Publications:

Olagoke O, Aziz A, Zhu LH, Read TD, Dean D. Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline. NAR Genom Bioinform. 2025 Mar;7(1):lqae187. doi: 10.1093/nargab/lqae187. eCollection 2025 Mar. PubMed PMID: 39781511; PubMed Central PMCID: PMC11704784. 

Auchus IC, Brown J, Kama M, Vargo SG, Devi R, Singh J, Dean D. Enhanced Chlamydia trachomatis and Neisseria gonorrhoeae Sexually Transmitted Infections and Associated Risk Factors in Fiji Following the Coronavirus Disease 2019 Pandemic. Open Forum Infect Dis. 2025 Mar;12(3):ofaf101. doi: 10.1093/ofid/ofaf101. eCollection 2025 Mar. PubMed PMID: 40046883; PubMed Central PMCID: PMC11881064. 

Seth-Smith H, Bommana S, Dean D, Read TD, Marti H. Chlamydia suis undergoes interclade recombination promoting Tet-island exchange. BMC Genomics. 2024 Jul 26;25(1):724. doi: 10.1186/s12864-024-10606-6. PubMed PMID: 39060998; PubMed Central PMCID: PMC11282597. 

Bommana S, Hu Y-J, Kama M, Wang R, Kodimerla R, Jijakli K, Read TD, Dean D. Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji. mBio. 2024 Jan 16;15(1):e0306323. doi: 10.1128/mbio.03063-23. Epub 2023 Dec 20. PubMed PMID: 38117091; PubMed Central PMCID: PMC10790706. 

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. Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae. New Microbes New Infect. 2023 Sep;54:101158. doi: 10.1016/j.nmni.2023.101158. eCollection 2023 Sep. PubMed PMID: 37416863; PubMed Central PMCID: PMC10320375. 

Joseph SJ, Bommana S, Ziklo N, Kama M, Dean D, Read TD. Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis. Front Microbiol. 2023;14:1154664. doi: 10.3389/fmicb.2023.1154664. eCollection 2023. PubMed PMID: 37056744; PubMed Central PMCID: PMC10086254. 

Auchus IC, Kama M, Bhuiyan RA, Brown J, Dean D. Chlamydial and gonorrheal neglected sexually transmitted diseases among Pacific Islanders of the Western Pacific Region-A narrative review and call to action. PLoS Negl Trop Dis. 2023 Mar;17(3):e0011171. doi: 10.1371/journal.pntd.0011171. eCollection 2023 Mar. Review. PubMed PMID: 36928890; PubMed Central PMCID: PMC10019716. 

Joseph SJ, Bommana S, Ziklo N, Kama M, Dean D, Read TD. Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis. bioRxiv. 2023 Jan 26;. doi: 10.1101/2023.01.25.525576. PubMed PMID: 36747780; PubMed Central PMCID: PMC9901013. 

Wongsamart R, Bhattarakasol P, Chaiwongkot A, Wongsawaeng D, Okada PA, Palaga T, Leelahavanichkul A, Khovidhunkit W, Dean D, Somboonna N. Multiplex recombinase polymerase amplification for high-risk and low-risk type HPV detection, as potential local use in single tube. Sci Rep. 2023 Jan 16;13(1):829. doi: 10.1038/s41598-023-28038-9. PubMed PMID: 36646782; PubMed Central PMCID: PMC9841928. 

Bommana S, Richards G, Kama M, Kodimerla R, Jijakli K, Read TD, Dean D. 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. Microbiol Spectr. 2022 Jun 29;10(3):e0010522. doi: 10.1128/spectrum.00105-22. Epub 2022 May 17. PubMed PMID: 35579443; PubMed Central PMCID: PMC9241848. 

de Vries HJC, Pannekoek Y, Dean D, Bavoil PM, Borel N, Greub G, Morré SA. Call for consensus in Chlamydia trachomatis nomenclature: moving from biovars, serovars, and serotypes to genovariants and genotypes. Clin Microbiol Infect. 2022 Jun;28(6):761-763. doi: 10.1016/j.cmi.2022.02.013. Epub 2022 Feb 21. PubMed PMID: 35202789. 

Borel N, Greub G. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Chlamydiae, minutes of the closed meeting, 07 October 2021, via Webex. Int J Syst Evol Microbiol. 2022 Feb;72(2). doi: 10.1099/ijsem.0.005213. PubMed PMID: 35133257. 

Marti H, Bommana S, Read TD, Pesch T, Prähauser B, Dean D, Borel N. Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants. Front Microbiol. 2021;12:630293. doi: 10.3389/fmicb.2021.630293. eCollection 2021. PubMed PMID: 34276577; PubMed Central PMCID: PMC8278220. 

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 in a Low-Resource Setting with High Rates of Chlamydia trachomatis Urogenital Infections in Fiji. J Clin Microbiol. 2021 Jun 18;59(7):e0018221. doi: 10.1128/JCM.00182-21. Epub 2021 Jun 18. PubMed PMID: 33910964; PubMed Central PMCID: PMC8218753. 

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). doi: 10.1128/mBio.00605-21. PubMed PMID: 33975934; PubMed Central PMCID: PMC8262981. 

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 Mar 26;6(3):742-751. doi: 10.1021/acssensors.0c01405. Epub 2021 Jan 13. PubMed PMID: 33439634. 

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 3;6(2). doi: 10.1128/mSphere.01302-20. PubMed PMID: 33658279; PubMed Central PMCID: PMC8546720. 

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. doi: 10.3389/fimmu.2020.555305. eCollection 2020. PubMed PMID: 33193323; PubMed Central PMCID: PMC7649141. 

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 May 8;10(1):7768. doi: 10.1038/s41598-020-64710-0. PubMed PMID: 32385390; PubMed Central PMCID: PMC7211006. 

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 Jan;14(1):e0008022. doi: 10.1371/journal.pntd.0008022. eCollection 2020 Jan. PubMed PMID: 31971951; PubMed Central PMCID: PMC6999915. 

Dean D, Ziklo N, Somboonna N, Suh JH, Ferrin T. Reply to Rockey et al., "Genomics and Chlamydial Persistence In Vivo".mBio. 2019 Dec 17;10(6). doi: 10.1128/mBio.02957-19. PubMed PMID: 31848290; PubMed Central PMCID: PMC6918091. 

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 αββα Tetramer of the Tryptophan Synthase Operon. mBio. 2019 Jul 16;10(4). doi: 10.1128/mBio.01464-19. PubMed PMID: 31311884; PubMed Central PMCID: PMC6635532. 

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 Mar 19;10(2). doi: 10.1128/mBio.00225-19. PubMed PMID: 30890604; PubMed Central PMCID: PMC6426598. 

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 Dec 21;9(1):5444. doi: 10.1038/s41467-018-07852-0. PubMed PMID: 30575720; PubMed Central PMCID: PMC6303365. 

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 Dec;12(12):e0006900. doi: 10.1371/journal.pntd.0006900. eCollection 2018 Dec. PubMed PMID: 30571705; PubMed Central PMCID: PMC6301561. 

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. doi: 10.3389/fmicb.2018.01414. eCollection 2018. PubMed PMID: 30018602; PubMed Central PMCID: PMC6037721. 

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 Feb;20(2). doi: 10.1111/cmi.12801. Epub 2017 Dec 12. PubMed PMID: 29117636; PubMed Central PMCID: PMC5764794. 

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 Jan;98(1):216-220. doi: 10.4269/ajtmh.17-0102. Epub 2018 Jan 1. PubMed PMID: 29141720; PubMed Central PMCID: PMC5928690. 

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. doi: 10.3389/fmicb.2017.02195. eCollection 2017. PubMed PMID: 29180986; PubMed Central PMCID: PMC5693916. 

Choopara I, Arunrut N, Kiatpathomchai W, Dean D, Somboonna N. Corrigendum: Rapid and visual Chlamydia trachomatis detection using loop-mediated isothermal amplification and hydroxynaphthol blue. Lett Appl Microbiol. 2017 Oct;65(4):343. doi: 10.1111/lam.12786. PubMed PMID: 28913832. 

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. doi: 10.1371/journal.pone.0178653. eCollection 2017. PubMed PMID: 28562672; PubMed Central PMCID: PMC5451082. 

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. doi: 10.1371/journal.pone.0174701. eCollection 2017. PubMed PMID: 28410368; PubMed Central PMCID: PMC5391922. 

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. doi: 10.3389/fmicb.2017.00156. eCollection 2017. PubMed PMID: 28223970; PubMed Central PMCID: PMC5293829. 

Choopara I, Arunrut N, Kiatpathomchai W, Dean D, Somboonna N. Rapid and visual Chlamydia trachomatis detection using loop-mediated isothermal amplification and hydroxynaphthol blue. Lett Appl Microbiol. 2017 Jan;64(1):51-56. doi: 10.1111/lam.12675. Epub 2016 Nov 21. PubMed PMID: 27689353. 

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 Sep 16;6:33442. doi: 10.1038/srep33442. PubMed PMID: 27633769; PubMed Central PMCID: PMC5025774. 

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 Sep 2;8(8):2613-23. doi: 10.1093/gbe/evw182. PubMed PMID: 27576537; PubMed Central PMCID: PMC5010913. 

Gwyn S, Mitchell A, Dean D, Mkocha H, Handali S, Martin DL. Lateral flow-based antibody testing for Chlamydia trachomatis. J Immunol Methods. 2016 Aug;435:27-31. doi: 10.1016/j.jim.2016.05.008. Epub 2016 May 18. PubMed PMID: 27208400. 

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. doi: 10.1038/srep23148. PubMed PMID: 26988341; PubMed Central PMCID: PMC4796813. 

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. doi: 10.1016/j.celrep.2015.12.051. Epub 2016 Jan 7. PubMed PMID: 26774481; PubMed Central PMCID: PMC4868501. 

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. doi: 10.1093/gbe/evv201. PubMed PMID: 26507799; PubMed Central PMCID: PMC4994753. 

Patel S, Vajdy M. Induction of cellular and molecular immunomodulatory pathways by vitamin A and flavonoids. Expert Opin Biol Ther. 2015;15(10):1411-28. doi: 10.1517/14712598.2015.1066331. Epub 2015 Jul 17. Review. PubMed PMID: 26185959; PubMed Central PMCID: PMC4832596. 

Wolff BJ, Morrison SS, Pesti D, Ganakammal SR, Srinivasamoorthy G, Changayil S, Weil MR, MacCannell D, Rowe L, Frace M, Ritchie BW, Dean D, Winchell JM. Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes. Microbiology (Reading). 2015 Jul;161(7):1378-91. doi: 10.1099/mic.0.000097. Epub 2015 Apr 17. PubMed PMID: 25887617; PubMed Central PMCID: PMC4635502. 

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. doi: 10.7717/peerj.806. eCollection 2015. PubMed PMID: 25780762; PubMed Central PMCID: PMC4358642. 

Acharya A, Sen P, Aran K, Gardner A, Rafi M, Kim H, Webb M, Dean D, Murthy N. A turn-off fluorescent substrate for horseradish peroxidase improves the sensitivity of ELISAs. J. Polym. Sci. A Polym. Chem.. 2015 January; 53(2):206-210. doi: 10.1002/pola.27376.

Read TD, Massey RC. Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology. Genome Med. 2014;6(11):109. doi: 10.1186/s13073-014-0109-z. eCollection 2014. PubMed PMID: 25593593; PubMed Central PMCID: PMC4295408. 

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. doi: 10.3201/2011.140604. PubMed PMID: 25340463; PubMed Central PMCID: PMC4214310. 

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. doi: 10.1371/journal.pone.0099290. eCollection 2014. PubMed PMID: 24971628; PubMed Central PMCID: PMC4074039. 

Al-Kuhlani M, Rothschild 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. doi: 10.1371/journal.pone.0093939. eCollection 2014. PubMed PMID: 24695582; PubMed Central PMCID: PMC3973638. 

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. doi: 10.3201/eid1912.130656. PubMed PMID: 24274654; PubMed Central PMCID: PMC3840858. 

Acharya AP, Nafisi PM, Gardner A, Mackay JL, Kundu K, Kumar S, Murthy N. A fluorescent peroxidase probe increases the sensitivity of commercial ELISAs by two orders of magnitude. Chem Commun (Camb). 2013 Nov 14;49(88):10379-81. doi: 10.1039/c3cc44783a. PubMed PMID: 24071916; PubMed Central PMCID: PMC4011665. 

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. doi: 10.1111/cmi.12071. Epub 2012 Dec 16. PubMed PMID: 23163821; PubMed Central PMCID: PMC3593943. 
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). doi: 10.1128/mBio.00604-12. PubMed PMID: 23532978; PubMed Central PMCID: PMC3622922. 
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. doi: 10.1371/journal.pone.0051685. Epub 2012 Dec 14. PubMed PMID: 23272140; PubMed Central PMCID: PMC3522697. 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. doi: 10.1093/molbev/mss198. Epub 2012 Aug 13. PubMed PMID: 22891032; PubMed Central PMCID: PMC3494276. 

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. doi: 10.1016/j.biomaterials.2012.03.054. Epub 2012 Apr 9. PubMed PMID: 22494890; PubMed Central PMCID: PMC3341514. 

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. doi: 10.1371/journal.pone.0036843. Epub 2012 May 9. PubMed PMID: 22590624; PubMed Central PMCID: PMC3348897. 

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. doi: 10.1128/JB.06268-11. Epub 2011 Nov 28. PubMed PMID: 22123249; PubMed Central PMCID: PMC3264063. 

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. doi: 10.1186/1745-6150-6-28. PubMed PMID: 21615910; PubMed Central PMCID: PMC3126793. 

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. doi: 10.1128/mBio.00045-11. Print 2011. PubMed PMID: 21540364; PubMed Central PMCID: PMC3088116. 

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. doi: 10.1167/iovs.09-5113. Epub 2010 May 12. PubMed PMID: 20463311; PubMed Central PMCID: PMC3066612. 

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 9;5(6):e11026. doi: 10.1371/journal.pone.0011026. PubMed PMID: 20543948; PubMed Central PMCID: PMC2882946. 

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. doi: 10.1128/JB.01462-09. Epub 2010 Mar 16. PubMed PMID: 20233927; PubMed Central PMCID: PMC2876499. 

Dean D. Psittacosis. British medical journal. 2010 January; 340:1. 

Dean D. Chlamydia trachomatis today: treatment, detection, immunogenetics and the need for a greater global understanding of chlamydial disease pathogenesis. Drugs Today (Barc). 2009 Nov;45 Suppl B(Suppl B):25-31. Review. PubMed PMID: 20011691; PubMed Central PMCID: PMC3278962. 

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. doi: 10.3201/eid1509.090272. PubMed PMID: 19788805; PubMed Central PMCID: PMC2819883. 

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. doi: 10.1128/IAI.01566-08. Epub 2009 Jun 1. PubMed PMID: 19487469; PubMed Central PMCID: PMC2715660. 

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. doi: 10.1371/journal.pone.0003600. Epub 2008 Oct 31. PubMed PMID: 18974840; PubMed Central PMCID: PMC2572999. 

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. doi: 10.1371/journal.pntd.0000264. PubMed PMID: 18628987; PubMed Central PMCID: PMC2442224. 

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. doi: 10.3201/eid1403.071071. PubMed PMID: 18325260; PubMed Central PMCID: PMC2570839.

Dean D, Kandel RP, Adhikari HK, Hessel T. Multiple Chlamydiaceae species in trachoma: implications for disease pathogenesis and control.PLoS Med. 2008 Jan 3;5(1):e14. doi: 10.1371/journal.pmed.0050014. PubMed PMID: 18177205; PubMed Central PMCID: PMC2174965. 

Wang A, Dean D. Apoptosis, cell signaling and human diseases: molecular mechanisms. Journal of the American Medical Association. 2007 November; 298(18):2203.

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. doi: 10.1371/journal.pone.0000878. PubMed PMID: 17849007; PubMed Central PMCID: PMC1963315. 

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. doi: 10.1128/JB.00378-06. Epub 2006 Dec 8. PubMed PMID: 17158668; PubMed Central PMCID: PMC1855709. 

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. doi: 10.1101/gr.5674706. Epub 2006 Nov 7. PubMed PMID: 17090662; PubMed Central PMCID: PMC1716266. 

Wang A, Dean D. Apoptosis, Cell Signaling and Human Diseases: Molecular Mechanisms. JAMA : the journal of the American Medical Association. 2007; 298:2203-4. 

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. doi: 10.1016/S1473-3099(06)70661-2. PubMed PMID: 17182334. 

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. doi: 10.1001/jama.296.12.1488. PubMed PMID: 17003397. 

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 Aug;90(8):943-8. doi: 10.1136/bjo.2006.093104. Epub 2006 May 10. PubMed PMID: 16687452; PubMed Central PMCID: PMC1857215. 

Millman K, Black CM, Stamm WE, Jones RB, Hook EW 3rd, 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. doi: 10.1016/j.micinf.2005.08.012. Epub 2006 Jan 5. PubMed PMID: 16527508. 

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. doi: 10.1016/j.micinf.2005.05.014. Epub 2005 Jul 13. PubMed PMID: 16289001. 

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. doi: 10.1128/JB.188.1.275-286.2006. PubMed PMID: 16352844; PubMed Central PMCID: PMC1317584. 

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. doi: 10.1161/01.ATV.0000189157.88630.d1. Epub 2005 Oct 6. PubMed PMID: 16210572. 

Hsieh JC, Tham DM, Feng W, Huang F, Embaie S, Liu K, Dean D, Hertle R, Fitzgerald DJ, Mrsny RJ. Intranasal immunization strategy to impede pilin-mediated binding of Pseudomonas aeruginosa to airway epithelial cells. Infect Immun. 2005 Nov;73(11):7705-17. doi: 10.1128/IAI.73.11.7705-7717.2005. PubMed PMID: 16239575; PubMed Central PMCID: PMC1273878. 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. doi: 10.1016/j.micinf.2004.11.014. Epub 2005 Feb 24. PubMed PMID: 15784185. lGomes 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. doi: 10.1128/JB.186.13.4295-4306.2004. PubMed PMID: 15205432; PubMed Central PMCID: PMC421610.

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. doi: 10.1128/JB.186.8.2457-2465.2004. PubMed PMID: 15060049; PubMed Central PMCID: PMC412158. 

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. doi: 10.1001/archopht.122.4.511. PubMed PMID: 15078668. 

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. doi: 10.1016/j.ajog.2003.09.063. PubMed PMID: 15041995. 

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. doi: 10.1016/j.vaccine.2003.08.038. PubMed PMID: 14741161. sDean 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. doi: 10.1097/00043426-200301000-00010. PubMed PMID: 12544773. 

Dean D, Suchland RJ, Stamm WE. Reply: Persistence of Chlamydia trachomatis Infections: Bacterium and Host Based?. Journal of Infectious Diseases. 2001 December; 184(12):1632-1633. 

Johnston SC, Messina LM, Browner WS, Lawton MT, Morris C, Dean D. C-reactive protein levels and viable Chlamydia pneumoniae in carotid artery atherosclerosis. Stroke. 2001 Dec 1;32(12):2748-52. doi: 10.1161/hs1201.099631. PubMed PMID: 11739967. 

Millman KL, Tavaré S, Dean D. Recombination in the ompA gene but not the omcB gene of Chlamydia contributes to serovar-specific differences in tissue tropism, immune surveillance, and persistence of the organism. J Bacteriol. 2001 Oct;183(20):5997-6008. doi: 10.1128/JB.183.20.5997-6008.2001. PubMed PMID: 11567000; PubMed Central PMCID: PMC99679. 

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 Aug;69(8):4996-5000. doi: 10.1128/IAI.69.8.4996-5000.2001. PubMed PMID: 11447178; PubMed Central PMCID: PMC98592. 

Dean D, Powers VC. Persistent Chlamydia trachomatis infections resist apoptotic stimuli. Infect Immun. 2001 Apr;69(4):2442-7. doi: 10.1128/IAI.69.4.2442-2447.2001. PubMed PMID: 11254605; PubMed Central PMCID: PMC98177. 

Dean D, Suchland R, Stamm W. Persistence of Chlamydia trachomatis infections. The Journal of infectious diseases. 2001; 184:1632-4. 

Dean D, Suchland RJ, Stamm WE. Evidence for long-term cervical persistence of Chlamydia trachomatis by omp1 genotyping. J Infect Dis.2000 Sep;182(3):909-16. doi: 10.1086/315778. Epub 2000 Aug 17. PubMed PMID: 10950788. 

Plank R, Dean D. Overview of the epidemiology, microbiology, and pathogenesis of Leptospira spp. in humans. Microbes Infect. 2000 Aug;2(10):1265-76. doi: 10.1016/s1286-4579(00)01280-6. Review. PubMed PMID: 11008116. 

Vichinsky EP, Neumayr LD, Earles AN, Williams R, Lennette ET, Dean D, Nickerson B, Orringer E, McKie V, Bellevue R, Daeschner C, Manci EA. Causes and outcomes of the acute chest syndrome in sickle cell disease. National Acute Chest Syndrome Study Group. N Engl J Med.2000 Jun 22;342(25):1855-65. doi: 10.1056/NEJM200006223422502. PubMed PMID: 10861320.

Knox CM, Cevallos V, Margolis TP, Dean D. Identification of bacterial pathogens in patients with endophthalmitis by 16S ribosomal DNA typing.Am J Ophthalmol. 1999 Oct;128(4):511-2. doi: 10.1016/s0002-9394(99)00181-6. PubMed PMID: 10577597. 

Wang G, Xu X, Pace B, Dean DA, Glazer PM, Chan P, Goodman SR, Shokolenko I. Peptide nucleic acid (PNA) binding-mediated induction of human gamma-globin gene expression. Nucleic Acids Res. 1999 Jul 1;27(13):2806-13. doi: 10.1093/nar/27.13.2806. PubMed PMID: 10373600; PubMed Central PMCID: PMC148492. 

Dean D, Millman K. Phylogenetic analysis of Chlamydia trachomatis. Infect Immun. 1999 Feb;67(2):1009-10. doi: 10.1128/IAI.67.2.1009-1010.1999. PubMed PMID: 10075515; PubMed Central PMCID: PMC96422. 

Dean D. Genotyping Chlamydia trachomatis by PCR. Methods Mol Med. 1999;20:151-70. doi: 10.1385/0-89603-535-2:151. PubMed PMID: 21390734. 

Lin JS, Donegan SP, Heeren TC, Greenberg M, Flaherty EE, Haivanis R, Su XH, Dean D, Newhall WJ, Knapp JS, Sarafian SK, Rice RJ, Morse SA, Rice PA. Transmission of Chlamydia trachomatis and Neisseria gonorrhoeae among men with urethritis and their female sex partners. J Infect Dis. 1998 Dec;178(6):1707-12. doi: 10.1086/314485. PubMed PMID: 9815223. 

Knox CM, Cevellos V, Dean D. 16S ribosomal DNA typing for identification of pathogens in patients with bacterial keratitis. J Clin Microbiol.1998 Dec;36(12):3492-6. doi: 10.1128/JCM.36.12.3492-3496.1998. PubMed PMID: 9817860; PubMed Central PMCID: PMC105227. 

Lietman TM, Dhital SP, Dean D. Conjunctival impression cytology for vitamin A deficiency in the presence of infectious trachoma. Br J Ophthalmol. 1998 Oct;82(10):1139-42. doi: 10.1136/bjo.82.10.1139. PubMed PMID: 9924300; PubMed Central PMCID: PMC1722377. 

Lietman T, Brooks D, Moncada J, Schachter J, Dawson C, Dean D. Chronic follicular conjunctivitis associated with Chlamydia psittaci or Chlamydia pneumoniae. Clin Infect Dis. 1998 Jun;26(6):1335-40. doi: 10.1086/516373. PubMed PMID: 9636859. 

Chu KM, Rathinam R, Namperumalsamy P, Dean D. Identification of Leptospira species in the pathogenesis of uveitis and determination of clinical ocular characteristics in south India. J Infect Dis. 1998 May;177(5):1314-21. doi: 10.1086/515273. PubMed PMID: 9593018. 

Molestina RE, Dean D, Miller RD, Ramirez JA, Summersgill JT. 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 Apr;66(4):1370-6. doi: 10.1128/IAI.66.4.1370-1376.1998. PubMed PMID: 9529055; PubMed Central PMCID: PMC108062. 

Dean D, Ferrero D, McCarthy M. Comparison of performance and cost-effectiveness of direct fluorescent-antibody, ligase chain reaction, and PCR assays for verification of chlamydial enzyme immunoassay results for populations with a low to moderate prevalence of Chlamydia trachomatis infection. J Clin Microbiol. 1998 Jan;36(1):94-9. doi: 10.1128/JCM.36.1.94-99.1998. PubMed PMID: 9431928; PubMed Central PMCID: PMC124815. selRathinam SR, Rathnam S, Selvaraj S, Dean D, Nozik RA, Namperumalsamy P. Uveitis associated with an epidemic outbreak of leptospirosis.Am J Ophthalmol. 1997 Jul;124(1):71-9. doi: 10.1016/s0002-9394(14)71646-0. PubMed PMID: 9222235. 

Dean D, 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 Feb 1;99(3):475-83. doi: 10.1172/JCI119182. PubMed PMID: 9022081; PubMed Central PMCID: PMC507821. 

Ramirez JA. Isolation of Chlamydia pneumoniae from the coronary artery of a patient with coronary atherosclerosis. The Chlamydia pneumoniae/Atherosclerosis Study Group. Ann Intern Med. 1996 Dec 15;125(12):979-82. doi: 10.7326/0003-4819-125-12-199612150-00008. PubMed PMID: 8967709. 

Dean D, Oudens E, Bolan G, Padian N, Schachter J. Major outer membrane protein variants of Chlamydia trachomatis are associated with severe upper genital tract infections and histopathology in San Francisco. J Infect Dis. 1995 Oct;172(4):1013-22. doi: 10.1093/infdis/172.4.1013. PubMed PMID: 7561174. 

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 May;20(5):1179-85. doi: 10.1093/clinids/20.5.1179. PubMed PMID: 7619997. 

Weinstock H, Dean D, Bolan G. Chlamydia trachomatis infections. Infect Dis Clin North Am. 1994 Dec;8(4):797-819. Review. PubMed PMID: 7890933. 

Dean D, Stephens RS. Identification of individual genotypes of Chlamydia trachomatis from experimentally mixed serovars and mixed infections among trachoma patients. J Clin Microbiol. 1994 Jun;32(6):1506-10. doi: 10.1128/jcm.32.6.1506-1510.1994. PubMed PMID: 8077396; PubMed Central PMCID: PMC264028. 

Dean D, Schachter J, Dawson CR, Stephens RS. Comparison of the major outer membrane protein variant sequence regions of B/Ba isolates: a molecular epidemiologic approach to Chlamydia trachomatis infections. J Infect Dis. 1992 Aug;166(2):383-92. doi: 10.1093/infdis/166.2.383. PubMed PMID: 1634810. 

Dean D, Patton M, Stephens RS. Direct sequence evaluation of the major outer membrane protein gene variant regions of Chlamydia trachomatis subtypes D', I', and L2'. Infect Immun. 1991 Apr;59(4):1579-82. doi: 10.1128/iai.59.4.1579-1582.1991. PubMed PMID: 1706325; PubMed Central PMCID: PMC257882. selDean D, Palmer L, Pant CR, Courtright P, Falkow S, O'Hanley P, Falkow S. Use of a Chlamydia trachomatis DNA probe for detection of ocular chlamydiae. J Clin Microbiol. 1989 May;27(5):1062-7. doi: 10.1128/jcm.27.5.1062-1067.1989. PubMed PMID: 2663912; PubMed Central PMCID: PMC267483. selDean D, Pant CR, O'Hanley P, Falkow,S. Improved sensitivity of a modified polymerase chain reaction amplified DNA probe in comparison with serial tissue culture passage fr detection of Chlamydia trachomatis in conjunctival specimens from nepal. Diagn Microbiol Infect Dis. 1989 Mar-Apr;12(2):133-7. doi: 10.1016/0732-8893(89)90003-5. PubMed PMID: 2752712.

Book Chapters:

Kohlhoff S, Hammerschlag MR and Dean D. Chlamydia pneumoniae. In:  Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases, 10th Edition. Bennett, J, Dolin R, Mandell GL, eds. Elsevier. Part III Infectious Diseases and Their Etiologic Agents, Chapter 188. 2025

Dean D. Psittacosis. British Medical Journal. Best Medical Practice. 2025

Dean D. Chlamydia trachomatis Pathogenicity and Disease. In: Chlamydial Infection: A Clinical and Public Health Perspective. Issues Infect Dis. Ed: CM Black. Basel, Karger, vol 7, 2013: pgs 25–60

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., Part IV, Urogenital Pathogens; 2012; pgs 327-349

Dean D.  Pathogenesis of Chlamydial Ocular Infections.  In: Duane’s Foundations of Clinical Ophthalmology.  Tasman W, Jaeger EA, eds.  Lippincott Williams & Wilkins, Philadelphia, PA. Volume 2; Chapter 77; 2010; pgs 678-702

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.  Part 1, General Aspects. 2009; pgs 21-32