Skip Navigation
Search Menu
Find an Expert


Rupak Shivakoti, M.S.P.H., Ph.D.

Photo of Dr. Rupak Shivakoti, M.S.P.H., Ph.D.

Instructor of Medicine

Research Interests: Immunology; Infectious diseases; Epidemiology; Nutrition; Human Immunodeficiency Virus (HIV); Tuberculosis; Micronutrient deficiencies; Gut microbiome; Inflammation; HIV-infected pregnant women; Infant outcomes; Maternal-infant populations; Adverse birth outcomes; Preterm birth; Resource-limited countries; India more


Dr. Rupak Shivakoti is an instructor of medicine at the Johns Hopkins University School of Medicine. 

He completed an undergraduate degree in biology from DePauw University. He earned both an M.S.P.H. in international health and a Ph.D. in molecular microbiology and immunology from the Johns Hopkins Bloomberg School of Public Health. He completed a post-doctoral fellowship in clinical global health education at CCGHE.

Dr. Shivakoti’s research focuses primarily on epidemiological studies that examine the roles of immunology and nutrition in HIV and tuberculosis infection. He also serves on the faculty of the Johns Hopkins Center for Clinical Global Health Education (CCGHE).

He joined the Johns Hopkins faculty in 2016. more


  • Instructor of Medicine

Departments / Divisions



  • B.A., DePauw University (Indiana) (2007)
  • M.S.P.H., Johns Hopkins University (Maryland) (2013)
  • Ph.D., Johns Hopkins University (Maryland) (2013)

Research & Publications

Research Summary

Dr. Shivakoti’s research focuses primarily on epidemiological studies that assess the role of immunology and nutrition within the context of HIV and tuberculosis infection.

Since 2013, he has studied how micronutrient deficiencies and inflammation affect HIV treatment outcomes in adults from resource-limited countries. In other studies, he is evaluating risk factors for infant outcomes among HIV-infected and uninfected maternal-infant populations from Pune, India.

He was awarded a 2016 Pathway to Independence Award (K99/R00 grant) to serve as the principal investigator of a study of HIV-infected and uninfected pregnant women from India. The study aims to determine the association of maternal inflammation, diet and gut microbiome during pregnancy with adverse birth outcomes, including preterm birth.

Dr. Shivakoti is also principal investigator of two Johns Hopkins Center for AIDS Research (CFAR) grants, including one examining the temporal dynamics of the gut microbiome during pregnancy among HIV-infected and uninfected women.

Selected Publications

Shivakoti R, Sharma D, Mamoon G, Pham K. "Association of HIV infection with extrapulmonary tuberculosis: a systematic review." Infection. 2016 Nov 9. [Epub ahead of print] Review

Balagopal A, Gupte N, Shivakoti R, Cox AL, Yang WT, Berendes S, Mwelase N, Kanyama C, Pillay S, Samaneka W, Santos B, Poongulali S, Tripathy S, Riviere C, Lama JR, Cardoso SW, Sugandhavesa P, Semba RD, Hakim J, Hosseinipour MC, Kumarasamy N, Sanne I, Asmuth D, Campbell T, Bollinger RC, Gupta A. "Continued elevation of interleukin-18 and interferon-γ after initiation of antiretroviral therapy and clinical failure in a diverse multicountry human immunodeficiency virus cohort." Open Forum Infect Dis. 2016 Jul 27;3(3):ofw118

Shivakoti R, Yang WT, Berendes S, Mwelase N, Kanyama C, Pillay S, Samaneka W, Santos B, Poongulali S, Tripathy S, Riviere C, Lama JR, Cardoso SW, Sugandhavesa P, Balagopal A, Gupte N, Semba RD, Campbell TB, Bollinger RC, Gupta A; NWCS 319 and PEARLS Study Team. "Persistently elevated C-reactive protein level in the first year of antiretroviral therapy, despite virologic suppression, is associated with HIV disease progression in resource-constrained settings." J Infect Dis. 2016 Apr 1;213(7):1074-8. doi: 10.1093/infdis/jiv573

Fiebelkorn AP, Coleman LA, Belongia EA, Freeman SK, York D, Bi D, Kulkarni A, Audet S, Mercader S, McGrew M, Hickman CJ, Bellini WJ, Shivakoti R, Griffin DE, Beeler J. "Measles virus neutralizing antibody response, cell-mediated immunity, and immunoglobulin G antibody avidity before and after receipt of a third dose of measles, mumps, and rubella vaccine in young adults." J Infect Dis. 2016 Apr 1;213(7):1115-23. doi: 10.1093/infdis/jiv555

Shivakoti R, Gupta A, Ray JC, Uprety P, Gupte N, Bhosale R, Mave V, Patil S, Balasubramanian U, Kinikar A, Bharadwaj R, Bollinger RC, Persaud D. "Soluble CD14: an independent biomarker for the risk of mother-to-child transmission of HIV in a setting of preexposure and postexposure antiretroviral prophylaxis." J Infect Dis. 2016 Mar 1;213(5):762-5. doi: 10.1093/infdis/jiv479

Activities & Honors


  • Pathway to Independence Award (K99/R00), Maternal Inflammation, Diet, and Gut Microbiome in HIV: Impact on Infant Outcomes, National Institutes of Health, 2016
  • Center For AIDS Research (CFAR) Scholar Award, National Institutes of Health, 2016
  • CFAR International Research Scholar Award, Temporal dynamics of gut microbiota in HIV-infected pregnant women, National Institutes of Health, 2015
  • Ujala Scholar, Center for Clinical Global Health Education, Johns Hopkins University, 2014
Is this you? Edit Profile