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Stuart Campbell Ray, MD

Director, Infectious Diseases Fellowship Training Program
Professor of Medicine

See Research on Pubmed | See Research on Google Scholar

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The Johns Hopkins Hospital

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  • Director, Infectious Diseases Fellowship Training Program
  • Faculty Leader, Janeway Firm of the Osler Internal Medicine Residency Program
  • Professor of Medicine
  • Professor of Oncology

Centers & Institutes

  • Infectious Diseases Center for Viral Hepatitis Research
  • NanoBio Technology, Institute for
  • Sidney Kimmel Comprehensive Cancer Center


Chronic Viral Hepatitis, Hepatitis, HIV/AIDS, Infectious Disease, Infectious Diseases, Internal Medicine

Research Interests

HIV pathogenesis; Computational biology; Viral Evolution; Hepatitis C immunology; Hepatitis C virology

Technology Expertise

computational biology, virology, immunology


Stuart C. Ray, MD FIDSA serves as Fellowship Program Director and Professor in the Division of Infectious Diseases within the Department of Medicine, with secondary appointments in Viral Oncology and Health Sciences Informatics, at the Johns Hopkins University School of Medicine. He directs the virology laboratory and is a clinical investigator in the Center for Viral Hepatitis Research in the Division of Infectious Diseases. He is a faculty member of the Graduate Immunology program, the Graduate Pharmacology program, and of the Barker Firm of the Osler Medical Service. Dr. Ray received his M.D. from Vanderbilt University School of Medicine in 1990. After an internship and residency at Johns Hopkins Hospital, he continued there as an Assistant Chief of Service and fellow in Infectious Diseases. During his fellowship, he studied the immunology and sequence variation of HIV in the laboratory of Dr. Robert Bollinger. During that time, he developed an interest in HIV sequence variation during antiretroviral therapy in a productive collaboration with Dr. Robert Siliciano that continues to the present. In 1997 Dr. Ray joined the Johns Hopkins faculty, and under the mentorship of Dr. David Thomas shifted his primary research focus to hepatitis C virus (HCV). His laboratory work has focused on the sequence variation of HCV during acute and chronic infection, developing and applying computational and molecular biology tools to underlying mechanisms including stochastic variation, immune selection, and viral fitness. He continues to care for inpatients and outpatients with HIV, HCV, and other infectious diseases.


  • English


American Association for the Study of Liver Disease

American College of Physicians

American Society for Microbiology

American Society for Virology

American Society of Clinical Investigation

European Association for the Study of the Liver

Infectious Diseases Society of America

International Society for Computational Biology

Society for Molecular Biology and Evolution

Society of Industrial and Applied Mathematics

Additional Resources

Additional Resources +
  • Education +


    • Vanderbilt University School of Medicine (Nashville TN ) (1990)


    • Johns Hopkins University School of Medicine / Internal Medicine (Baltimore MD ) (1993)


    • Johns Hopkins University School of Medicine / Infectious Diseases (Baltimore MD ) (1997)


    • Infectious Disease, American Board of Internal Medicine (2014)
    • Internal Medicine, American Board of Internal Medicine (2014)
  • Research & Publications +

    Research Summary

    Dr. Ray's research focuses on hepatitis C virus (HCV) sequence evolution and persistence. HCV affects more than 4 million people in the United States (four times as many as are infected with HIV-1) and 200 million worldwide. HCV-related liver disease is the number one indication for liver transplantation in the U.S., and the consequences of HCV infection in terms of death and disability is expected to rise over the next 20 years. Approximately 20 percent of infected individuals will progress to liver cancer. Current interferon-based treatment is cost prohibitive for developing nations and useful in only 20 percent to 50 percent of cases. Vaccine development for HCV has potential for therapeutic intervention as well as prevention. Dr. Ray collaborates with Dr. Andrea Cox in Cancer Immunology to evaluate the influence of quasi-species evolution on immune responses, and computational approaches for using this variation in rational vaccine design.

    Selected Publications View all on PubMed

    1. Bailey, J.R.; Lassen, K.G.; Yang, H.C.; Quinn, T.C.; Ray, S.C.; Blankson, J.N.; Siliciano, R.F. Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy. J Virol. 2006 May;80(10):4758-4770.
    2. Bailey, J.R.; Sedaghat, A.R.; Kieffer, T.; Brennan, T.; Lee, P.K.; Wind-Rotolo, M.; Haggerty, C.M.; Kamireddi, A.R.; Liu, Y.; Lee, J.; Persaud, D.; Gallant, J.E.; Cofrancesco, J., Jr.; Quinn, T.C.; Wilke, C.O.; Ray, S.C.; Siliciano, J.D.; Nettles, R.E.; Siliciano, R.F. Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells. J Virol. 2006 Jul;80(13):6441-6457.
    3. Ziemniak, C.; George-Agwu, A.; Moss, W.J.; Ray, S.C.; Persaud, D. A sensitive genotyping assay for detection of drug resistance mutations in reverse transcriptase of HIV-1 subtypes B and C in samples stored as dried blood spots or frozen RNA extracts. J Virol Methods. 2006 Sep;136(1-2):238-247.
    4. Wang, X.H.; Netski, D.M.; Astemborski, J.; Mehta, S.H.; Torbenson, M.S.; Thomas, D.L.; Ray, S.C. Progression of fibrosis during chronic hepatitis C is associated with rapid virus evolution. J Virol. 2007 Jun;81(12):6513-6522.
    5. Agwu, A.; Lindsey, J.C.; Ferguson, K.; Zhang, H.; Spector, S.; Rudy, B.J.; Ray, S.C.; Douglas, S.D.; Flynn, P.M.; Persaud, D. Analyses of HIV-1 drug-resistance profiles among infected adolescents experiencing delayed antiretroviral treatment switch after initial nonsuppressive highly active antiretroviral therapy. AIDS patient care and STDs. 2008 Jul;22(7):545-552.
    6. Andrade, A.; Bailey, J.R.; Xu, J.; Philp, F.H.; Quinn, T.C.; Williams, T.M.; Ray, S.C.; Thomas, D.L.; Blankson, J.N. CD4+ T cell depletion in an untreated HIV type 1-infected human leukocyte antigen-B*5801-positive patient with an undetectable viral load. Clin Infect Dis. 2008 Apr 15;46(8):e78-82.
    7. Bailey, J.R.; O'Connell, K.; Yang, H.C.; Han, Y.; Xu, J.; Jilek, B.; Williams, T.M.; Ray, S.C.; Siliciano, R.F.; Blankson, J.N. Transmission of human immunodeficiency virus type 1 from a patient who developed AIDS to an elite suppressor. J Virol. 2008 Aug;82(15):7395-7410.
    8. Balagopal, A.; Philp, F.H.; Astemborski, J.; Block, T.M.; Mehta, A.; Long, R.; Kirk, G.D.; Mehta, S.H.; Cox, A.L.; Thomas, D.L.; Ray, S.C. Human immunodeficiency virus-related microbial translocation and progression of hepatitis C. Gastroenterology. 2008 Jul;135(1):226-233.
    9. Dowd, K.A.; Hershow, R.C.; Yawetz, S.; Larussa, P.; Diaz, C.; Landesman, S.H.; Paul, M.E.; Read, J.S.; Lu, M.; Thomas, D.L.; Netski, D.M.; Ray, S.C. Maternal neutralizing antibody and transmission of hepatitis C virus to infants. J Infect Dis. 2008 Dec 1;198(11):1651-1655.
    10. Hoffman, C.J.; Ray, S.C. Severe pruritus after completing pegylated interferon for hepatitis C. The AIDS reader. 2008 Nov;18(11):562-565.
    11. Netski, D.M.; Mao, Q.; Ray, S.C.; Klein, R.S. Genetic divergence of hepatitis C virus: The role of HIV-related immunosuppression. J Acquir Immune Defic Syndr. 2008 Oct 1;49(2):136-141.
    12. Rutebemberwa, A.; Ray, S.C.; Astemborski, J.; Levine, J.; Liu, L.; Dowd, K.A.; Clute, S.; Wang, C.; Korman, A.; Sette, A.; Sidney, J.; Pardoll, D.M.; Cox, A.L. High-programmed death-1 levels on hepatitis C virus-specific T cells during acute infection are associated with viral persistence and require preservation of cognate antigen during chronic infection. J Immunol. 2008 Dec 15;181(12):8215-8225.
    13. Vivekanandan, P.; Kannangai, R.; Ray, S.C.; Thomas, D.L.; Torbenson, M. Comprehensive genetic and epigenetic analysis of occult hepatitis B from liver tissue samples. Clin Infect Dis. 2008 Apr 15;46(8):1227-1236.
    14. Wolfl, M.; Rutebemberwa, A.; Mosbruger, T.; Mao, Q.; Li, H.M.; Netski, D.; Ray, S.C.; Pardoll, D.; Sidney, J.; Sette, A.; Allen, T.; Kuntzen, T.; Kavanagh, D.G.; Kuball, J.; Greenberg, P.D.; Cox, A.L. Hepatitis C virus immune escape via exploitation of a hole in the T cell repertoire. J Immunol. 2008 Nov 1;181(9):6435-6446.
    15. Balagopal, A.; Ray, S.C.; De Oca, R.M.; Sutcliffe, C.G.; Vivekanandan, P.; Higgins, Y.; Mehta, S.H.; Moore, R.D.; Sulkowski, M.S.; Thomas, D.L.; Torbenson, M.S. Kupffer cells are depleted with HIV immunodeficiency and partially recovered with antiretroviral immune reconstitution. AIDS. 2009 Nov 27;23(18):2397-2404.
    16. Dowd, K.A.; Netski, D.M.; Wang, X.H.; Cox, A.L.; Ray, S.C. Selection pressure from neutralizing antibodies drives sequence evolution during acute infection with hepatitis C virus. Gastroenterology. 2009 Jun;136(7):2377-2386.
    17. Fan, X.; Mao, Q.; Zhou, D.; Lu, Y.; Xing, J.; Xu, Y.; Ray, S.C.; Di Bisceglie, A.M. High diversity of hepatitis C viral quasispecies is associated with early virological response in patients undergoing antiviral therapy. Hepatology. 2009 Dec;50(6):1765-1772.
    18. Keerthikumar, S.; Raju, R.; Kandasamy, K.; Hijikata, A.; Ramabadran, S.; Balakrishnan, L.; Ahmed, M.; Rani, S.; Selvan, L.D.; Somanathan, D.S.; Ray, S.; Bhattacharjee, M.; Gollapudi, S.; Ramachandra, Y.L.; Bhadra, S.; Bhattacharyya, C.; Imai, K.; Nonoyama, S.; Kanegane, H.; Miyawaki, T.; Pandey, A.; Ohara, O.; Mohan, S. RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Res. 2009 Jan;37(Database issue):D863-867.
    19. Keshava Prasad, T.S.; Goel, R.; Kandasamy, K.; Keerthikumar, S.; Kumar, S.; Mathivanan, S.; Telikicherla, D.; Raju, R.; Shafreen, B.; Venugopal, A.; Balakrishnan, L.; Marimuthu, A.; Banerjee, S.; Somanathan, D.S.; Sebastian, A.; Rani, S.; Ray, S.; Harrys Kishore, C.J.; Kanth, S.; Ahmed, M.; Kashyap, M.K.; Mohmood, R.; Ramachandra, Y.L.; Krishna, V.; Rahiman, B.A.; Mohan, S.; Ranganathan, P.; Ramabadran, S.; Chaerkady, R.; Pandey, A. Human Protein Reference Database-2009 update. Nucleic Acids Res. 2009 Jan;37(Database issue):D767-772.
    20. O'Connell, K.A.; Xu, J.; Durbin, A.P.; Apuzzo, L.G.; Imteyaz, H.; Williams, T.M.; Ray, S.C.; Margolick, J.B.; Siliciano, R.F.; Blankson, J.N. HIV-1 evolution following transmission to an HLA-B*5801-positive patient. J Infect Dis. 2009 Dec 15;200(12):1820-1824.
    21. Osburn, W.O.; Fisher, B.E.; Dowd, K.A.; Urban, G.; Liu, L.; Ray, S.C.; Thomas, D.L.; Cox, A.L. Spontaneous Control of Primary Hepatitis C Virus Infection and Immunity Against Persistent Reinfection. Gastroenterology. 2009 Sep 24.
    22. Ray, S.C.; Thomas, D.L. Hepatitis C In: Mandell, G.L.; Bennett, J.E.; Dolin, R., editors. Seventh ed, Principles and Practices of Infectious Diseases Philadelphia: Churchill Livingstone; 2009.
    23. Shiu, C.; Cunningham, C.K.; Greenough, T.; Muresan, P.; Sanchez-Merino, V.; Carey, V.; Jackson, J.B.; Ziemniak, C.; Fox, L.; Belzer, M.; Ray, S.C.; Luzuriaga, K.; Persaud, D.; Pediatric, A.C.T.G.P.T. Identification of ongoing human immunodeficiency virus type 1 (HIV-1) replication in residual viremia during recombinant HIV-1 poxvirus immunizations in patients with clinically undetectable viral loads on durable suppressive highly active antiretroviral therapy. J Virol. 2009 Oct;83(19):9731-9742.
    24. Wind-Rotolo, M.; Durand, C.; Cranmer, L.; Reid, A.; Martinson, N.; Doherty, M.; Jilek, B.L.; Kagaayi, J.; Kizza, A.; Pillay, V.; Laeyendecker, O.; Reynolds, S.J.; Eshleman, S.H.; Lau, B.; Ray, S.C.; Siliciano, J.D.; Quinn, T.C.; Siliciano, R.F. Identification of nevirapine-resistant HIV-1 in the latent reservoir after single-dose nevirapine to prevent mother-to-child transmission of HIV-1. J Infect Dis. 2009 May 1;199(9):1301-1309.
    25. Fletcher, N.F.; Yang, J.P.; Farquhar, M.J.; Hu, K.; Davis, C.; He, Q.; Dowd, K.; Ray, S.C.; Krieger, S.E.; Neyts, J.; Baumert, T.F.; Balfe, P.; McKeating, J.A.; Wong-Staal, F. Hepatitis C virus infection of neuroepithelioma cell lines. Gastroenterology. 2010 Oct;139(4):1365-1374.
    26. Liu, L.; Fisher, B.E.; Dowd, K.A.; Astemborski, J.; Cox, A.L.; Ray, S.C. Acceleration of hepatitis C virus envelope evolution in humans is consistent with progressive humoral immune selection during the transition from acute to chronic infection. J Virol. 2010 May;84(10):5067-5077.
    27. O'Connell, K.A.; Brennan, T.P.; Bailey, J.R.; Ray, S.C.; Siliciano, R.F.; Blankson, J.N. Control of HIV-1 in elite suppressors despite ongoing replication and evolution in plasma virus. J Virol. 2010 Jul;84(14):7018-7028.
    28. Osburn, W.O.; Fisher, B.E.; Dowd, K.A.; Urban, G.; Liu, L.; Ray, S.C.; Thomas, D.L.; Cox, A.L. Spontaneous control of primary hepatitis C virus infection and immunity against persistent reinfection. Gastroenterology. 2010 Jan;138(1):315-324.
    29. Salgado, M.; Brennan, T.P.; O'Connell, K.A.; Bailey, J.R.; Ray, S.C.; Siliciano, R.F.; Blankson, J.N. Evolution of the HIV-1 nef gene in HLA-B*57 positive elite suppressors. Retrovirology. 2010;7:94.
    30. Thio, C.L.; Ray, S.C.; Datta, S.; Panigrahi, R.; Biswas, A.; Chakravarty, R. Genetic linkage of hepatitis B virus in peripheral blood leukocytes provides evidence for contamination. J Virol. 2010 Feb;84(4):2184-2186.
    31. Towler, W.I.; James, M.M.; Ray, S.C.; Wang, L.; Donnell, D.; Mwatha, A.; Guay, L.; Nakabiito, C.; Musoke, P.; Jackson, J.B.; Eshleman, S.H. Analysis of HIV diversity using a high-resolution melting assay. AIDS Res Hum Retroviruses. 2010 Aug;26(8):913-918.


  • Academic Affiliations & Courses +

    Graduate Program Affiliation

    Immunology, Pharmacology

  • Activities & Honors +


    Fellow, Infectious Diseases Society of America (elected 2008)

    American Society of Clinical Investigation (elected 2009)

  • Videos & Media +
  • Events +
  • Contact & Locations +


    The Johns Hopkins Hospital
    600 N. Wolfe Street
    Sheikh Zayed Tower
    Rangos 530
    Baltimore, MD 21287
    Phone: 410-614-2891
    Appointment Phone: 410-583-2736
    Fax: 443-769-1221
    Location Map


    • Medicine - Infectious Diseases
    • Medicine - Health Sciences Informatics

    For Research Inquiries Contact

    Center for Viral Hepatitis Research
    855 N. Wolfe St, suite 530
    Baltimore, MD 21205

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