bruno WJ, Nunes A, Santos N, Florindo C, Borrego MJ, Dean D. Evolution of Chlamydia trachomatis diversity occurs by widespread interstrain recombination involving hotspots. Genome Res. 2007 Jan; 17(1):50-60.
Atik B, Thanh TT, Luong VQ, Lagree S, Dean D. Impact of annual targeted treatment on infectious trachoma and susceptibility to reinfection. JAMA. 2006 Sep 27; 296(12):1488-97.
Millman K, Black CM, Stamm WE, Jones RB, Hook EW, Martin DH, Bolan G, Tavaré S, Dean D. Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and lack of association between ompA polymorphisms and clinical phenotypes. Microbes Infect. 2006 Mar; 8(3):604-11.
Gomes JP, Nunes A, Bruno WJ, Borrego MJ, Florindo C, 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. J Bacteriol. 2006 Jan; 188(1):275-86.
Johnston SC, Zhang H, Messina LM, Lawton MT, Dean D. Chlamydia pneumoniae burden in carotid arteries is associated with upregulation of plaque interleukin-6 and elevated C-reactive protein in serum. Arterioscler Thromb Vasc Biol. 2005 Dec; 25(12):2648-53.
Gomes JP, Borrego MJ, Atik B, Santo I, Azevedo J, Brito de Sá A, Nogueira P, Dean D. Correlating Chlamydia trachomatis infectious load with urogenital ecological success and disease pathogenesis. Microbes Infect. 2006 Jan; 8(1):16-26.
Gomes JP, Hsia RC, Mead S, Borrego MJ, Dean D. Immunoreactivity and differential developmental expression of known and putative Chlamydia trachomatis membrane proteins for biologically variant serovars representing distinct disease groups. Microbes Infect. 2005 Mar; 7(3):410-20.
Gomes JP, Bruno WJ, 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. J Bacteriol. 2004 Jul; 186(13):4295-306.
Millman K, Black CM, Johnson RE, Stamm WE, Jones RB, Hook EW, Martin DH, Bolan G, Tavaré S, Dean D. Population-based genetic and evolutionary analysis of Chlamydia trachomatis urogenital strain variation in the United States. J Bacteriol. 2004 Apr; 186(8):2457-65.
Zhang H, Kandel RP, Sharma B, Dean D. Risk factors for recurrence of postoperative trichiasis: implications for trachoma blindness prevention. Arch Ophthalmol. 2004 Apr; 122(4):511-6.
Shrier LA, Dean D, Klein E, Harter K, Rice PA. Limitations of screening tests for the detection of Chlamydia trachomatis in asymptomatic adolescent and young adult women. Am J Obstet Gynecol. 2004 Mar; 190(3):654-62.
Frick KD, Colchero MA, Dean D. Modeling the economic net benefit of a potential vaccination program against ocular infection with Chlamydia trachomatis. Vaccine. 2004 Jan 26; 22(5-6):689-96.
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. Chlamydia pneumoniae and acute chest syndrome in patients with sickle cell disease. J Pediatr Hematol Oncol. 2003 Jan; 25(1):46-55.