Deborah Dean, MD, MPH
An Overview
Scientists & Staff
Positions & Awards


Phone: 510-450-7655

CHORI Staff Directory
CHORI Intranet


Peer-Reviewed Publications (21st century)

  1. Dean D, Palmer L, Pant CR, Courtright P, Falkow S.  Use of a Chlamydia trachomatis DNA probe for detection of ocular chlamydiae.  J Clin Microbiol  1989;27:1062-67. PMCID: PMC267483
  2. Dean D, Pant CR, O'Hanley P.  Improved sensitivity of a modified polymerase chain reaction amplified DNA probe in comparison with serial tissue culture passage for detection of Chlamydia trachomatis in conjunctival specimens from Nepal.  Diag Microbiol Infect Dis  1989;12:133-37. PMID: 2752712
  3. Dean D, Patton M, Stephens RS.  Direct sequence evaluation of the major outer membrane protein gene variant regions of Chlamydia trachomatis subtypes D', I', L2'Infect Immun  1991;59:1579-82. PMCID: PMC257882
  4. Dean D, Schachter J, Dawson C, Stephens RS.  Comparison of the major outer membrane protein sequence variant regions of B/Ba isolates:  A molecular epidemiologic approach to Chlamydia trachomatis infections.  J Infect Dis  1992;166:383-392. PMID: 1634810
  5. Dean D, Stephens RS.  Identification of individual genotypes of Chlamydia trachomatis in experimentally mixed infections and mixed infections among trachoma patients.  J Clin Microbiol  1994;32(6):1506-10.  PMCID: PMC264028
  6. Dean D, Shama A, Schachter J, Dawson CR.  Molecular identification of an avian strain of Chlamydia psittaci causing severe keratoconjunctivitis in a bird fancier.  Clin Infect Dis  1995;20:1179-85. PMID: 7619997
  7. Dean D, Oudens EM, Bolan G, Padian N, Schachter J.  Major outer membrane protein variants of Chlamydia trachomatis are associated with severe genital tract infections and histopathology in San FranciscoJ Infect Dis  1995;172:1013-22. PMID: 7561174
  8. Ramirez JA, Ahkee S, Ganzel B, Ogend L, Gaydos CA, Quinn TC, Hammerschlag MR, Roblin PM, Lebar W, Cho CC, Campbell LA, Grayston JT, Patton DL, Dean D, Schachter J, Summersgill J.  Isolation of Chlamydia pneumoniae from the coronary artery of a patient with coronary arteriosclerosis.  Ann Inter Med  1996;125:979-82.  PMID: 8967709
  9. Rathinam R, Ratnam S, Selvaraj S, Dean D, Nozik R, Namperumalsamy P.  Uveitis associated with an outbreak of leptospirosis.  Am J Ophthalmol  1997;124:71-9.  PMID: 9222235
  10. Dean D and Millman K.  Molecular and Mutation Trends Analyses of omp1 Alleles for Serovar E of Chlamydia trachomatis:  Implications for the Immunopathogenesis of Disease.  J Clin Invest  1997;99:475-83. PMCID: PMC507821
  11. Dean D, Ferrero D, McCarthy M.  Comparison of performance and cost effectiveness of direct fluorescent-antibody, ligase chain reaction, PCR assays for verification of chlamydial enzyme immunoassay results for low to moderate prevalence of Chlamydia trachomatis infectionJ Clin Micro  1998;36:94-9. PMCID: PMC124815
  12. Molestina RE, Dean D, Miller RD, Ramirez JA, Summersgill J.  Characterization of a strain of Chlamydia pneumoniae isolated from a coronary atheroma by analysis of the omp1 gene and biological activity in human endothelial cells.  Infect Immun  1998;66:1370-6. PMCID: PMC108062
  13. Chu K, Rathinam R, Namperumalsamy P, Dean D.  Identification of Leptospira spp. in the pathogenesis of uveitis and determination of clinical ocular characteristics in South India.  J Infect Dis  1998;177:1314-21. PMID: 9593018
  14. Lietman T, Brooks D, Moncada J, Schachter J, Dawson CR, Dean D.  Chronic follicular conjunctivitis associated with Chlamydia pneumoniae and Chlamydia psittaciClin Infect Dis  1998;26:1335-40.  PMID: 9636859
  15. Lietman T, Dhital SP, Dean D.  Conjunctival impression cytology for vitamin A deficiency in the presence of infectious trachoma.  Br J Ophthalmol 1998;83:1139-42. PMCID: PMC1722377
  16. Lin J-S, Donegan SP, Newhall WJ, Dean D, Heeren T, Su X-H, Greenberg M, Rice PA. Transmission of Chlamydia trachomatis from men with urethritis to their female sex-partnersJ Infect Dis  1998;178:1707-12. PMID: 9815223
  17. Knox M, Cevallos V, Dean D.  16s Ribosomal RNA typing for bacterial keratitis.  J Clin Microbiol  1998;36:3492-6.  PMCID: PMC105227
  18. Dean D, Millman K.  Phylogenetic analysis of Chlamydia trachomatisInfect Immun 1999;67:1009-10. PMCID: PMC96422
  19. Knox M, Cevallos V, Margolis T, Dean D.  Identification of bacterial pathogens in patients with endophthalmitis by 16s ribosomal DNA typing.  Am J Ophthal  1999;128:511-3. PMID: 10577597
  20. Vichinsky EP, Neumayr LD, Earles AN, Williams R, Lennette ET, Dean D, Nickerson B, McKie V, Bellevue R, Daeschner C, Aboud M, Orringer E, Moncino M, Ware R, Ballas SK, Manci-Gardener E, Causes and outcomes of the acute chest syndrome in sickle cell disease. National Acute Chest Syndrome Study Group.  NEJM 2000;342:1855-65. PMID: 10861320
  21. Plank R, Dean D. Overview of the epidemiology, microbiology, and pathogenesis of Leptospira spp. in humans (peer reviewed review).  Microbes Infect  2000;2:1265-76.  PMID: 11008116
  22. Dean D, Suchland R, Stamm W.  Evidence of long-term cervical persistence of Chlamydia trachomatis by omp1 genotyping.  J Infect Dis  2000;182:909-16.  PMID: 10950788
  23. Dean D, Powers VC.  Persistent Chlamydia trachomatis Infections Resist Apoptotic Stimuli. Infect Immun 2001;69:2442-7.  PMCID: PMC98177
  24. Hessel T, Dhital SP, Plank R, Dean D. Immune response to chlamydial 60-kilodalton heat shock protein in tears from Nepali trachoma patients.  Infect Immun 2001;69:4996-5000.  PMCID: PMC98592 
  25. Millman K, Tavere S, Dean D. Recombination in the ompA gene but not the omcB gene of Chlamydia contribute to serovar specific differences in tissue tropism, immune surveillance and persistence of the organism.  J Bacteriol  2001;183:5997-6008. PMCID: PMC99679
  26. Johnston SC, Messina LM, Browner WS, Morris C, Dean D. C-reactive protein and viable Chlamydia pneumoniae in carotid artery atherosclerosis.  Stroke  2001;32:2748-2752.  PMID: 11739967
  27. Dean D, Suchland R, Stamm W.  Persistence of Chlamydia trachomatis infections.  J Infect Dis  2001;184:1632-3.  doi:10.1086/324670
  28. Dean D, Neumayr L, Kleman K, Vichinsky E. Chlamydia pneumoniae and acute chest syndrome in patients with sickle cell disease.   J Ped Hem/Onc  2003;25:46-55.  PMID: 12544773
  29. Frick K, Colchero MA, Dean D. Modeling the economic net benefit of a potential vaccination program against ocular infection with Chlamydia trachomatis. Vaccine 2004;22:689-96.  PMID: 14741161
  30. Millman K, Black CM, Johnson R, Stamm WE, Jones R, Hook E, Martin D, 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;186:2457-65.  PMCID: PMC412158
  31. 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 Gynecol2004;190:654-62. PMID: 15041995
  32. Gomes JP, Bruno WJ, Borrego MJ, Dean D. Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C relative to ompA and evidence for horizontal gene transfer.  J Bacteriol  2004: 186:4295-306. PMCID: PMC421610
  33. Zhang H, Kandel RP, Sharma B, Dean D. Risk factors for recurrence of postoperative trichiasis:  implications for trachoma blindness prevention.  Archives of Ophthalmol 2004;122:511-6.  PMID: 15078668
  34. Gomes JP, Hsia R-c, 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;7:410-20.  PMID: 15784185
  35. Hsieh JC, Tham DM, Feng W, Huang F, Embaie S, Liu K, Dean D, FitzGerald DJ and Mrsny RJ. An Intranasal immunization strategy to impede pilin-mediated binding of Pseudomonas aeruginosa to airway epithelial cells and neutralize cytotoxic actions of this pathogen. Infect Immun 2005;73:7705-7717.  PMCID: PMC1273878
  36. 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;25:2648-53. PMID: 16210572
  37. 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;8:16-26. PMID: 16289001
  38. Gomes JP, Bruno WJ, Borrego MJ, Nunes A, Florindo C, Dean D.  Polymorphisms in the nine polymorphic membrane proteins of Chlamydia trachomatis across all serovars:  Evidence for Da recombination and correlation with tissue tropism.  J Bacteriol  2006;188:275-86.  PMCID: PMC1317584
  39. Millman K, Black CM, Stamm WE, Jones R, Hook E, Martin D, Bolan G, Tavaré S, Dean D. Population-based genetic epidemiologic analysis of Chlamydia trachomatis serotypes and ompA polymorphisms associated with clinical phenotypes.  Microbes Infect 2006;8:604-11. PMID: 16527508
  40. Zhang H, Kandel RP, Atakari HK,  Dean D. Impact of oral azithromycin on recurrence of trachomatous trichiasis in Nepal over 1 year. Br J Ophthalmol  2006;90:943-948. PMCID: PMC1857215
  41. Atik B, Thanh TTK, Luong VQ , Lagree S, Dean D.   Impact of Annual Targeted Treatment on Infectious Trachoma and Susceptibility to Reinfection. JAMA  2006;296:1488-97.  PMID: 17003397
  42. 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 Research 2007;1:50-60.  PMCID: PMC1716266
  43. Liu Z, Rank R, Kaltenboek B, Magnino S, Dean D, Plaut R, Read T, Myers G, Bavoil, PM. Genomic plasticity of the rrn-nqrF intergenic segment in the ChlamydiaceaeJ Bacteriol  2007;189;2128-2132.  PMCID: PMC1855709
  44. Dean D, Atik B, Thanh TT, Luong VQ, Lagree S. Evaluating the “A” component of the SAFE strategy.  Lancet Infectious Diseases  2007;7:2-3. PMID: 17182334
  45. 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;2:e878 doi:10.1371/journal.pone.0000878.  PMCID: PMC1963315
  46. Wang A, Dean D. Apoptosis, cell signaling and human diseases: molecular mechanisms. JAMA 2007;298:2203-4. PMID: 18316188
  47. Dean D, Kandel RP, Atakari HK , Hessel T. Multiple Chlamydiaceae species in trachoma: implications for disease pathogenesis and control. PLoS Medicine  2008;5:e14. PMCID: PMC2174965
  48. Somboonna N, Mead S, Lui J, Dean D. Discovering and differentiating new and emerging clonal populations of Chlamydia trachomatis with a novel shotgun cell culture harvest assay.   Emerging Infect Dis  2008;14:445-53. PMCID: PMC2570839
  49. Skwor T, Atik B, Kandel RP, Atakari HK, Dean D. Role of secreted conjunctival mucosal cytokine and chemokine proteins in different stages of Trachomatous disease. PLoS Neglected Trop Dis  2008;2:e264. PMCID: PMC2442224
  50. Atik B, Skwor TA, Kandel RP, Atakari 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:e3600. PMCID: PMC2572999
  51. Tan C, Hsia R,  Shou H, Haggarty C, Gaydos C, Dean D, Scurlock A, Wilson DP, Bavoil PM. C. trachomatis-infected patients display variable antibody profiles against the nine-member polymorphic membrane protein family. Infect Immunity 2009;77:3218-26. PMCID: PMC2715660
  52. Dean D, Bruno WJ, Wan R, Gomes JP, Devignot S, Mehari T, Servaas A. Morre, Myers G, Read TD, Spratt BG. Predicting phenotype and emerging strains among Chlamydia trachomatis infections. Emerging Infectious Diseases 2009;15:1385-94.  PMCID: PMC2819883
  53. Dean D. Psitacosis - Monograph.  British Medical Journal. 2010;
  54. Dean D. Chlamydia trachomatis today: treatment, detection, immunogenetics and the need for a greater global understanding of chlamydial disease pathogenesis. Drugs Today.  2009:45 Suppl B:25-31.  PMID: 20011691
  55. Wang A, Johnston SC, Chou J, Dean D. A systemic network for Chlamydia pneumoniae entry into human cells.  J Bacteriol   2010;192: 2809–2815. PMCID: PMC2876499
  56. Atik B, Johnston SC, Dean D.  Association of carotid plaque Lp-PLA2 with macrophages and Chlamydia pneumoniae, but not serum Lp-PLA2 mass or activity levels, among patients at risk for stroke. PLoS ONE  2010;5: e11026. PMCID: PMC2882946
  57. Skwor T, Basaravi S, Khan A, Kandel RP, Sharma B, Dean D. Characterization of the humoral immune responses to chlamydial heat shock protein 60, protease-like activity factor and hypothetical protein CT795 in inflammatory and severe trachoma. IOVS  2010;51:5128-36.  PMCID: PMC3066612
  58. Somboonna N, Wan R, Ojcius DM, Pettengill M, Chang A, Joseph S, Hsu RJ, Read TD, and Dean D. Hypervirulent Chlamydia trachomatis clinical strain is a recombinant between lymphogranuloma venereum (L2) and D lineages. mBio  2011;2(3):doi:10.1128/mBio.00045-11.
  59. Joseph SJ, Didelot X, Gandhi K, Dean D, Read TD. Interplay of recombination and selection in the genomes of Chlamydia trachomatis. Biology Direct  2011;6:28.  PMCID: PMC3126793
  60. Srinivasan T, Bruno WJ, Wan R, Yen A, Duong J, and 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;194:617-26. PMCID: PMC3264063.
  61. Bhattarai SR, Yoo SY, Lee SW, and Dean D. Novel engineered phage-based therapeutic materials inhibiting Chlamydia trachomatis intracellular infection. Biomaterials  2012;33:5166-74. PMCID: PMC3341514.
  62. Soupene E, Rothschild J, Kuypers FA, and Dean D. Eukaryotic protein recruitment into the Chlamydia inclusion: implications for survival and growth. PLoS ONE 2012;7(5):e36843. PMCID: PMC3348897.
  63. 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;29:3933-46. PMCID: PMC3494276
  64. 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 2012; Nov 16. doi: 10.1111/cmi.12071 [Epub ahead of print]
  65. Dean D, Turingan RS, Rothschild J, Zolotova A, Thomann HU, Joseph, SJ, Read TD, Selden RF. A Multiplexed PCR Assay for Sensitive and Specific Point-of-Care Detection of C. trachomatis. PLoS ONE 2012;7(12);e51685. PMCID: PMC3522697
  66. 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;4(2). doi: 10.1128/mBio.00604-12. PMCID: PMC3622922
  67. Dean D, Rothschild J, Ruettger A, Kandel RP, Sachse K. Chlamydiaceae Microarray Typing of Conjunctival Samples:  Discovering Species Distribution Among a Trachoma Endemic Population in Nepal. 2013; submitted.
  68. Batteiger B,, Wan R, Williams JA, Van Der Pol B,  Fortenberry JD, He L, Ma A, and Dean D. Tracking partner concordance using Chlamydia trachomatis MLST. 2013; submitted.
  69. Al-Kuhlani M, Rothchild J, Pal S, de la Maza LM, Ouburg S, Morré SA, Dean D, and Ojcius DM. Human TRAIL-R1 is a negative regulator of pro-inflammatory response induced by Chlamydia trachomatis. 2013 Submitted.
  70. Atik B, Johnston SC, Madden E, Balakrishnan P, Erlich JH, Dean D. Single nucleotide polymorphisms in C3, CCR2 and SDF1 are associated with Chlamydia pneumoniae infection among patients with carotid atherosclerosis. 2013; submitted.

Book Chapters

  1. Dean D.  Molecular characterization of new Chlamydia trachomatis serological variants from a trachoma endemic region of Africa.  In:  Chlamydial Infections.  Orfila J, et al. eds.  Societa Editrice Esculapio, Bologna;  1994; pp. 259-62.
  2. Weinstock HS, Dean D, Bolan G.  Chlamydia trachomatis Infections.  In:  Sexually Transmitted Diseases in the AIDS Era; Part II.  Infectious Disease Clinics of North America; WB Saunders, Philadelphia;  1994.  pg. 797-819.
  3. Dean DChlamydia trachomatis Sexually Transmitted Diseases.  In:  Pathology of Infectious Diseases.  Connor DH, Schwartz DA, Chandler FW, eds.  Appleton and Lange Publishers, Stamford, Conn. 1997: pgs 473-90
  4. Dean D.  Trachoma.  In:  Pathology of Infectious Diseases.  Connor DH, Schwartz DA, Chandler FW, eds.  Appleton and Lange Publishers, Stamford, Conn. 1997: pgs 498-507
  5. Dean D.  Typing of Chlamydia trachomatis. In:  Molecular Protocols for Sexually Transmitted Diseases.  Methods in Molecular Medicine Series.  Peeling R, Sparling PF, eds. Humana Press, Inc, Totowa, NJ. 1999;pgs 151-70.
  6. Dean D.  Pathogenesis of Chlamydial Ocular Infections.  In: Duane’s Foundations of Clinical Ophthalmology.  Tasman W, Jaeger EA, eds.  Lippincott Williams & Wilkins, Philadelphia, PA. 2002;Volume 2; Chapter 77; pgs 1-20.
  7. Dean D, Myers G, Read T. Lessons and challenges arising from the “first wave” of chlamydial genomics.  In: Chlamydia: Genomics, Pathogenesis and Implications for Control.  Editors: Patrik Bavoil and Priscilla Wyrick.   Horizon Scientific Press, Norwich, UK.  2006; Chapter 1; pgs 1-24.
  8.   Dean D, Millman K. The Evolution of Chlamydiaceae and Chlamydiaceae Infections.  In: Evolutionary Biology of Bacterial and Fungal Pathogens.  Baquero F, Nombell C, Cassell GH, Gutierrez JA, eds.  ASM Press, Washington D.C. 2007:Chpt 40; pgs 475-488.
  9. Somboonna N, Dean D. Limited genomes and gene transfer in the evolution of intracellular parasitism and symbiosis. In: Intracellular Niches of Pathogens – A Microbe’s Guide through the Host Cell.  Editors:  Schaible UE and Haas A. Wiley-VCH Publishers.  2009; Part 1,  General Aspects, 2, ; pages 21-32.
  10. Dean D.  Pathogenesis of Chlamydial Ocular Infections.  In: Duane’s Foundations of Clinical Ophthalmology.  Tasman W, Jaeger EA, eds.  Lippincott Williams & Wilkins, Philadelphia, PA. 2010;Volume 2; Chapter 77; pgs 678-702.
  11. Skwor T, Dean D. Molecular approaches to typing chlamydiae.  In:  Molecular typing in bacterial infections.  Eds: McKee ML and de Filippis I, Humana Press, Inc. 2012; Part IV Urogenital Pathogens; pgs 327-349.
  12. Dean D.  Chlamydia trachomatis Pathogenicity and Disease. In: Chlamydia Infections: A Clinical and Public Health Perspective. Ed. Black C. Centers for Disease Control and Prevention. 2013; In Press.


Dean D. The Impact of Comparative and Functional Genomics on Chlamydial Disease Pathogenesis and Global Disease Control.  Imperial College Press, London, UK.  2013; In Preparation

Revised: Thursday, April 16, 2020 3:02 PM


© 2005 Children's Hospital Oakland Research Institute
5700 Martin Luther King Jr Way • Oakland, California 94609
Phone 510-450-7600 • Fax 510-450-7910
Site MapDisclaimer