Peer-reviewed

Pappas RS, Sweetman BJ, Ray S, and Hellerqvist CG. Monomer sequence determination of carbohydrates using fast-atom bombardment mass spectrometry of periodate oxidized acetate ester derivatives. Carbohydrate Research 1990; 197:1-14.

Cavener DR and Ray SC. Eukaryotic start and stop translation sites. Nucl Acids Res 1991; 19:3185-3192.

Ray SC, Siliciano RF, and Bollinger RC. Vaccines and immunotherapy for human immunodeficiency virus type 1 (HIV-1) infection: a brief review. Venereology 1993; 6:93-94.

Baskar PV, Ray SC, Rao R, Quinn TC, Hildreth JEK, and Bollinger RC. The presence of HIV-1 similar to North American strains in India. AIDS Res Human Retroviruses 1994; 10:1039-1041.

Markham RB, Yu X, Farzadegan H, Ray SC, and Vlahov D. HIV-1 env and p17gag sequence variation in polymerase chain reaction positive, seronegative injection drug users. JID 1995; 171:797-804.

Strunnikova N, Ray SC, Livingston RA, Rubalcaba E, and Viscidi RP. Convergent evolution within the V3 Loop domain of Human Immunodeficiency Virus type 1 in association with disease progression. J Virol 1995; 69:7548-7558.

Heldman AW, Hartert TV, Ray SC, Daoud EG, Kowalski TE, Pompili VJ, Sisson SD, Tidmore WC, vom Eigen KA, Goodman SN, Lietman PS, Petty BG, and Flexner C. Oral antibiotic treatment of right-sided Staphylococcal endocarditis in injection drug users: prospective randomized comparison with parenteral therapy. Am J Med 1996; 101:68-76.

Schwartz DH, Viscidi R, Laeyendecker O, Song H, Ray SC, Michael N. Predominance of defective proviral sequences in an HIV+ long-term non-progressor. Immunol Lett 1996; 51:3-6.

Pan D, Hsu K, and Ray SC. Ecchymoses and eschars at sites of injection. Lancet 1997; 349:1364.

Lubaki N, Ray SC, Dhruva B, Quinn TC, Siliciano RF, and Bollinger RC. Characterization of a polyclonal cytolytic T lymphocyte response to Human Immunodeficiency Virus in persons without clinical progression. JID 1997; 6:1360-1367.

Ray SC, Lubaki N, Dhruva BR, Siliciano RF, and Bollinger RC. Autologous strain-specific cytolytic T lymphocyte responses directed against Human Immunodeficiency Virus type 1 env. AIDS Res Hum Retrov 1998;14: 3-13.

Strunnikova N, Ray SC, Lancioni C, Nguyen M, and Viscidi RP. Evolution of Human Immunodeficiency Virus type 1 in relation to disease progression in children. J Human Virol 1998; 1:224-239.

Wang Y-M, Ray SC, Laeyendecker O, Ticehurst JR, and Thomas DT. Assessment of Hepatitis C Virus sequence complexity by the electrophoretic mobility of both single- and double-stranded DNA. J Clin Micro 1998; 36(10):2982-2989.

Ray S. Capnocytophaga canimorsus sepsis [letter] N Engl J Med 1999;340(19):1513-4.

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, and Ray SC. Full-length Human Immunodeficiency Virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of inter-subtype recombination. J Virol 1999; 73(1):152-160.

Dibbern DA and Ray SC. Recrudescence of treated neurosyphilis in an HIV-positive host. Mayo Clin Proc 1999; 74(1):53-56.

Echavarria MS, Ray SC, Ambinder R, Dumler JS, and Charache P. PCR detection of adenovirus in a bone marrow transplant recipient: hemorrhagic cystitis as a presenting manifestation of disseminated disease. J Clin Micro 1999; 37(3):686-689.

Ray SC, Wang Y-M, Laeyendecker O, Ticehurst JR, Villano SA, Thomas DL. Acute Hepatitis C Virus structural gene sequences as predictors of persistent viremia: Hypervariable region 1 as a decoy. J Virol 1999; 73(4):2938-46.

Ray SC, Mao Q, Lanford RE, Bassett S, Laeyendecker OB, Wang Y-M, Thomas DT. Hypervariable region 1 sequence stability during hepatitis C virus replication in chimpanzees. J Virol 2000; 74(7):3058-66.

Thomas DL, Astemborski J, Vlahov D, Strathdee SA, Ray SC, Nelson KE, Galai N, Nolt KR, Laeyendecker O, Todd JA. Determinants of the quantity of hepatitis C virus RNA. J Infect Dis 2000; 181(3):844-851.

Persaud D, Pierson T, Ruff C, Finzi D, Chadwick KR, Margolick JB, Ruff A, Hutton N, Ray S, Siliciano RF. A stable latent reservoir for HIV-1 in resting CD4+ T lymphocytes in infected children. J Clin Invest 2000; 105(7):995-1003.

Ray SC, Arthur RR, Carella A, Bukh J, and Thomas DL. Genetic epidemiology of hepatitis C virus throughout Egypt. J Infect Dis 2000; 182(3):698-707.

Nousbaum J-B, Polyak SJ, Ray SC, Sullivan DG, Larson AM, Carithers RL Jr, Gretch DR. Prospective characterization of full-length hepatitis C virus NS5A quasispecies during induction and combination antiviral therapy. J Virology 2000; 74(19):9028-9038.

Mao Q, Ray SC, Laeyendecker O, Ticehurst JR, Strathdee SA, Vlahov D, and Thomas DL. HIV seroconversion and evolution of the hepatitis C quasispecies. J Virology 2001; 75(7):3259-67.

Hermankova M, Ray SC, Ruff C, Powell Davis M, Ingersoll R, D’Aquila RT, Quinn TC, Siliciano JD, Siliciano RF, Persaud D, Stasis in the drug resistance profiles of HIV-1 in the plasma of infected children and adults on protease inhibitor-containing combination therapy with <50 copies/ml of plasma HIV-1 RNA. JAMA 2001; 286(2): 196-207.

Dumler JS, Barbet AF, Bekker CPJ, Dasch GA, Palmer GH, Ray SC, Rikihisa Y, Rurangirwa FR. Reorganization of Genera in the Families Rickettsiaceae and Anaplasmataceae in the Order Rickettsiales; Unification of Some Species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia, and Ehrlichia with Neorickettsia; Descriptions of Five New Species Combinations; and Designation of Ehrlichia equi and "HGE agent" as Subjective Synonyms of Ehrlichia phagocytophila. Int J Syst Evol Microbiol 2001; 51: 2145-2165.

Thimme R, Oldach D, Chang K-M, Steiger C, Ray SC, and Chisari FV. Determinants of viral clearance and persistence during acute hepatitis C virus infection. J Exp Med 2001; 194: 1395-1406.

Wilson LE, Umemura T, Astemborski J, Ray SC, Alter HJ, Strathdee SA, Vlahov D, and Thomas DL. SEN Virus and Injection Drug Users. JID 2001; 184(10): 1315-9.

Mehta SH, Cox A, Hoover DR, Wang X-H, Mao Q, Ray S, Strathdee SA, Vlahov D, and Thomas DL. Protection against persistence of Hepatitis C. Lancet 2002; 359(9316): 1478-83.

Sulkowski MS, Ray SC, and Thomas DL. Needlestick transmission of hepatitis C. JAMA 2002; 287(10): 2406-13.

Ruff CT, Ray SC, Kwon P, Zinn R, Pendleton A, Hutton N, Ashworth R, Gange S, Quinn TC, Siliciano RF, and Persaud D. Persistence of Wild Type Virus and Lack of Temporal Structure in the Latent Reservoir for HIV-1 in Pediatric Patients with Extensive Antiretroviral Exposure. J Virology 2002; 76(18): 9481-92.

Wilbe K, Salminen M, Laukannen T, McCutchan F, Ray SC, Albert J, and Leitner T. Characterization of novel recombinant HIV-1 genomes using the branching index. Virology 2003; 316: 116-25.

Persaud D, Siberry GK, Ahonkhai A, Kajdas J, Monie D, Hutton N, Watson DC, Quinn TC, Ray SC, and Siliciano RF. Continued production of drug-sensitive human immunodeficiency virus type 1 in children on combination antiretroviral therapy who have undetectable viral loads. J Virology 2004;78(2):968-79.

Lanford RE, Guerra B, Chavez D, Bigger C, Brasky KM, Wang XH, Ray SC, and Thomas DL. Cross-genotype immunity to hepatitis C virus. J Virology 2004;78(3):1575-81.

Kieffer TL, Finucane MM, Nettles RE, Quinn TC, Broman KW, Ray SC, Persaud D, and Siliciano RF. Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads. J Infect Dis 2004; 189:1452.

Liu Z, Netski D, Mao Q, Laeyendecker O, Ticehurst J.R., Wang X.-H., Thomas DL, and Ray SC. Accurate representation of the hepatitis C virus quasispecies in 5.2-kilobase amplicons. J Clin Microbiol 2004; 42(9):4223-9.

Kieffer TL, Kwon P, Nettles RE, Han Y, Ray SC, and Siliciano RF. G->A hypermutation in protease and RT regions of HIV-1 residing in resting CD4+ T cells in vivo. J Virology 2005; 79(3):1975-80.

Li K, Foy E, Ferreon JC, Nakamura M, Ferreon ACM, Ikeda M, Ray SC, Gale M, and Lemon SM. Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF. Proc Natl Acad Sci (USA) 2005; 102(8): 2992-7.

Nettles RE, Kieffer TL, Kwon P, Monie D, Han Y, Parsons T, Cofrancesco J Jr, Gallant JE, Quinn TC, Jackson B, Flexner C, Carson K, Ray S, Persaud D, Siliciano RF. Intermittent HIV-1 viremia (Blips) and drug resistance in patients receiving HAART. JAMA 2005;293(7):817-29.

Laeyendecker O, Zhang GW, Quinn TC, Garten R, Ray SC, Lai S, Liu W, Chen J, Yu XF. Molecular Epidemiology of HIV-1 Subtypes in Southern China. J AIDS. 2005;38(3):356-362.

Monie D, Simmons RP, Nettles RE, Kieffer TL, Zhou Y, Zhang H, Karmon S, Ingersoll R, Chadwick K, Zhang H, Margolick JB, Quinn TC, Ray SC, Wind-Rotolo M, Miller M, Persaud D, Siliciano RF. A Novel Assay Allows Genotyping of the Latent Reservoir for Human Immunodeficiency Virus Type 1 in the Resting CD4+ T Cells of Viremic Patients. J Virol. 2005; 79(8):5185-202.

Cox AL, Netski DM, Mosbruger T, Sherman SG, Strathdee S, Ompad D, Vlahov D, Chien D, Shyamala V, Ray SC, and Thomas DL. Prospective evaluation of community-acquired acute hepatitis C. Clin Infect Dis 2005; 40(7):951-8.

Cox AL, Mosbruger T, Mao Q, Liu Z, Wang XH, Yang HC, Sidney J, Sette A, Pardoll D, Thomas DL, Ray SC. Cellular immune selection with hepatitis C virus persistence in humans. J Exp Med. 2005; 201(11):1741-52.

Ray SC, Fanning L, Wang XH, Netski DM, Kenny-Walsh E, Thomas DL. Divergent and convergent evolution after a common-source outbreak of hepatitis C virus. J Exp Med. 2005; 201(11):1753-9.

Cox AL, Mosbruger T, Lauer GM, Pardoll D, Thomas DL, Ray SC. Comprehensive analyses of CD8+ T cell responses during longitudinal study of acute human hepatitis C. Hepatology. 2005;42(1):104-112.

Netski DM, Mosbruger T, Depla E, Maertens G, Ray SC, Hamilton RG, Roundtree S, Thomas DL, McKeating J, and Cox AL. Humoral immune response in acute HCV infection. Clin Infect Dis 2005; 41(5):667-75. Invited editorial 1. Ray SC, Quinn TC. Sex and the genetic diversity of HIV-1. Nature Med 2000;6(1):23-25.

Book Chapter

Thomas DL, Ray SC, Lemon SM. Hepatitis C. In: Mandell GL, Bennett JE, Dolin R, eds. Principles and Practices of Infectious Diseases. Sixth ed. Philadelphia: Churchhill Livingstone; 2004:1736-60.