PUBLICATIONS

Featured Recent Publications

2026

• Garcia, M. A., Farrell-Sherman, A., Aydin, B., Zhuo, J., Fray, E. J., Zinsser, A. M., Lai, J., Sowers, K., Li, H., Lopez, B. M., Abeyta-Lopez, A., Chu, T., Lubbeck, D., Chae, M., Bachmann, N., Varriale, J., Westfall, D. H., Hoh, R., Dalhuisen, T., Simonetti, F. R., … Siliciano, J. D. (2026). Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir. Proceedings of the National Academy of Sciences of the United States of America, 123(27), e2608337123. https://doi.org/10.1073/pnas.2608337123, PMID: 42391404, PMCID: PMC13342869.
• Box, J. R., Camilo-Contreras, A., Dragoni, F., Yue, F. Y., Matveev, V., Foley, J., Zhang, J., Mok, Y. W., DeSousa, M., Lai, J., Mulcare, Z., Bakewell, Z., Poulin, S., Chano, F., Fortin, C., Tremblay, C., Blankson, J. N., Krishnan, S., Weld, E. D., Basseth, C., … Simonetti, F. R. (2026). 5′ leader defects drive persistent HIV-1 viremia on long-term ART. Nature communications, 17(1), 4725. https://doi.org/10.1038/s41467-026-73475-5, PMID: 42259781, PMCID: PMC13246943.
• Ma, T., George, A. F., Li, Z., Thomas, R., Yin, K., Shin, M. G., Montano, M., Matsui, Y., Ashokkumar, M., Young, K., Prigann, J., Frouard, J., Leddy, S., Adiba, M., Herrde, C., Lange, U. C., Feschotte, C., Nixon, D. F., Browne, E. P., Archin, N. M., … Roan, N. R. (2026). Multiomic analysis of ART-interruption cohorts identifies cell-extrinsic and -intrinsic mechanisms driving lymphocyte-mediated control of HIV rebound. Immunity, 59(5), 1454–1472.e9. https://doi.org/10.1016/j.immuni.2026.01.029, PMID: 41864210, PMCID: PMC13245417.
• Bachmann, N., Kim, B., Simonetti, F. R., Kovacs, C. M., Hoh, R., Deeks, S. G., Siliciano, J. D., & Siliciano, R. F. (2026). HIV-1 infection does not confer intrinsic resistance to cell death induced by cytotoxic T lymphocytes. bioRxiv : the preprint server for biology, 2026.03.23.713717. https://doi.org/10.64898/2026.03.23.713717, PMID: 41929103, PMCID: PMC13041980
• Fisher, K.†, Garcia, M. A.†, Frattari, G. S.†, Naasz, C.†, Zhuo, J.†, Rosás-Umbert, M., Dietz, L. L., Juhl, A. K., Falling Iversen, E., Olesen, R., Schleimann, M. H., Pahus, M. H., Johansen, I. S., Henderson, M., Carrere, L., Roseto, I., Gao, C., Yu, X. G., Fray, E. J., Aydin, B., … Søgaard, O. S. (2026). Autologous neutralizing antibodies and polyfunctional T cells contribute to long-term HIV-1 post-intervention control. Nature immunology, 27(4), 812–826. https://doi.org/10.1038/s41590-026-02448-z, PMID: 41776101, PMCID: PMC13043296
• Sulaiman, A., Tamil Selvan, M., Yang, P., Zhu, X., Eby, Y., Benner, S. E., Fernandez, R. E., Hussain, S., Brown, D., Desai, N., Florman, S., Rana, M. M., Friedman-Moraco, R., Pereira, M. R., Mehta, S., Stock, P., Gilbert, A., Morris, M. I., Stosor, V., Mehta, S. A., … Tobian, A. A. (2026). Allograft Rejection and the Latent HIV Reservoir in Kidney Transplant Recipients with HIV. The Journal of infectious diseases, jiag154. Advance online publication. https://doi.org/10.1093/infdis/jiag154, PMID: 41823991, PMCID: PMC13046422

2025

• Pathirage, R., Dutta, M., Parsons, R. J., Lella, M., Atwood, E., Zhang, Q. E., May, A., Johnson, A., Huang, X., Flemming, J., Kumar, U., Marayati, B. F., Spurrier, M. A., Liu, C., Zhuo, J., Song, K., Adhikari, R. D., Sammour, S., Ilevbare, V., Abram, C., … Acharya, P. (2025). An integrated workflow for structural virology with a 100 keV electron microscope. bioRxiv : the preprint server for biology, 2025.12.08.693081. https://doi.org/10.64898/2025.12.08.693081, PMID: 41427412 , PMCID: PMC12713605
• Rhodehouse, K., Zitzmann, C., Ravi, M., Armstrong, C., Moskovljevic, M., Moore, H. P., Schill, C., Fray, E. J., Kumar, M. R., Penney, T., Krzykwa, C., Stauss, M. R., Wiseman, R. W., O’Connor, D. H., Fennessey, C. M., Keele, B. F., Lifson, J. D., Ribeiro, R. M., Perelson, A. S., Hoxie, J. A., … Siliciano, R. F. (2026). Dynamics of natural and pharmacologic control of an SIV variant with an envelope trafficking defect. The Journal of experimental medicine, 223(2), e20251172. https://doi.org/10.1084/jem.20251172, PMID: 41348110, PMCID: PMC12679998
• Hariharan, V., White, J. A., Dragoni, F., Fray, E. J., Pathoulas, N., Moskovljevic, M., Zhang, H., Singhal, A., Lai, J., Beg, S. A., Scully, E. P., Gilliams, E. A., Block, D. S., Keruly, J., Moore, R. D., Siliciano, J. D., Simonetti, F. R., & Siliciano, R. F. (2025). Superinfection promotes replication and diversification of defective HIV-1 proviruses in people with non-suppressible viraemia. Nature microbiology, 10(11), 2736–2748. https://doi.org/10.1038/s41564-025-02135-z, PMID: 41044362, PMCID: PMC12578631
• Obregon-Perko, V., Awasthi, A., Barfield, R., Berendam, S. J., Yagnik, B., Styles, T., Tharp, G., Gupta, P. M., Mensah, G., Neja, M., Kumar, M., Fray, E., Bu, F., Pollara, J., Tuyishime, M., Ferrari, G., Siliciano, J. D., Siliciano, R. F., Mavigner, M., Silvestri, G., … Chahroudi, A. (2025). Identifying correlates of viral rebound timing and viral control in SHIV-infected infant macaques after ART interruption. Science translational medicine, 17(822), eadq1965. https://doi.org/10.1126/scitranslmed.adq1965, PMID: 41160668, PMCID: PMC12646350
• Reeves, D. B., Rigau, D. N., Romero, A., Zhang, H., Simonetti, F. R., Varriale, J., Hoh, R., Zhang, L., Smith, K. N., Montaner, L. J., Rubin, L. H., Gange, S. J., Roan, N. R., Tien, P. C., Margolick, J. B., Peluso, M. J., Deeks, S. G., Schiffer, J. T., Siliciano, J. D., Siliciano, R. F., … Antar, A. A. R. (2025). Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. Cell systems, 16(10), 101402. https://doi.org/10.1016/j.cels.2025.101402, PMID: 40987290, PMCID: PMC12694735
• Yuan, Z., Board, N. L., Zhao, M., Zu, G., Sengupta, S., Li, Q., Siliciano, J. D., Siliciano, R. F., & Montaner, L. J. (2025). A TCR-mimic bispecific antibody reduces HIV-1 provirus and delays viral rebound in HLA-matched humanized mice. bioRxiv : the preprint server for biology, 2025.10.06.680344. https://doi.org/10.1101/2025.10.06.680344, PMID: 41279654, PMCID: PMC12632495
• McMyn, N. F., Varriale, J., Wu, H. W. S., Hariharan, V., Moskovljevic, M., Tan, T. S., Lai, J., Singhal, A., Lynn, K., Mounzer, K., Tebas, P., Montaner, L. J., Hoh, R., Yu, X. G., Lichterfeld, M., Simonetti, F. R., Kovacs, C., Deeks, S. G., Siliciano, J. M., & Siliciano, R. F. (2025). Factors associated with resistance of HIV-1 reservoir viruses to neutralization by autologous IgG antibodies. The Journal of clinical investigation, 135(19), e194081. https://doi.org/10.1172/JCI194081, PMID: 40728901, PMCID: PMC12483561
• Wu, F., Moskovljevic, M., Dragoni, F., Jayaraman, S., Board, N. L., Camilo-Contreras, A., Bernal, S., Hariharan, V., Zhang, H., Lai, J., Singhal, A., Poulin, S., Chano, F., Chamberland, A., Tremblay, C., Zoltick, M., Hoffmann, C. J., Jones, J. L., Larman, H. B., Montaner, L. J., … Simonetti, F. R. (2025). Proviruses in CD4⁺T cells reactive to autologous antigens contribute to nonsuppressible HIV-1 viremia. Science translational medicine, 17(811), eadu4643. https://doi.org/10.1126/scitranslmed.adu4643, PMID: 40802737, PMCID: PMC12363666
• Quinn, S. L., George, M., Ventura, J. D., Fray, E. J., Aid, M., Walker-Sperling, V. E. K., Siliciano, J. D., Siliciano, R. F., Nguyen, S., Barouch, D. H., & Shalek, A. K. (2025). Longitudinal transcriptomic analysis of SIV-infected rhesus macaques reveals peripheral immune dynamics throughout untreated SIV infection and long-term antiretroviral therapy. bioRxiv : the preprint server for biology, 2025.08.08.669172. https://doi.org/10.1101/2025.08.08.669172, PMID: 40832257, PMCID: PMC12363852
• Sambaturu, N., Fray, E. J., Hariharan, V., Wu, F., Zitzmann, C., Simonetti, F. R., Barouch, D. H., Siliciano, J. D., Siliciano, R. F., Ribeiro, R. M., Perelson, A. S., Molina-París, C., & Leitner, T. (2025). SIV proviruses seeded later in infection are harbored in short-lived CD4⁺T cells. Cell reports, 44(5), 115663. https://doi.org/10.1016/j.celrep.2025.115663, PMID: 40327506, PMCID: PMC12160121
• Song, B., Liu, D., Dai, W., McMyn, N. F., Wang, Q., Yang, D., Krejci, A., Vasilyev, A., Untermoser, N., Loregger, A., Song, D., Williams, B., Rosen, B., Cheng, X., Chao, L., Kale, H. T., Zhang, H., Diao, Y., Bürckstümmer, T., Siliciano, J. D., … Li, W. (2025). Decoding heterogeneous single-cell perturbation responses. Nature cell biology, 27(3), 493–504. https://doi.org/10.1038/s41556-025-01626-9, PMID: 40011559, PMCID: PMC11906366

2024

• Moskovljevic, M., Dragoni, F., Board, N. L., Wu, F., Lai, J., Zhang, H., White, J. R., Hoh, R., Lynn, K., Tebas, P., Mounzer, K., Deeks, S. G., Montaner, L. J., Siliciano, J. D., Siliciano, R. F., & Simonetti, F. R. (2024). Cognate antigen engagement induces HIV-1 expression in latently infected CD4⁺T cells from people on long-term antiretroviral therapy. Immunity, 57(12), 2928–2944.e6. https://doi.org/10.1016/j.immuni.2024.11.002, PMID: 39612916, PMCID: PMC11896817
• Mainou, E., Berendam, S. J., Obregon-Perko, V., Uffman, E. A., Phan, C. T., Shaw, G. M., Bar, K. J., Kumar, M. R., Fray, E. J., Siliciano, J. M., Siliciano, R. F., Silvestri, G., Permar, S. R., Fouda, G. G., McCarthy, J., Chahroudi, A., Conway, J. M., & Chan, C. (2024). Assessing the impact of autologous virus neutralizing antibodies on viral rebound time in postnatally SHIV-infected ART-treated infant rhesus macaques. Epidemics, 48, 100780. https://doi.org/10.1016/j.epidem.2024.100780, PMID: 38964130, PMCID: PMC11518701
• Mainou, E., Berendam, S. J., Obregon-Perko, V., Uffman, E. A., Phan, C. T., Shaw, G. M., Bar, K. J., Kumar, M. R., Fray, E. J., Siliciano, J. M., Siliciano, R. F., Silvestri, G., Permar, S. R., Fouda, G. G., McCarthy, J., Chahroudi, A., Chan, C., & Conway, J. M. (2024). Comparative analysis of within-host dynamics of acute infection and viral rebound dynamics in postnatally SHIV-infected ART-treated infant rhesus macaques. bioRxiv : the preprint server for biology, 2024.05.21.595130. https://doi.org/10.1101/2024.05.21.595130, PMID: 38826467, PMCID: PMC11142125
• Lim, S. Y., Lee, J., Osuna, C. E., Vikhe, P., Schalk, D. R., Chen, E., Fray, E., Kumar, M., Schultz-Darken, N., Rakasz, E., Capuano, S., Ladd, R. A., Gil, H. M., Evans, D. T., Jeng, E. K., Seaman, M., Martin, M., Van Dorp, C., Perelson, A. S., Wong, H. C., … Whitney, J. B. (2024). Induction of durable remission by dual immunotherapy in SHIV-infected ART-suppressed macaques. Science, 383(6687), 1104–1111. https://doi.org/10.1126/science.adf7966, PMID: 38422185, PMCID: PMC11022498
• Board, N. L., Yuan, Z., Wu, F., Moskovljevic, M., Ravi, M., Sengupta, S., Mun, S. S., Simonetti, F. R., Lai, J., Tebas, P., Lynn, K., Hoh, R., Deeks, S. G., Siliciano, J. D., Montaner, L. J., & Siliciano, R. F. (2024). Bispecific antibodies promote natural killer cell-mediated elimination of HIV-1 reservoir cells. Nature immunology, 25(3), 462–470. https://doi.org/10.1038/s41590-023-01741-5, PMID: 38278966, PMCID: PMC10907297
• Siliciano, J. D., & Siliciano, R. F. (2024). HIV cure: The daunting scale of the problem. Science, 383(6684), 703–705. https://doi.org/10.1126/science.adk1831, PMID: 38359111
• Kufera, J. T., Armstrong, C., Wu, F., Singhal, A., Zhang, H., Lai, J., Wilkins, H. N., Simonetti, F. R., Siliciano, J. D., & Siliciano, R. F. (2024). CD4+ T cells with latent HIV-1 have reduced proliferative responses to T cell receptor stimulation. The Journal of experimental medicine, 221(3), e20231511. https://doi.org/10.1084/jem.20231511, PMID: 38270554, PMCID: PMC10818065

2023

• Benner, S. E., Zhu, X., Hussain, S., Florman, S., Eby, Y., Fernandez, R. E., Ostrander, D., Rana, M., Ottmann, S., Hand, J., Price, J. C., Pereira, M. R., Wojciechowski, D., Simkins, J., Stosor, V., Mehta, S. A., Aslam, S., Malinis, M., Haidar, G., Massie, A., … Tobian, A. A. R. (2023). HIV-Positive Liver Transplant Does not Alter the Latent Viral Reservoir in Recipients With Antiretroviral Therapy-Suppressed HIV. The Journal of infectious diseases, 228(9), 1274–1279. https://doi.org/10.1093/infdis/jiad241, PMID: 37379584, PMCID: PMC10629701
• Kumar, M. R., Fray, E. J., Bender, A. M., Zitzmann, C., Ribeiro, R. M., Perelson, A. S., Barouch, D. H., Siliciano, J. D., & Siliciano, R. F. (2023). Biphasic decay of intact SHIV genomes following initiation of antiretroviral therapy complicates analysis of interventions targeting the reservoir. Proceedings of the National Academy of Sciences of the United States of America, 120(43), e2313209120. https://doi.org/10.1073/pnas.2313209120, PMID: 37844236, PMCID: PMC10614214
• McMyn, N. F., Varriale, J., Fray, E. J., Zitzmann, C., MacLeod, H., Lai, J., Singhal, A., Moskovljevic, M., Garcia, M. A., Lopez, B. M., Hariharan, V., Rhodehouse, K., Lynn, K., Tebas, P., Mounzer, K., Montaner, L. J., Benko, E., Kovacs, C., Hoh, R., Simonetti, F. R., … Siliciano, J. M. (2023). The latent reservoir of inducible, infectious HIV-1 does not decrease despite decades of antiretroviral therapy. The Journal of clinical investigation, 133(17), e171554. https://doi.org/10.1172/JCI171554, PMID: 37463049, PMCID: PMC10471168
• Wu, H. L., Busman-Sahay, K., Weber, W. C., Waytashek, C. M., Boyle, C. D., Bateman, K. B., Reed, J. S., Hwang, J. M., Shriver-Munsch, C., Swanson, T., Northrup, M., Armantrout, K., Price, H., Robertson-LeVay, M., Uttke, S., Kumar, M. R., Fray, E. J., Taylor-Brill, S., Bondoc, S., Agnor, R., … Sacha, J. B. (2023). Allogeneic immunity clears latent virus following allogeneic stem cell transplantation in SIV-infected ART-suppressed macaques. Immunity, 56(7), 1649–1663.e5. https://doi.org/10.1016/j.immuni.2023.04.019, PMID: 37236188, PMCID: PMC10524637
• Sengupta, S., Zhang, J., Reed, M. C., Yu, J., Kim, A., Boronina, T. N., Board, N. L., Wrabl, J. O., Shenderov, K., Welsh, R. A., Yang, W., Timmons, A. E., Hoh, R., Cole, R. N., Deeks, S. G., Siliciano, J. D., Siliciano, R. F., & Sadegh-Nasseri, S. (2023). A cell-free antigen processing system informs HIV-1 epitope selection and vaccine design. The Journal of experimental medicine, 220(7), e20221654. https://doi.org/10.1084/jem.20221654, PMID: 37058141, PMCID: PMC10114365
• White, J. A., Wu, F., Yasin, S., Moskovljevic, M., Varriale, J., Dragoni, F., Camilo-Contreras, A., Duan, J., Zheng, M. Y., Tadzong, N. F., Patel, H. B., Quiambao, J. M. C., Rhodehouse, K., Zhang, H., Lai, J., Beg, S. A., Delannoy, M., Kilcrease, C., Hoffmann, C. J., Poulin, S., … Simonetti, F. R. (2023). Clonally expanded HIV-1 proviruses with 5′-leader defects can give rise to nonsuppressible residual viremia. The Journal of clinical investigation, 133(6), e165245. https://doi.org/10.1172/JCI165245, PMID: 36602866, PMCID: PMC10014112
• Fray, E. J., Wu, F., Simonetti, F. R., Zitzmann, C., Sambaturu, N., Molina-Paris, C., Bender, A. M., Liu, P. T., Ventura, J. D., Wiseman, R. W., O’Connor, D. H., Geleziunas, R., Leitner, T., Ribeiro, R. M., Perelson, A. S., Barouch, D. H., Siliciano, J. D., & Siliciano, R. F. (2023). Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants. Cell host & microbe, 31(3), 356–372.e5. https://doi.org/10.1016/j.chom.2023.01.016, PMID: 36809762, PMCID: PMC10583177
• Lopez, B., & Siliciano, R. F. (2023). Analyzing the unperturbed HIV-1 T cell reservoir. Trends in immunology, 44(3), 147–149. https://doi.org/10.1016/j.it.2023.01.007, PMID: 36739207
• Statzu, M., Jin, W., Fray, E. J., Wong, A. K. H., Kumar, M. R., Ferrer, E., Docken, S. S., Pinkevych, M., McBrien, J. B., Fennessey, C. M., Keele, B. F., Liang, S., Harper, J. L., Mutascio, S., Franchitti, L., Wang, H., Cicetti, D., Bosinger, S. E., Carnathan, D. G., Vanderford, T. H., … Silvestri, G. (2023). CD8⁺lymphocytes do not impact SIV reservoir establishment under ART. Nature microbiology, 8(2), 299–308. https://doi.org/10.1038/s41564-022-01311-9, PMID: 36690860, PMCID: PMC9894752

2022

• Benner, S. E., Eby, Y., Zhu, X., Fernandez, R. E., Patel, E. U., Ruff, J. E., Habtehyimer, F., Schmidt, H. A., Kirby, C. S., Hussain, S., Ostrander, D., Desai, N. M., Florman, S., Rana, M. M., Friedman-Moraco, R., Pereira, M. R., Mehta, S., Stock, P., Gilbert, A., Morris, M. I., … Tobian, A. A. (2022). The effect of induction immunosuppression for kidney transplant on the latent HIV reservoir. JCI insight, 7(21), e162968. https://doi.org/10.1172/jci.insight.162968, PMID: 36345940, PMCID: PMC9675561
• Dai, W., Wu, F., McMyn, N., Song, B., Walker-Sperling, V. E., Varriale, J., Zhang, H., Barouch, D. H., Siliciano, J. D., Li, W., & Siliciano, R. F. (2022). Genome-wide CRISPR screens identify combinations of candidate latency reversing agents for targeting the latent HIV-1 reservoir. Science translational medicine, 14(667), eabh3351. https://doi.org/10.1126/scitranslmed.abh3351, PMID: 36260688, PMCID: PMC9705157
• White, J. A., Kufera, J. T., Bachmann, N., Dai, W., Simonetti, F. R., Armstrong, C., Lai, J., Beg, S., Siliciano, J. D., & Siliciano, R. F. (2022). Measuring the latent reservoir for HIV-1: Quantification bias in near full-length genome sequencing methods. PLoS pathogens, 18(9), e1010845. https://doi.org/10.1371/journal.ppat.1010845, PMID: 36074794, PMCID: PMC9488763
• Board, N. L., Moskovljevic, M., Wu, F., Siliciano, R. F., & Siliciano, J. D. (2022). Engaging innate immunity in HIV-1 cure strategies. Nature reviews. Immunology, 22(8), 499–512. https://doi.org/10.1038/s41577-021-00649-1, PMID: 34824401
• Walker-Sperling, V. E. K., Mercado, N. B., Chandrashekar, A., Borducchi, E. N., Liu, J., Nkolola, J. P., Lewis, M., Murry, J. P., Yang, Y., Geleziunas, R., Robb, M. L., Michael, N. L., Pau, M. G., Wegmann, F., Schuitemaker, H., Fray, E. J., Kumar, M. R., Siliciano, J. D., Siliciano, R. F., & Barouch, D. H. (2022). Therapeutic efficacy of combined active and passive immunization in ART-suppressed, SHIV-infected rhesus macaques. Nature communications, 13(1), 3463. https://doi.org/10.1038/s41467-022-31196-5, PMID: 35710819, PMCID: PMC9203527
• Ventura, J. D., Nkolola, J. P., Chandrashekar, A., Borducchi, E. N., Liu, J., Mercado, N. B., Hope, D. L., Giffin, V. M., McMahan, K., Geleziunas, R., Murry, J. P., Yang, Y., Lewis, M. G., Pau, M. G., Wegmann, F., Schuitemaker, H., Fray, E. J., Kumar, M. R., Siliciano, J. D., Siliciano, R. F., … Barouch, D. H. (2022). Therapeutic efficacy of an Ad26/MVA vaccine with SIV gp140 protein and vesatolimod in ART-suppressed rhesus macaques. NPJ vaccines, 7(1), 53. https://doi.org/10.1038/s41541-022-00477-x, PMID: 35585080, PMCID: PMC9117189
• Sengupta, S., Board, N. L., Wu, F., Moskovljevic, M., Douglass, J., Zhang, J., Reinhold, B. R., Duke-Cohan, J., Yu, J., Reed, M. C., Tabdili, Y., Azurmendi, A., Fray, E. J., Zhang, H., Hsiue, E. H., Jenike, K., Ho, Y. C., Gabelli, S. B., Kinzler, K. W., Vogelstein, B., … Siliciano, R. F. (2022). TCR-mimic bispecific antibodies to target the HIV-1 reservoir. Proceedings of the National Academy of Sciences of the United States of America, 119(15), e2123406119. https://doi.org/10.1073/pnas.2123406119, PMID: 35394875, PMCID: PMC9169739
• White, J. A., Simonetti, F. R., Beg, S., McMyn, N. F., Dai, W., Bachmann, N., Lai, J., Ford, W. C., Bunch, C., Jones, J. L., Ribeiro, R. M., Perelson, A. S., Siliciano, J. D., & Siliciano, R. F. (2022). Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proceedings of the National Academy of Sciences of the United States of America, 119(6), e2120326119. https://doi.org/10.1073/pnas.2120326119, PMID: 35110411, PMCID: PMC8833145
• Siliciano, J. D., & Siliciano, R. F. (2022). In Vivo Dynamics of the Latent Reservoir for HIV-1: New Insights and Implications for Cure. Annual review of pathology, 17, 271–294. https://doi.org/10.1146/annurev-pathol-050520-112001, PMID: 34736342
• Turk, G., Seiger, K., Lian, X., Sun, W., Parsons, E. M., Gao, C., Rassadkina, Y., Polo, M. L., Czernikier, A., Ghiglione, Y., Vellicce, A., Varriale, J., Lai, J., Yuki, Y., Martin, M., Rhodes, A., Lewin, S. R., Walker, B. D., Carrington, M., Siliciano, R., … Yu, X. G. (2022). A Possible Sterilizing Cure of HIV-1 Infection Without Stem Cell Transplantation. Annals of internal medicine, 175(1), 95–100. https://doi.org/10.7326/L21-0297, PMID: 34781719, PMCID: PMC9215120

2021

• Rasmussen, T. A., Rajdev, L., Rhodes, A., Dantanarayana, A., Tennakoon, S., Chea, S., Spelman, T., Lensing, S., Rutishauser, R., Bakkour, S., Busch, M., Siliciano, J. D., Siliciano, R. F., Einstein, M. H., Dittmer, D. P., Chiao, E., Deeks, S. G., Durand, C., & Lewin, S. R. (2021). Impact of Anti-PD-1 and Anti-CTLA-4 on the Human Immunodeficiency Virus (HIV) Reservoir in People Living With HIV With Cancer on Antiretroviral Therapy: The AIDS Malignancy Consortium 095 Study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 73(7), e1973–e1981. https://doi.org/10.1093/cid/ciaa1530, PMID: 33677480, PMCID: PMC8492152
• Rasmussen, T. A., Rajdev, L., Rhodes, A., Dantanarayana, A., Tennakoon, S., Chea, S., Spelman, T., Lensing, S., Rutishauser, R., Bakkour, S., Busch, M., Siliciano, J. D., Siliciano, R. F., Einstein, M. H., Dittmer, D. P., Chiao, E., Deeks, S. G., Durand, C., & Lewin, S. R. (2021). Impact of Anti-PD-1 and Anti-CTLA-4 on the Human Immunodeficiency Virus (HIV) Reservoir in People Living With HIV With Cancer on Antiretroviral Therapy: The AIDS Malignancy Consortium 095 Study. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 73(7), e1973–e1981. https://doi.org/10.1093/cid/ciaa1530, PMID: 33677480, PMCID: PMC8492152
• Martin, A. R., Bender, A. M., Hackman, J., Kwon, K. J., Lynch, B. A., Bruno, D., Martens, C., Beg, S., Florman, S. S., Desai, N., Segev, D., Laird, G. M., Siliciano, J. D., Quinn, T. C., Tobian, A. A. R., Durand, C. M., Siliciano, R. F., & Redd, A. D. (2021). Similar Frequency and Inducibility of Intact Human Immunodeficiency Virus-1 Proviruses in Blood and Lymph Nodes. The Journal of infectious diseases, 224(2), 258–268. https://doi.org/10.1093/infdis/jiaa736, PMID: 33269401, PMCID: PMC8280486
• Kirk, G. D., Astemborski, J., Mehta, S. H., Ritter, K. D., Laird, G. M., Bordi, R., Sekaly, R., Siliciano, J. D., & Siliciano, R. F. (2021). Nonstructured Treatment Interruptions Are Associated With Higher Human Immunodeficiency Virus Reservoir Size Measured by Intact Proviral DNA Assay in People Who Inject Drugs. The Journal of infectious diseases, 223(11), 1905–1913. https://doi.org/10.1093/infdis/jiaa634, PMID: 33037877, PMCID: PMC8176633
• Cadena, A. M., Ventura, J. D., Abbink, P., Borducchi, E. N., Tuyishime, H., Mercado, N. B., Walker-Sperling, V., Siamatu, M., Liu, P. T., Chandrashekar, A., Nkolola, J. P., McMahan, K., Kordana, N., Hamza, V., Bondzie, E. A., Fray, E., Kumar, M., Fischinger, S., Shin, S. A., Lewis, M. G., … Barouch, D. H. (2021). Persistence of viral RNA in lymph nodes in ART-suppressed SIV/SHIV-infected Rhesus Macaques. Nature communications, 12(1), 1474. https://doi.org/10.1038/s41467-021-21724-0, PMID: 33674572, PMCID: PMC7935896
• Gaebler, C., Falcinelli, S. D., Stoffel, E., Read, J., Murtagh, R., Oliveira, T. Y., Ramos, V., Lorenzi, J. C. C., Kirchherr, J., James, K. S., Allard, B., Baker, C., Kuruc, J. D., Caskey, M., Archin, N. M., Siliciano, R. F., Margolis, D. M., & Nussenzweig, M. C. (2021). Sequence Evaluation and Comparative Analysis of Novel Assays for Intact Proviral HIV-1 DNA. Journal of virology, 95(6), e01986-20. https://doi.org/10.1128/JVI.01986-20, PMID: 33361426, PMCID: PMC8094944
• Simonetti, F. R., Zhang, H., Soroosh, G. P., Duan, J., Rhodehouse, K., Hill, A. L., Beg, S. A., McCormick, K., Raymond, H. E., Nobles, C. L., Everett, J. K., Kwon, K. J., White, J. A., Lai, J., Margolick, J. B., Hoh, R., Deeks, S. G., Bushman, F. D., Siliciano, J. D., & Siliciano, R. F. (2021). Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo. The Journal of clinical investigation, 131(3), e145254. https://doi.org/10.1172/JCI145254, PMID: 33301425, PMCID: PMC7843227
• Siliciano, J. D., & Siliciano, R. F. (2021). Low Inducibility of Latent Human Immunodeficiency Virus Type 1 Proviruses as a Major Barrier to Cure. The Journal of infectious diseases, 223(12 Suppl 2), 13–21. https://doi.org/10.1093/infdis/jiaa649, PMID: 33586775
• Gondim, M. V. P., Sherrill-Mix, S., Bibollet-Ruche, F., Russell, R. M., Trimboli, S., Smith, A. G., Li, Y., Liu, W., Avitto, A. N., DeVoto, J. C., Connell, J., Fenton-May, A. E., Pellegrino, P., Williams, I., Papasavvas, E., Lorenzi, J. C. C., Salantes, D. B., Mampe, F., Monroy, M. A., Cohen, Y. Z., … Hahn, B. H. (2021). Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption. Science translational medicine, 13(576), eabd8179. https://doi.org/10.1126/scitranslmed.abd8179, PMID: 33441429, PMCID: PMC7923595

2020

• Obregon-Perko, V., Bricker, K. M., Mensah, G., Uddin, F., Kumar, M. R., Fray, E. J., Siliciano, R. F., Schoof, N., Horner, A., Mavigner, M., Liang, S., Vanderford, T., Sass, J., Chan, C., Berendam, S. J., Bar, K. J., Shaw, G. M., Silvestri, G., Fouda, G. G., Permar, S. R., … Chahroudi, A. (2020). Simian-Human Immunodeficiency Virus SHIV.C.CH505 Persistence in ART-Suppressed Infant Macaques Is Characterized by Elevated SHIV RNA in the Gut and a High Abundance of Intact SHIV DNA in Naive CD4⁺T Cells. Journal of virology, 95(2), e01669-20. https://doi.org/10.1128/JVI.01669-20, PMID: 33087463, PMCID: PMC7944446
• Yukl, S. A., Khan, S., Chen, T. H., Trapecar, M., Wu, F., Xie, G., Telwatte, S., Fulop, D., Pico, A. R., Laird, G. M., Ritter, K. D., Jones, N. G., Lu, C. M., Siliciano, R. F., Roan, N. R., Milush, J. M., Somsouk, M., Deeks, S. G., Hunt, P. W., & Sanjabi, S. (2020). Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103⁺and Gut CD4⁺ T Cells. Journal of virology, 95(2), e01331-20. https://doi.org/10.1128/JVI.01331-20, PMID: 33115867, PMCID: PMC7944458
• Bertagnolli, L. N., Varriale, J., Sweet, S., Brockhurst, J., Simonetti, F. R., White, J., Beg, S., Lynn, K., Mounzer, K., Frank, I., Tebas, P., Bar, K. J., Montaner, L. J., Siliciano, R. F., & Siliciano, J. D. (2020). Autologous IgG antibodies block outgrowth of a substantial but variable fraction of viruses in the latent reservoir for HIV-1. Proceedings of the National Academy of Sciences of the United States of America, 117(50), 32066–32077. https://doi.org/10.1073/pnas.2020617117, PMID: 33239444, PMCID: PMC7749285
• Siliciano, J. D., & Siliciano, R. F. (2020). Nonsuppressible HIV-1 viremia: a reflection of how the reservoir persists. The Journal of clinical investigation, 130(11), 5665–5667. https://doi.org/10.1172/JCI141497, PMID: 33016925, PMCID: PMC7598039
• Song, N., Sengupta, S., Khoruzhenko, S., Welsh, R. A., Kim, A., Kumar, M. R., Sønder, S. U., Sidhom, J. W., Zhang, H., Jie, C., Siliciano, R. F., & Sadegh-Nasseri, S. (2020). Multiple genetic programs contribute to CD4 T cell memory differentiation and longevity by maintaining T cell quiescence. Cellular immunology, 357, 104210. https://doi.org/10.1016/j.cellimm.2020.104210, PMID: 32987276, PMCID: PMC7737224
• Jiang, C., Lian, X., Gao, C., Sun, X., Einkauf, K. B., Chevalier, J. M., Chen, S. M. Y., Hua, S., Rhee, B., Chang, K., Blackmer, J. E., Osborn, M., Peluso, M. J., Hoh, R., Somsouk, M., Milush, J., Bertagnolli, L. N., Sweet, S. E., Varriale, J. A., Burbelo, P. D., … Yu, X. G. (2020). Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature, 585(7824), 261–267. https://doi.org/10.1038/s41586-020-2651-8, PMID: 32848246, PMCID: PMC7837306
• Abdel-Mohsen, M., Richman, D., Siliciano, R. F., Nussenzweig, M. C., Howell, B. J., Martinez-Picado, J., Chomont, N., Bar, K. J., Yu, X. G., Lichterfeld, M., Alcami, J., Hazuda, D., Bushman, F., Siliciano, J. D., Betts, M. R., Spivak, A. M., Planelles, V., Hahn, B. H., Smith, D. M., Ho, Y. C., … BEAT-HIV Delaney Collaboratory to Cure HIV-1 infection (2020). Recommendations for measuring HIV reservoir size in cure-directed clinical trials. Nature medicine, 26(9), 1339–1350. https://doi.org/10.1038/s41591-020-1022-1, PMID: 32895573, PMCID: PMC7703694
• Durand, C. M., Capoferri, A. A., Redd, A. D., Zahurak, M., Rosenbloom, D. I. S., Cash, A., Avery, R. K., Bolaños-Meade, J., Bollard, C. M., Bullen, C. K., Flexner, C., Fuchs, E. J., Gallant, J., Gladstone, D. E., Gocke, C. D., Jones, R. J., Kasamon, Y. L., Lai, J., Levis, M., Luznik, L., … Ambinder, R. F. (2020). Allogeneic bone marrow transplantation with post-transplant cyclophosphamide for patients with HIV and haematological malignancies: a feasibility study. The lancet. HIV, 7(9), e602–e610. https://doi.org/10.1016/S2352-3018(20)30073-4, PMID: 32649866, PMCID: PMC7484204
• Simonetti, F. R., White, J. A., Tumiotto, C., Ritter, K. D., Cai, M., Gandhi, R. T., Deeks, S. G., Howell, B. J., Montaner, L. J., Blankson, J. N., Martin, A., Laird, G. M., Siliciano, R. F., Mellors, J. W., & Siliciano, J. D. (2020). Intact proviral DNA assay analysis of large cohorts of people with HIV provides a benchmark for the frequency and composition of persistent proviral DNA. Proceedings of the National Academy of Sciences of the United States of America, 117(31), 18692–18700. https://doi.org/10.1073/pnas.2006816117, PMID: 32690683, PMCID: PMC7414172
• Timmons, A., Fray, E., Kumar, M., Wu, F., Dai, W., Bullen, C. K., Kim, P., Hetzel, C., Yang, C., Beg, S., Lai, J., Pomerantz, J. L., Yukl, S. A., Siliciano, J. D., & Siliciano, R. F. (2020). HSF1 inhibition attenuates HIV-1 latency reversal mediated by several candidate LRAs In Vitro and Ex Vivo. Proceedings of the National Academy of Sciences of the United States of America, 117(27), 15763–15771. https://doi.org/10.1073/pnas.1916290117, PMID: 32571938, PMCID: PMC7959657
• Antar, A. A., Jenike, K. M., Jang, S., Rigau, D. N., Reeves, D. B., Hoh, R., Krone, M. R., Keruly, J. C., Moore, R. D., Schiffer, J. T., Nonyane, B. A., Hecht, F. M., Deeks, S. G., Siliciano, J. D., Ho, Y. C., & Siliciano, R. F. (2020). Longitudinal study reveals HIV-1-infected CD4+ T cell dynamics during long-term antiretroviral therapy. The Journal of clinical investigation, 130(7), 3543–3559. https://doi.org/10.1172/JCI135953, PMID: 32191639, PMCID: PMC7324206
• Peluso, M. J., Bacchetti, P., Ritter, K. D., Beg, S., Lai, J., Martin, J. N., Hunt, P. W., Henrich, T. J., Siliciano, J. D., Siliciano, R. F., Laird, G. M., & Deeks, S. G. (2020). Differential decay of intact and defective proviral DNA in HIV-1-infected individuals on suppressive antiretroviral therapy. JCI insight, 5(4), e132997. https://doi.org/10.1172/jci.insight.132997, PMID: 32045386, PMCID: PMC7101154
• Kwon, K. J., Timmons, A. E., Sengupta, S., Simonetti, F. R., Zhang, H., Hoh, R., Deeks, S. G., Siliciano, J. D., & Siliciano, R. F. (2020). Different human resting memory CD4⁺T cell subsets show similar low inducibility of latent HIV-1 proviruses. Science translational medicine, 12(528), eaax6795. https://doi.org/10.1126/scitranslmed.aax6795, PMID: 31996465, PMCID: PMC7875249

2019

• Silverman, K., Holtyn, A. F., Rodewald, A. M., Siliciano, R. F., Jarvis, B. P., Subramaniam, S., Leoutsakos, J. M., Getty, C. A., Ruhs, S., Marzinke, M. A., & Fingerhood, M. (2019). Incentives for Viral Suppression in People Living with HIV: A Randomized Clinical Trial. AIDS and behavior, 23(9), 2337–2346. https://doi.org/10.1007/s10461-019-02592-8, PMID: 31297681, PMCID: PMC6768703
• Bender, A. M., Simonetti, F. R., Kumar, M. R., Fray, E. J., Bruner, K. M., Timmons, A. E., Tai, K. Y., Jenike, K. M., Antar, A. A. R., Liu, P. T., Ho, Y. C., Raugi, D. N., Seydi, M., Gottlieb, G. S., Okoye, A. A., Del Prete, G. Q., Picker, L. J., Mankowski, J. L., Lifson, J. D., Siliciano, J. D., … Siliciano, R. F. (2019). The Landscape of Persistent Viral Genomes in ART-Treated SIV, SHIV, and HIV-2 Infections. Cell host & microbe, 26(1), 73–85.e4. https://doi.org/10.1016/j.chom.2019.06.005, PMID: 31295427, PMCID: PMC6724192
• Bruner, K. M., Wang, Z., Simonetti, F. R., Bender, A. M., Kwon, K. J., Sengupta, S., Fray, E. J., Beg, S. A., Antar, A. A. R., Jenike, K. M., Bertagnolli, L. N., Capoferri, A. A., Kufera, J. T., Timmons, A., Nobles, C., Gregg, J., Wada, N., Ho, Y. C., Zhang, H., Margolick, J. B., … Siliciano, R. F. (2019). A quantitative approach for measuring the reservoir of latent HIV-1 proviruses. Nature, 566(7742), 120–125. https://doi.org/10.1038/s41586-019-0898-8, PMID: 30700913, PMCID: PMC6447073

2018

• Bertagnolli, L. N., White, J. A., Simonetti, F. R., Beg, S. A., Lai, J., Tomescu, C., Murray, A. J., Antar, A. A. R., Zhang, H., Margolick, J. B., Hoh, R., Deeks, S. G., Tebas, P., Montaner, L. J., Siliciano, R. F., Laird, G. M., & Siliciano, J. D. (2018). The role of CD32 during HIV-1 infection. Nature, 561(7723), E17–E19. https://doi.org/10.1038/s41586-018-0494-3, PMID: 30232425, PMCID: PMC6442722
• Hill, A. L., Rosenbloom, D. I. S., Nowak, M. A., & Siliciano, R. F. (2018). Insight into treatment of HIV infection from viral dynamics models. Immunological reviews, 285(1), 9–25. https://doi.org/10.1111/imr.12698, PMID: 30129208, PMCID: PMC6155466
• El-Diwany, R., Soliman, M., Sugawara, S., Breitwieser, F., Skaist, A., Coggiano, C., Sangal, N., Chattergoon, M., Bailey, J. R., Siliciano, R. F., Blankson, J. N., Ray, S. C., Wheelan, S. J., Thomas, D. L., & Balagopal, A. (2018). CMPK2 and BCL-G are associated with type 1 interferon-induced HIV restriction in humans. Science advances, 4(8), eaat0843. https://doi.org/10.1126/sciadv.aat0843, PMID: 30083606, PMCID: PMC6070316
• Salantes, D. B., Zheng, Y., Mampe, F., Srivastava, T., Beg, S., Lai, J., Li, J. Z., Tressler, R. L., Koup, R. A., Hoxie, J., Abdel-Mohsen, M., Sherrill-Mix, S., McCormick, K., Overton, E. T., Bushman, F. D., Learn, G. H., Siliciano, R. F., Siliciano, J. M., Tebas, P., & Bar, K. J. (2018). HIV-1 latent reservoir size and diversity are stable following brief treatment interruption. The Journal of clinical investigation, 128(7), 3102–3115. https://doi.org/10.1172/JCI120194, PMID: 29911997, PMCID: PMC6026010
• Huang, S. H., Ren, Y., Thomas, A. S., Chan, D., Mueller, S., Ward, A. R., Patel, S., Bollard, C. M., Cruz, C. R., Karandish, S., Truong, R., Macedo, A. B., Bosque, A., Kovacs, C., Benko, E., Piechocka-Trocha, A., Wong, H., Jeng, E., Nixon, D. F., Ho, Y. C., … Jones, R. B. (2018). Latent HIV reservoirs exhibit inherent resistance to elimination by CD8+ T cells. The Journal of clinical investigation, 128(2), 876–889. https://doi.org/10.1172/JCI97555, PMID: 29355843, PMCID: PMC5785246
• Sengupta, S., & Siliciano, R. F. (2018). Targeting the Latent Reservoir for HIV-1. Immunity, 48(5), 872–895. https://doi.org/10.1016/j.immuni.2018.04.030, PMID: 29768175, PMCID: PMC6196732
• Wang, Z., Gurule, E. E., Brennan, T. P., Gerold, J. M., Kwon, K. J., Hosmane, N. N., Kumar, M. R., Beg, S. A., Capoferri, A. A., Ray, S. C., Ho, Y. C., Hill, A. L., Siliciano, J. D., & Siliciano, R. F. (2018). Expanded cellular clones carrying replication-competent HIV-1 persist, wax, and wane. Proceedings of the National Academy of Sciences of the United States of America, 115(11), E2575–E2584. https://doi.org/10.1073/pnas.1720665115, PMID: 29483265, PMCID: PMC5856552
• Pohlmeyer, C. W., Laskey, S. B., Beck, S. E., Xu, D. C., Capoferri, A. A., Garliss, C. C., May, M. E., Livingston, A., Lichmira, W., Moore, R. D., Leffell, M. S., Butler, N. J., Thorne, J. E., Flynn, J. A., Siliciano, R. F., & Blankson, J. N. (2018). Cross-reactive microbial peptides can modulate HIV-specific CD8+ T cell responses. PloS one, 13(2), e0192098. https://doi.org/10.1371/journal.pone.0192098, PMID: 29466365, PMCID: PMC5821448
• Wang, Z., Simonetti, F. R., Siliciano, R. F., & Laird, G. M. (2018). Measuring replication competent HIV-1: advances and challenges in defining the latent reservoir. Retrovirology, 15(1), 21. https://doi.org/10.1186/s12977-018-0404-7, PMID: 29433524, PMCID: PMC5810003

2017

• Rosenbloom, D. I. S., Hill, A. L., Laskey, S. B., & Siliciano, R. F. (2017). Re-evaluating evolution in the HIV reservoir. Nature, 551(7681), E6–E9. https://doi.org/10.1038/nature24634, PMID: 29168805, PMCID: PMC6103791
• Henrich, T. J., Hatano, H., Bacon, O., Hogan, L. E., Rutishauser, R., Hill, A., Kearney, M. F., Anderson, E. M., Buchbinder, S. P., Cohen, S. E., Abdel-Mohsen, M., Pohlmeyer, C. W., Fromentin, R., Hoh, R., Liu, A. Y., McCune, J. M., Spindler, J., Metcalf-Pate, K., Hobbs, K. S., Thanh, C., … Deeks, S. G. (2017). HIV-1 persistence following extremely early initiation of antiretroviral therapy (ART) during acute HIV-1 infection: An observational study. PLoS medicine, 14(11), e1002417. https://doi.org/10.1371/journal.pmed.1002417, PMID: 29112956, PMCID: PMC5675377
• Siliciano, J. D., & Siliciano, R. F. (2018). Assays to Measure Latency, Reservoirs, and Reactivation. Current topics in microbiology and immunology, 417, 23–41. https://doi.org/10.1007/82_2017_75, PMID: 29071475
• Shan, L., Deng, K., Gao, H., Xing, S., Capoferri, A. A., Durand, C. M., Rabi, S. A., Laird, G. M., Kim, M., Hosmane, N. N., Yang, H. C., Zhang, H., Margolick, J. B., Li, L., Cai, W., Ke, R., Flavell, R. A., Siliciano, J. D., & Siliciano, R. F. (2017). Transcriptional Reprogramming during Effector-to-Memory Transition Renders CD4⁺T Cells Permissive for Latent HIV-1 Infection. Immunity, 47(4), 766–775.e3. https://doi.org/10.1016/j.immuni.2017.09.014, PMID: 29045905, PMCID: PMC5948104
• Prodger, J. L., Lai, J., Reynolds, S. J., Keruly, J. C., Moore, R. D., Kasule, J., Kityamuweesi, T., Buule, P., Serwadda, D., Nason, M., Capoferri, A. A., Porcella, S. F., Siliciano, R. F., Redd, A. D., Siliciano, J. D., & Quinn, T. C. (2017). Reduced Frequency of Cells Latently Infected With Replication-Competent Human Immunodeficiency Virus-1 in Virally Suppressed Individuals Living in Rakai, Uganda. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 65(8), 1308–1315. https://doi.org/10.1093/cid/cix478, PMID: 28535179, PMCID: PMC5850010
• Hill, A. L., Rosenbloom, D. I. S., Goldstein, E., Hanhauser, E., Kuritzkes, D. R., Siliciano, R. F., & Henrich, T. J. (2017). Correction: Real-Time Predictions of Reservoir Size and Rebound Time during Antiretroviral Therapy Interruption Trials for HIV. PLoS pathogens, 13(7), e1006488. https://doi.org/10.1371/journal.ppat.1006488, PMID: 28683094, PMCID: PMC5500350
• Kwon, K. J., & Siliciano, R. F. (2017). HIV persistence: clonal expansion of cells in the latent reservoir. The Journal of clinical investigation, 127(7), 2536–2538. https://doi.org/10.1172/JCI95329, PMID: 28628041, PMCID: PMC5490744
• Pollack, R. A., Jones, R. B., Pertea, M., Bruner, K. M., Martin, A. R., Thomas, A. S., Capoferri, A. A., Beg, S. A., Huang, S. H., Karandish, S., Hao, H., Halper-Stromberg, E., Yong, P. C., Kovacs, C., Benko, E., Siliciano, R. F., & Ho, Y. C. (2017). Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape. Cell host & microbe, 21(4), 494–506.e4. https://doi.org/10.1016/j.chom.2017.03.008, PMID: 28407485, PMCID: PMC5433942
• Hosmane, N. N., Kwon, K. J., Bruner, K. M., Capoferri, A. A., Beg, S., Rosenbloom, D. I., Keele, B. F., Ho, Y. C., Siliciano, J. D., & Siliciano, R. F. (2017). Proliferation of latently infected CD4⁺T cells carrying replication-competent HIV-1: Potential role in latent reservoir dynamics. The Journal of experimental medicine, 214(4), 959–972. https://doi.org/10.1084/jem.20170193, PMID: 28341641, PMCID: PMC5379987
• Martin, A. R., Pollack, R. A., Capoferri, A., Ambinder, R. F., Durand, C. M., & Siliciano, R. F. (2017). Rapamycin-mediated mTOR inhibition uncouples HIV-1 latency reversal from cytokine-associated toxicity. The Journal of clinical investigation, 127(2), 651–656. https://doi.org/10.1172/JCI89552, PMID: 28094770, PMCID: PMC5272184
• Lusic, M., & Siliciano, R. F. (2017). Nuclear landscape of HIV-1 infection and integration. Nature reviews. Microbiology, 15(2), 69–82. https://doi.org/10.1038/nrmicro.2016.162, PMID: 27941817
• Gama, L., Abreu, C. M., Shirk, E. N., Price, S. L., Li, M., Laird, G. M., Pate, K. A., Wietgrefe, S. W., O’Connor, S. L., Pianowski, L., Haase, A. T., Van Lint, C., Siliciano, R. F., Clements, J. E., & LRA-SIV Study Group (2017). Reactivation of simian immunodeficiency virus reservoirs in the brain of virally suppressed macaques. AIDS (London, England), 31(1), 5–14. https://doi.org/10.1097/QAD.0000000000001267, PMID: 27898590, PMCID: PMC5131686

2016

• Besnard, E., Hakre, S., Kampmann, M., Lim, H. W., Hosmane, N. N., Martin, A., Bassik, M. C., Verschueren, E., Battivelli, E., Chan, J., Svensson, J. P., Gramatica, A., Conrad, R. J., Ott, M., Greene, W. C., Krogan, N. J., Siliciano, R. F., Weissman, J. S., & Verdin, E. (2016). The mTOR Complex Controls HIV Latency. Cell host & microbe, 20(6), 785–797. https://doi.org/10.1016/j.chom.2016.11.001, PMID: 27978436, PMCID: PMC5354304
• Laskey, S. B., & Siliciano, R. F. (2016). Quantitative evaluation of the antiretroviral efficacy of dolutegravir. JCI insight, 1(19), e90033. https://doi.org/10.1172/jci.insight.90033, PMID: 27882352, PMCID: PMC5111505
• Hansen, E. C., Ransom, M., Hesselberth, J. R., Hosmane, N. N., Capoferri, A. A., Bruner, K. M., Pollack, R. A., Zhang, H., Drummond, M. B., Siliciano, J. M., Siliciano, R., & Stivers, J. T. (2016). Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. eLife, 5, e18447. https://doi.org/10.7554/eLife.18447, PMID: 27644592, PMCID: PMC5030084
• Bruner, K. M., Murray, A. J., Pollack, R. A., Soliman, M. G., Laskey, S. B., Capoferri, A. A., Lai, J., Strain, M. C., Lada, S. M., Hoh, R., Ho, Y. C., Richman, D. D., Deeks, S. G., Siliciano, J. D., & Siliciano, R. F. (2016). Defective proviruses rapidly accumulate during acute HIV-1 infection. Nature medicine, 22(9), 1043–1049. https://doi.org/10.1038/nm.4156, PMID: 27500724, PMCID: PMC5014606
• Hill, A. L., Rosenbloom, D. I., Siliciano, J. D., & Siliciano, R. F. (2016). Insufficient Evidence for Rare Activation of Latent HIV in the Absence of Reservoir-Reducing Interventions. PLoS pathogens, 12(8), e1005679. https://doi.org/10.1371/journal.ppat.1005679, PMID: 27560936, PMCID: PMC4999146
• Laskey, S. B., Pohlmeyer, C. W., Bruner, K. M., & Siliciano, R. F. (2016). Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality. PLoS pathogens, 12(8), e1005689. https://doi.org/10.1371/journal.ppat.1005689, PMID: 27494508, PMCID: PMC4975415
• Murray, A. J., Kwon, K. J., Farber, D. L., & Siliciano, R. F. (2016). The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence. Journal of immunology, 197(2), 407–417. https://doi.org/10.4049/jimmunol.1600343, PMID: 27382129, PMCID: PMC4936486
• Sunshine, S., Kirchner, R., Amr, S. S., Mansur, L., Shakhbatyan, R., Kim, M., Bosque, A., Siliciano, R. F., Planelles, V., Hofmann, O., Ho Sui, S., & Li, J. Z. (2016). HIV Integration Site Analysis of Cellular Models of HIV Latency with a Probe-Enriched Next-Generation Sequencing Assay. Journal of virology, 90(9), 4511–4519. https://doi.org/10.1128/JVI.01617-15, PMID: 26912621, PMCID: PMC4836361
• Hill, A. L., Rosenbloom, D. I., Goldstein, E., Hanhauser, E., Kuritzkes, D. R., Siliciano, R. F., & Henrich, T. J. (2016). Real-Time Predictions of Reservoir Size and Rebound Time during Antiretroviral Therapy Interruption Trials for HIV. PLoS pathogens, 12(4), e1005535. https://doi.org/10.1371/journal.ppat.1005535, PMID: 27119536, PMCID: PMC4847932
• Kim, M., & Siliciano, R. F. (2016). Genome editing for clinical HIV isolates. Nature biotechnology, 34(4), 388–389. https://doi.org/10.1038/nbt.3531, PMID: 27054991
• Kim, M., & Siliciano, R. F. (2016). Reservoir expansion by T-cell proliferation may be another barrier to curing HIV infection. Proceedings of the National Academy of Sciences of the United States of America, 113(7), 1692–1694. https://doi.org/10.1073/pnas.1600097113, PMID: 26862166, PMCID: PMC4763749
• Siliciano, J. D., & Siliciano, R. F. (2016). Recent developments in the effort to cure HIV infection: going beyond N = 1. The Journal of clinical investigation, 126(2), 409–414. https://doi.org/10.1172/JCI86047, PMID: 26829622, PMCID: PMC4731192
• Martin, A. R., & Siliciano, R. F. (2016). Progress Toward HIV Eradication: Case Reports, Current Efforts, and the Challenges Associated with Cure. Annual review of medicine, 67, 215–228. https://doi.org/10.1146/annurev-med-011514-023043, PMID: 26526767
• Laird, G. M., Rosenbloom, D. I., Lai, J., Siliciano, R. F., & Siliciano, J. D. (2016). Measuring the Frequency of Latent HIV-1 in Resting CD4⁺ T Cells Using a Limiting Dilution Coculture Assay.Methods in molecular biology (Clifton, N.J.), 1354, 239–253. https://doi.org/10.1007/978-1-4939-3046-3_16, PMID: 26714716
• Churchill, M. J., Deeks, S. G., Margolis, D. M., Siliciano, R. F., & Swanstrom, R. (2016). HIV reservoirs: what, where and how to target them. Nature reviews. Microbiology, 14(1), 55–60. https://doi.org/10.1038/nrmicro.2015.5, PMID: 26616417

2015

• Rosenbloom, D. I., Elliott, O., Hill, A. L., Henrich, T. J., Siliciano, J. M., & Siliciano, R. F. (2015). Designing and Interpreting Limiting Dilution Assays: General Principles and Applications to the Latent Reservoir for Human Immunodeficiency Virus-1. Open forum infectious diseases, 2(4), ofv123. https://doi.org/10.1093/ofid/ofv123, PMID: 26478893, PMCID: PMC4602119
• Siliciano, J. M., & Siliciano, R. F. (2015). The Remarkable Stability of the Latent Reservoir for HIV-1 in Resting Memory CD4+ T Cells. The Journal of infectious diseases, 212(9), 1345–1347. https://doi.org/10.1093/infdis/jiv219, PMID: 25877551
• Gray, W. T., Frey, K. M., Laskey, S. B., Mislak, A. C., Spasov, K. A., Lee, W. G., Bollini, M., Siliciano, R. F., Jorgensen, W. L., & Anderson, K. S. (2015). Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance. ACS medicinal chemistry letters, 6(10), 1075–1079. https://doi.org/10.1021/acsmedchemlett.5b00254, PMID: 26487915, PMCID: PMC4601059
• Sampah, M. E., Laird, G. M., Blankson, J. N., Siliciano, R. F., & Coleman, J. S. (2015). Medroxyprogesterone acetate increases HIV-1 infection of unstimulated peripheral blood mononuclear cells in vitro. AIDS (London, England), 29(10), 1137–1146. https://doi.org/10.1097/QAD.0000000000000681, PMID: 26035316, PMCID: PMC4453018
• Laird, G. M., Bullen, C. K., Rosenbloom, D. I., Martin, A. R., Hill, A. L., Durand, C. M., Siliciano, J. D., & Siliciano, R. F. (2015). Ex vivo analysis identifies effective HIV-1 latency-reversing drug combinations. The Journal of clinical investigation, 125(5), 1901–1912. https://doi.org/10.1172/JCI80142, PMID: 25822022, PMCID: PMC4463209
• Bruner, K. M., Hosmane, N. N., & Siliciano, R. F. (2015). Towards an HIV-1 cure: measuring the latent reservoir. Trends in microbiology, 23(4), 192–203. https://doi.org/10.1016/j.tim.2015.01.013, PMID: 25747663, PMCID: PMC4386620
• Cohn, L. B., Silva, I. T., Oliveira, T. Y., Rosales, R. A., Parrish, E. H., Learn, G. H., Hahn, B. H., Czartoski, J. L., McElrath, M. J., Lehmann, C., Klein, F., Caskey, M., Walker, B. D., Siliciano, J. D., Siliciano, R. F., Jankovic, M., & Nussenzweig, M. C. (2015). HIV-1 integration landscape during latent and active infection. Cell, 160(3), 420–432. https://doi.org/10.1016/j.cell.2015.01.020, PMID: 25635456, PMCID: PMC4371550
• Deng, K., Pertea, M., Rongvaux, A., Wang, L., Durand, C. M., Ghiaur, G., Lai, J., McHugh, H. L., Hao, H., Zhang, H., Margolick, J. B., Gurer, C., Murphy, A. J., Valenzuela, D. M., Yancopoulos, G. D., Deeks, S. G., Strowig, T., Kumar, P., Siliciano, J. D., Salzberg, S. L., … Siliciano, R. F. (2015). Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature, 517(7534), 381–385. https://doi.org/10.1038/nature14053, PMID: 25561180, PMCID: PMC4406054
• Zarr, M., & Siliciano, R. (2015). Stoichiometric parameters of HIV-1 entry. Virology, 474, 1–9. https://doi.org/10.1016/j.virol.2014.10.007, PMID: 25463598

2014

• Kim, M., Hosmane, N. N., Bullen, C. K., Capoferri, A., Yang, H. C., Siliciano, J. D., & Siliciano, R. F. (2014). A primary CD4(+) T cell model of HIV-1 latency established after activation through the T cell receptor and subsequent return to quiescence. Nature protocols, 9(12), 2755–2770. https://doi.org/10.1038/nprot.2014.188, PMID: 25375990, PMCID: PMC4378543
• Deeks, S. G., & Siliciano, R. (2014). HIV Prevention and Treatment Fields Join Forces. EBioMedicine, 1(1), 4–5. https://doi.org/10.1016/j.ebiom.2014.10.009, PMID: 26137503, PMCID: PMC4457402
• Laskey, S. B., & Siliciano, R. F. (2014). A mechanistic theory to explain the efficacy of antiretroviral therapy. Nature reviews. Microbiology, 12(11), 772–780. https://doi.org/10.1038/nrmicro3351, PMID: 25263222
• Cockerham, L. R., Siliciano, J. D., Sinclair, E., O’Doherty, U., Palmer, S., Yukl, S. A., Strain, M. C., Chomont, N., Hecht, F. M., Siliciano, R. F., Richman, D. D., & Deeks, S. G. (2014). CD4+ and CD8+ T cell activation are associated with HIV DNA in resting CD4+ T cells. PloS one, 9(10), e110731. https://doi.org/10.1371/journal.pone.0110731, PMID: 25340755, PMCID: PMC4207702
• Hill, A. L., Rosenbloom, D. I., Fu, F., Nowak, M. A., & Siliciano, R. F. (2014). Predicting the outcomes of treatment to eradicate the latent reservoir for HIV-1. Proceedings of the National Academy of Sciences of the United States of America, 111(37), 13475–13480. https://doi.org/10.1073/pnas.1406663111, PMID: 25097264, PMCID: PMC4169952
• Siliciano, J. D., & Siliciano, R. F. (2014). AIDS/HIV. Rekindled HIV infection. Science, 345(6200), 1005–1006. https://doi.org/10.1126/science.1259452, PMID: 25170139
• Deng, K., Siliciano, R. Early treatment may not be early enough. Nature512, 35–36 (2014). https://doi.org/10.1038/nature13647
• Siliciano, J. D., & Siliciano, R. F. (2014). Recent developments in the search for a cure for HIV-1 infection: targeting the latent reservoir for HIV-1. The Journal of allergy and clinical immunology, 134(1), 12–19. https://doi.org/10.1016/j.jaci.2014.05.026, PMID: 25117799
• Dar, R. D., Hosmane, N. N., Arkin, M. R., Siliciano, R. F., & Weinberger, L. S. (2014). Screening for noise in gene expression identifies drug synergies. Science, 344(6190), 1392–1396. https://doi.org/10.1126/science.1250220, PMID: 24903562, PMCID: PMC4122234
• Shan, L., & Siliciano, R. F. (2014). Unraveling the relationship between microbial translocation and systemic immune activation in HIV infection. The Journal of clinical investigation, 124(6), 2368–2371. https://doi.org/10.1172/JCI75799, PMID: 24837427, PMCID: PMC4089457
• Ho, Y. C., Laird, G. M., & Siliciano, R. F. (2014). Measuring reversal of HIV-1 latency ex vivo using cells from infected individuals. Proceedings of the National Academy of Sciences of the United States of America, 111(19), 6860–6861. https://doi.org/10.1073/pnas.1405194111, PMID: 24799684, PMCID: PMC4024879
• Siliciano R. F. (2014). Opening Fronts in HIV Vaccine Development: Targeting reservoirs to clear and cure. Nature medicine, 20(5), 480–481. https://doi.org/10.1038/nm.3550, PMID: 24804757
• Laird, G. M., Eisele, E. E., Rabi, S. A., Nikolaeva, D., & Siliciano, R. F. (2014). A novel cell-based high-throughput screen for inhibitors of HIV-1 gene expression and budding identifies the cardiac glycosides. The Journal of antimicrobial chemotherapy, 69(4), 988–994. https://doi.org/10.1093/jac/dkt471, PMID: 24275119, PMCID: PMC3956374
• Bullen, C. K., Laird, G. M., Durand, C. M., Siliciano, J. D., & Siliciano, R. F. (2014). New ex vivo approaches distinguish effective and ineffective single agents for reversing HIV-1 latency in vivo. Nature medicine, 20(4), 425–429. https://doi.org/10.1038/nm.3489, PMID: 24658076, PMCID: PMC3981911
• Salgado, M., Swanson, M. D., Pohlmeyer, C. W., Buckheit, R. W., 3rd, Wu, J., Archin, N. M., Williams, T. M., Margolis, D. M., Siliciano, R. F., Garcia, J. V., & Blankson, J. N. (2014). HLA-B*57 elite suppressor and chronic progressor HIV-1 isolates replicate vigorously and cause CD4+ T cell depletion in humanized BLT mice. Journal of virology, 88(6), 3340–3352. https://doi.org/10.1128/JVI.03380-13, PMID: 24390323, PMCID: PMC3957943
• Spivak, A. M., Andrade, A., Eisele, E., Hoh, R., Bacchetti, P., Bumpus, N. N., Emad, F., Buckheit, R., 3rd, McCance-Katz, E. F., Lai, J., Kennedy, M., Chander, G., Siliciano, R. F., Siliciano, J. D., & Deeks, S. G. (2014). A pilot study assessing the safety and latency-reversing activity of disulfiram in HIV-1-infected adults on antiretroviral therapy. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 58(6), 883–890. https://doi.org/10.1093/cid/cit813, PMID: 24336828, PMCID: PMC3935499
• Cox, A. L., & Siliciano, R. F. (2014). HIV: Not-so-innocent bystanders. Nature, 505(7484), 492–493. https://doi.org/10.1038/505492a, PMID: 24451540, PMCID: PMC4434588
• Durand, C. M., & Siliciano, R. F. (2014). Dual zinc-finger nucleases block HIV infection. Blood, 123(1), 2–3. https://doi.org/10.1182/blood-2013-11-535542, PMID: 24385492
• Shan, L., Xing, S., Yang, H. C., Zhang, H., Margolick, J. B., & Siliciano, R. F. (2014). Unique characteristics of histone deacetylase inhibitors in reactivation of latent HIV-1 in Bcl-2-transduced primary resting CD4+ T cells. The Journal of antimicrobial chemotherapy, 69(1), 28–33. https://doi.org/10.1093/jac/dkt338, PMID: 23999005, PMCID: PMC3861332

2013

• Spina, C. A., Anderson, J., Archin, N. M., Bosque, A., Chan, J., Famiglietti, M., Greene, W. C., Kashuba, A., Lewin, S. R., Margolis, D. M., Mau, M., Ruelas, D., Saleh, S., Shirakawa, K., Siliciano, R. F., Singhania, A., Soto, P. C., Terry, V. H., Verdin, E., Woelk, C., … Planelles, V. (2013). An in-depth comparison of latent HIV-1 reactivation in multiple cell model systems and resting CD4+ T cells from aviremic patients. PLoS pathogens, 9(12), e1003834. https://doi.org/10.1371/journal.ppat.1003834, PMID: 24385908, PMCID: PMC3873446
• Cox, A. L., & Siliciano, R. F. (2013). Making sense of HIV innate sensing. Immunity, 39(6), 998–1000. https://doi.org/10.1016/j.immuni.2013.11.014, PMID: 24332027, PMCID: PMC4434593
• Pohlmeyer, C. W., Buckheit, R. W., 3rd, Siliciano, R. F., & Blankson, J. N. (2013). CD8+ T cells from HLA-B*57 elite suppressors effectively suppress replication of HIV-1 escape mutants. Retrovirology, 10, 152. https://doi.org/10.1186/1742-4690-10-152, PMID: 24330837, PMCID: PMC3878989
• Chen, I., Khaki, L., Lindsey, J. C., Fry, C., Cousins, M. M., Siliciano, R. F., Violari, A., Palumbo, P., & Eshleman, S. H. (2013). Association of pol diversity with antiretroviral treatment outcomes among HIV-infected African children. PloS one, 8(11), e81213. https://doi.org/10.1371/journal.pone.0081213, PMID: 24312277, PMCID: PMC3842253
• Avery, L. B., Zarr, M. A., Bakshi, R. P., Siliciano, R. F., & Hendrix, C. W. (2013). Increasing extracellular protein concentration reduces intracellular antiretroviral drug concentration and antiviral effect. AIDS research and human retroviruses, 29(11), 1434–1442. https://doi.org/10.1089/AID.2013.0031, PMID: 23601085, PMCID: PMC3809607
• Ho, Y. C., Shan, L., Hosmane, N. N., Wang, J., Laskey, S. B., Rosenbloom, D. I., Lai, J., Blankson, J. N., Siliciano, J. D., & Siliciano, R. F. (2013). Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell, 155(3), 540–551. https://doi.org/10.1016/j.cell.2013.09.020, PMID: 24243014, PMCID: PMC3896327
• Dobrowsky, T. M., Rabi, S. A., Nedellec, R., Daniels, B. R., Mullins, J. I., Mosier, D. E., Siliciano, R. F., & Wirtz, D. (2013). Adhesion and fusion efficiencies of human immunodeficiency virus type 1 (HIV-1) surface proteins. Scientific reports, 3, 3014. https://doi.org/10.1038/srep03014, PMID: 24145278, PMCID: PMC3804852
• Siliciano, J. D., & Siliciano, R. F. (2013). Recent trends in HIV-1 drug resistance. Current opinion in virology, 3(5), 487–494. https://doi.org/10.1016/j.coviro.2013.08.007, PMID: 24021560, PMCID: PMC3963152
• Rabi, S. A., Laird, G. M., Durand, C. M., Laskey, S., Shan, L., Bailey, J. R., Chioma, S., Moore, R. D., & Siliciano, R. F. (2013). Multi-step inhibition explains HIV-1 protease inhibitor pharmacodynamics and resistance. The Journal of clinical investigation, 123(9), 3848–3860. https://doi.org/10.1172/JCI67399, PMID: 23979165, PMCID: PMC4381280
• Shen, A., Baker, J. J., Scott, G. L., Davis, Y. P., Ho, Y. Y., & Siliciano, R. F. (2013). Endothelial cell stimulation overcomes restriction and promotes productive and latent HIV-1 infection of resting CD4+ T cells. Journal of virology, 87(17), 9768–9779. https://doi.org/10.1128/JVI.01478-13, PMID: 23824795, PMCID: PMC3754127
• Sherrill-Mix, S., Lewinski, M. K., Famiglietti, M., Bosque, A., Malani, N., Ocwieja, K. E., Berry, C. C., Looney, D., Shan, L., Agosto, L. M., Pace, M. J., Siliciano, R. F., O’Doherty, U., Guatelli, J., Planelles, V., & Bushman, F. D. (2013). HIV latency and integration site placement in five cell-based models. Retrovirology, 10, 90. https://doi.org/10.1186/1742-4690-10-90, PMID: 23953889, PMCID: PMC3765678
• Siliciano, J. D., & Siliciano, R. F. (2013). HIV-1 eradication strategies: design and assessment. Current opinion in HIV and AIDS, 8(4), 318–325. https://doi.org/10.1097/COH.0b013e328361eaca, PMID: 23698561, PMCID: PMC3963140
• Buckheit, R. W., 3rd, Siliciano, R. F., & Blankson, J. N. (2013). Primary CD8+ T cells from elite suppressors effectively eliminate non-productively HIV-1 infected resting and activated CD4+ T cells. Retrovirology, 10, 68. https://doi.org/10.1186/1742-4690-10-68, PMID: 23816179, PMCID: PMC3702406
• Xing, S., & Siliciano, R. F. (2013). Targeting HIV latency: pharmacologic strategies toward eradication. Drug discovery today, 18(11-12), 541–551. https://doi.org/10.1016/j.drudis.2012.12.008, PMID: 23270785, PMCID: PMC3672351
• Shan, L., & Siliciano, R. F. (2013). From reactivation of latent HIV-1 to elimination of the latent reservoir: the presence of multiple barriers to viral eradication. BioEssays : news and reviews in molecular, cellular and developmental biology, 35(6), 544–552. https://doi.org/10.1002/bies.201200170, PMID: 23613347, PMCID: PMC4386637
• Shan, L., Rabi, S. A., Laird, G. M., Eisele, E. E., Zhang, H., Margolick, J. B., & Siliciano, R. F. (2013). A novel PCR assay for quantification of HIV-1 RNA. Journal of virology, 87(11), 6521–6525. https://doi.org/10.1128/JVI.00006-13, PMID: 23536672, PMCID: PMC3648108
• Laird, G. M., Eisele, E. E., Rabi, S. A., Lai, J., Chioma, S., Blankson, J. N., Siliciano, J. D., & Siliciano, R. F. (2013). Rapid quantification of the latent reservoir for HIV-1 using a viral outgrowth assay. PLoS pathogens, 9(5), e1003398. https://doi.org/10.1371/journal.ppat.1003398, PMID: 23737751, PMCID: PMC3667757
• Yukl, S. A., Boritz, E., Busch, M., Bentsen, C., Chun, T. W., Douek, D., Eisele, E., Haase, A., Ho, Y. C., Hütter, G., Justement, J. S., Keating, S., Lee, T. H., Li, P., Murray, D., Palmer, S., Pilcher, C., Pillai, S., Price, R. W., Rothenberger, M., … Deeks, S. G. (2013). Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient. PLoS pathogens, 9(5), e1003347. https://doi.org/10.1371/journal.ppat.1003347, PMID: 23671416, PMCID: PMC3649997
• Gandhi, R. T., Bosch, R. J., Aga, E., Bedison, M. A., Bastow, B., Schmitz, J. L., Siliciano, J. D., Siliciano, R. F., Eron, J. J., Mellors, J. W., & ACTG A5173 team (2013). Residual plasma viraemia and infectious HIV-1 recovery from resting memory CD4 cells in patients on antiretroviral therapy: results from ACTG A5173. Antiviral therapy, 18(4), 607–613. https://doi.org/10.3851/IMP2543, PMID: 23411421, PMCID: PMC3887470
• Eriksson, S., Graf, E. H., Dahl, V., Strain, M. C., Yukl, S. A., Lysenko, E. S., Bosch, R. J., Lai, J., Chioma, S., Emad, F., Abdel-Mohsen, M., Hoh, R., Hecht, F., Hunt, P., Somsouk, M., Wong, J., Johnston, R., Siliciano, R. F., Richman, D. D., O’Doherty, U., … Siliciano, J. D. (2013). Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS pathogens, 9(2), e1003174. https://doi.org/10.1371/journal.ppat.1003174, PMID: 23459007, PMCID: PMC3573107
• Weil, A. F., Ghosh, D., Zhou, Y., Seiple, L., McMahon, M. A., Spivak, A. M., Siliciano, R. F., & Stivers, J. T. (2013). Uracil DNA glycosylase initiates degradation of HIV-1 cDNA containing misincorporated dUTP and prevents viral integration. Proceedings of the National Academy of Sciences of the United States of America, 110(6), E448–E457. https://doi.org/10.1073/pnas.1219702110, PMID: 23341616, PMCID: PMC3568341
• Boehm, D., Calvanese, V., Dar, R. D., Xing, S., Schroeder, S., Martins, L., Aull, K., Li, P. C., Planelles, V., Bradner, J. E., Zhou, M. M., Siliciano, R. F., Weinberger, L., Verdin, E., & Ott, M. (2013). BET bromodomain-targeting compounds reactivate HIV from latency via a Tat-independent mechanism. Cell cycle (Georgetown, Tex.), 12(3), 452–462. https://doi.org/10.4161/cc.23309, PMID: 23255218, PMCID: PMC3587446

2012

• Zinchenko, M. K., & Siliciano, R. F. (2012). Editorial: JQ1: giving HIV-1 expression a boost by blocking bromodomains?. Journal of leukocyte biology, 92(6), 1127–1129. https://doi.org/10.1189/jlb.0712358, PMID: 23204259
• Durand, C. M., Blankson, J. N., & Siliciano, R. F. (2012). Developing strategies for HIV-1 eradication. Trends in immunology, 33(11), 554–562. https://doi.org/10.1016/j.it.2012.07.001, PMID: 22867874, PMCID: PMC3963166
• Deng, K., Zink, M. C., Clements, J. E., & Siliciano, R. F. (2012). A quantitative measurement of antiviral activity of anti-human immunodeficiency virus type 1 drugs against simian immunodeficiency virus infection: dose-response curve slope strongly influences class-specific inhibitory potential. Journal of virology, 86(20), 11368–11372. https://doi.org/10.1128/JVI.01563-12, PMID: 22875968, PMCID: PMC3457139
• Eisele, E., & Siliciano, R. F. (2012). Redefining the viral reservoirs that prevent HIV-1 eradication. Immunity, 37(3), 377–388. https://doi.org/10.1016/j.immuni.2012.08.010, PMID: 22999944, PMCID: PMC3963158
• Rosenbloom, D. I., Hill, A. L., Rabi, S. A., Siliciano, R. F., & Nowak, M. A. (2012). Antiretroviral dynamics determines HIV evolution and predicts therapy outcome. Nature medicine, 18(9), 1378–1385. https://doi.org/10.1038/nm.2892, PMID: 22941277, PMCID: PMC3490032
• Thayil, S. M., Ho, Y. C., Bollinger, R. C., Blankson, J. N., Siliciano, R. F., Karakousis, P. C., & Page, K. R. (2012). Mycobacterium tuberculosis complex enhances susceptibility of CD4 T cells to HIV through a TLR2-mediated pathway. PloS one, 7(7), e41093. https://doi.org/10.1371/journal.pone.0041093, PMID: 22844428, PMCID: PMC3402510
• Shan, L., Deng, K., Shroff, N. S., Durand, C. M., Rabi, S. A., Yang, H. C., Zhang, H., Margolick, J. B., Blankson, J. N., & Siliciano, R. F. (2012). Stimulation of HIV-1-specific cytolytic T lymphocytes facilitates elimination of latent viral reservoir after virus reactivation. Immunity, 36(3), 491–501. https://doi.org/10.1016/j.immuni.2012.01.014, PMID: 22406268, PMCID: PMC3501645
• Goldberg, D. E., Siliciano, R. F., & Jacobs, W. R., Jr (2012). Outwitting evolution: fighting drug-resistant TB, malaria, and HIV. Cell, 148(6), 1271–1283. https://doi.org/10.1016/j.cell.2012.02.021, PMID: 22424234, PMCID: PMC3322542
• Durand, C. M., Ghiaur, G., Siliciano, J. D., Rabi, S. A., Eisele, E. E., Salgado, M., Shan, L., Lai, J. F., Zhang, H., Margolick, J., Jones, R. J., Gallant, J. E., Ambinder, R. F., & Siliciano, R. F. (2012). HIV-1 DNA is detected in bone marrow populations containing CD4+ T cells but is not found in purified CD34+ hematopoietic progenitor cells in most patients on antiretroviral therapy. The Journal of infectious diseases, 205(6), 1014–1018. https://doi.org/10.1093/infdis/jir884, PMID: 22275402, PMCID: PMC3282572
• Jilek, B. L., Zarr, M., Sampah, M. E., Rabi, S. A., Bullen, C. K., Lai, J., Shen, L., & Siliciano, R. F. (2012). A quantitative basis for antiretroviral therapy for HIV-1 infection. Nature medicine, 18(3), 446–451. https://doi.org/10.1038/nm.2649, PMID: 22344296, PMCID: PMC3296892
• Xing, S., Bhat, S., Shroff, N. S., Zhang, H., Lopez, J. A., Margolick, J. B., Liu, J. O., & Siliciano, R. F. (2012). Novel structurally related compounds reactivate latent HIV-1 in a bcl-2-transduced primary CD4+ T cell model without inducing global T cell activation. The Journal of antimicrobial chemotherapy, 67(2), 398–403. https://doi.org/10.1093/jac/dkr496, PMID: 22160146, PMCID: PMC3254198
• Buckheit, R. W., 3rd, Allen, T. G., Alme, A., Salgado, M., O’Connell, K. A., Huculak, S., Falade-Nwulia, O., Williams, T. M., Gallant, J. E., Siliciano, R. F., & Blankson, J. N. (2012). Host factors dictate control of viral replication in two HIV-1 controller/chronic progressor transmission pairs. Nature communications, 3, 716. https://doi.org/10.1038/ncomms1697, PMID: 22395607, PMCID: PMC3549550

2011

• Salgado, M., Rabi, S. A., O’Connell, K. A., Buckheit, R. W., 3rd, Bailey, J. R., Chaudhry, A. A., Breaud, A. R., Marzinke, M. A., Clarke, W., Margolick, J. B., Siliciano, R. F., & Blankson, J. N. (2011). Prolonged control of replication-competent dual- tropic human immunodeficiency virus-1 following cessation of highly active antiretroviral therapy. Retrovirology, 8, 97. https://doi.org/10.1186/1742-4690-8-97, PMID: 22141397, PMCID: PMC3293762
• Siliciano R. F. (2011). Measurement of antiviral activity in drugs for HIV-1. The Lancet. Infectious diseases, 11(12), 888–889. https://doi.org/10.1016/S1473-3099(11)70250-X, PMID: 21933753
• O’Connell, K. A., Rabi, S. A., Siliciano, R. F., & Blankson, J. N. (2011). CD4+ T cells from elite suppressors are more susceptible to HIV-1 but produce fewer virions than cells from chronic progressors. Proceedings of the National Academy of Sciences of the United States of America, 108(37), E689–E698. https://doi.org/10.1073/pnas.1108866108, PMID: 21873218, PMCID: PMC3174588
• O’Connell, K. A., Hegarty, R. W., Siliciano, R. F., & Blankson, J. N. (2011). Viral suppression of multiple escape mutants by de novo CD8(+) T cell responses in a human immunodeficiency virus-1 infected elite suppressor. Retrovirology, 8, 63. https://doi.org/10.1186/1742-4690-8-63, PMID: 21812985, PMCID: PMC3173334
• Shen, L., Rabi, S. A., Sedaghat, A. R., Shan, L., Lai, J., Xing, S., & Siliciano, R. F. (2011). A critical subset model provides a conceptual basis for the high antiviral activity of major HIV drugs. Science translational medicine, 3(91), 91ra63. https://doi.org/10.1126/scitranslmed.3002304, PMID: 21753122, PMCID: PMC3488347
• Spivak, A. M., Rabi, S. A., McMahon, M. A., Shan, L., Sedaghat, A. R., Wilke, C. O., & Siliciano, R. F. (2011). Short communication: dynamic constraints on the second phase compartment of HIV-infected cells. AIDS research and human retroviruses, 27(7), 759–761. https://doi.org/10.1089/AID.2010.0199, PMID: 21105850, PMCID: PMC3123527
• Xing, S., Bullen, C. K., Shroff, N. S., Shan, L., Yang, H. C., Manucci, J. L., Bhat, S., Zhang, H., Margolick, J. B., Quinn, T. C., Margolis, D. M., Siliciano, J. D., & Siliciano, R. F. (2011). Disulfiram reactivates latent HIV-1 in a Bcl-2-transduced primary CD4+ T cell model without inducing global T cell activation. Journal of virology, 85(12), 6060–6064. https://doi.org/10.1128/JVI.02033-10, PMID: 21471244, PMCID: PMC3126325
• Shan, L., Yang, H. C., Rabi, S. A., Bravo, H. C., Shroff, N. S., Irizarry, R. A., Zhang, H., Margolick, J. B., Siliciano, J. D., & Siliciano, R. F. (2011). Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model. Journal of virology, 85(11), 5384–5393. https://doi.org/10.1128/JVI.02536-10, PMID: 21430059, PMCID: PMC3094997
• Sampah, M. E., Shen, L., Jilek, B. L., & Siliciano, R. F. (2011). Dose-response curve slope is a missing dimension in the analysis of HIV-1 drug resistance. Proceedings of the National Academy of Sciences of the United States of America, 108(18), 7613–7618. https://doi.org/10.1073/pnas.1018360108, PMID: 21502494, PMCID: PMC3088572
• McMahon, M. A., Parsons, T. L., Shen, L., Siliciano, J. D., & Siliciano, R. F. (2011). Consistent inhibition of HIV-1 replication in CD4+ T cells by acyclovir without detection of human herpesviruses. Journal of virology, 85(9), 4618–4622. https://doi.org/10.1128/JVI.02423-10, PMID: 21325417, PMCID: PMC3126274
• Rabi, S. A., O’Connell, K. A., Nikolaeva, D., Bailey, J. R., Jilek, B. L., Shen, L., Page, K. R., Siliciano, R. F., & Blankson, J. N. (2011). Unstimulated primary CD4+ T cells from HIV-1-positive elite suppressors are fully susceptible to HIV-1 entry and productive infection. Journal of virology, 85(2), 979–986. https://doi.org/10.1128/JVI.01721-10, PMID: 21068257, PMCID: PMC3020020

2010

• Kohli, R. M., Maul, R. W., Guminski, A. F., McClure, R. L., Gajula, K. S., Saribasak, H., McMahon, M. A., Siliciano, R. F., Gearhart, P. J., & Stivers, J. T. (2010). Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. The Journal of biological chemistry, 285(52), 40956–40964. https://doi.org/10.1074/jbc.M110.177402, PMID: 20929867, PMCID: PMC3003395
• Bellows, M. L., Taylor, M. S., Cole, P. A., Shen, L., Siliciano, R. F., Fung, H. K., & Floudas, C. A. (2010). Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework. Biophysical journal, 99(10), 3445–3453. https://doi.org/10.1016/j.bpj.2010.09.050, PMID: 21081094, PMCID: PMC2980751
• Salgado, M., Brennan, T. P., O’Connell, K. A., Bailey, J. R., Ray, S. C., Siliciano, R. F., & Blankson, J. N. (2010). Evolution of the HIV-1 nef gene in HLA-B*57 positive elite suppressors. Retrovirology, 7, 94. https://doi.org/10.1186/1742-4690-7-94, PMID: 21059238, PMCID: PMC2993647
• Shen, L., & Siliciano, R. F. (2010). Achieving a quantitative understanding of antiretroviral drug efficacy. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 51(9), 1105–1107. https://doi.org/10.1086/656688, PMID: 20925507
• Siliciano, J. D., & Siliciano, R. F. (2010). Biomarkers of HIV replication. Current opinion in HIV and AIDS, 5(6), 491–497. https://doi.org/10.1097/COH.0b013e32833f206f, PMID: 20978392
• Kim, H. N., Wang, J., Hughes, J., Coombs, R., Sanchez, J., Reid, S., Delany-Moretlwe, S., Cowan, F., Fuchs, J., Eshleman, S. H., Khaki, L., McMahon, M. A., Siliciano, R. F., Wald, A., & Celum, C. (2010). Effect of acyclovir on HIV-1 set point among herpes simplex virus type 2-seropositive persons during early HIV-1 infection. The Journal of infectious diseases, 202(5), 734–738. https://doi.org/10.1086/655662, PMID: 20649426, PMCID: PMC2964878
• Siliciano R. F. (2010). What do we need to do to cure HIV infection. Topics in HIV medicine : a publication of the International AIDS Society, USA, 18(3), 104–108. PMID: 20921575
• Dobrowsky, T. M., Daniels, B. R., Siliciano, R. F., Sun, S. X., & Wirtz, D. (2010). Organization of cellular receptors into a nanoscale junction during HIV-1 adhesion. PLoS computational biology, 6(7), e1000855. https://doi.org/10.1371/journal.pcbi.1000855, PMID: 20657663, PMCID: PMC2904768
• O’Connell, K. A., Brennan, T. P., Bailey, J. R., Ray, S. C., Siliciano, R. F., & Blankson, J. N. (2010). Control of HIV-1 in elite suppressors despite ongoing replication and evolution in plasma virus. Journal of virology, 84(14), 7018–7028. https://doi.org/10.1128/JVI.00548-10, PMID: 20444904, PMCID: PMC2898225
• Spivak, A. M., & Siliciano, R. F. (2010). Using highly active antiretroviral therapy to decrease perioperative HIV-1 transmission risk. AIDS (London, England), 24(10), 1603–1604. https://doi.org/10.1097/QAD.0b013e32832f3155, PMID: 20539094, PMCID: PMC4509634
• Szeto, G. L., Brice, A. K., Yang, H. C., Barber, S. A., Siliciano, R. F., & Clements, J. E. (2010). Minocycline attenuates HIV infection and reactivation by suppressing cellular activation in human CD4+ T cells. The Journal of infectious diseases, 201(8), 1132–1140. https://doi.org/10.1086/651277, PMID: 20205570, PMCID: PMC3739045
• Spivak, A. M., Brennan, T. P., O’Connell, K. A., Sydnor, E., Williams, T. M., Siliciano, R. F., Gallant, J. E., & Blankson, J. N. (2010). A case of seronegative HIV-1 infection. The Journal of infectious diseases, 201(3), 341–345. https://doi.org/10.1086/649822, PMID: 20039801, PMCID: PMC2821828
• Gandhi, R. T., Bosch, R. J., Aga, E., Albrecht, M., Demeter, L. M., Dykes, C., Bastow, B., Para, M., Lai, J., Siliciano, R. F., Siliciano, J. D., Eron, J. J., & AIDS Clinical Trials Group A5173 Team (2010). No evidence for decay of the latent reservoir in HIV-1-infected patients receiving intensive enfuvirtide-containing antiretroviral therapy. The Journal of infectious diseases, 201(2), 293–296. https://doi.org/10.1086/649569, PMID: 20001856, PMCID: PMC2887684
• McMahon, M. A., Siliciano, J. D., Kohli, R. M., & Siliciano, R. F. (2010). Sensitivity of V75I HIV-1 reverse transcriptase mutant selected in vitro by acyclovir to anti-HIV drugs. AIDS (London, England), 24(2), 319–323. https://doi.org/10.1097/QAD.0b013e32833424e5, PMID: 20009920

2009

• 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. (2009). HIV-1 evolution following transmission to an HLA-B*5801-positive patient. The Journal of infectious diseases, 200(12), 1820–1824. https://doi.org/10.1086/648377, PMID: 19909081, PMCID: PMC2779566
• Shen, L., Rabi, S. A., & Siliciano, R. F. (2009). A novel method for determining the inhibitory potential of anti-HIV drugs. Trends in pharmacological sciences, 30(12), 610–616. https://doi.org/10.1016/j.tips.2009.09.003, PMID: 19837466, PMCID: PMC3385974
• McMahon, M. A., Shen, L., & Siliciano, R. F. (2009). New approaches for quantitating the inhibition of HIV-1 replication by antiviral drugs in vitro and in vivo. Current opinion in infectious diseases, 22(6), 574–582. https://doi.org/10.1097/QCO.0b013e328332c54d, PMID: 19841584, PMCID: PMC3939826
• Yang, H. C., Xing, S., Shan, L., O’Connell, K., Dinoso, J., Shen, A., Zhou, Y., Shrum, C. K., Han, Y., Liu, J. O., Zhang, H., Margolick, J. B., & Siliciano, R. F. (2009). Small-molecule screening using a human primary cell model of HIV latency identifies compounds that reverse latency without cellular activation. The Journal of clinical investigation, 119(11), 3473–3486. https://doi.org/10.1172/JCI39199, PMID: 19805909, PMCID: PMC2769176
• Dinoso, J. B., Rabi, S. A., Blankson, J. N., Gama, L., Mankowski, J. L., Siliciano, R. F., Zink, M. C., & Clements, J. E. (2009). A simian immunodeficiency virus-infected macaque model to study viral reservoirs that persist during highly active antiretroviral therapy. Journal of virology, 83(18), 9247–9257. https://doi.org/10.1128/JVI.00840-09, PMID: 19570871, PMCID: PMC2738256
• Brennan, T. P., Woods, J. O., Sedaghat, A. R., Siliciano, J. D., Siliciano, R. F., & Wilke, C. O. (2009). Analysis of human immunodeficiency virus type 1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. Journal of virology, 83(17), 8470–8481. https://doi.org/10.1128/JVI.02568-08, PMID: 19535437, PMCID: PMC2738142
• Dinoso, J. B., Kim, S. Y., Wiegand, A. M., Palmer, S. E., Gange, S. J., Cranmer, L., O’Shea, A., Callender, M., Spivak, A., Brennan, T., Kearney, M. F., Proschan, M. A., Mican, J. M., Rehm, C. A., Coffin, J. M., Mellors, J. W., Siliciano, R. F., & Maldarelli, F. (2009). Treatment intensification does not reduce residual HIV-1 viremia in patients on highly active antiretroviral therapy. Proceedings of the National Academy of Sciences of the United States of America, 106(23), 9403–9408. https://doi.org/10.1073/pnas.0903107106, PMID: 19470482, PMCID: PMC2685743
• O’Connell, K. A., Han, Y., Williams, T. M., Siliciano, R. F., & Blankson, J. N. (2009). Role of natural killer cells in a cohort of elite suppressors: low frequency of the protective KIR3DS1 allele and limited inhibition of human immunodeficiency virus type 1 replication in vitro. Journal of virology, 83(10), 5028–5034. https://doi.org/10.1128/JVI.02551-08, PMID: 19211742, PMCID: PMC2682110
• 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. (2009). Identification of nevirapine-resistant HIV-1 in the latent reservoir after single-dose nevirapine to prevent mother-to-child transmission of HIV-1. The Journal of infectious diseases, 199(9), 1301–1309. https://doi.org/10.1086/597759, PMID: 19338474, PMCID: PMC2703715
• Yang, H. C., Shen, L., Siliciano, R. F., & Pomerantz, J. L. (2009). Isolation of a cellular factor that can reactivate latent HIV-1 without T cell activation. Proceedings of the National Academy of Sciences of the United States of America, 106(15), 6321–6326. https://doi.org/10.1073/pnas.0809536106, PMID: 19336585, PMCID: PMC2663775
• Lassen, K. G., Lobritz, M. A., Bailey, J. R., Johnston, S., Nguyen, S., Lee, B., Chou, T., Siliciano, R. F., Markowitz, M., & Arts, E. J. (2009). Elite suppressor-derived HIV-1 envelope glycoproteins exhibit reduced entry efficiency and kinetics. PLoS pathogens, 5(4), e1000377. https://doi.org/10.1371/journal.ppat.1000377, PMID: 19360131, PMCID: PMC2661022
• Sedaghat, A. R., Siliciano, R. F., & Wilke, C. O. (2009). Constraints on the dominant mechanism for HIV viral dynamics in patients on raltegravir. Antiviral therapy, 14(2), 263–271. PMID: 19430101, PMCID: PMC2980788
• Brennan, T. P., Woods, J. O., Sedaghat, A. R., Siliciano, J. D., Siliciano, R. F., & Wilke, C. O. (2009). Analysis of human immunodeficiency virus type 1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. Journal of virology, 83(17), 8470–8481. https://doi.org/10.1128/JVI.02568-08, PMID: 19535437, PMCID: PMC2738142
• Bailey, J. R., Brennan, T. P., O’Connell, K. A., Siliciano, R. F., & Blankson, J. N. (2009). Evidence of CD8+ T-cell-mediated selective pressure on human immunodeficiency virus type 1 nef in HLA-B*57+ elite suppressors. Journal of virology, 83(1), 88–97. https://doi.org/10.1128/JVI.01958-08, PMID: 18945771, PMCID: PMC2612327

2008

• Blankson, J. N., & Siliciano, R. F. (2008). Elite suppression of HIV-1 replication. Immunity, 29(6), 845–847. https://doi.org/10.1016/j.immuni.2008.12.002, PMID: 19100698
• McMahon, M. A., Siliciano, J. D., Lai, J., Liu, J. O., Stivers, J. T., Siliciano, R. F., & Kohli, R. M. (2008). The antiherpetic drug acyclovir inhibits HIV replication and selects the V75I reverse transcriptase multidrug resistance mutation. The Journal of biological chemistry, 283(46), 31289–31293. https://doi.org/10.1074/jbc.C800188200, PMID: 18818198, PMCID: PMC2581555
• O’Connell, K., & Siliciano, R. F. (2008). Immune alteration fends off AIDS. Nature medicine, 14(10), 1016–1018. https://doi.org/10.1038/nm1008-1016, PMID: 18841135
• Zhou, Y., Shen, L., Yang, H. C., & Siliciano, R. F. (2008). Preferential cytolysis of peripheral memory CD4+ T cells by in vitro X4-tropic human immunodeficiency virus type 1 infection before the completion of reverse transcription. Journal of virology, 82(18), 9154–9163. https://doi.org/10.1128/JVI.00773-08, PMID: 18596085, PMCID: PMC2546913
• Chase, A. J., Yang, H. C., Zhang, H., Blankson, J. N., & Siliciano, R. F. (2008). Preservation of FoxP3+ regulatory T cells in the peripheral blood of human immunodeficiency virus type 1-infected elite suppressors correlates with low CD4+ T-cell activation. Journal of virology, 82(17), 8307–8315. https://doi.org/10.1128/JVI.00520-08, PMID: 18579608, PMCID: PMC2519624
• Han, Y., Lin, Y. B., An, W., Xu, J., Yang, H. C., O’Connell, K., Dordai, D., Boeke, J. D., Siliciano, J. D., & Siliciano, R. F. (2008). Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough. Cell host & microbe, 4(2), 134–146. https://doi.org/10.1016/j.chom.2008.06.008, PMID: 18692773, PMCID: PMC2604135
• 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. (2008). Transmission of human immunodeficiency virus type 1 from a patient who developed AIDS to an elite suppressor. Journal of virology, 82(15), 7395–7410. https://doi.org/10.1128/JVI.00800-08, PMID: 18495769, PMCID: PMC2493308
• Dobrowsky, T. M., Zhou, Y., Sun, S. X., Siliciano, R. F., & Wirtz, D. (2008). Monitoring early fusion dynamics of human immunodeficiency virus type 1 at single-molecule resolution. Journal of virology, 82(14), 7022–7033. https://doi.org/10.1128/JVI.00053-08, PMID: 18480458, PMCID: PMC2446967
• Dinoso, J. B., Kim, S. Y., Siliciano, R. F., & Blankson, J. N. (2008). A comparison of viral loads between HIV-1-infected elite suppressors and individuals who receive suppressive highly active antiretroviral therapy. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 47(1), 102–104. https://doi.org/10.1086/588791, PMID: 18494606, PMCID: PMC2564994
• Shen, L., Peterson, S., Sedaghat, A. R., McMahon, M. A., Callender, M., Zhang, H., Zhou, Y., Pitt, E., Anderson, K. S., Acosta, E. P., & Siliciano, R. F. (2008). Dose-response curve slope sets class-specific limits on inhibitory potential of anti-HIV drugs. Nature medicine, 14(7), 762–766. https://doi.org/10.1038/nm1777, PMID: 18552857, PMCID: PMC2743464
• Shen, L., & Siliciano, R. F. (2008). Viral reservoirs, residual viremia, and the potential of highly active antiretroviral therapy to eradicate HIV infection. The Journal of allergy and clinical immunology, 122(1), 22–28. https://doi.org/10.1016/j.jaci.2008.05.033, PMID: 18602567, PMCID: PMC6812482
• Halwani, R., Boyer, J. D., Yassine-Diab, B., Haddad, E. K., Robinson, T. M., Kumar, S., Parkinson, R., Wu, L., Sidhu, M. K., Phillipson-Weiner, R., Pavlakis, G. N., Felber, B. K., Lewis, M. G., Shen, A., Siliciano, R. F., Weiner, D. B., & Sekaly, R. P. (2008). Therapeutic vaccination with simian immunodeficiency virus (SIV)-DNA + IL-12 or IL-15 induces distinct CD8 memory subsets in SIV-infected macaques. Journal of immunology (Baltimore, Md. : 1950), 180(12), 7969–7979. https://doi.org/10.4049/jimmunol.180.12.7969, PMID: 18523260
• Sasadeusz, J., Audsley, J., Mijch, A., Baden, R., Caro, J., Hunter, H., Matthews, G., McMahon, M. A., Olender, S. A., Siliciano, R. F., Lewin, S. R., & Thio, C. L. (2008). The anti-HIV activity of entecavir: a multicentre evaluation of lamivudine-experienced and lamivudine-naive patients. AIDS (London, England), 22(8), 947–955. https://doi.org/10.1097/QAD.0b013e3282ffde91, PMID: 18453854, PMCID: PMC2722443
• Sedaghat, A. R., Dinoso, J. B., Shen, L., Wilke, C. O., & Siliciano, R. F. (2008). Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle. Proceedings of the National Academy of Sciences of the United States of America, 105(12), 4832–4837. https://doi.org/10.1073/pnas.0711372105, PMID: 18362342, PMCID: PMC2290747
• Gandhi, S. K., Siliciano, J. D., Bailey, J. R., Siliciano, R. F., & Blankson, J. N. (2008). Role of APOBEC3G/F-mediated hypermutation in the control of human immunodeficiency virus type 1 in elite suppressors. Journal of virology, 82(6), 3125–3130. https://doi.org/10.1128/JVI.01533-07, PMID: 18077705, PMCID: PMC2259015
• Domaoal, R. A., McMahon, M., Thio, C. L., Bailey, C. M., Tirado-Rives, J., Obikhod, A., Detorio, M., Rapp, K. L., Siliciano, R. F., Schinazi, R. F., & Anderson, K. S. (2008). Pre-steady-state kinetic studies establish entecavir 5′-triphosphate as a substrate for HIV-1 reverse transcriptase. The Journal of biological chemistry, 283(9), 5452–5459. https://doi.org/10.1074/jbc.M707834200, PMID: 17962184, PMCID: PMC7748947
• Han, Y., Lai, J., Barditch-Crovo, P., Gallant, J. E., Williams, T. M., Siliciano, R. F., & Blankson, J. N. (2008). The role of protective HCP5 and HLA-C associated polymorphisms in the control of HIV-1 replication in a subset of elite suppressors. AIDS, 22(4), 541–544. https://doi.org/10.1097/QAD.0b013e3282f470e4, PMID: 18301071
• Sedaghat, A. R., German, J., Teslovich, T. M., Cofrancesco, J., Jr, Jie, C. C., Talbot, C. C., Jr, & Siliciano, R. F. (2008). Chronic CD4+ T-cell activation and depletion in human immunodeficiency virus type 1 infection: type I interferon-mediated disruption of T-cell dynamics. Journal of virology, 82(4), 1870–1883. https://doi.org/10.1128/JVI.02228-07, PMID: 18077723, PMCID: PMC2258719
• Sedaghat, A. R., Siliciano, R. F., & Wilke, C. O. (2008). Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART. BMC infectious diseases, 8, 2. https://doi.org/10.1186/1471-2334-8-2, PMID: 18171475, PMCID: PMC2254415
• Halwani, R., Boyer, J. D., Yassine-Diab, B., Haddad, E. K., Robinson, T. M., Kumar, S., Parkinson, R., Wu, L., Sidhu, M. K., Phillipson-Weiner, R., Pavlakis, G. N., Felber, B. K., Lewis, M. G., Shen, A., Siliciano, R. F., Weiner, D. B., & Sekaly, R. P. (2008). Therapeutic vaccination with simian immunodeficiency virus (SIV)-DNA + IL-12 or IL-15 induces distinct CD8 memory subsets in SIV-infected macaques. Journal of immunology, 180(12), 7969–7979. https://doi.org/10.4049/jimmunol.180.12.7969, PMID: 18523260

2007

• Chase, A. J., Sedaghat, A. R., German, J. R., Gama, L., Zink, M. C., Clements, J. E., & Siliciano, R. F. (2007). Severe depletion of CD4+ CD25+ regulatory T cells from the intestinal lamina propria but not peripheral blood or lymph nodes during acute simian immunodeficiency virus infection. Journal of virology, 81(23), 12748–12757. https://doi.org/10.1128/JVI.00841-07, PMID: 17855517, PMCID: PMC2169083
• Han, Y., & Siliciano, R. F. (2007). Keeping quiet: microRNAs in HIV-1 latency. Nature medicine, 13(10), 1138–1140. https://doi.org/10.1038/nm1007-1138, PMID: 17917655
• Sedaghat, A. R., Siliciano, J. D., Brennan, T. P., Wilke, C. O., & Siliciano, R. F. (2007). Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. PLoS pathogens, 3(8), e122. https://doi.org/10.1371/journal.ppat.0030122, PMID: 17784786, PMCID: PMC1959378
• Bailey, J. R., Zhang, H., Wegweiser, B. W., Yang, H. C., Herrera, L., Ahonkhai, A., Williams, T. M., Siliciano, R. F., & Blankson, J. N. (2007). Evolution of HIV-1 in an HLA-B*57-positive patient during virologic escape. The Journal of infectious diseases, 196(1), 50–55. https://doi.org/10.1086/518515, PMID: 17538883
• McMahon, M. A., Jilek, B. L., Brennan, T. P., Shen, L., Zhou, Y., Wind-Rotolo, M., Xing, S., Bhat, S., Hale, B., Hegarty, R., Chong, C. R., Liu, J. O., Siliciano, R. F., & Thio, C. L. (2007). The HBV drug entecavir – effects on HIV-1 replication and resistance. The New England journal of medicine, 356(25), 2614–2621. https://doi.org/10.1056/NEJMoa067710, PMID: 17582071, PMCID: PMC3069686
• Siliciano, J. D., Lai, J., Callender, M., Pitt, E., Zhang, H., Margolick, J. B., Gallant, J. E., Cofrancesco, J., Jr, Moore, R. D., Gange, S. J., & Siliciano, R. F. (2007). Stability of the latent reservoir for HIV-1 in patients receiving valproic acid. The Journal of infectious diseases, 195(6), 833–836. https://doi.org/10.1086/511823, PMID: 17299713
• Blankson, J. N., Bailey, J. R., Thayil, S., Yang, H. C., Lassen, K., Lai, J., Gandhi, S. K., Siliciano, J. D., Williams, T. M., & Siliciano, R. F. (2007). Isolation and characterization of replication-competent human immunodeficiency virus type 1 from a subset of elite suppressors. Journal of virology, 81(5), 2508–2518. https://doi.org/10.1128/JVI.02165-06, PMID: 17151109, PMCID: PMC1865922
• Shen, A., Yang, H. C., Zhou, Y., Chase, A. J., Boyer, J. D., Zhang, H., Margolick, J. B., Zink, M. C., Clements, J. E., & Siliciano, R. F. (2007). Novel pathway for induction of latent virus from resting CD4(+) T cells in the simian immunodeficiency virus/macaque model of human immunodeficiency virus type 1 latency. Journal of virology, 81(4), 1660–1670. https://doi.org/10.1128/JVI.01396-06, PMID: 17151130, PMCID: PMC1797567
• Han, Y., Wind-Rotolo, M., Yang, H. C., Siliciano, J. D., & Siliciano, R. F. (2007). Experimental approaches to the study of HIV-1 latency. Nature reviews. Microbiology, 5(2), 95–106. https://doi.org/10.1038/nrmicro1580, PMID: 17224919
• Peterson, S., Reid, A. P., Kim, S., & Siliciano, R. F. (2007). Treatment implications of the latent reservoir for HIV-1. Advances in pharmacology, 55, 411–425. https://doi.org/10.1016/S1054-3589(07)55012-X, PMID: 17586322

2006

• Nettles, R. E., Kieffer, T. L., Parsons, T., Johnson, J., Cofrancesco, J., Jr, Gallant, J. E., Carson, K. A., Siliciano, R. F., & Flexner, C. (2006). Marked intraindividual variability in antiretroviral concentrations may limit the utility of therapeutic drug monitoring. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 42(8), 1189–1196. https://doi.org/10.1086/501458, PMID: 16575741
• 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. (2006). 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. Journal of virology, 80(13), 6441–6457. https://doi.org/10.1128/JVI.00591-06, PMID: 16775332, PMCID: PMC1488985
• Lassen, K. G., Ramyar, K. X., Bailey, J. R., Zhou, Y., & Siliciano, R. F. (2006). Nuclear retention of multiply spliced HIV-1 RNA in resting CD4+ T cells. PLoS pathogens, 2(7), e68. https://doi.org/10.1371/journal.ppat.0020068, PMID: 16839202, PMCID: PMC1487174
• Bailey, J. R., Lassen, K. G., Yang, H. C., Quinn, T. C., Ray, S. C., Blankson, J. N., & Siliciano, R. F. (2006). 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. Journal of virology, 80(10), 4758–4770. https://doi.org/10.1128/JVI.80.10.4758-4770.2006, PMID: 16641269, PMCID: PMC1472047
• Bailey, J. R., Williams, T. M., Siliciano, R. F., & Blankson, J. N. (2006). Maintenance of viral suppression in HIV-1-infected HLA-B*57+ elite suppressors despite CTL escape mutations. The Journal of experimental medicine, 203(5), 1357–1369. https://doi.org/10.1084/jem.20052319, PMID: 16682496, PMCID: PMC2121215
• Lee, P. K., Kieffer, T. L., Siliciano, R. F., & Nettles, R. E. (2006). HIV-1 viral load blips are of limited clinical significance. The Journal of antimicrobial chemotherapy, 57(5), 803–805. https://doi.org/10.1093/jac/dkl092, PMID: 16533823
• Nettles, R. E., Kieffer, T. L., Parsons, T., Johnson, J., Cofrancesco, J., Jr, Gallant, J. E., Carson, K. A., Siliciano, R. F., & Flexner, C. (2006). Marked intraindividual variability in antiretroviral concentrations may limit the utility of therapeutic drug monitoring. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 42(8), 1189–1196. https://doi.org/10.1086/501458, PMID: 16575741
• Siliciano, J. D., & Siliciano, R. F. (2006). The latent reservoir for HIV-1 in resting CD4+ T cells: a barrier to cure. Current opinion in HIV and AIDS, 1(2), 121–128. https://doi.org/10.1097/01.COH.0000209582.82328.b8, PMID: 19372795
• Blankson, J. N., Bailey, J. R., & Siliciano, R. F. (2006). Crosscurrents in HIV-1 evolution. Nature immunology, 7(2), 121–122. https://doi.org/10.1038/ni0206-121, PMID: 16424885
• Haggerty, C. M., Pitt, E., & Siliciano, R. F. (2006). The latent reservoir for HIV-1 in resting CD4+ T cells and other viral reservoirs during chronic infection: insights from treatment and treatment-interruption trials. Current opinion in HIV and AIDS, 1(1), 62–68. https://doi.org/10.1097/01.COH.0000191897.78309.70, PMID: 19372786
• Chase, A., Zhou, Y., & Siliciano, R. F. (2006). HIV-1-induced depletion of CD4+ T cells in the gut: mechanism and therapeutic implications. Trends in pharmacological sciences, 27(1), 4–7. https://doi.org/10.1016/j.tips.2005.11.005, PMID: 16337692
• 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. (2006). 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. Journal of virology, 80(13), 6441–6457. https://doi.org/10.1128/JVI.00591-06, PMID: 16775332, PMCID: PMC1488985

2005

• Nettles, R. E., Keiffer, T. L., Cofrancesco, J., Jr, Gallant, J. E., Quinn, T., Jackson, B., Flexner, C., Carson, K. A., Wu, A. W., & Siliciano, R. F. (2005). Psychological distress and physical pain appear to have no short-term adverse impact on plasma HIV-1 RNA levels in patients on successful HAART. HIV clinical trials, 6(5), 262–271. https://doi.org/10.1310/5X2L-MVY7-YQTB-EBAJ, PMID: 16425464
• Siliciano R. F. (2005). Scientific rationale for antiretroviral therapy in 2005: viral reservoirs and resistance evolution. Topics in HIV medicine : a publication of the International AIDS Society, USA, 13(3), 96–100. PMID: 16170226
• Carruth, L. M., Zink, M. C., Tarwater, P. M., Miller, M. D., Li, M., Queen, L. A., Mankowski, J. L., Shen, A., Siliciano, R. F., & Clements, J. E. (2005). SIV-specific T lymphocyte responses in PBMC and lymphoid tissues of SIV-infected pigtailed macaques during suppressive combination antiretroviral therapy. Journal of medical primatology, 34(3), 109–121. https://doi.org/10.1111/j.1600-0684.2005.00103.x, PMID: 15860119
• Blankson, J. N., Siliciano, J. D., & Siliciano, R. F. (2005). The Effect of early treatment on the latent reservoir of HIV-1. The Journal of infectious diseases, 191(9), 1394–1396. https://doi.org/10.1086/428783, PMID: 15809894
• Monie, D., Simmons, R. P., Nettles, R. E., Kieffer, T. L., Zhou, Y., Zhang, H., Karmon, S., Ingersoll, R., Chadwick, K., Zhang, H., Margolick, J. B., Quinn, T. C., Ray, S. C., Wind-Rotolo, M., Miller, M., Persaud, D., & Siliciano, R. F. (2005). A novel assay allows genotyping of the latent reservoir for human immunodeficiency virus type 1 in the resting CD4+ T cells of viremic patients. Journal of virology, 79(8), 5185–5202. https://doi.org/10.1128/JVI.79.8.5185-5202.2005, PMID: 15795302, PMCID: PMC1069549
• Boyer, J. D., Robinson, T. M., Maciag, P. C., Peng, X., Johnson, R. S., Pavlakis, G., Lewis, M. G., Shen, A., Siliciano, R., Brown, C. R., Weiner, D. B., & Paterson, Y. (2005). DNA prime Listeria boost induces a cellular immune response to SIV antigens in the rhesus macaque model that is capable of limited suppression of SIV239 viral replication. Virology, 333(1), 88–101. https://doi.org/10.1016/j.virol.2004.12.026, PMID: 15708595
• Nettles, R. E., Kieffer, T. L., Kwon, P., Monie, D., Han, Y., Parsons, T., Cofrancesco, J., Jr, Gallant, J. E., Quinn, T. C., Jackson, B., Flexner, C., Carson, K., Ray, S., Persaud, D., & Siliciano, R. F. (2005). Intermittent HIV-1 viremia (Blips) and drug resistance in patients receiving HAART. JAMA, 293(7), 817–829. https://doi.org/10.1001/jama.293.7.817, PMID: 15713771
• Zhou, Y., Zhang, H., Siliciano, J. D., & Siliciano, R. F. (2005). Kinetics of human immunodeficiency virus type 1 decay following entry into resting CD4+ T cells. Journal of virology, 79(4), 2199–2210. https://doi.org/10.1128/JVI.79.4.2199-2210.2005, PMID: 15681422, PMCID: PMC546571
• Kieffer, T. L., Kwon, P., Nettles, R. E., Han, Y., Ray, S. C., & Siliciano, R. F. (2005). G–>A hypermutation in protease and reverse transcriptase regions of human immunodeficiency virus type 1 residing in resting CD4+ T cells in vivo. Journal of virology, 79(3), 1975–1980. https://doi.org/10.1128/JVI.79.3.1975-1980.2005, PMID: 15650227, PMCID: PMC544145
• Wong, S. B., & Siliciano, R. F. (2005). Contribution of virus-like particles to the immunogenicity of human immunodeficiency virus type 1 Gag-derived vaccines in mice. Journal of virology, 79(3), 1701–1712. https://doi.org/10.1128/JVI.79.3.1701-1712.2005, PMID: 15650195, PMCID: PMC544117
• Siliciano, J. D., & Siliciano, R. F. (2005). Enhanced culture assay for detection and quantitation of latently infected, resting CD4+ T-cells carrying replication-competent virus in HIV-1-infected individuals. Methods in molecular biology, 304, 3–15. https://doi.org/10.1385/1-59259-907-9:003, PMID: 16061962
• Siliciano, J. M., & Siliciano, R. F. (2005). Targeting HIV reservoirs with valproic acid. The Hopkins HIV report : a bimonthly newsletter for healthcare providers, 17(5), 8–9. PMID: 16419304

2004

• Lassen, K., Han, Y., Zhou, Y., Siliciano, J., & Siliciano, R. F. (2004). The multifactorial nature of HIV-1 latency. Trends in molecular medicine, 10(11), 525–531. https://doi.org/10.1016/j.molmed.2004.09.006, PMID: 15519278
• Nettles, R. E., Kieffer, T. L., Simmons, R. P., Cofrancesco, J., Jr, Moore, R. D., Gallant, J. E., Persaud, D., & Siliciano, R. F. (2004). Genotypic resistance in HIV-1-infected patients with persistently detectable low-level viremia while receiving highly active antiretroviral therapy. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 39(7), 1030–1037. https://doi.org/10.1086/423388, PMID: 15472857
• Lassen, K. G., Bailey, J. R., & Siliciano, R. F. (2004). Analysis of human immunodeficiency virus type 1 transcriptional elongation in resting CD4+ T cells in vivo. Journal of virology, 78(17), 9105–9114. https://doi.org/10.1128/JVI.78.17.9105-9114.2004, PMID: 15308706, PMCID: PMC506937
• Wong, S. B., Buck, C. B., Shen, X., & Siliciano, R. F. (2004). An evaluation of enforced rapid proteasomal degradation as a means of enhancing vaccine-induced CTL responses. Journal of immunology (Baltimore, Md. : 1950), 173(5), 3073–3083. https://doi.org/10.4049/jimmunol.173.5.3073, PMID: 15322167
• Simmons, R., & Siliciano, R. F. (2004). Can antiretroviral therapy ever be stopped? An update. The AIDS reader, 14(8), 435–442. PMID: 15338523
• Bailey, J., Blankson, J. N., Wind-Rotolo, M., & Siliciano, R. F. (2004). Mechanisms of HIV-1 escape from immune responses and antiretroviral drugs. Current opinion in immunology, 16(4), 470–476. https://doi.org/10.1016/j.coi.2004.05.005, PMID: 15245741
• Wang, Z., La Rosa, C., Mekhoubad, S., Lacey, S. F., Villacres, M. C., Markel, S., Longmate, J., Ellenhorn, J. D., Siliciano, R. F., Buck, C., Britt, W. J., & Diamond, D. J. (2004). Attenuated poxviruses generate clinically relevant frequencies of CMV-specific T cells. Blood, 104(3), 847–856. https://doi.org/10.1182/blood-2003-10-3469, PMID: 15090456
• Kieffer, T., & Siliciano, R. (2004). Averting the evolution of drug resistance. The Hopkins HIV report : a bimonthly newsletter for healthcare providers, 16(4), 9–10. PMID: 15386837
• Siliciano, J. D., & Siliciano, R. F. (2004). A long-term latent reservoir for HIV-1: discovery and clinical implications. The Journal of antimicrobial chemotherapy, 54(1), 6–9. https://doi.org/10.1093/jac/dkh292, PMID: 15163657
• Han, Y., Lassen, K., Monie, D., Sedaghat, A. R., Shimoji, S., Liu, X., Pierson, T. C., Margolick, J. B., Siliciano, R. F., & Siliciano, J. D. (2004). Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. Journal of virology, 78(12), 6122–6133. https://doi.org/10.1128/JVI.78.12.6122-6133.2004, PMID: 15163705, PMCID: PMC416493
• Kieffer, T. L., Finucane, M. M., Nettles, R. E., Quinn, T. C., Broman, K. W., Ray, S. C., Persaud, D., & Siliciano, R. F. (2004). Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads. The Journal of infectious diseases, 189(8), 1452–1465. https://doi.org/10.1086/382488, PMID: 15073683
• Zhang, H., Zhou, Y., Alcock, C., Kiefer, T., Monie, D., Siliciano, J., Li, Q., Pham, P., Cofrancesco, J., Persaud, D., & Siliciano, R. F. (2004). Novel single-cell-level phenotypic assay for residual drug susceptibility and reduced replication capacity of drug-resistant human immunodeficiency virus type 1. Journal of virology, 78(4), 1718–1729. https://doi.org/10.1128/jvi.78.4.1718-1729.2004, PMID: 14747537, PMCID: PMC369469
• Persaud, D., Siberry, G. K., Ahonkhai, A., Kajdas, J., Monie, D., Hutton, N., Watson, D. C., Quinn, T. C., Ray, S. C., & Siliciano, R. F. (2004). Continued production of drug-sensitive human immunodeficiency virus type 1 in children on combination antiretroviral therapy who have undetectable viral loads. Journal of virology, 78(2), 968–979. https://doi.org/10.1128/jvi.78.2.968-979.2004, PMID: 14694128, PMCID: PMC368798
• Wong, S. B., Buck, C. B., Shen, X., & Siliciano, R. F. (2004). An evaluation of enforced rapid proteasomal degradation as a means of enhancing vaccine-induced CTL responses. Journal of immunology (Baltimore, Md. : 1950), 173(5), 3073–3083. https://doi.org/10.4049/jimmunol.173.5.3073, PMID: 15322167
• Persaud, D., Siberry, G. K., Ahonkhai, A., Kajdas, J., Monie, D., Hutton, N., Watson, D. C., Quinn, T. C., Ray, S. C., & Siliciano, R. F. (2004). Continued production of drug-sensitive human immunodeficiency virus type 1 in children on combination antiretroviral therapy who have undetectable viral loads. Journal of virology, 78(2), 968–979. https://doi.org/10.1128/jvi.78.2.968-979.2004, PMID: 14694128, PMCID: PMC368798
• Kieffer, T. L., Finucane, M. M., Nettles, R. E., Quinn, T. C., Broman, K. W., Ray, S. C., Persaud, D., & Siliciano, R. F. (2004). Genotypic analysis of HIV-1 drug resistance at the limit of detection: virus production without evolution in treated adults with undetectable HIV loads. The Journal of infectious diseases, 189(8), 1452–1465. https://doi.org/10.1086/382488, PMID: 15073683
• Zhang, H., Zhou, Y., Alcock, C., Kiefer, T., Monie, D., Siliciano, J., Li, Q., Pham, P., Cofrancesco, J., Persaud, D., & Siliciano, R. F. (2004). Novel single-cell-level phenotypic assay for residual drug susceptibility and reduced replication capacity of drug-resistant human immunodeficiency virus type 1. Journal of virology, 78(4), 1718–1729. https://doi.org/10.1128/jvi.78.4.1718-1729.2004, PMID: 14747537, PMCID: PMC369469
• Han, Y., Lassen, K., Monie, D., Sedaghat, A. R., Shimoji, S., Liu, X., Pierson, T. C., Margolick, J. B., Siliciano, R. F., & Siliciano, J. D. (2004). Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. Journal of virology, 78(12), 6122–6133. https://doi.org/10.1128/JVI.78.12.6122-6133.2004, PMID: 15163705, PMCID: PMC416493

2003

• Mansharamani, M., Graham, D. R., Monie, D., Lee, K. K., Hildreth, J. E., Siliciano, R. F., & Wilson, K. L. (2003). Barrier-to-autointegration factor BAF binds p55 Gag and matrix and is a host component of human immunodeficiency virus type 1 virions. Journal of virology, 77(24), 13084–13092. https://doi.org/10.1128/jvi.77.24.13084-13092.2003, PMID: 14645565, PMCID: PMC296067
• Daftarian, P., Ali, S., Sharan, R., Lacey, S. F., La Rosa, C., Longmate, J., Buck, C., Siliciano, R. F., & Diamond, D. J. (2003). Immunization with Th-CTL fusion peptide and cytosine-phosphate-guanine DNA in transgenic HLA-A2 mice induces recognition of HIV-infected T cells and clears vaccinia virus challenge. Journal of immunology, 171(8), 4028–4039. https://doi.org/10.4049/jimmunol.171.8.4028, PMID: 14530323
• Hermankova, M., Siliciano, J. D., Zhou, Y., Monie, D., Chadwick, K., Margolick, J. B., Quinn, T. C., & Siliciano, R. F. (2003). Analysis of human immunodeficiency virus type 1 gene expression in latently infected resting CD4+ T lymphocytes in vivo. Journal of virology, 77(13), 7383–7392. https://doi.org/10.1128/jvi.77.13.7383-7392.2003, PMID: 12805437, PMCID: PMC164778
• Siliciano, J. D., Kajdas, J., Finzi, D., Quinn, T. C., Chadwick, K., Margolick, J. B., Kovacs, C., Gange, S. J., & Siliciano, R. F. (2003). Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nature medicine, 9(6), 727–728. https://doi.org/10.1038/nm880, PMID: 12754504
• Shen, A., Zink, M. C., Mankowski, J. L., Chadwick, K., Margolick, J. B., Carruth, L. M., Li, M., Clements, J. E., & Siliciano, R. F. (2003). Resting CD4+ T lymphocytes but not thymocytes provide a latent viral reservoir in a simian immunodeficiency virus-Macaca nemestrina model of human immunodeficiency virus type 1-infected patients on highly active antiretroviral therapy. Journal of virology, 77(8), 4938–4949. https://doi.org/10.1128/jvi.77.8.4938-4949.2003, PMID: 12663799, PMCID: PMC152116
• Persaud, D., Zhou, Y., Siliciano, J. M., & Siliciano, R. F. (2003). Latency in human immunodeficiency virus type 1 infection: no easy answers. Journal of virology, 77(3), 1659–1665. https://doi.org/10.1128/jvi.77.3.1659-1665.2003, PMID: 12525599, PMCID: PMC140995
• Shen, A., Zink, M. C., Mankowski, J. L., Chadwick, K., Margolick, J. B., Carruth, L. M., Li, M., Clements, J. E., & Siliciano, R. F. (2003). Resting CD4+ T lymphocytes but not thymocytes provide a latent viral reservoir in a simian immunodeficiency virus-Macaca nemestrina model of human immunodeficiency virus type 1-infected patients on highly active antiretroviral therapy. Journal of virology, 77(8), 4938–4949. https://doi.org/10.1128/jvi.77.8.4938-4949.2003, PMID: 12663799, PMCID: PMC152116
• Daftarian, P., Ali, S., Sharan, R., Lacey, S. F., La Rosa, C., Longmate, J., Buck, C., Siliciano, R. F., & Diamond, D. J. (2003). Immunization with Th-CTL fusion peptide and cytosine-phosphate-guanine DNA in transgenic HLA-A2 mice induces recognition of HIV-infected T cells and clears vaccinia virus challenge. Journal of immunology, 171(8), 4028–4039. https://doi.org/10.4049/jimmunol.171.8.4028, PMID: 14530323

2002

• Shen, X., Wong, S. B., Buck, C. B., Zhang, J., & Siliciano, R. F. (2002). Direct priming and cross-priming contribute differentially to the induction of CD8+ CTL following exposure to vaccinia virus via different routes. Journal of immunology, 169(8), 4222–4229. https://doi.org/10.4049/jimmunol.169.8.4222, PMID: 12370352
• Ruff, C. T., Ray, S. C., Kwon, P., Zinn, R., Pendleton, A., Hutton, N., Ashworth, R., Gange, S., Quinn, T. C., Siliciano, R. F., & Persaud, D. (2002). Persistence of wild-type virus and lack of temporal structure in the latent reservoir for human immunodeficiency virus type 1 in pediatric patients with extensive antiretroviral exposure. Journal of virology, 76(18), 9481–9492. https://doi.org/10.1128/jvi.76.18.9481-9492.2002, PMID: 12186930, PMCID: PMC136462
• Pierson, T. C., Zhou, Y., Kieffer, T. L., Ruff, C. T., Buck, C., & Siliciano, R. F. (2002). Molecular characterization of preintegration latency in human immunodeficiency virus type 1 infection. Journal of virology, 76(17), 8518–8531. https://doi.org/10.1128/jvi.76.17.8518-8513.2002, PMID: 12163571, PMCID: PMC136977
• Blankson, J. N., Gallant, J. E., Quinn, T. C., Bartlett, J. G., & Siliciano, R. F. (2002). Loss of HIV-1-specific immunity during treatment interruption in 2 chronically infected patients. JAMA, 288(2), 162–164. https://doi.org/10.1001/jama.288.2.162-a, PMID: 12095377
• Pierson, T. C., Kieffer, T. L., Ruff, C. T., Buck, C., Gange, S. J., & Siliciano, R. F. (2002). Intrinsic stability of episomal circles formed during human immunodeficiency virus type 1 replication. Journal of virology, 76(8), 4138–4144. https://doi.org/10.1128/jvi.76.8.4138-4144.2002, PMID: 11907256, PMCID: PMC136068
• Hermankova, M., Siliciano, J. D., Zhou, Y., Monie, D., Chadwick, K., Margolick, J. B., Quinn, T. C., & Siliciano, R. F. (2003). Analysis of human immunodeficiency virus type 1 gene expression in latently infected resting CD4+ T lymphocytes in vivo. Journal of virology, 77(13), 7383–7392. https://doi.org/10.1128/jvi.77.13.7383-7392.2003, PMID: 12805437, PMCID: PMC164778
• Saavedra-Lozano, J., McCoig, C., Xu, J., Cao, Y., Keiser, P., Ghetie, V., Siliciano, R. F., Siliciano, J. D., Picker, L. J., Ramilo, O., & Vitetta, E. S. (2002). An anti-CD45RO immunotoxin kills latently infected human immunodeficiency virus (HIV) CD4 T cells in the blood of HIV-positive persons. The Journal of infectious diseases, 185(3), 306–314. https://doi.org/10.1086/338565, PMID: 11807712
• Blankson, J. N., Persaud, D., & Siliciano, R. F. (2002). The challenge of viral reservoirs in HIV-1 infection. Annual review of medicine, 53, 557–593. https://doi.org/10.1146/annurev.med.53.082901.104024, PMID: 11818490
• Ruff, C. T., Ray, S. C., Kwon, P., Zinn, R., Pendleton, A., Hutton, N., Ashworth, R., Gange, S., Quinn, T. C., Siliciano, R. F., & Persaud, D. (2002). Persistence of wild-type virus and lack of temporal structure in the latent reservoir for human immunodeficiency virus type 1 in pediatric patients with extensive antiretroviral exposure. Journal of virology, 76(18), 9481–9492. https://doi.org/10.1128/jvi.76.18.9481-9492.2002, PMID: 12186930, PMCID: PMC136462
• Shen, X., Wong, S. B., Buck, C. B., Zhang, J., & Siliciano, R. F. (2002). Direct priming and cross-priming contribute differentially to the induction of CD8+ CTL following exposure to vaccinia virus via different routes. Journal of immunology, 169(8), 4222–4229. https://doi.org/10.4049/jimmunol.169.8.4222, PMID: 12370352

2001

• Hermankova, M., Ray, S. C., Ruff, C., Powell-Davis, M., Ingersoll, R., D’Aquila, R. T., Quinn, T. C., Siliciano, J. D., Siliciano, R. F., & Persaud, D. (2001). HIV-1 drug resistance profiles in children and adults with viral load of <50 copies/ml receiving combination therapy. JAMA, 286(2), 196–207. https://doi.org/10.1001/jama.286.2.196, PMID: 11448283
• Blankson, J. N., & Siliciano, R. F. (2001). MHC class II genotype and the control of viremia in HIV-1-infected individuals on highly active antiretroviral therapy. The Journal of clinical investigation, 107(5), 549–551. https://doi.org/10.1172/JCI12430, PMID: 11238554, PMCID: PMC199437
• Blankson, J. N., Gallant, J. E., & Siliciano, R. F. (2001). Proliferative responses to human immunodeficiency virus type 1 (HIV-1) antigens in HIV-1-infected patients with immune reconstitution. The Journal of infectious diseases, 183(4), 657–661. https://doi.org/10.1086/318545, PMID: 11170994
• Blankson, J. N., & Siliciano, R. F. (2001). Structured therapeutic interruptions: a review. The Hopkins HIV report : a bimonthly newsletter for healthcare providers, 13(1), 1–13. PMID: 12184252
• Buck, C. B., Shen, X., Egan, M. A., Pierson, T. C., Walker, C. M., & Siliciano, R. F. (2001). The human immunodeficiency virus type 1 gag gene encodes an internal ribosome entry site. Journal of virology, 75(1), 181–191. https://doi.org/10.1128/JVI.75.1.181-191.2001, PMID: 11119587, PMCID: PMC113911
• Blankson, J. N., Gallant, J. E., & Siliciano, R. F. (2001). Proliferative responses to human immunodeficiency virus type 1 (HIV-1) antigens in HIV-1-infected patients with immune reconstitution. The Journal of infectious diseases, 183(4), 657–661. https://doi.org/10.1086/318545, PMID: 11170994

2000

• Gupta, K., Ott, D., Hope, T. J., Siliciano, R. F., & Boeke, J. D. (2000). A human nuclear shuttling protein that interacts with human immunodeficiency virus type 1 matrix is packaged into virions. Journal of virology, 74(24), 11811–11824. https://doi.org/10.1128/jvi.74.24.11811-11824.2000, PMID: 11090181, PMCID: PMC112464
• Shen, A., Siliciano, J. D., Pierson, T. C., Buck, C. B., & Siliciano, R. F. (2000). Establishment of latent HIV-1 infection of resting CD4(+) T lymphocytes does not require inactivation of Vpr. Virology, 278(1), 227–233. https://doi.org/10.1006/viro.2000.0650, PMID: 11112497
• Blankson, J. N., Finzi, D., Pierson, T. C., Sabundayo, B. P., Chadwick, K., Margolick, J. B., Quinn, T. C., & Siliciano, R. F. (2000). Biphasic decay of latently infected CD4+ T cells in acute human immunodeficiency virus type 1 infection. The Journal of infectious diseases, 182(6), 1636–1642. https://doi.org/10.1086/317615, PMID: 11069234
• Shen, X., & Siliciano, R. F. (2000). Preventing AIDS but not HIV-1 infection with a DNA vaccine. Science, 290(5491), 463–465. https://doi.org/10.1126/science.290.5491.463, PMID: 11183769
• Siliciano, J. D., & Siliciano, R. F. (2000). Latency and viral persistence in HIV-1 infection. The Journal of clinical investigation, 106(7), 823–825. https://doi.org/10.1172/JCI11246, PMID: 11018068, PMCID: PMC517817
• Martinez-Picado, J., DePasquale, M. P., Kartsonis, N., Hanna, G. J., Wong, J., Finzi, D., Rosenberg, E., Gunthard, H. F., Sutton, L., Savara, A., Petropoulos, C. J., Hellmann, N., Walker, B. D., Richman, D. D., Siliciano, R., & D’Aquila, R. T. (2000). Antiretroviral resistance during successful therapy of HIV type 1 infection. Proceedings of the National Academy of Sciences of the United States of America, 97(20), 10948–10953. https://doi.org/10.1073/pnas.97.20.10948, PMID: 11005867, PMCID: PMC27129
• Pierson, T., Hoffman, T. L., Blankson, J., Finzi, D., Chadwick, K., Margolick, J. B., Buck, C., Siliciano, J. D., Doms, R. W., & Siliciano, R. F. (2000). Characterization of chemokine receptor utilization of viruses in the latent reservoir for human immunodeficiency virus type 1. Journal of virology, 74(17), 7824–7833. https://doi.org/10.1128/jvi.74.17.7824-7833.2000, PMID: 10933689, PMCID: PMC112312
• Blankson, J., & Siliciano, R. F. (2000). Interleukin 2 treatment for HIV infection. JAMA, 284(2), 236–238. https://doi.org/10.1001/jama.284.2.236, PMID: 10889599
• Finzi, D., & Siliciano, R. F. (2000). Taking aim at HIV replication. Nature medicine, 6(7), 735–736. https://doi.org/10.1038/77444, PMID: 10888911
• Persaud, D., Pierson, T., Ruff, C., Finzi, D., Chadwick, K. R., Margolick, J. B., Ruff, A., Hutton, N., Ray, S., & Siliciano, R. F. (2000). A stable latent reservoir for HIV-1 in resting CD4(+) T lymphocytes in infected children. The Journal of clinical investigation, 105(7), 995–1003. https://doi.org/10.1172/JCI9006, PMID: 10749578, PMCID: PMC377486
• Pierson, T., McArthur, J., & Siliciano, R. F. (2000). Reservoirs for HIV-1: mechanisms for viral persistence in the presence of antiviral immune responses and antiretroviral therapy. Annual review of immunology, 18, 665–708. https://doi.org/10.1146/annurev.immunol.18.1.665, PMID: 10837072
• Siliciano R. (2000). Can antiretroviral therapy ever be stopped?. The AIDS reader, 10(4), 224–229. PMID: 10808605
• Shen, X., & Siliciano, R. F. (2000). Preventing AIDS but not HIV-1 infection with a DNA vaccine. Science, 290(5491), 463–465. https://doi.org/10.1126/science.290.5491.463, PMID: 11183769

1999

• Lori, F., Jessen, H., Lieberman, J., Finzi, D., Rosenberg, E., Tinelli, C., Walker, B., Siliciano, R. F., & Lisziewicz, J. (1999). Treatment of human immunodeficiency virus infection with hydroxyurea, didanosine, and a protease inhibitor before seroconversion is associated with normalized immune parameters and limited viral reservoir. The Journal of infectious diseases, 180(6), 1827–1832. https://doi.org/10.1086/315113, PMID: 10558937
• Siliciano R. (1999). HARRT for life. The Hopkins HIV report : a bimonthly newsletter for healthcare providers, 11(4), 2. PMID: 11366922
• Carruth, L. M., Greten, T. F., Murray, C. E., Castro, M. G., Crone, S. N., Pavlat, W., Schneck, J. P., & Siliciano, R. F. (1999). An algorithm for evaluating human cytotoxic T lymphocyte responses to candidate AIDS vaccines. AIDS research and human retroviruses, 15(11), 1021–1034. https://doi.org/10.1089/088922299310539, PMID: 10445814
• Lisziewicz, J., Rosenberg, E., Lieberman, J., Jessen, H., Lopalco, L., Siliciano, R., Walker, B., & Lori, F. (1999). Control of HIV despite the discontinuation of antiretroviral therapy. The New England journal of medicine, 340(21), 1683–1684. https://doi.org/10.1056/NEJM199905273402114, PMID: 10348681
• Finzi, D., Blankson, J., Siliciano, J. D., Margolick, J. B., Chadwick, K., Pierson, T., Smith, K., Lisziewicz, J., Lori, F., Flexner, C., Quinn, T. C., Chaisson, R. E., Rosenberg, E., Walker, B., Gange, S., Gallant, J., & Siliciano, R. F. (1999). Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nature medicine, 5(5), 512–517. https://doi.org/10.1038/8394, PMID: 10229227
• Ferris, R. L., Hall, C., Sipsas, N. V., Safrit, J. T., Trocha, A., Koup, R. A., Johnson, R. P., & Siliciano, R. F. (1999). Processing of HIV-1 envelope glycoprotein for class I-restricted recognition: dependence on TAP1/2 and mechanisms for cytosolic localization. Journal of immunology, 162(3), 1324–1332. PMID: 9973386
• Ferris, R. L., Hall, C., Sipsas, N. V., Safrit, J. T., Trocha, A., Koup, R. A., Johnson, R. P., & Siliciano, R. F. (1999). Processing of HIV-1 envelope glycoprotein for class I-restricted recognition: dependence on TAP1/2 and mechanisms for cytosolic localization. Journal of immunology (Baltimore, Md. : 1950), 162(3), 1324–1332. PMID: 9973386
• Tobery, T., & Siliciano, R. F. (1999). Cutting edge: induction of enhanced CTL-dependent protective immunity in vivo by N-end rule targeting of a model tumor antigen. Journal of immunology, 162(2), 639–642. PMID: 9916680

1998

• Contreras, C. E., Ploton, I. N., Siliciano, R. F., Karp, C. L., Viscidi, R., & Kumar, N. (1998). Mapping of specific and promiscuous HLA-DR-restricted T-cell epitopes on the Plasmodium falciparum 27-kilodalton sexual stage-specific antigen. Infection and immunity, 66(8), 3579–3590. https://doi.org/10.1128/IAI.66.8.3579-3590.1998, PMID: 9673236, PMCID: PMC108389
• Lisziewicz, J., Jessen, H., Finzi, D., Siliciano, R. F., & Lori, F. (1998). HIV-1 suppression by early treatment with hydroxyurea, didanosine, and a protease inhibitor. Lancet (London, England), 352(9123), 199–200. https://doi.org/10.1016/S0140-6736(98)24029-3, PMID: 9683211
• Finzi, D., & Siliciano, R. F. (1998). Viral dynamics in HIV-1 infection. Cell, 93(5), 665–671. https://doi.org/10.1016/s0092-8674(00)81427-0, PMID: 9630210
• Agosto, M., Allan, J., Benson, C., Berger, E. A., Blumenthal, R., Burton, D., Clements, J., Coffin, J., Connor, R., Cullen, B., Desrosiers, R., Dimitrov, D., Doms, R., Emerman, M., Feinberg, M., Fultz, P., Gerard, C., Gonsalves, G., Haase, A., Haigwood, N., … Zingale, D. (1998). AIDS vaccine development. Science, 280(5365), 803–805. PMID: 9599148
• Clements-Mann, M. L., Weinhold, K., Matthews, T. J., Graham, B. S., Gorse, G. J., Keefer, M. C., McElrath, M. J., Hsieh, R. H., Mestecky, J., Zolla-Pazner, S., Mascola, J., Schwartz, D., Siliciano, R., Corey, L., Wright, P. F., Belshe, R., Dolin, R., Jackson, S., Xu, S., Fast, P., … Paoletti, E. (1998). Immune responses to human immunodeficiency virus (HIV) type 1 induced by canarypox expressing HIV-1MN gp120, HIV-1SF2 recombinant gp120, or both vaccines in seronegative adults. NIAID AIDS Vaccine Evaluation Group. The Journal of infectious diseases, 177(5), 1230–1246. https://doi.org/10.1086/515288, PMID: 9593008
• Siliciano R. F. (1998). A reservoir for HIV in patients on combination antiretroviral therapy. The Hopkins HIV report : a bimonthly newsletter for healthcare providers, 10(1), 1–11. PMID: 11365130
• Johnson, R. P., Siliciano, R. F., & McElrath, M. J. (1998). Cellular immune responses to HIV-1. AIDS (London, England), 12 Suppl A, S113–S120. PMID: 9632992
• Ray, S. C., Lubaki, N., Dhruva, B. R., Siliciano, R. F., & Bollinger, R. C. (1998). Autologous strain-specific cytolytic T lymphocyte responses directed against human immunodeficiency virus type 1 Env. AIDS research and human retroviruses, 14(1), 3–13. https://doi.org/10.1089/aid.1998.14.3, PMID: 9453246

1997

• Finzi, D., Hermankova, M., Pierson, T., Carruth, L. M., Buck, C., Chaisson, R. E., Quinn, T. C., Chadwick, K., Margolick, J., Brookmeyer, R., Gallant, J., Markowitz, M., Ho, D. D., Richman, D. D., & Siliciano, R. F. (1997). Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science, 278(5341), 1295–1300. https://doi.org/10.1126/science.278.5341.1295, PMID: 9360927
• Ehret, R., Heinkelein, M., Siliciano, R. F., & Jassoy, C. (1997). Human immunodeficiency virus glycoprotein-specific CD4+ cytotoxic T lymphocytes are involved in two types of cytotoxicity: antigen-specific and cell-cell fusion-related cell lysis. AIDS research and human retroviruses, 13(12), 1017–1021. https://doi.org/10.1089/aid.1997.13.1017, PMID: 9264288
• Chun, T. W., Chadwick, K., Margolick, J., & Siliciano, R. F. (1997). Differential susceptibility of naive and memory CD4+ T cells to the cytopathic effects of infection with human immunodeficiency virus type 1 strain LAI. Journal of virology, 71(6), 4436–4444. https://doi.org/10.1128/JVI.71.6.4436-4444.1997, PMID: 9151834, PMCID: PMC191662
• Lubaki, N. M., Ray, S. C., Dhruva, B., Quinn, T. C., Siliciano, R. F., & Bollinger, R. C. (1997). Characterization of a polyclonal cytolytic T lymphocyte response to human immunodeficiency virus in persons without clinical progression. The Journal of infectious diseases, 175(6), 1360–1367. https://doi.org/10.1086/516468, PMID: 9180175
• Chun, T. W., Carruth, L., Finzi, D., Shen, X., DiGiuseppe, J. A., Taylor, H., Hermankova, M., Chadwick, K., Margolick, J., Quinn, T. C., Kuo, Y. H., Brookmeyer, R., Zeiger, M. A., Barditch-Crovo, P., & Siliciano, R. F. (1997). Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature, 387(6629), 183–188. https://doi.org/10.1038/387183a0, PMID: 9144289
• Ruff, A. L., Guarnieri, F. G., Staveley-O’Carroll, K., Siliciano, R. F., & August, J. T. (1997). The enhanced immune response to the HIV gp160/LAMP chimeric gene product targeted to the lysosome membrane protein trafficking pathway. The Journal of biological chemistry, 272(13), 8671–8678. https://doi.org/10.1074/jbc.272.13.8671, PMID: 9079699
• Tobery, T. W., & Siliciano, R. F. (1997). Targeting of HIV-1 antigens for rapid intracellular degradation enhances cytotoxic T lymphocyte (CTL) recognition and the induction of de novo CTL responses in vivo after immunization. The Journal of experimental medicine, 185(5), 909–920. https://doi.org/10.1084/jem.185.5.909, PMID: 9120397, PMCID: PMC2196169
• Egan, M. A., Carruth, L. M., Rowell, J. F., Yu, X., & Siliciano, R. F. (1997). The ins and outs of HIV endocytosis. Trends in cell biology, 7(2), 49. https://doi.org/10.1016/S0962-8924(97)82670-0, PMID: 17708904
• McElrath, M. J., Siliciano, R. F., & Weinhold, K. J. (1997). HIV type 1 vaccine-induced cytotoxic T cell responses in phase I clinical trials: detection, characterization, and quantitation. AIDS research and human retroviruses, 13(3), 211–216. https://doi.org/10.1089/aid.1997.13.211, PMID: 9115806
• Liu, A. Y., Torchia, B. S., Migeon, B. R., & Siliciano, R. F. (1997). The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4+ T cells. Genomics, 39(2), 171–184. https://doi.org/10.1006/geno.1996.4463, PMID: 9027504

1996

• Egan, M. A., Carruth, L. M., Rowell, J. F., Yu, X., & Siliciano, R. F. (1996). Human immunodeficiency virus type 1 envelope protein endocytosis mediated by a highly conserved intrinsic internalization signal in the cytoplasmic domain of gp41 is suppressed in the presence of the Pr55gag precursor protein. Journal of virology, 70(10), 6547–6556. https://doi.org/10.1128/JVI.70.10.6547-6556.1996, PMID: 8794289, PMCID: PMC190695
• Bollinger, R. C., Egan, M. A., Chun, T. W., Mathieson, B., & Siliciano, R. F. (1996). Cellular immune responses to HIV-1 in progressive and non-progressive infections. AIDS (London, England), 10 Suppl A, S85–S96. https://doi.org/10.1097/00002030-199601001-00013, PMID: 8883615
• Ferris, R. L., Buck, C., Hammond, S. A., Woods, A. S., Cotter, R. J., Takiguchi, M., Igarashi, Y., Ichikawa, Y., & Siliciano, R. F. (1996). Class I-restricted presentation of an HIV-1 gp41 epitope containing an N-linked glycosylation site. Implications for the mechanism of processing of viral envelope proteins. Journal of immunology, 156(2), 834–840. PMID: 8543840

1995

• Chun, T. W., Finzi, D., Margolick, J., Chadwick, K., Schwartz, D., & Siliciano, R. F. (1995). In vivo fate of HIV-1-infected T cells: quantitative analysis of the transition to stable latency. Nature medicine, 1(12), 1284–1290. https://doi.org/10.1038/nm1295-1284, PMID: 7489410
• Rowell, J. F., Ruff, A. L., Guarnieri, F. G., Staveley-O’Carroll, K., Lin, X., Tang, J., August, J. T., & Siliciano, R. F. (1995). Lysosome-associated membrane protein-1-mediated targeting of the HIV-1 envelope protein to an endosomal/lysosomal compartment enhances its presentation to MHC class II-restricted T cells. Journal of immunology, 155(4), 1818–1828. PMID: 7636236
• Rowell, J. F., Stanhope, P. E., & Siliciano, R. F. (1995). Endocytosis of endogenously synthesized HIV-1 envelope protein. Mechanism and role in processing for association with class II MHC. Journal of immunology, 155(1), 473–488. PMID: 7602119
• Egan, M. A., Pavlat, W. A., Tartaglia, J., Paoletti, E., Weinhold, K. J., Clements, M. L., & Siliciano, R. F. (1995). Induction of human immunodeficiency virus type 1 (HIV-1)-specific cytolytic T lymphocyte responses in seronegative adults by a nonreplicating, host-range-restricted canarypox vector (ALVAC) carrying the HIV-1MN env gene. The Journal of infectious diseases, 171(6), 1623–1627. https://doi.org/10.1093/infdis/171.6.1623, PMID: 7769304
• Hammond, S. A., Johnson, R. P., Kalams, S. A., Walker, B. D., Takiguchi, M., Safrit, J. T., Koup, R. A., & Siliciano, R. F. (1995). An epitope-selective, transporter associated with antigen presentation (TAP)-1/2-independent pathway and a more general TAP-1/2-dependent antigen-processing pathway allow recognition of the HIV-1 envelope glycoprotein by CD8+ CTL. Journal of immunology, 154(11), 6140–6156. PMID: 7538543
• Siliciano, R. F., & Soloski, M. J. (1995). MHC class I-restricted processing of transmembrane proteins. Mechanism and biologic significance. Journal of immunology, 155(1), 2–5. PMID: 7602096

1994

• Lubaki, M. N., Egan, M. A., Siliciano, R. F., Weinhold, K. J., & Bollinger, R. C. (1994). A novel method for detection and ex vivo expansion of HIV type 1-specific cytolytic T lymphocytes. AIDS research and human retroviruses, 10(11), 1427–1431. https://doi.org/10.1089/aid.1994.10.1427, PMID: 7888197
• Miskovsky, E. P., Liu, A. Y., Pavlat, W., Viveen, R., Stanhope, P. E., Finzi, D., Fox, W. M., 3rd, Hruban, R. H., Podack, E. R., & Siliciano, R. F. (1994). Studies of the mechanism of cytolysis by HIV-1-specific CD4+ human CTL clones induced by candidate AIDS vaccines. Journal of immunology, 153(6), 2787–2799. PMID: 7915742
• Johnson, R. P., Hammond, S. A., Trocha, A., Siliciano, R. F., & Walker, B. D. (1994). Induction of a major histocompatibility complex class I-restricted cytotoxic T-lymphocyte response to a highly conserved region of human immunodeficiency virus type 1 (HIV-1) gp120 in seronegative humans immunized with a candidate HIV-1 vaccine. Journal of virology, 68(5), 3145–3153. https://doi.org/10.1128/JVI.68.5.3145-3153.1994, PMID: 7908700, PMCID: PMC236805
• Johnson, R. P., Hammond, S. A., Trocha, A., Siliciano, R. F., & Walker, B. D. (1994). Epitope specificity of MHC restricted cytotoxic T lymphocytes induced by candidate HIV-1 vaccine. AIDS research and human retroviruses, 10 Suppl 2, S73–S75. PMID: 7532425

1993

• Bollinger, R. C., Quinn, T. C., Liu, A. Y., Stanhope, P. E., Hammond, S. A., Viveen, R., Clements, M. L., & Siliciano, R. F. (1993). Cytokines from vaccine-induced HIV-1 specific cytotoxic T lymphocytes: effects on viral replication. AIDS research and human retroviruses, 9(11), 1067–1077. https://doi.org/10.1089/aid.1993.9.1067, PMID: 7906131
• Callahan, K. M., Rowell, J. F., Soloski, M. J., Machamer, C. E., & Siliciano, R. F. (1993). HIV-1 envelope protein is expressed on the surface of infected cells before its processing and presentation to class II-restricted T lymphocytes. Journal of immunology, 151(6), 2928–2942.
• Schwartz, D. H., Gorse, G., Clements, M. L., Belshe, R., Izu, A., Duliege, A. M., Berman, P., Twaddell, T., Stablein, D., & Sposto, R. (1993). Induction of HIV-1-neutralising and syncytium-inhibiting antibodies in uninfected recipients of HIV-1IIIB rgp120 subunit vaccine. Lancet, 342(8863), 69–73. https://doi.org/10.1016/0140-6736(93)91283-r, PMID: 8100910
• Hammond, S. A., Bollinger, R. C., Tobery, T. W., & Silliciano, R. F. (1993). Transporter-independent processing of HIV-1 envelope protein for recognition by CD8+ T cells. Nature, 364(6433), 158–161. https://doi.org/10.1038/364158a0, PMID: 8321286
• Stanhope, P. E., Clements, M. L., & Siliciano, R. F. (1993). Human CD4+ cytolytic T lymphocyte responses to a human immunodeficiency virus type 1 gp160 subunit vaccine. The Journal of infectious diseases, 168(1), 92–100. https://doi.org/10.1093/infdis/168.1.92, PMID: 8099941
• Stanhope, P. E., Liu, A. Y., Pavlat, W., Pitha, P. M., Clements, M. L., & Siliciano, R. F. (1993). An HIV-1 envelope protein vaccine elicits a functionally complex human CD4+ T cell response that includes cytolytic T lymphocytes. Journal of immunology, 150(10), 4672–4686. PMID: 8097759
• Siliciano R. F. (1993). CD4+ T cell epitopes in HIV-1 proteins. Chemical immunology, 56, 127–149. PMID: 7680866

1992

• Hammond, S. A., Bollinger, R. C., Stanhope, P. E., Quinn, T. C., Schwartz, D., Clements, M. L., & Siliciano, R. F. (1992). Comparative clonal analysis of human immunodeficiency virus type 1 (HIV-1)-specific CD4+ and CD8+ cytolytic T lymphocytes isolated from seronegative humans immunized with candidate HIV-1 vaccines. The Journal of experimental medicine, 176(6), 1531–1542. https://doi.org/10.1084/jem.176.6.1531, PMID: 1460417, PMCID: PMC2119456
• Siliciano, R. F., Bollinger, R. C., Callahan, K. M., Hammond, S. A., Liu, A. Y., Miskovsky, E. P., Rowell, J. F., & Stanhope, P. E. (1992). Clonal analysis of T-cell responses to the HIV-1 envelope proteins in AIDS vaccine recipients. AIDS research and human retroviruses, 8(8), 1349–1352. https://doi.org/10.1089/aid.1992.8.1349, PMID: 1361352
• Liu, A. Y., Miskovsky, E. P., Stanhope, P. E., & Siliciano, R. F. (1992). Production of transmembrane and secreted forms of tumor necrosis factor (TNF)-alpha by HIV-1-specific CD4+ cytolytic T lymphocyte clones. Evidence for a TNF-alpha-independent cytolytic mechanism. Journal of immunology, 148(12), 3789–3798. PMID: 1351088

1991

• Novotny, J., Ganju, R. K., Smiley, S. T., Hussey, R. E., Luther, M. A., Recny, M. A., Siliciano, R. F., & Reinherz, E. L. (1991). A soluble, single-chain T-cell receptor fragment endowed with antigen-combining properties. Proceedings of the National Academy of Sciences of the United States of America, 88(19), 8646–8650. https://doi.org/10.1073/pnas.88.19.8646, PMID: 1924326, PMCID: PMC52566
• Diamond, D. J., Szalay, P., Symer, D., Hao, P., Shin, H. S., Dintzis, R. Z., Dintzis, H. M., Reinherz, E. L., & Siliciano, R. F. (1991). Major histocompatibility complex independent T cell receptor-antigen interaction: functional analysis using fluorescein derivatives. The Journal of experimental medicine, 174(1), 229–241. https://doi.org/10.1084/jem.174.1.229, PMID: 2056277, PMCID: PMC2118876
• Hammond, S. A., Obah, E., Stanhope, P., Monell, C. R., Strand, M., Robbins, F. M., Bias, W. B., Karr, R. W., Koenig, S., & Siliciano, R. F. (1991). Characterization of a conserved T cell epitope in HIV-1 gp41 recognized by vaccine-induced human cytolytic T cells. Journal of immunology,146(5), 1470–1477. PMID: 1704395

1990

• Orentas, R. J., Hildreth, J. E., Obah, E., Polydefkis, M., Smith, G. E., Clements, M. L., & Siliciano, R. F. (1990). Induction of CD4+ human cytolytic T cells specific for HIV-infected cells by a gp160 subunit vaccine. Science, 248(4960), 1234–1237. https://doi.org/10.1126/science.2190315, PMID: 2190315
• Callahan, K. M., Fort, M. M., Obah, E. A., Reinherz, E. L., & Siliciano, R. F. (1990). Genetic variability in HIV-1 gp120 affects interactions with HLA molecules and T cell receptor. Journal of immunology, 144(9), 3341–3346. PMID: 1970352
• Koyasu, S., Lawton, T., Novick, D., Recny, M. A., Siliciano, R. F., Wallner, B. P., & Reinherz, E. L. (1990). Role of interaction of CD2 molecules with lymphocyte function-associated antigen 3 in T-cell recognition of nominal antigen. Proceedings of the National Academy of Sciences of the United States of America, 87(7), 2603–2607. https://doi.org/10.1073/pnas.87.7.2603, PMID: 1690889, PMCID: PMC53738
• Polydefkis, M., Koenig, S., Flexner, C., Obah, E., Gebo, K., Chakrabarti, S., Earl, P. L., Moss, B., & Siliciano, R. F. (1990). Anchor sequence-dependent endogenous processing of human immunodeficiency virus 1 envelope glycoprotein gp160 for CD4+ T cell recognition. The Journal of experimental medicine, 171(3), 875–887. https://doi.org/10.1084/jem.171.3.875, PMID: 1968506, PMCID: PMC2187764

1989

• Siliciano, R. F., Knall, C., Lawton, T., Berman, P., Gregory, T., & Reinherz, E. L. (1989). Recognition of HIV glycoprotein gp120 by T cells. Role of monocyte CD4 in the presentation of gp120. Journal of immunology, 142(5), 1506–1511. PMID: 2537355

1988

• Siliciano, R. F., Lawton, T., Knall, C., Karr, R. W., Berman, P., Gregory, T., & Reinherz, E. L. (1988). Analysis of host-virus interactions in AIDS with anti-gp120 T cell clones: effect of HIV sequence variation and a mechanism for CD4+ cell depletion. Cell, 54(4), 561–575. https://doi.org/10.1016/0092-8674(88)90078-5, PMID: 2969774
• Hussey, R. E., Richardson, N. E., Kowalski, M., Brown, N. R., Chang, H. C., Siliciano, R. F., Dorfman, T., Walker, B., Sodroski, J., & Reinherz, E. L. (1988). A soluble CD4 protein selectively inhibits HIV replication and syncytium formation. Nature, 331(6151), 78–81. https://doi.org/10.1038/331078a0, PMID: 2829023