Research Summary

My cancer-related research centers around Kaposi sarcoma (KS) and its etiologic agent, Kaposi’s sarcoma-associated herpesvirus (KSHV), with work both in the US and in Africa.

My qualifications for research include both theoretical background and practical experience. I am Director of the UCSF Training in Clinical Research (TICR) Program, which provides graduate-level didactic training in clinical, epidemiologic, and translational research methods to graduate students, post-doctoral fellows, and junior faculty members at UCSF. The TICR Program, which is supported by the UCSF NIH-sponsored Clinical and Translational Science Award (CTSA), includes 33 different courses spanning “laboratory to human subjects” translational research, traditional clinical and epidemiologic research, and “evidence to practice” implementation science research. In direct teaching, I am the course director of “Epidemiologic Methods,” the program’s foundational course in research methods, and the “Master’s Program Seminar Series.” On a practical level, I have extensive experience in both observational and experimental research in both the US and Africa. In the US, I am Co-Director of the Population and Clinical Sciences Core of the UCSF NIH-sponsored Center for AIDS Research (CFAR), which manages the 1800-subject UCSF SCOPE cohort, a vehicle that has supported collaborative research leading to over 200 publications since 2000. In Africa, I am the Principal Investigator (PI) for U54 CA190153 (a project which focuses on the early detection and prevention of KS in Uganda); PI for the UCSF component of the East Africa International Epidemiologic Databases to Evaluate AIDS (IeDEA) Consortium (U01 AI069911), in which I direct the working group on cancer; PI for the recently completed R01 CA119903 (a randomized trial for the therapy of KS in Africa); PI for the recently completed D43 CA153717 (a training grant related to KS in Uganda); and Director of the Data Coordinating Center for the 750-subject Mbarara-based Uganda AIDS Rural Treatment Outcomes (UARTO) Cohort. UARTO, which has spun off over 50 publications from collaborative projects since 2006, is a microscopic complement of IeDEA. In all of this work, I have had broad experience with study design, instrument development, study recruitment/ retention, data collection, quality enhancement, data reporting, biostatistical analysis, manuscript preparation, and financial management.

Research Funding

  • July 13, 2020 - June 30, 2025 - United States-East Africa HIV-Associated Malignancy Research Center (USEAHAMRC) for Career Development and the Prevention, Early Detection and Efficient Linkage to Care for Virus-related Cancers , Principal Investigator . Sponsor: NIH, Sponsor Award ID: U54CA254571
  • August 10, 2019 - April 30, 2024 - Training in Clinical and Epidemiological Research for Liberia (TRACER) , Principal Investigator . Sponsor: NIH, Sponsor Award ID: U2RTW011281
  • September 30, 1988 - August 31, 2022 - UCSF-Gladstone Center for AIDS Research , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P30AI027763
  • August 17, 2016 - July 31, 2022 - Early Stage Diagnosis of Kaposi's Sarcoma in Limited Resource Settings using KS-Detect , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: UH3CA202723
  • September 24, 2001 - August 31, 2021 - Center for AIDS Prevention Studies , Co-Investigator . Sponsor: NIH, Sponsor Award ID: P30MH062246
  • September 17, 2014 - August 31, 2020 - Uganda-UCSF Consortium on Prevention and Early Detection of HIV-Associated Cancer , Principal Investigator . Sponsor: NIH, Sponsor Award ID: U54CA190153
  • August 17, 2016 - July 31, 2018 - Early Stage Diagnosis of Kaposi's Sarcoma in Limited Resource Settings using KS-Detect , Co-Principal Investigator . Sponsor: NIH, Sponsor Award ID: UH2CA202723
  • September 9, 2010 - August 31, 2015 - Uganda-UCSF Research Training in HIV-Associated Malignancies , Principal Investigator . Sponsor: NIH, Sponsor Award ID: D43CA153717
  • September 30, 2005 - July 31, 2012 - Antiretroviral Therapy of AIDS-Related Kaposi's Sarcoma in Africa , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA119903

Education

Johns Hopkins University; Baltimore, Maryland, BA, 1979-83, Biology
University of Pennsylvania; Philadelphia, MD, 1983-88, Medicine
UC, San Francisco, 1988-89, Medicine - Internship
UC, San Francisco, 1989-91, Medicine - Residency 
UC, San Francisco, 1991-92, Medicine - Chief Residency
UC, Berkeley, MPH, 1992-93, Epidemiology
UC, San Francisco, 1993-97, Infectious Diseases - Fellowship
UC, San Francisco, 1993-97, AIDS Prevention - Fellowship

Honors & Awards

  • 1982
    Phi Beta Kappa
  • 1988
    Alpha Omega Alpha
  • 1988
    Merck Manual Award, University of Pennsylvania School of Medicine
  • 1989
    Diplomate, National Board of Medical Examiners
  • 1991
    Diplomate, American Board of Internal Medicine
  • 1996
    Diplomate, American Board of Internal Medicine, Subspecialty in Infectious Diseases
  • 1998
    New Investigator Award, UCSF Center for AIDS Research (CFAR)
  • 2009
    Stephen B. Hulley Award for Excellence in Instruction in Methods of Clinical Research at UCSF

Selected Publications

  1. Moses JS, Pau AK, Kuriakose S, Grandits G, Reilly C, Sherman BT, Chang W, Dai L, Khan MA, Highbarger H, Mannah M, McCullough J, Chorley C, Morlu I, Dorbor J, Bongolee OT, Slewion R, Akpa E, Wilson B, Poole AL, Kopka SL, Miller T, Nuta CJ, Lindan C, Glidden D, Martin JN, Johnson KL, Dewar RL, Wachekwa I, Migueles SA HIV-1 suppression and rare dolutegravir resistance in antiretroviral-experienced people with HIV in Liberia.  View on PubMed
  2. Coates SJ, Yang F, Hill C, Xue Z, Rajaraman S, Semeere A, Ayanga R, Laker-Oketta M, Byakwaga H, Lukande R, Semakadde M, Kanyesigye M, Wenger M, LeBoit P, McCalmont T, Cesarman E, Erickson D, Maurer T, Antani S, Martin J Artificial Intelligence-based Diagnosis of Kaposi Sarcoma using Photographs in Dark-skinned Patients.  View on PubMed
  3. Lage SL, Bricker-Holt K, Rocco JM, Rupert A, Donovan FX, Abramzon YA, Chandrasekharappa SC, McNinch C, Cook L, Amaral EP, Rosenfeld G, Dalhuisen T, Eun A, Hoh R, Fehrman E, Martin JN, Deeks SG, Henrich TJ, Peluso MJ, Sereti I Persistent immune dysregulation and metabolic alterations following SARS-CoV-2 infection.  View on PubMed
  4. Hussain I, Boza J, Lukande R, Ayanga R, Semeere A, Cesarman E, Martin J, Maurer T, Erickson D Automated Detection of Kaposi Sarcoma-Associated Herpesvirus-Infected Cells in Immunohistochemical Images of Skin Biopsies.  View on PubMed
  5. Omoding D, Musinguzi N, Boum Y, Muzoora C, Kigozi S, Hunt PW, Martin JN, Bangsberg DR, Haberer JE, Siedner MJ, McCluskey SM, Lee GQ. Subtypes A1 and D, and recombinant HIV-1 natural polymorphisms associated with lenacapavir drug resistance in Uganda. J Antimicrob Chemother. 2025 Apr 02; 80(4):955-961.  View on PubMed
  6. Fallah MP, Van Ryn C, Moses JS, Badio M, Fayiah T, Johnson K, Gayedyu-Dennis D, Eghrari AO, Weiser SD, Porco TC, Martin JN, Peluso MJ, McIlwain DR, Dighero-Kemp B, Higgs E, Hensley LE, Rutherford GW, Reilly C, Kelly JD Associations of inflammatory markers with post-acute clinical findings among survivors of Ebola virus disease with and without viral RNA shedding in the semen in Liberia: a nested case-control study.  View on PubMed
  7. Garcia-Knight MA, Kelly JD, Lu S, Tassetto M, Goldberg SA, Zhang A, Pineda-Ramirez J, Anglin K, Davidson MC, Chen JY, Fortes-Cobby M, Park S, Martinez A, So M, Donovan A, Viswanathan B, Richardson ET, McIlwain DR, Gaudilliere B, Rutishauser RL, Chenna A, Petropoulos C, Wrin T, Deeks SG, Abedi GR, Saydah S, Martin JN, Briggs Hagen M, Midgley CM, Peluso MJ, Andino R Circulating neutralizing antibodies and SARS-CoV-2 variant replication following postvaccination infections.  View on PubMed
  8. Wang Y, Gornalusse GG, Siegel DA, Barbehenn A, Hoh R, Martin J, Hecht F, Pilcher C, Semenova L, Murdoch DM, Margolis DM, Levy CN, Jerome KR, Rudin CD, Hladik F, Deeks SG, Lee SA, Browne EP NF-κB dependent gene expression and plasma IL-1β, TNFα and GCSF drive transcriptomic diversity and CD4:CD8 ratio in people with HIV on ART.  View on PubMed
  9. Drainas AP, McIlwain DR, Dallas A, Chu T, Delgado-González A, Baron M, Angulo-Ibáñez M, Trejo A, Bai Y, Hickey JW, Lu G, Lu S, Pineda-Ramirez J, Anglin K, Richardson ET, Prostko JC, Frias E, Servellita V, Brazer N, Chiu CY, Peluso MJ, Martin JN, Wirz OF, Pham TD, Boyd SD, Kelly JD, Sage J, Nolan GP, Rovira-Clavé X. High-throughput multiplexed serology via the mass-spectrometric analysis of isotopically barcoded beads. Nat Biomed Eng. 2025 Feb 12.  View on PubMed
  10. Shah DP, Thaweethai T, Karlson EW, Bonilla H, Horne BD, Mullington JM, Wisnivesky JP, Hornig M, Shinnick DJ, Klein JD, Erdmann NB, Brosnahan SB, Lee-Iannotti JK, Metz TD, Maughan C, Ofotokun I, Reeder HT, Stiles LE, Shaukat A, Hess R, Ashktorab H, Bartram L, Bassett IV, Becker JH, Brim H, Charney AW, Chopra T, Clifton RG, Deeks SG, Erlandson KM, Fierer DS, Flaherman VJ, Fonseca V, Gander JC, Hodder SL, Jacoby VL, Kotini-Shah P, Krishnan JA, Kumar A, Levy BD, Lieberman D, Lin JJ, Martin JN, McComsey GA, Moukabary T, Okumura MJ, Peluso MJ, Rosen CJ, Saade G, Shah PK, Sherif ZA, Taylor BS, Tuttle KR, Urdaneta AE, Wallick JA, Wiley Z, Zhang D, Horwitz LI, Foulkes AS, Singer NG, RECOVER Consortium. Sex Differences in Long COVID. JAMA Netw Open. 2025 Jan 02; 8(1):e2455430.  View on PubMed
  11. Tsao T, Buck AM, Grimbert L, LaFranchi BH, Altamirano Poblano B, Fehrman EA, Dalhuisen T, Hsue PY, Kelly JD, Martin JN, Deeks SG, Hunt PW, Peluso MJ, Aguilar OA, Henrich TJ. Long COVID is associated with lower percentages of mature, cytotoxic NK cell phenotypes. J Clin Invest. 2024 Dec 17; 135(4).  View on PubMed
  12. Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso MJ, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA Rapid biphasic decay of intact and defective HIV DNA reservoir during acute treated HIV disease.  View on PubMed
  13. Jamal A, Dalhuisen T, Gallego Márquez N, Dziarski AD, Uy J, Walch SN, Thomas SA, Fehrman EA, Romero AE, Zelaya AS, Akasreku EA, Adeagbo TV, Pasetes EC, Akbas SY, Azola AM, Deeks SG, Kelly JD, Martin JN, Henrich TJ, Landay AL, Peluso MJ, Antar AAR. Post-SARS-CoV-2 Onset Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Symptoms in Two Cohort Studies of COVID-19 Recovery. medRxiv. 2024 Nov 08.  View on PubMed
  14. Swank Z, Borberg E, Chen Y, Senussi Y, Chalise S, Manickas-Hill Z, Yu XG, Li JZ, Alter G, Henrich TJ, Kelly JD, Hoh R, Goldberg SA, Deeks SG, Martin JN, Peluso MJ, Talla A, Li X, Skene P, Bumol TF, Torgerson TR, Czartoski JL, McElrath MJ, Karlson EW, Walt DR, RECOVER consortium authors. Measurement of circulating viral antigens post-SARS-CoV-2 infection in a multicohort study. Clin Microbiol Infect. 2024 Dec; 30(12):1599-1605.  View on PubMed
  15. Kadama-Makanga P, Semeere A, Laker-Oketta M, Mubiru M, Lukande R, Huchko M, Freeman E, Kulkarni N, Martin J, Kang D, Nakalembe M Usability of a smartphone-compatible, confocal micro-endoscope for cervical cancer screening in resource-limited settings.  View on PubMed
  16. Lu S, Peluso MJ, Glidden DV, Davidson MC, Lugtu K, Pineda-Ramirez J, Tassetto M, Garcia-Knight M, Zhang A, Goldberg SA, Chen JY, Fortes-Cobby M, Park S, Martinez A, So M, Donovan A, Viswanathan B, Hoh R, Donohue K, McIlwain DR, Gaudiliere B, Anglin K, Yee BC, Chenna A, Winslow JW, Petropoulos CJ, Deeks SG, Briggs-Hagen M, Andino R, Midgley CM, Martin JN, Saydah S, Kelly JD. Early biological markers of post-acute sequelae of SARS-CoV-2 infection. Nat Commun. 2024 Aug 29; 15(1):7466.  View on PubMed
  17. Byakwaga H, Semeere A, Laker-Oketta M, Busakhala N, Freeman E, Rotich E, Wenger M, Kadama-Makanga P, Kisuya J, Semakadde M, Mwine B, Kasozi C, Mwebesa B, Maurer T, Glidden DV, Wools-Kaloustian K, Kambugu A, Martin J. Survival Following Diagnosis of HIV-Associated Kaposi Sarcoma Among Adults in East Africa in the "Treat-All" Era. medRxiv. 2024 Aug 28.  View on PubMed
  18. Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso MJ, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA Rapid Biphasic Decay of Intact and Defective HIV DNA Reservoir During Acute Treated HIV Disease.  View on PubMed
  19. Hussain I, Boza J, Lukande R, Ayanga R, Semeere A, Cesarman E, Martin J, Maurer T, Erickson D Automated detection of Kaposi sarcoma-associated herpesvirus infected cells in immunohistochemical images of skin biopsies.  View on PubMed
  20. Peluso MJ, Ryder D, Flavell RR, Wang Y, Levi J, LaFranchi BH, Deveau TM, Buck AM, Munter SE, Asare KA, Aslam M, Koch W, Szabo G, Hoh R, Deswal M, Rodriguez AE, Buitrago M, Tai V, Shrestha U, Lu S, Goldberg SA, Dalhuisen T, Vasquez JJ, Durstenfeld MS, Hsue PY, Kelly JD, Kumar N, Martin JN, Gambhir A, Somsouk M, Seo Y, Deeks SG, Laszik ZG, VanBrocklin HF, Henrich TJ. Tissue-based T cell activation and viral RNA persist for up to 2 years after SARS-CoV-2 infection. Sci Transl Med. 2024 Jul 03; 16(754):eadk3295.  View on PubMed

Go to UCSF Profiles, powered by CTSI