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    Steven Deeks, MD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentMedicine
    AddressSFGH Bldg 80
    Phone415-476-4082x404

       Biography 
       Education and Training
      Institution Degree School or Department Year
      University of California, San FranciscoResidency School of Medicine
      University of California, San FranciscoM.D. Medicine1990

       Overview 
       Overview
      Steven G. Deeks, MD, is a Professor of Medicine in Residence at the University of California, San Francisco (UCSF) and a faculty member in the Positive Health Program (AIDS Program) at San Francisco General Hospital. Dr. Deeks has been engaged in HIV research and clinical care since 1993. He is an expert on the role of chronic inflammation in untreated and treated HIV disease. His research has several linked objectives, including: (1) to determine the mechanisms which contribute to this persistent inflammation during therapy, (2) to characterize the impact of persistent inflammation during antiretroviral therapy on end-organ disease and function, (3) to determine the impact of inflammation and immune dysfunction on HIV persistence during effective therapy and (4) to develop novel therapeutic interventions which reduce chronic inflammation and/or the size of the latent reservoir.

      Dr. Deeks has published over 300 peer-review articles, editorials and invited reviews on these and related topics. He has been the recipient of several NIH grants. He is the principle investigator of NIH-funded international collaboratory aimed at developing therapeutic interventions to cure HIV infection (DARE). He is the co-chair of the “Towards an HIV Cure” International Working Group and a member of the Office of AIDS Research Advisory Council (ORAC). He was elected to the American Society for Clinical Investigation (ASCI). In addition to his clinical and translational investigation, Dr. Deeks maintains a primary care clinic for HIV infected patients, and is a member of the Department on Health and Human Services Panel on Antiretroviral Guidelines for Adults and Adolescents.


       ORNG Applications 
       Websites
       In The News
       NIH Grants Awarded
       Global Health
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       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Cockerham LR, Deeks SG. Biomarker reveals HIV's hidden reservoir. Elife. 2014; 3.
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      2. Klatt NR, Bosinger SE, Peck M, Richert-Spuhler LE, Heigele A, Gile JP, Patel N, Taaffe J, Julg B, Camerini D, Torti C, Martin JN, Deeks SG, Sinclair E, Hecht FM, Lederman MM, Paiardini M, Kirchhoff F, Brenchley JM, Hunt PW, Silvestri G. Limited HIV Infection of Central Memory and Stem Cell Memory CD4+ T Cells Is Associated with Lack of Progression in Viremic Individuals. PLoS Pathog. 2014 Aug; 10(8):e1004345.
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      3. Seu L, Ortiz GM, Burt TD, Deeks SG, Martin JN, McCune JM. Levels of circulating myeloid subpopulations and of heme oxygenase-1 do not predict CD4(+) T cell recovery after the initiation of antiretroviral therapy for HIV disease. AIDS Res Ther. 2014; 11:27.
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      4. Borges AH, Weitz JI, Collins G, Baker JV, Lévy Y, Davey RT, Phillips AN, Neaton JD, Lundgren JD, Deeks SG. Markers of inflammation and activation of coagulation are associated with anaemia in antiretroviral-treated HIV disease. AIDS. 2014 Jul 31; 28(12):1791-6.
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      5. Lewin SR, Deeks SG, Barré-Sinoussi F. Towards a cure for HIV-are we making progress? Lancet. 2014 Jul 19; 384(9939):209-11.
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      6. Deeks SG, Hunt PW. Antiretroviral therapy: stubborn limitations persist. Lancet. 2014 Jul 19; 384(9939):214-6.
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      7. Michaud HA, SenGupta D, de Mulder M, Deeks SG, Martin JN, Kobie JJ, Sacha JB, Nixon DF. Cutting Edge: An Antibody Recognizing Ancestral Endogenous Virus Glycoproteins Mediates Antibody-Dependent Cellular Cytotoxicity on HIV-1-Infected Cells. J Immunol. 2014 Jul 14.
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      8. Barouch DH, Deeks SG. Immunologic strategies for HIV-1 remission and eradication. Science. 2014 Jul 11; 345(6193):169-74.
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      9. Li P, Fujimoto K, Bourguingnon L, Yukl S, Deeks S, Wong JK. Exogenous and endogenous hyaluronic acid reduces HIV infection of CD4(+) T cells. Immunol Cell Biol. 2014 Jun 24.
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      10. Scherzer R, Gandhi M, Estrella MM, Tien PC, Deeks SG, Grunfeld C, Peralta CA, Shlipak MG. A chronic kidney disease risk score to determine tenofovir safety in a prospective cohort of HIV-positive male veterans. AIDS. 2014 Jun 1; 28(9):1289-95.
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      11. Tandon R, Chew GM, Byron MM, Borrow P, Niki T, Hirashima M, Barbour JD, Norris PJ, Lanteri MC, Martin JN, Deeks SG, Ndhlovu LC. Galectin-9 Is Rapidly Released During Acute HIV-1 Infection and Remains Sustained at High Levels Despite Viral Suppression Even in Elite Controllers. AIDS Res Hum Retroviruses. 2014 Jul; 30(7):654-64.
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      12. Cockerham LR, Jain V, Sinclair E, Glidden DV, Hartogenesis W, Hatano H, Hunt PW, Martin JN, Pilcher CD, Sekaly R, Mccune JM, Hecht FM, Deeks SG. Programmed death 1 expression on CD4+ and CD8+ T cells in treated and untreated HIV disease. AIDS. 2014 May 26.
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      13. Serrano-Villar S, Sainz T, Lee SA, Hunt PW, Sinclair E, Shacklett BL, Ferre AL, Hayes TL, Somsouk M, Hsue PY, Van Natta ML, Meinert CL, Lederman MM, Hatano H, Jain V, Huang Y, Hecht FM, Martin JN, McCune JM, Moreno S, Deeks SG. HIV-Infected Individuals with Low CD4/CD8 Ratio despite Effective Antiretroviral Therapy Exhibit Altered T Cell Subsets, Heightened CD8+ T Cell Activation, and Increased Risk of Non-AIDS Morbidity and Mortality. PLoS Pathog. 2014 May; 10(5):e1004078.
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      14. Asher AK, Santos GM, Evans J, Dokubo EK, Lee TH, Martin JN, Deeks SG, Tobler LH, Busch M, Hunt PW, Page K. A closer look at hepatitis C clearance in HIV controllers: a response. AIDS. 2014 May 15; 28(8):1241-2.
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      15. Tenorio AR, Zheng Y, Bosch RJ, Krishnan S, Rodriguez B, Hunt PW, Plants J, Seth A, Wilson CC, Deeks SG, Lederman MM, Landay AL. Soluble Markers of Inflammation and Coagulation but Not T-Cell Activation Predict Non-AIDS-Defining Morbid Events During Suppressive Antiretroviral Treatment. J Infect Dis. 2014 Oct 15; 210(8):1248-59.
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      16. Symons J, Vandekerckhove L, Hütter G, Wensing AM, van Ham PM, Deeks SG, Nijhuis M. Dependence on the CCR5 Coreceptor for Viral Replication Explains the Lack of Rebound of CXCR4-Predicted HIV Variants in the Berlin Patient. Clin Infect Dis. 2014 Aug 15; 59(4):596-600.
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      17. Hunt PW, Sinclair E, Rodriguez B, Shive C, Clagett B, Funderburg N, Robinson J, Huang Y, Epling L, Martin JN, Deeks SG, Meinert CL, Van Natta ML, Jabs DA, Lederman MM. Gut Epithelial Barrier Dysfunction and Innate Immune Activation Predict Mortality in Treated HIV Infection. J Infect Dis. 2014 Apr 21.
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      18. Gopal S, Patel MR, Achenbach CJ, Yanik EL, Cole SR, Napravnik S, Burkholder GA, Mathews WC, Rodriguez B, Deeks SG, Mayer KH, Moore RD, Kitahata MM, Richards KL, Eron JJ. Lymphoma immune reconstitution inflammatory syndrome in the center for AIDS research network of integrated clinical systems cohort. Clin Infect Dis. 2014 Jul 15; 59(2):279-86.
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      19. Siewe B, Wallace J, Rygielski S, Stapleton JT, Martin J, Deeks SG, Landay A. Regulatory B Cells Inhibit Cytotoxic T Lymphocyte (CTL) Activity and Elimination of Infected CD4 T Cells after In Vitro Reactivation of HIV Latent Reservoirs. PLoS One. 2014; 9(4):e92934.
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      20. Stock PG, Barin B, Hatano H, Rogers RL, Roland ME, Lee TH, Busch M, Deeks SG. Reduction of HIV Persistence Following Transplantation in HIV-Infected Kidney Transplant Recipients. Am J Transplant. 2014 May; 14(5):1136-41.
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      21. Byakwaga H, Boum Y, Huang Y, Muzoora C, Kembabazi A, Weiser SD, Bennett J, Cao H, Haberer JE, Deeks SG, Bangsberg DR, McCune JM, Martin JN, Hunt PW. The Kynurenine Pathway of Tryptophan Catabolism, CD4+ T-Cell Recovery, and Mortality Among HIV-Infected Ugandans Initiating Antiretroviral Therapy. J Infect Dis. 2014 Apr 3.
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      22. Lee SA, Sinclair E, Jain V, Huang Y, Epling L, Van Natta M, Meinert CL, Martin JN, McCune JM, Deeks SG, Lederman MM, Hecht FM, Hunt PW. Low Proportions of CD28- CD8+ T cells Expressing CD57 Can Be Reversed by Early ART Initiation and Predict Mortality in Treated HIV Infection. J Infect Dis. 2014 Mar 21.
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      23. Bashirova AA, Martin-Gayo E, Jones DC, Qi Y, Apps R, Gao X, Burke PS, Taylor CJ, Rogich J, Wolinsky S, Bream JH, Duggal P, Hussain S, Martinson J, Weintrob A, Kirk GD, Fellay J, Buchbinder SP, Goedert JJ, Deeks SG, Pereyra F, Trowsdale J, Lichterfeld M, Telenti A, Walker BD, Allen RL, Carrington M, Yu XG. LILRB2 Interaction with HLA Class I Correlates with Control of HIV-1 Infection. PLoS Genet. 2014 Mar; 10(3):e1004196.
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      24. Lee SA, Sinclair E, Hatano H, Hsue PY, Epling L, Hecht FM, Bangsberg DR, Martin JN, McCune JM, Deeks SG, Hunt PW. Impact of HIV on CD8+ T Cell CD57 Expression Is Distinct from That of CMV and Aging. PLoS One. 2014; 9(2):e89444.
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      25. Parikh RV, Scherzer R, Nitta EM, Leone A, Hur S, Mistry V, Macgregor JS, Martin JN, Deeks SG, Ganz P, Hsue PY. Increased levels of asymmetric dimethylarginine are associated with pulmonary arterial hypertension in HIV infection. AIDS. 2014 Feb 20; 28(4):511-9.
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      26. Payne RP, Branch S, Kløverpris H, Matthews PC, Koofhethile CK, Strong T, Adland E, Leitman E, Frater J, Ndung'u T, Hunter E, Haubrich R, Mothe B, Edwards A, Riddell L, Chen F, Harrigan PR, Brumme ZL, Mallal S, John M, Jooste JP, Shapiro R, Deeks SG, Walker BD, Brander C, Landis C, Carlson JM, Prado JG, Goulder PJ. Differential Escape Patterns within the Dominant HLA-B*57:03-Restricted HIV Gag Epitope Reflect Distinct Clade-Specific Functional Constraints. J Virol. 2014 May; 88(9):4668-78.
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      27. Dunham RM, Vujkovic-Cvijin I, Yukl SA, Broadhurst MJ, Loke P, Albright RG, Wong JK, Lederman MM, Somsouk M, Hunt PW, Martin JN, Deeks SG, McCune JM. Discordance Between Peripheral and Colonic Markers of Inflammation During Suppressive ART. J Acquir Immune Defic Syndr. 2014 Feb 1; 65(2):133-41.
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      28. Yukl SA, Sinclair E, Somsouk M, Hunt PW, Epling L, Killian M, Girling V, Li P, Havlir DV, Deeks SG, Wong JK, Hatano H. A comparison of methods for measuring rectal HIV levels suggests that HIV DNA resides in cells other than CD4+ T cells, including myeloid cells. AIDS. 2014 Jan 28; 28(3):439-42.
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      29. Michaud HA, de Mulder M, Sengupta D, Deeks SG, Martin JN, Pilcher CD, Hecht FM, Sacha JB, Nixon DF. Trans-activation, post-transcriptional maturation, and induction of antibodies to HERV-K (HML-2) envelope transmembrane protein in HIV-1 infection. Retrovirology. 2014; 11(1):10.
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      30. Heredia A, Davis C, Amin MN, Le NM, Wainberg MA, Oliveira M, Deeks SG, Wang LX, Redfield RR. Targeting host nucleotide biosynthesis with resveratrol inhibits emtricitabine-resistant HIV-1. AIDS. 2014 Jan 28; 28(3):317-23.
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      31. Emu B, Moretto WJ, Hoh R, Krone M, Martin JN, Nixon DF, Deeks SG, McCune JM. Composition and Function of T Cell Subpopulations Are Slow to Change Despite Effective Antiretroviral Treatment of HIV Disease. PLoS One. 2014 Jan 21; 9(1):e85613.
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      32. Boufassa F, Lechenadec J, Meyer L, Costagliola D, Hunt PW, Pereyra F, Deeks S, Pancino G, Taulera O, Lichterfeld M, Delobel P, Saez-Cirion A, Lambotte O. Blunted Response to Combination Antiretroviral Therapy in HIV Elite Controllers: An International HIV Controller Collaboration. PLoS One. 2014 Jan 17; 9(1):e85516.
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      33. Hatano H, Bacchetti P, Hsue PY, Deeks SG. Reply to Karch et al. J Infect Dis. 2014 Jul 1; 210(1):159-60.
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      34. Seu L, Ortiz GM, Epling L, Sinclair E, Swainson LA, Bajpai UD, Huang Y, Deeks SG, Hunt PW, Martin JN, McCune JM. Higher CD27(+)CD8(+) T Cells Percentages during Suppressive Antiretroviral Therapy Predict Greater Subsequent CD4(+) T Cell Recovery in Treated HIV Infection. PLoS One. 2013; 8(12):e84091.
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      35. Milush JM, López-Vergès S, York VA, Deeks SG, Martin JN, Hecht FM, Lanier LL, Nixon DF. CD56negCD16+ NK cells are activated mature NK cells with impaired effector function during HIV-1 infection. Retrovirology. 2013; 10(1):158.
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      36. Spivak AM, Andrade A, Eisele E, Hoh R, Bacchetti P, Bumpus NN, Emad F, Buckheit R, McCance-Katz EF, Lai J, Kennedy M, Chander G, Siliciano RF, Siliciano JD, Deeks SG. A Pilot Study Assessing the Safety and Latency-Reversing Activity of Disulfiram in HIV-1-Infected Adults on Antiretroviral Therapy. Clin Infect Dis. 2014 Mar; 58(6):883-90.
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      37. Burbelo PD, Bayat A, Rhodes CS, Hoh R, Martin JN, Fromentin R, Chomont N, Hütter G, Kovacs JA, Deeks SG. HIV Antibody Characterization as a Method to Quantify Reservoir Size During Curative Interventions. J Infect Dis. 2014 May; 209(10):1613-7.
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      38. Josefsson L, von Stockenstrom S, Faria NR, Sinclair E, Bacchetti P, Killian M, Epling L, Tan A, Ho T, Lemey P, Shao W, Hunt PW, Somsouk M, Wylie W, Douek DC, Loeb L, Custer J, Hoh R, Poole L, Deeks SG, Hecht F, Palmer S. The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):E4987-96.
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      39. Kulkarni S, Qi Y, O'huigin C, Pereyra F, Ramsuran V, McLaren P, Fellay J, Nelson G, Chen H, Liao W, Bass S, Apps R, Gao X, Yuki Y, Lied A, Ganesan A, Hunt PW, Deeks SG, Wolinsky S, Walker BD, Carrington M. Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20705-10.
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      40. Asher AK, Santos GM, Evans J, Dokubo EK, Lee TH, Martin JN, Deeks SG, Tobler LH, Busch M, Hunt PW, Page K. Human leukocyte antigen B*57 does not fully explain hepatitis C clearance in HIV controllers. AIDS. 2013 Nov 13; 27(17):2691-6.
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      41. Picker LJ, Deeks SG. HIV: Antibodies advance the search for a cure. Nature. 2013 Nov 14; 503(7475):207-8.
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      42. Deeks SG, Lewin SR, Havlir DV. The end of AIDS: HIV infection as a chronic disease. Lancet. 2013 Nov 2; 382(9903):1525-33.
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      43. Abdel-Mohsen M, Deng X, Liegler T, Guatelli JC, Salama MS, Ghanem Hel-D, Rauch A, Ledergerber B, Deeks SG, Günthard HF, Wong JK, Pillai SK. Effects of Alpha Interferon Treatment on Intrinsic Anti-HIV-1 Immunity In Vivo. J Virol. 2014 Jan; 88(1):763-7.
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      44. Deeks SG, Tracy R, Douek DC. Systemic effects of inflammation on health during chronic HIV infection. Immunity. 2013 Oct 17; 39(4):633-45.
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      45. Abdel-Mohsen M, Raposo RA, Deng X, Li M, Liegler T, Sinclair E, Salama MS, Ghanem Hel-D, Hoh R, Wong JK, David M, Nixon DF, Deeks SG, Pillai SK. Expression profile of host restriction factors in HIV-1 elite controllers. Retrovirology. 2013; 10(1):106.
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      46. Hatano H, Yukl SA, Ferre AL, Graf EH, Somsouk M, Sinclair E, Abdel-Mohsen M, Liegler T, Harvill K, Hoh R, Palmer S, Bacchetti P, Hunt PW, Martin JN, McCune JM, Tracy RP, Busch MP, O'Doherty U, Shacklett BL, Wong JK, Deeks SG. Prospective antiretroviral treatment of asymptomatic, HIV-1 infected controllers. PLoS Pathog. 2013; 9(10):e1003691.
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      47. Hunt PW, Lederman MM, Deeks SG. Response: Maraviroc intensification and microbial translocation. Blood. 2013 Sep 26; 122(13):2283-4.
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      48. Gopal S, Patel MR, Yanik EL, Cole SR, Achenbach CJ, Napravnik S, Burkholder GA, Reid EG, Rodriguez B, Deeks SG, Mayer KH, Moore RD, Kitahata MM, Richards KL, Eron JJ. Association of early HIV viremia with mortality after HIV-associated lymphoma. AIDS. 2013 Sep 24; 27(15):2365-73.
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      49. Hatano H, Somsouk M, Sinclair E, Harvill K, Gilman L, Cohen M, Hoh R, Hunt PW, Martin JN, Wong JK, Deeks SG, Yukl SA. Comparison of HIV DNA and RNA in gut-associated lymphoid tissue of HIV-infected controllers and noncontrollers. AIDS. 2013 Sep 10; 27(14):2255-60.
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      50. Lok JJ, Hunt PW, Collier AC, Benson CA, Witt MD, Luque AE, Deeks SG, Bosch RJ. The impact of age on the prognostic capacity of CD8+ T-cell activation during suppressive antiretroviral therapy. AIDS. 2013 Aug 24; 27(13):2101-10.
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      51. Hatano H, Strain MC, Scherzer R, Bacchetti P, Wentworth D, Hoh R, Martin JN, McCune JM, Neaton JD, Tracy RP, Hsue PY, Richman DD, Deeks SG. Increase in 2-long terminal repeat circles and decrease in D-dimer after raltegravir intensification in patients with treated HIV infection: a randomized, placebo-controlled trial. J Infect Dis. 2013 Nov 1; 208(9):1436-42.
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      52. Graf EH, Pace MJ, Peterson BA, Lynch LJ, Chukwulebe SB, Mexas AM, Shaheen F, Martin JN, Deeks SG, Connors M, Migueles SA, O'Doherty U. Gag-positive reservoir cells are susceptible to HIV-specific cytotoxic T lymphocyte mediated clearance. PLoS One. 2013; 8(8):e71879.
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      53. Li L, Deng X, Linsuwanon P, Bangsberg D, Bwana MB, Hunt P, Martin JN, Deeks SG, Delwart E. AIDS alters the commensal plasma virome. J Virol. 2013 Oct; 87(19):10912-5.
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      54. Gopal S, Patel MR, Yanik EL, Cole SR, Achenbach CJ, Napravnik S, Burkholder GA, Reid EG, Rodriguez B, Deeks SG, Mayer KH, Moore RD, Kitahata MM, Eron JJ, Richards KL. Temporal trends in presentation and survival for HIV-associated lymphoma in the antiretroviral therapy era. J Natl Cancer Inst. 2013 Aug 21; 105(16):1221-9.
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      55. Patterson S, Moran P, Epel E, Sinclair E, Kemeny ME, Deeks SG, Bacchetti P, Acree M, Epling L, Kirschbaum C, Hecht FM. Cortisol patterns are associated with T cell activation in HIV. PLoS One. 2013; 8(7):e63429.
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      56. McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, Carrington M, Cossarizza A, Dalmau J, Deeks SG, Delaneau O, De Luca A, Goedert JJ, Haas D, Herbeck JT, Kathiresan S, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, O'Brien SJ, Pereyra F, Plummer FA, Poli G, Qi Y, Rucart P, Sandhu MS, Shea PR, Schuitemaker H, Theodorou I, Vannberg F, Veldink J, Walker BD, Weintrob A, Winkler CA, Wolinsky S, Telenti A, Goldstein DB, de Bakker PI, Zagury JF, Fellay J. Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS Pathog. 2013; 9(7):e1003515.
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      57. Unemori P, Leslie KS, Hunt PW, Sinclair E, Epling L, Mitsuyasu R, Effros RB, Dock J, Dollard SG, Deeks SG, Martin JN, Maurer TA. Immunosenescence is associated with presence of Kaposi's sarcoma in antiretroviral treated HIV infection. AIDS. 2013 Jul 17; 27(11):1735-42.
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      58. Jain V, Hartogensis W, Bacchetti P, Hunt PW, Hatano H, Sinclair E, Epling L, Lee TH, Busch MP, McCune JM, Pilcher CD, Hecht FM, Deeks SG. Antiretroviral therapy initiated within 6 months of HIV infection is associated with lower T-cell activation and smaller HIV reservoir size. J Infect Dis. 2013 Oct 15; 208(8):1202-11.
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      59. Yukl SA, Shergill AK, Ho T, Killian M, Girling V, Epling L, Li P, Wong LK, Crouch P, Deeks SG, Havlir DV, McQuaid K, Sinclair E, Wong JK. The distribution of HIV DNA and RNA in cell subsets differs in gut and blood of HIV-positive patients on ART: implications for viral persistence. J Infect Dis. 2013 Oct 15; 208(8):1212-20.
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      60. Vujkovic-Cvijin I, Dunham RM, Iwai S, Maher MC, Albright RG, Broadhurst MJ, Hernandez RD, Lederman MM, Huang Y, Somsouk M, Deeks SG, Hunt PW, Lynch SV, McCune JM. Dysbiosis of the gut microbiota is associated with hiv disease progression and tryptophan catabolism. Sci Transl Med. 2013 Jul 10; 5(193):193ra91.
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      61. Klatt NR, Chomont N, Douek DC, Deeks SG. Immune activation and HIV persistence: implications for curative approaches to HIV infection. Immunol Rev. 2013 Jul; 254(1):326-42.
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      62. Ranasinghe S, Cutler S, Davis I, Lu R, Soghoian DZ, Qi Y, Sidney J, Kranias G, Flanders MD, Lindqvist M, Kuhl B, Alter G, Deeks SG, Walker BD, Gao X, Sette A, Carrington M, Streeck H. Association of HLA-DRB1-restricted CD4? T cell responses with HIV immune control. Nat Med. 2013 Jul; 19(7):930-3.
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      63. Yukl SA, Boritz E, Busch M, Bentsen C, Chun TW, Douek D, Eisele E, Haase A, Ho YC, Hütter G, Justement JS, Keating S, Lee TH, Li P, Murray D, Palmer S, Pilcher C, Pillai S, Price RW, Rothenberger M, Schacker T, Siliciano J, Siliciano R, Sinclair E, Strain M, Wong J, Richman D, Deeks SG. Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient. PLoS Pathog. 2013; 9(5):e1003347.
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      64. Parikh RV, Scherzer R, Grunfeld C, Nitta EM, Leone A, Martin JN, Deeks SG, Ganz P, Hsue PY. Elevated levels of asymmetric dimethylarginine are associated with lower CD4+ count and higher viral load in HIV-infected individuals. Atherosclerosis. 2013 Jul; 229(1):246-52.
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      65. Hunt PW, Shulman NS, Hayes TL, Dahl V, Somsouk M, Funderburg NT, McLaughlin B, Landay AL, Adeyemi O, Gilman LE, Clagett B, Rodriguez B, Martin JN, Schacker TW, Shacklett BL, Palmer S, Lederman MM, Deeks SG. The immunologic effects of maraviroc intensification in treated HIV-infected individuals with incomplete CD4+ T-cell recovery: a randomized trial. Blood. 2013 Jun 6; 121(23):4635-46.
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      66. Apps R, Qi Y, Carlson JM, Chen H, Gao X, Thomas R, Yuki Y, Del Prete GQ, Goulder P, Brumme ZL, Brumme CJ, John M, Mallal S, Nelson G, Bosch R, Heckerman D, Stein JL, Soderberg KA, Moody MA, Denny TN, Zeng X, Fang J, Moffett A, Lifson JD, Goedert JJ, Buchbinder S, Kirk GD, Fellay J, McLaren P, Deeks SG, Pereyra F, Walker B, Michael NL, Weintrob A, Wolinsky S, Liao W, Carrington M. Influence of HLA-C expression level on HIV control. Science. 2013 Apr 5; 340(6128):87-91.
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      67. Katlama C, Deeks SG, Autran B, Martinez-Picado J, van Lunzen J, Rouzioux C, Miller M, Vella S, Schmitz JE, Ahlers J, Richman DD, Sekaly RP. Barriers to a cure for HIV: new ways to target and eradicate HIV-1 reservoirs. Lancet. 2013 Jun 15; 381(9883):2109-17.
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      68. Rodger AJ, Lodwick R, Schechter M, Deeks S, Amin J, Gilson R, Paredes R, Bakowska E, Engsig FN, Phillips A. Mortality in well controlled HIV in the continuous antiretroviral therapy arms of the SMART and ESPRIT trials compared with the general population. AIDS. 2013 Mar 27; 27(6):973-9.
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      69. Champiat S, Garrison KE, Raposo RA, Burwitz BJ, Reed J, Tandon R, York VA, Newman LP, Nimityongskul FA, Wilson NA, Almeida RR, Martin JN, Deeks SG, Rosenberg MG, Wiznia AA, Spotts GE, Pilcher CD, Hecht FM, Ostrowski MA, Sacha JB, Nixon DF. T cells target APOBEC3 proteins in human immunodeficiency virus type 1-infected humans and simian immunodeficiency virus-infected Indian rhesus macaques. J Virol. 2013 Jun; 87(11):6073-80.
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      70. Eriksson S, Graf EH, Dahl V, Strain MC, Yukl SA, Lysenko ES, Bosch RJ, Lai J, Chioma S, Emad F, Abdel-Mohsen M, Hoh R, Hecht F, Hunt P, Somsouk M, Wong J, Johnston R, Siliciano RF, Richman DD, O'Doherty U, Palmer S, Deeks SG, Siliciano JD. Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies. PLoS Pathog. 2013 Feb; 9(2):e1003174.
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      71. Justice AC, Modur SP, Tate JP, Althoff KN, Jacobson LP, Gebo KA, Kitahata MM, Horberg MA, Brooks JT, Buchacz K, Rourke SB, Rachlis A, Napravnik S, Eron J, Willig JH, Moore R, Kirk GD, Bosch R, Rodriguez B, Hogg RS, Thorne J, Goedert JJ, Klein M, Gill J, Deeks S, Sterling TR, Anastos K, Gange SJ. Predictive accuracy of the Veterans Aging Cohort Study index for mortality with HIV infection: a North American cross cohort analysis. J Acquir Immune Defic Syndr. 2013 Feb 1; 62(2):149-63.
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      72. Deeks S, Drosten C, Picker L, Subbarao K, Suzich J. Roadblocks to translational challenges on viral pathogenesis. Nat Med. 2013 Jan; 19(1):30-4.
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      73. Eriksson EM, Keh CE, Deeks SG, Martin JN, Hecht FM, Nixon DF. Differential expression of CD96 surface molecule represents CD8? T cells with dissimilar effector function during HIV-1 infection. PLoS One. 2012; 7(12):e51696.
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      74. Leeansyah E, Ganesh A, Quigley MF, Sönnerborg A, Andersson J, Hunt PW, Somsouk M, Deeks SG, Martin JN, Moll M, Shacklett BL, Sandberg JK. Activation, exhaustion, and persistent decline of the antimicrobial MR1-restricted MAIT-cell population in chronic HIV-1 infection. Blood. 2013 Feb 14; 121(7):1124-35.
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      75. Lauring AS, Lee TH, Martin JN, Hunt PW, Deeks SG, Busch M. Lack of evidence for mtDNA as a biomarker of innate immune activation in HIV infection. PLoS One. 2012; 7(11):e50486.
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      76. Hatano H, Scherzer R, Wu Y, Harvill K, Maka K, Hoh R, Sinclair E, Palmer S, Martin JN, Busch MP, Deeks SG, Hsue PY. A randomized controlled trial assessing the effects of raltegravir intensification on endothelial function in treated HIV infection. J Acquir Immune Defic Syndr. 2012 Nov 1; 61(3):317-25.
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      77. Underwood MR, Johns BA, Sato A, Martin JN, Deeks SG, Fujiwara T. The activity of the integrase inhibitor dolutegravir against HIV-1 variants isolated from raltegravir-treated adults. J Acquir Immune Defic Syndr. 2012 Nov 1; 61(3):297-301.
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      78. Azzoni L, Foulkes AS, Papasavvas E, Mexas AM, Lynn KM, Mounzer K, Tebas P, Jacobson JM, Frank I, Busch MP, Deeks SG, Carrington M, O'Doherty U, Kostman J, Montaner LJ. Pegylated Interferon alfa-2a monotherapy results in suppression of HIV type 1 replication and decreased cell-associated HIV DNA integration. J Infect Dis. 2013 Jan 15; 207(2):213-22.
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      79. Hatano H, Jain V, Hunt PW, Lee TH, Sinclair E, Do TD, Hoh R, Martin JN, McCune JM, Hecht F, Busch MP, Deeks SG. Cell-based measures of viral persistence are associated with immune activation and programmed cell death protein 1 (PD-1)-expressing CD4+ T cells. J Infect Dis. 2013 Jul; 208(1):50-6.
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      80. Shaw JM, Hunt PW, Critchfield JW, McConnell DH, Garcia JC, Pollard RB, Somsouk M, Deeks SG, Shacklett BL. Short communication: HIV+ viremic slow progressors maintain low regulatory T cell numbers in rectal mucosa but exhibit high T cell activation. AIDS Res Hum Retroviruses. 2013 Jan; 29(1):172-7.
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      81. Dunham RM, Gordon SN, Vaccari M, Piatak M, Huang Y, Deeks SG, Lifson J, Franchini G, McCune JM. Preclinical evaluation of HIV eradication strategies in the simian immunodeficiency virus-infected rhesus macaque: a pilot study testing inhibition of indoleamine 2,3-dioxygenase. AIDS Res Hum Retroviruses. 2013 Feb; 29(2):207-14.
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      82. Deeks SG, Gandhi RT, Chae CU, Lewandrowski KB. Case records of the Massachusetts General Hospital. Case 30-2012. A 54-year-old woman with HIV infection, dyspnea, and chest pain. N Engl J Med. 2012 Sep 27; 367(13):1246-54.
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      83. Lee GQ, Swenson LC, Poon AF, Martin JN, Hatano H, Deeks SG, Harrigan PR. Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing. PLoS One. 2012; 7(9):e46181.
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      84. Selby VN, Scherzer R, Barnett CF, MacGregor JS, Morelli J, Donovan C, Deeks SG, Martin JN, Hsue PY. Doppler echocardiography does not accurately estimate pulmonary artery systolic pressure in HIV-infected patients. AIDS. 2012 Sep 24; 26(15):1967-9.
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      85. Tomescu C, Duh FM, Hoh R, Viviani A, Harvill K, Martin MP, Carrington M, Deeks SG, Montaner LJ. Impact of protective killer inhibitory receptor/human leukocyte antigen genotypes on natural killer cell and T-cell function in HIV-1-infected controllers. AIDS. 2012 Sep 24; 26(15):1869-78.
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      86. Geng EH, Hare CB, Kahn JO, Jain V, Van Nunnery T, Christopoulos KA, Deeks SG, Gandhi M, Havlir DV. The effect of a "universal antiretroviral therapy" recommendation on HIV RNA levels among HIV-infected patients entering care with a CD4 count greater than 500/µL in a public health setting. Clin Infect Dis. 2012 Dec; 55(12):1690-7.
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      87. Deeks SG. HIV infection, lymphoid fibrosis, and disease. Blood. 2012 Aug 30; 120(9):1753-4.
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      88. Li JZ, Gallien S, Do TD, Martin JN, Deeks S, Kuritzkes DR, Hatano H. Prevalence and significance of HIV-1 drug resistance mutations among patients on antiretroviral therapy with detectable low-level viremia. Antimicrob Agents Chemother. 2012 Nov; 56(11):5998-6000.
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      89. Ormsby CE, Sengupta D, Tandon R, Deeks SG, Martin JN, Jones RB, Ostrowski MA, Garrison KE, Vázquez-Pérez JA, Reyes-Terán G, Nixon DF. Human endogenous retrovirus expression is inversely associated with chronic immune activation in HIV-1 infection. PLoS One. 2012; 7(8):e41021.
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      90. Lim H, Kane L, Schwartz JB, Hesdorffer CS, Deeks SG, Greig N, Ferrucci L, Goetzl EJ. Lenalidomide enhancement of human T cell functions in human immunodeficiency virus (HIV)-infected and HIV-negative CD4 T lymphocytopenic patients. Clin Exp Immunol. 2012 Aug; 169(2):182-9.
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      91. Deeks SG. HIV: Shock and kill. Nature. 2012 Jul 26; 487(7408):439-40.
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      93. Deeks SG, Barré-Sinoussi F. Public health: Towards a cure for HIV. Nature. 2012 Jul 19; 487(7407):293-4.
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      94. High KP, Brennan-Ing M, Clifford DB, Cohen MH, Currier J, Deeks SG, Deren S, Effros RB, Gebo K, Goronzy JJ, Justice AC, Landay A, Levin J, Miotti PG, Munk RJ, Nass H, Rinaldo CR, Shlipak MG, Tracy R, Valcour V, Vance DE, Walston JD, Volberding P. HIV and aging: state of knowledge and areas of critical need for research. A report to the NIH Office of AIDS Research by the HIV and Aging Working Group. J Acquir Immune Defic Syndr. 2012 Jul 1; 60 Suppl 1:S1-18.
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      95. Champiat S, Raposo RA, Maness NJ, Lehman JL, Purtell SE, Hasenkrug AM, Miller JC, Dean H, Koff WC, Hong MA, Martin JN, Deeks SG, Spotts GE, Pilcher CD, Hecht FM, Kallas EG, Garrison KE, Nixon DF. Influence of HAART on alternative reading frame immune responses over the course of HIV-1 infection. PLoS One. 2012; 7(6):e39311.
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      96. McLaren PJ, Ripke S, Pelak K, Weintrob AC, Patsopoulos NA, Jia X, Erlich RL, Lennon NJ, Kadie CM, Heckerman D, Gupta N, Haas DW, Deeks SG, Pereyra F, Walker BD, de Bakker PI. Fine-mapping classical HLA variation associated with durable host control of HIV-1 infection in African Americans. Hum Mol Genet. 2012 Oct 1; 21(19):4334-47.
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      97. Deeks SG, Verdin E, McCune JM. Immunosenescence and HIV. Curr Opin Immunol. 2012 Aug; 24(4):501-6.
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      98. Hsue PY, Deeks SG, Hunt PW. Immunologic basis of cardiovascular disease in HIV-infected adults. J Infect Dis. 2012 Jun; 205 Suppl 3:S375-82.
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      99. Ho JE, Scherzer R, Hecht FM, Maka K, Selby V, Martin JN, Ganz P, Deeks SG, Hsue PY. The association of CD4+ T-cell counts and cardiovascular risk in treated HIV disease. AIDS. 2012 Jun 1; 26(9):1115-20.
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      100. Scholler J, Brady TL, Binder-Scholl G, Hwang WT, Plesa G, Hege KM, Vogel AN, Kalos M, Riley JL, Deeks SG, Mitsuyasu RT, Bernstein WB, Aronson NE, Levine BL, Bushman FD, June CH. Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci Transl Med. 2012 May 2; 4(132):132ra53.
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      101. Hsue PY, Scherzer R, Hunt PW, Schnell A, Bolger AF, Kalapus SC, Maka K, Martin JN, Ganz P, Deeks SG. Carotid Intima-Media Thickness Progression in HIV-Infected Adults Occurs Preferentially at the Carotid Bifurcation and Is Predicted by Inflammation. J Am Heart Assoc. 2012 Apr; 1(2).
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      102. Scherzer R, Estrella M, Li Y, Choi AI, Deeks SG, Grunfeld C, Shlipak MG. Association of tenofovir exposure with kidney disease risk in HIV infection. AIDS. 2012 Apr 24; 26(7):867-75.
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      103. Armah KA, McGinnis K, Baker J, Gibert C, Butt AA, Bryant KJ, Goetz M, Tracy R, Oursler KK, Rimland D, Crothers K, Rodriguez-Barradas M, Crystal S, Gordon A, Kraemer K, Brown S, Gerschenson M, Leaf DA, Deeks SG, Rinaldo C, Kuller LH, Justice A, Freiberg M. HIV status, burden of comorbid disease, and biomarkers of inflammation, altered coagulation, and monocyte activation. Clin Infect Dis. 2012 Jul; 55(1):126-36.
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      104. Sacre K, Hunt PW, Hsue PY, Maidji E, Martin JN, Deeks SG, Autran B, McCune JM. A role for cytomegalovirus-specific CD4+CX3CR1+ T cells and cytomegalovirus-induced T-cell immunopathology in HIV-associated atherosclerosis. AIDS. 2012 Apr 24; 26(7):805-14.
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      105. Parrinello CM, Sinclair E, Landay AL, Lurain N, Sharrett AR, Gange SJ, Xue X, Hunt PW, Deeks SG, Hodis HN, Kaplan RC. Cytomegalovirus immunoglobulin G antibody is associated with subclinical carotid artery disease among HIV-infected women. J Infect Dis. 2012 Jun 15; 205(12):1788-96.
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      106. Hsue PY, Scherzer R, Grunfeld C, Nordstrom SM, Schnell A, Kohl LP, Nitta E, Martin JN, Deeks SG, Weiss EJ. HIV infection is associated with decreased thrombin generation. Clin Infect Dis. 2012 Apr; 54(8):1196-203.
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      107. Tassiopoulos K, Landay A, Collier AC, Connick E, Deeks SG, Hunt P, Lewis DE, Wilson C, Bosch R. CD28-negative CD4+ and CD8+ T cells in antiretroviral therapy-naive HIV-infected adults enrolled in adult clinical trials group studies. J Infect Dis. 2012 Jun; 205(11):1730-8.
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      108. Baum PD, Young JJ, Schmidt D, Zhang Q, Hoh R, Busch M, Martin J, Deeks S, McCune JM. Blood T-cell receptor diversity decreases during the course of HIV infection, but the potential for a diverse repertoire persists. Blood. 2012 Apr 12; 119(15):3469-77.
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      109. Chen H, Hayashi G, Lai OY, Dilthey A, Kuebler PJ, Wong TV, Martin MP, Fernandez Vina MA, McVean G, Wabl M, Leslie KS, Maurer T, Martin JN, Deeks SG, Carrington M, Bowcock AM, Nixon DF, Liao W. Psoriasis patients are enriched for genetic variants that protect against HIV-1 disease. PLoS Genet. 2012 Feb; 8(2):e1002514.
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      110. Justice AC, Freiberg MS, Tracy R, Kuller L, Tate JP, Goetz MB, Fiellin DA, Vanasse GJ, Butt AA, Rodriguez-Barradas MC, Gibert C, Oursler KA, Deeks SG, Bryant K. Does an index composed of clinical data reflect effects of inflammation, coagulation, and monocyte activation on mortality among those aging with HIV? Clin Infect Dis. 2012 Apr; 54(7):984-94.
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      111. Kiem HP, Jerome KR, Deeks SG, McCune JM. Hematopoietic-stem-cell-based gene therapy for HIV disease. Cell Stem Cell. 2012 Feb 3; 10(2):137-47.
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      112. Gandhi RT, Deeks SG. Plasma HIV-1 RNA levels during antiretroviral therapy: how low is low enough? Clin Infect Dis. 2012 Mar 1; 54(5):733-5.
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      113. Papasavvas E, Hsue P, Reynolds G, Pistilli M, Hancock A, Martin JN, Deeks SG, Montaner LJ. Increased CD34+/KDR+ cells are not associated with carotid artery intima-media thickness progression in chronic HIV-positive subjects. Antivir Ther. 2012; 17(3):557-63.
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      114. Deepe RN, Kistner-Griffin E, Martin JN, Deeks SG, Pandey JP. Epistatic interactions between Fc (GM) and Fc?R genes and the host control of human immunodeficiency virus replication. Hum Immunol. 2012 Mar; 73(3):263-6.
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      115. Hsue PY, Ordovas K, Lee T, Reddy G, Gotway M, Schnell A, Ho JE, Selby V, Madden E, Martin JN, Deeks SG, Ganz P, Waters DD. Carotid intima-media thickness among human immunodeficiency virus-infected patients without coronary calcium. Am J Cardiol. 2012 Mar 1; 109(5):742-7.
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      116. Eriksson EM, Milush JM, Ho EL, Batista MD, Holditch SJ, Keh CE, Norris PJ, Keating SM, Deeks SG, Hunt PW, Martin JN, Rosenberg MG, Hecht FM, Nixon DF. Expansion of CD8+ T cells lacking Sema4D/CD100 during HIV-1 infection identifies a subset of T cells with decreased functional capacity. Blood. 2012 Jan 19; 119(3):745-55.
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      117. Hunt PW, Cao HL, Muzoora C, Ssewanyana I, Bennett J, Emenyonu N, Kembabazi A, Neilands TB, Bangsberg DR, Deeks SG, Martin JN. Impact of CD8+ T-cell activation on CD4+ T-cell recovery and mortality in HIV-infected Ugandans initiating antiretroviral therapy. AIDS. 2011 Nov 13; 25(17):2123-31.
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      118. Seu L, Burt TD, Witte JS, Martin JN, Deeks SG, McCune JM. Variations in the heme oxygenase-1 microsatellite polymorphism are associated with plasma CD14 and viral load in HIV-infected African-Americans. Genes Immun. 2012 Apr; 13(3):258-67.
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      119. Sips M, Sciaranghella G, Diefenbach T, Dugast AS, Berger CT, Liu Q, Kwon D, Ghebremichael M, Estes JD, Carrington M, Martin JN, Deeks SG, Hunt PW, Alter G. Altered distribution of mucosal NK cells during HIV infection. Mucosal Immunol. 2012 Jan; 5(1):30-40.
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      120. Geng EH, Kahn JS, Chang OC, Hare CB, Christopoulos KA, Jones D, Petersen ML, Deeks SG, Havlir DV, Gandhi M. The effect of AIDS Clinical Trials Group Protocol 5164 on the time from Pneumocystis jirovecii pneumonia diagnosis to antiretroviral initiation in routine clinical practice: a case study of diffusion, dissemination, and implementation. Clin Infect Dis. 2011 Nov; 53(10):1008-14.
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      121. Plaeger SF, Collins BS, Musib R, Deeks SG, Read S, Embry A. Immune activation in the pathogenesis of treated chronic HIV disease: a workshop summary. AIDS Res Hum Retroviruses. 2012 May; 28(5):469-77.
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      122. Appay V, Fastenackels S, Katlama C, Ait-Mohand H, Schneider L, Guihot A, Keller M, Grubeck-Loebenstein B, Simon A, Lambotte O, Hunt PW, Deeks SG, Costagliola D, Autran B, Sauce D. Old age and anti-cytomegalovirus immunity are associated with altered T-cell reconstitution in HIV-1-infected patients. AIDS. 2011 Sep 24; 25(15):1813-22.
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      123. Rajasuriar R, Booth DR, Gouillou M, Spelman T, James I, Solomon A, Chua K, Stewart G, Deeks S, Bangsberg DR, Muzoora C, Cameron PU, Hunt P, Martin J, Lewin SR. The role of SNPs in the a-chain of the IL-7R gene in CD4+ T-cell recovery in HIV-infected African patients receiving suppressive cART. Genes Immun. 2012 Jan; 13(1):83-93.
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      124. Sterling TR, Lau B, Zhang J, Freeman A, Bosch RJ, Brooks JT, Deeks SG, French A, Gange S, Gebo KA, John Gill M, Horberg MA, Jacobson LP, Kirk GD, Kitahata MM, Klein MB, Martin JN, Rodriguez B, Silverberg MJ, Willig JH, Eron JJ, Goedert JJ, Hogg RS, Justice AC, McKaig RG, Napravnik S, Thorne J, Moore RD. Risk factors for tuberculosis after highly active antiretroviral therapy initiation in the United States and Canada: implications for tuberculosis screening. J Infect Dis. 2011 Sep 15; 204(6):893-901.
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      125. Mugavero MJ, Napravnik S, Cole SR, Eron JJ, Lau B, Crane HM, Kitahata MM, Willig JH, Moore RD, Deeks SG, Saag MS. Viremia copy-years predicts mortality among treatment-naive HIV-infected patients initiating antiretroviral therapy. Clin Infect Dis. 2011 Nov; 53(9):927-35.
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      126. Deeks SG. HIV: How to escape treatment. Nature. 2011 Sep 1; 477(7362):36-7.
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      127. Shaw JM, Hunt PW, Critchfield JW, McConnell DH, Garcia JC, Pollard RB, Somsouk M, Deeks SG, Shacklett BL. Increased frequency of regulatory T cells accompanies increased immune activation in rectal mucosae of HIV-positive noncontrollers. J Virol. 2011 Nov; 85(21):11422-34.
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      128. Abraham AG, Lau B, Deeks S, Moore RD, Zhang J, Eron J, Harrigan R, Gill MJ, Kitahata M, Klein M, Napravnik S, Rachlis A, Rodriguez B, Rourke S, Benson C, Bosch R, Collier A, Gebo K, Goedert J, Hogg R, Horberg M, Jacobson L, Justice A, Kirk G, Martin J, McKaig R, Silverberg M, Sterling T, Thorne J, Willig J, Gange SJ. Missing data on the estimation of the prevalence of accumulated human immunodeficiency virus drug resistance in patients treated with antiretroviral drugs in north america. Am J Epidemiol. 2011 Sep 15; 174(6):727-35.
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      129. Dias PT, Hahn JA, Delwart E, Edlin B, Martin J, Lum P, Evans J, Kral A, Deeks S, Busch MP, Page K. Temporal changes in HCV genotype distribution in three different high risk populations in San Francisco, California. BMC Infect Dis. 2011; 11:208.
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      130. Geng EH, Glidden DV, Bwana MB, Musinguzi N, Emenyonu N, Muyindike W, Christopoulos KA, Neilands TB, Yiannoutsos CT, Deeks SG, Bangsberg DR, Martin JN. Retention in care and connection to care among HIV-infected patients on antiretroviral therapy in Africa: estimation via a sampling-based approach. PLoS One. 2011; 6(7):e21797.
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      131. Perelson AS, Deeks SG. Drug effectiveness explained: the mathematics of antiviral agents for HIV. Sci Transl Med. 2011 Jul 13; 3(91):91ps30.
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      132. Sandler NG, Koh C, Roque A, Eccleston JL, Siegel RB, Demino M, Kleiner DE, Deeks SG, Liang TJ, Heller T, Douek DC. Host response to translocated microbial products predicts outcomes of patients with HBV or HCV infection. Gastroenterology. 2011 Oct; 141(4):1220-30, 1230.e1-3.
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      133. Kitchen CM, Yeghiazarian L, Hoh R, McCune JM, Sinclair E, Martin JN, Deeks SG. Immune activation, CD4+ T cell counts, and viremia exhibit oscillatory patterns over time in patients with highly resistant HIV infection. PLoS One. 2011; 6(6):e21190.
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      134. Choi AI, Vittinghoff E, Deeks SG, Weekley CC, Li Y, Shlipak MG. Cardiovascular risks associated with abacavir and tenofovir exposure in HIV-infected persons. AIDS. 2011 Jun 19; 25(10):1289-98.
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      135. Bacchetti P, Deeks SG, McCune JM. Breaking free of sample size dogma to perform innovative translational research. Sci Transl Med. 2011 Jun 15; 3(87):87ps24.
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      136. Jha AR, Nixon DF, Rosenberg MG, Martin JN, Deeks SG, Hudson RR, Garrison KE, Pillai SK. Human endogenous retrovirus K106 (HERV-K106) was infectious after the emergence of anatomically modern humans. PLoS One. 2011; 6(5):e20234.
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      137. Hunt PW, Martin JN, Sinclair E, Epling L, Teague J, Jacobson MA, Tracy RP, Corey L, Deeks SG. Valganciclovir reduces T cell activation in HIV-infected individuals with incomplete CD4+ T cell recovery on antiretroviral therapy. J Infect Dis. 2011 May 15; 203(10):1474-83.
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      138. SenGupta D, Tandon R, Vieira RG, Ndhlovu LC, Lown-Hecht R, Ormsby CE, Loh L, Jones RB, Garrison KE, Martin JN, York VA, Spotts G, Reyes-Terán G, Ostrowski MA, Hecht FM, Deeks SG, Nixon DF. Strong human endogenous retrovirus-specific T cell responses are associated with control of HIV-1 in chronic infection. J Virol. 2011 Jul; 85(14):6977-85.
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      139. Yukl SA, Li P, Fujimoto K, Lampiris H, Lu CM, Hare CB, Deeks SG, Liegler T, Pandori M, Havlir DV, Wong JK. Modification of the Abbott RealTime assay for detection of HIV-1 plasma RNA viral loads less than one copy per milliliter. J Virol Methods. 2011 Aug; 175(2):261-5.
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      140. Kulkarni S, Savan R, Qi Y, Gao X, Yuki Y, Bass SE, Martin MP, Hunt P, Deeks SG, Telenti A, Pereyra F, Goldstein D, Wolinsky S, Walker B, Young HA, Carrington M. Differential microRNA regulation of HLA-C expression and its association with HIV control. Nature. 2011 Apr 28; 472(7344):495-8.
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      141. Jain V, Sucupira MC, Bacchetti P, Hartogensis W, Diaz RS, Kallas EG, Janini LM, Liegler T, Pilcher CD, Grant RM, Cortes R, Deeks SG, Hecht FM. Differential persistence of transmitted HIV-1 drug resistance mutation classes. J Infect Dis. 2011 Apr 15; 203(8):1174-81.
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      142. Hatano H, Hayes TL, Dahl V, Sinclair E, Lee TH, Hoh R, Lampiris H, Hunt PW, Palmer S, McCune JM, Martin JN, Busch MP, Shacklett BL, Deeks SG. A randomized, controlled trial of raltegravir intensification in antiretroviral-treated, HIV-infected patients with a suboptimal CD4+ T cell response. J Infect Dis. 2011 Apr 1; 203(7):960-8.
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      143. Sauce D, Larsen M, Fastenackels S, Pauchard M, Ait-Mohand H, Schneider L, Guihot A, Boufassa F, Zaunders J, Iguertsira M, Bailey M, Gorochov G, Duvivier C, Carcelain G, Kelleher AD, Simon A, Meyer L, Costagliola D, Deeks SG, Lambotte O, Autran B, Hunt PW, Katlama C, Appay V. HIV disease progression despite suppression of viral replication is associated with exhaustion of lymphopoiesis. Blood. 2011 May 12; 117(19):5142-51.
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      144. Kaplan RC, Sinclair E, Landay AL, Lurain N, Sharrett AR, Gange SJ, Xue X, Parrinello CM, Hunt P, Deeks SG, Hodis HN. T cell activation predicts carotid artery stiffness among HIV-infected women. Atherosclerosis. 2011 Jul; 217(1):207-13.
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      145. Duprez DA, Neuhaus J, Tracy R, Kuller LH, Deeks SG, Orkin C, Stoehr A, Woolley IJ, Neaton JD. N-terminal-proB-type natriuretic peptide predicts cardiovascular disease events in HIV-infected patients. AIDS. 2011 Mar 13; 25(5):651-7.
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      146. Hersperger AR, Martin JN, Shin LY, Sheth PM, Kovacs CM, Cosma GL, Makedonas G, Pereyra F, Walker BD, Kaul R, Deeks SG, Betts MR. Increased HIV-specific CD8+ T-cell cytotoxic potential in HIV elite controllers is associated with T-bet expression. Blood. 2011 Apr 7; 117(14):3799-808.
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      147. Hunt PW, Landay AL, Sinclair E, Martinson JA, Hatano H, Emu B, Norris PJ, Busch MP, Martin JN, Brooks C, McCune JM, Deeks SG. A low T regulatory cell response may contribute to both viral control and generalized immune activation in HIV controllers. PLoS One. 2011; 6(1):e15924.
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      148. Choi AI, Lo JC, Mulligan K, Schnell A, Kalapus SC, Li Y, Hunt PW, Martin JN, Deeks SG, Hsue PY. Association of vitamin D insufficiency with carotid intima-media thickness in HIV-infected persons. Clin Infect Dis. 2011 Apr 1; 52(7):941-4.
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      149. Sandler NG, Wand H, Roque A, Law M, Nason MC, Nixon DE, Pedersen C, Ruxrungtham K, Lewin SR, Emery S, Neaton JD, Brenchley JM, Deeks SG, Sereti I, Douek DC. Plasma levels of soluble CD14 independently predict mortality in HIV infection. J Infect Dis. 2011 Mar 15; 203(6):780-90.
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      150. Corrah TW, Goonetilleke N, Kopycinski J, Deeks SG, Cohen MS, Borrow P, McMichael A, Brackenridge S. Reappraisal of the relationship between the HIV-1-protective single-nucleotide polymorphism 35 kilobases upstream of the HLA-C gene and surface HLA-C expression. J Virol. 2011 Apr; 85(7):3367-74.
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      151. Hunt PW, Hatano H, Sinclair E, Lee TH, Busch MP, Martin JN, McCune JM, Deeks SG. HIV-specific CD4+ T cells may contribute to viral persistence in HIV controllers. Clin Infect Dis. 2011 Mar 1; 52(5):681-7.
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      152. Kaplan RC, Sinclair E, Landay AL, Lurain N, Sharrett AR, Gange SJ, Xue X, Hunt P, Karim R, Kern DM, Hodis HN, Deeks SG. T cell activation and senescence predict subclinical carotid artery disease in HIV-infected women. J Infect Dis. 2011 Feb 15; 203(4):452-63.
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      153. Favre D, Stoddart CA, Emu B, Hoh R, Martin JN, Hecht FM, Deeks SG, McCune JM. HIV disease progression correlates with the generation of dysfunctional naive CD8(low) T cells. Blood. 2011 Feb 17; 117(7):2189-99.
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      154. Deeks SG. HIV infection, inflammation, immunosenescence, and aging. Annu Rev Med. 2011; 62:141-55.
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      155. Althoff KN, Gebo KA, Gange SJ, Klein MB, Brooks JT, Hogg RS, Bosch RJ, Horberg MA, Saag MS, Kitahata MM, Eron JJ, Napravnik S, Rourke SB, Gill MJ, Rodriguez B, Sterling TR, Deeks SG, Martin JN, Jacobson LP, Kirk GD, Collier AC, Benson CA, Silverberg MJ, Goedert JJ, McKaig RG, Thorne J, Rachlis A, Moore RD, Justice AC. CD4 count at presentation for HIV care in the United States and Canada: are those over 50 years more likely to have a delayed presentation? AIDS Res Ther. 2010; 7:45.
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      156. Jain V, Liegler T, Vittinghoff E, Hartogensis W, Bacchetti P, Poole L, Loeb L, Pilcher CD, Grant RM, Deeks SG, Hecht FM. Transmitted drug resistance in persons with acute/early HIV-1 in San Francisco, 2002-2009. PLoS One. 2010; 5(12):e15510.
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      157. Lima VD, Bangsberg DR, Harrigan PR, Deeks SG, Yip B, Hogg RS, Montaner JS. Risk of viral failure declines with duration of suppression on highly active antiretroviral therapy irrespective of adherence level. J Acquir Immune Defic Syndr. 2010 Dec; 55(4):460-5.
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      158. Bangsberg DR, Ragland K, Monk A, Deeks SG. A single tablet regimen is associated with higher adherence and viral suppression than multiple tablet regimens in HIV+ homeless and marginally housed people. AIDS. 2010 Nov 27; 24(18):2835-40.
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      159. Vaidya NK, Rong L, Marconi VC, Kuritzkes DR, Deeks SG, Perelson AS. Treatment-mediated alterations in HIV fitness preserve CD4+ T cell counts but have minimal effects on viral load. PLoS Comput Biol. 2010; 6(11):e1001012.
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      160. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science. 2010 Dec 10; 330(6010):1551-7.
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      161. Lundgren JD, Baxter J, Deeks SG, Lane HC. Biomarkers in HIV disease. Curr Opin HIV AIDS. 2010 Nov; 5(6):459-62.
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      162. Hatano H, Delwart EL, Norris PJ, Lee TH, Neilands TB, Kelley CF, Hunt PW, Hoh R, Linnen JM, Martin JN, Busch MP, Deeks SG. Evidence of persistent low-level viremia in long-term HAART-suppressed, HIV-infected individuals. AIDS. 2010 Oct 23; 24(16):2535-9.
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      163. Althoff KN, Justice AC, Gange SJ, Deeks SG, Saag MS, Silverberg MJ, Gill MJ, Lau B, Napravnik S, Tedaldi E, Klein MB, Gebo KA. Virologic and immunologic response to HAART, by age and regimen class. AIDS. 2010 Oct 23; 24(16):2469-79.
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      164. Ferre AL, Hunt PW, McConnell DH, Morris MM, Garcia JC, Pollard RB, Yee HF, Martin JN, Deeks SG, Shacklett BL. HIV controllers with HLA-DRB1*13 and HLA-DQB1*06 alleles have strong, polyfunctional mucosal CD4+ T-cell responses. J Virol. 2010 Nov; 84(21):11020-9.
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      165. Cummins NW, Jiang W, McGinty J, Bren GD, Bosch RJ, Landay A, Deeks SG, Martin JN, Douek D, Lederman MM, Brenchley J, Badley AD. Intracellular Casp8p41 content is inversely associated with CD4 T cell count. J Infect Dis. 2010 Aug 15; 202(3):386-91.
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      166. Tilton JC, Wilen CB, Didigu CA, Sinha R, Harrison JE, Agrawal-Gamse C, Henning EA, Bushman FD, Martin JN, Deeks SG, Doms RW. A maraviroc-resistant HIV-1 with narrow cross-resistance to other CCR5 antagonists depends on both N-terminal and extracellular loop domains of drug-bound CCR5. J Virol. 2010 Oct; 84(20):10863-76.
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      167. Deeks SG, McCune JM. Can HIV be cured with stem cell therapy? Nat Biotechnol. 2010 Aug; 28(8):807-10.
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      168. Hatano H, Lampiris H, Fransen S, Gupta S, Huang W, Hoh R, Martin JN, Lalezari J, Bangsberg D, Petropoulos C, Deeks SG. Evolution of integrase resistance during failure of integrase inhibitor-based antiretroviral therapy. J Acquir Immune Defic Syndr. 2010 Aug; 54(4):389-93.
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      169. Ho JE, Deeks SG, Hecht FM, Xie Y, Schnell A, Martin JN, Ganz P, Hsue PY. Initiation of antiretroviral therapy at higher nadir CD4+ T-cell counts is associated with reduced arterial stiffness in HIV-infected individuals. AIDS. 2010 Jul 31; 24(12):1897-905.
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      170. Ferre AL, Lemongello D, Hunt PW, Morris MM, Garcia JC, Pollard RB, Yee HF, Martin JN, Deeks SG, Shacklett BL. Immunodominant HIV-specific CD8+ T-cell responses are common to blood and gastrointestinal mucosa, and Gag-specific responses dominate in rectal mucosa of HIV controllers. J Virol. 2010 Oct; 84(19):10354-65.
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      171. Saag M, Deeks SG. How do HIV elite controllers do what they do? Clin Infect Dis. 2010 Jul 15; 51(2):239-41.
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      172. Volberding PA, Deeks SG. Antiretroviral therapy and management of HIV infection. Lancet. 2010 Jul 3; 376(9734):49-62.
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      173. Althoff KN, Gange SJ, Klein MB, Brooks JT, Hogg RS, Bosch RJ, Horberg MA, Saag MS, Kitahata MM, Justice AC, Gebo KA, Eron JJ, Rourke SB, Gill MJ, Rodriguez B, Sterling TR, Calzavara LM, Deeks SG, Martin JN, Rachlis AR, Napravnik S, Jacobson LP, Kirk GD, Collier AC, Benson CA, Silverberg MJ, Kushel M, Goedert JJ, McKaig RG, Van Rompaey SE, Zhang J, Moore RD. Late presentation for human immunodeficiency virus care in the United States and Canada. Clin Infect Dis. 2010 Jun 1; 50(11):1512-20.
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      174. Geng EH, Glidden DV, Emenyonu N, Musinguzi N, Bwana MB, Neilands TB, Muyindike W, Yiannoutsos CT, Deeks SG, Bangsberg DR, Martin JN. Tracking a sample of patients lost to follow-up has a major impact on understanding determinants of survival in HIV-infected patients on antiretroviral therapy in Africa. Trop Med Int Health. 2010 Jun; 15 Suppl 1:63-9.
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      175. Favre D, Mold J, Hunt PW, Kanwar B, Loke P, Seu L, Barbour JD, Lowe MM, Jayawardene A, Aweeka F, Huang Y, Douek DC, Brenchley JM, Martin JN, Hecht FM, Deeks SG, McCune JM. Tryptophan catabolism by indoleamine 2,3-dioxygenase 1 alters the balance of TH17 to regulatory T cells in HIV disease. Sci Transl Med. 2010 May 19; 2(32):32ra36.
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      176. Owen RE, Heitman JW, Hirschkorn DF, Lanteri MC, Biswas HH, Martin JN, Krone MR, Deeks SG, Norris PJ. HIV+ elite controllers have low HIV-specific T-cell activation yet maintain strong, polyfunctional T-cell responses. AIDS. 2010 May 15; 24(8):1095-105.
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      177. Kosmrlj A, Read EL, Qi Y, Allen TM, Altfeld M, Deeks SG, Pereyra F, Carrington M, Walker BD, Chakraborty AK. Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature. 2010 May 20; 465(7296):350-4.
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      178. Jain V, Deeks SG. When to start antiretroviral therapy. Curr HIV/AIDS Rep. 2010 May; 7(2):60-8.
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      179. Hecht FM, Hartogensis W, Bragg L, Bacchetti P, Atchison R, Grant R, Barbour J, Deeks SG. HIV RNA level in early infection is predicted by viral load in the transmission source. AIDS. 2010 Apr 24; 24(7):941-5.
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      180. Probasco JC, Deeks SG, Lee E, Hoh R, Hunt PW, Liegler T, Price RW, Spudich SS. Cerebrospinal fluid in HIV-1 systemic viral controllers: absence of HIV-1 RNA and intrathecal inflammation. AIDS. 2010 Apr 24; 24(7):1001-5.
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      181. Geng EH, Bangsberg DR, Musinguzi N, Emenyonu N, Bwana MB, Yiannoutsos CT, Glidden DV, Deeks SG, Martin JN. Understanding reasons for and outcomes of patients lost to follow-up in antiretroviral therapy programs in Africa through a sampling-based approach. J Acquir Immune Defic Syndr. 2010 Mar; 53(3):405-11.
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      182. Loke P, Favre D, Hunt PW, Leung JM, Kanwar B, Martin JN, Deeks SG, McCune JM. Correlating cellular and molecular signatures of mucosal immunity that distinguish HIV controllers from noncontrollers. Blood. 2010 Apr 15; 115(15):e20-32.
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      183. Naeger DM, Martin JN, Sinclair E, Hunt PW, Bangsberg DR, Hecht F, Hsue P, McCune JM, Deeks SG. Cytomegalovirus-specific T cells persist at very high levels during long-term antiretroviral treatment of HIV disease. PLoS One. 2010; 5(1):e8886.
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      184. Choi AI, Li Y, Deeks SG, Grunfeld C, Volberding PA, Shlipak MG. Association between kidney function and albuminuria with cardiovascular events in HIV-infected persons. Circulation. 2010 Feb 9; 121(5):651-8.
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      185. Bangsberg DR, Deeks SG. Spending more to save more: interventions to promote adherence. Ann Intern Med. 2010 Jan 5; 152(1):54-6; W-13.
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      186. Thomas R, Apps R, Qi Y, Gao X, Male V, O'hUigin C, O'Connor G, Ge D, Fellay J, Martin JN, Margolick J, Goedert JJ, Buchbinder S, Kirk GD, Martin MP, Telenti A, Deeks SG, Walker BD, Goldstein D, McVicar DW, Moffett A, Carrington M. HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C. Nat Genet. 2009 Dec; 41(12):1290-4.
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      187. Hsue PY, Hunt PW, Ho JE, Farah HH, Schnell A, Hoh R, Martin JN, Deeks SG, Bolger AF. Impact of HIV infection on diastolic function and left ventricular mass. Circ Heart Fail. 2010 Jan; 3(1):132-9.
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      188. Deeks SG, Gange SJ, Kitahata MM, Saag MS, Justice AC, Hogg RS, Eron JJ, Brooks JT, Rourke SB, Gill MJ, Bosch RJ, Benson CA, Collier AC, Martin JN, Klein MB, Jacobson LP, Rodriguez B, Sterling TR, Kirk GD, Napravnik S, Rachlis AR, Calzavara LM, Horberg MA, Silverberg MJ, Gebo KA, Kushel MB, Goedert JJ, McKaig RG, Moore RD. Trends in multidrug treatment failure and subsequent mortality among antiretroviral therapy-experienced patients with HIV infection in North America. Clin Infect Dis. 2009 Nov 15; 49(10):1582-90.
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      189. Choi AI, Shlipak MG, Hunt PW, Martin JN, Deeks SG. HIV-infected persons continue to lose kidney function despite successful antiretroviral therapy. AIDS. 2009 Oct 23; 23(16):2143-9.
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      190. Rosenblum M, Deeks SG, van der Laan M, Bangsberg DR. The risk of virologic failure decreases with duration of HIV suppression, at greater than 50% adherence to antiretroviral therapy. PLoS One. 2009; 4(9):e7196.
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      191. Hsue PY, Hunt PW, Wu Y, Schnell A, Ho JE, Hatano H, Xie Y, Martin JN, Ganz P, Deeks SG. Association of abacavir and impaired endothelial function in treated and suppressed HIV-infected patients. AIDS. 2009 Sep 24; 23(15):2021-7.
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      192. Snyder-Cappione JE, Loo CP, Carvalho KI, Kuylenstierna C, Deeks SG, Hecht FM, Rosenberg MG, Sandberg JK, Kallas EG, Nixon DF. Lower cytokine secretion ex vivo by natural killer T cells in HIV-infected individuals is associated with higher CD161 expression. AIDS. 2009 Sep 24; 23(15):1965-70.
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      193. Gress RE, Deeks SG. Reduced thymus activity and infection prematurely age the immune system. J Clin Invest. 2009 Oct; 119(10):2884-7.
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      194. Deeks SG. Immune dysfunction, inflammation, and accelerated aging in patients on antiretroviral therapy. Top HIV Med. 2009 Sep-Oct; 17(4):118-23.
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      195. Jha AR, Pillai SK, York VA, Sharp ER, Storm EC, Wachter DJ, Martin JN, Deeks SG, Rosenberg MG, Nixon DF, Garrison KE. Cross-sectional dating of novel haplotypes of HERV-K 113 and HERV-K 115 indicate these proviruses originated in Africa before Homo sapiens. Mol Biol Evol. 2009 Nov; 26(11):2617-26.
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      196. Huang W, Toma J, Stawiski E, Fransen S, Wrin T, Parkin N, Whitcomb JM, Coakley E, Hecht FM, Deeks SG, Gandhi RT, Eshleman SH, Petropoulos CJ. Characterization of human immunodeficiency virus type 1 populations containing CXCR4-using variants from recently infected individuals. AIDS Res Hum Retroviruses. 2009 Aug; 25(8):795-802.
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      197. Garrison KE, Champiat S, York VA, Agrawal AT, Kallas EG, Martin JN, Hecht FM, Deeks SG, Nixon DF. Transcriptional errors in human immunodeficiency virus type 1 generate targets for T-cell responses. Clin Vaccine Immunol. 2009 Sep; 16(9):1369-71.
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      198. Murphy RL, Autran B, Katlama C, Brucker G, Debre P, Calvez V, Clotet B, Clumeck N, Costagliola D, Deeks SG, Dorrell L, Gatell J, Haase A, Klein M, Lazzarin A, McMichael AJ, Papagno L, Schacker TW, Wain-Hobson S, Walker BD, Youle M. A step ahead on the HIV collaboratory. Science. 2009 Jun 5; 324(5932):1264-5.
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      199. Hsue PY, Hunt PW, Schnell A, Kalapus SC, Hoh R, Ganz P, Martin JN, Deeks SG. Role of viral replication, antiretroviral therapy, and immunodeficiency in HIV-associated atherosclerosis. AIDS. 2009 Jun 1; 23(9):1059-67.
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      200. Jacobson MA, Ditmer DP, Sinclair E, Martin JN, Deeks SG, Hunt P, Mocarski ES, Shiboski C. Human herpesvirus replication and abnormal CD8+ T cell activation and low CD4+ T cell counts in antiretroviral-suppressed HIV-infected patients. PLoS One. 2009; 4(4):e5277.
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      201. Jiang W, Lederman MM, Hunt P, Sieg SF, Haley K, Rodriguez B, Landay A, Martin J, Sinclair E, Asher AI, Deeks SG, Douek DC, Brenchley JM. Plasma levels of bacterial DNA correlate with immune activation and the magnitude of immune restoration in persons with antiretroviral-treated HIV infection. J Infect Dis. 2009 Apr 15; 199(8):1177-85.
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      202. Kitahata MM, Gange SJ, Abraham AG, Merriman B, Saag MS, Justice AC, Hogg RS, Deeks SG, Eron JJ, Brooks JT, Rourke SB, Gill MJ, Bosch RJ, Martin JN, Klein MB, Jacobson LP, Rodriguez B, Sterling TR, Kirk GD, Napravnik S, Rachlis AR, Calzavara LM, Horberg MA, Silverberg MJ, Gebo KA, Goedert JJ, Benson CA, Collier AC, Van Rompaey SE, Crane HM, McKaig RG, Lau B, Freeman AM, Moore RD. Effect of early versus deferred antiretroviral therapy for HIV on survival. N Engl J Med. 2009 Apr 30; 360(18):1815-26.
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      203. Kelley CF, Kitchen CM, Hunt PW, Rodriguez B, Hecht FM, Kitahata M, Crane HM, Willig J, Mugavero M, Saag M, Martin JN, Deeks SG. Incomplete peripheral CD4+ cell count restoration in HIV-infected patients receiving long-term antiretroviral treatment. Clin Infect Dis. 2009 Mar 15; 48(6):787-94.
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      204. Tenorio AR, Jiang H, Zheng Y, Bastow B, Kuritzkes DR, Bartlett JA, Deeks SG, Landay AL, Riddler SA. Delaying a treatment switch in antiretroviral-treated HIV type 1-infected patients with detectable drug-resistant viremia does not have a profound effect on immune parameters: AIDS Clinical Trials Group Study A5115. AIDS Res Hum Retroviruses. 2009 Feb; 25(2):135-9.
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      205. Geng EH, Deeks SG. CD4+ T cell recovery with antiretroviral therapy: more than the sum of the parts. Clin Infect Dis. 2009 Feb 1; 48(3):362-4.
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      206. Deeks SG, Phillips AN. HIV infection, antiretroviral treatment, ageing, and non-AIDS related morbidity. BMJ. 2009; 338:a3172.
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      207. Contreras X, Schweneker M, Chen CS, McCune JM, Deeks SG, Martin J, Peterlin BM. Suberoylanilide hydroxamic acid reactivates HIV from latently infected cells. J Biol Chem. 2009 Mar 13; 284(11):6782-9.
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      208. Ferre AL, Hunt PW, Critchfield JW, Young DH, Morris MM, Garcia JC, Pollard RB, Yee HF, Martin JN, Deeks SG, Shacklett BL. Mucosal immune responses to HIV-1 in elite controllers: a potential correlate of immune control. Blood. 2009 Apr 23; 113(17):3978-89.
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      209. Paredes R, Sagar M, Marconi VC, Hoh R, Martin JN, Parkin NT, Petropoulos CJ, Deeks SG, Kuritzkes DR. In vivo fitness cost of the M184V mutation in multidrug-resistant human immunodeficiency virus type 1 in the absence of lamivudine. J Virol. 2009 Feb; 83(4):2038-43.
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      210. Hatano H, Delwart EL, Norris PJ, Lee TH, Dunn-Williams J, Hunt PW, Hoh R, Stramer SL, Linnen JM, McCune JM, Martin JN, Busch MP, Deeks SG. Evidence for persistent low-level viremia in individuals who control human immunodeficiency virus in the absence of antiretroviral therapy. J Virol. 2009 Jan; 83(1):329-35.
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      211. Petersen ML, van der Laan MJ, Napravnik S, Eron JJ, Moore RD, Deeks SG. Long-term consequences of the delay between virologic failure of highly active antiretroviral therapy and regimen modification. AIDS. 2008 Oct 18; 22(16):2097-106.
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      212. Marconi V, Bonhoeffer S, Paredes R, Lu J, Hoh R, Martin JN, Deeks SG, Kuritzkes DR. Viral dynamics and in vivo fitness of HIV-1 in the presence and absence of enfuvirtide. J Acquir Immune Defic Syndr. 2008 Aug 15; 48(5):572-6.
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      213. Probasco JC, Spudich SS, Critchfield J, Lee E, Lollo N, Deeks SG, Price RW. Failure of atorvastatin to modulate CSF HIV-1 infection: results of a pilot study. Neurology. 2008 Aug 12; 71(7):521-4.
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      214. Parienti JJ, Das-Douglas M, Massari V, Guzman D, Deeks SG, Verdon R, Bangsberg DR. Not all missed doses are the same: sustained NNRTI treatment interruptions predict HIV rebound at low-to-moderate adherence levels. PLoS One. 2008; 3(7):e2783.
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      215. Deeks SG. Transmitted minority drug-resistant HIV variants: a new epidemic? PLoS Med. 2008 Jul 29; 5(7):e164.
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      216. Schweneker M, Favre D, Martin JN, Deeks SG, McCune JM. HIV-induced changes in T cell signaling pathways. J Immunol. 2008 May 15; 180(10):6490-500.
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      217. Hsue PY, Deeks SG, Farah HH, Palav S, Ahmed SY, Schnell A, Ellman AB, Huang L, Dollard SC, Martin JN. Role of HIV and human herpesvirus-8 infection in pulmonary arterial hypertension. AIDS. 2008 Apr 23; 22(7):825-33.
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      218. Sinclair E, Ronquillo R, Lollo N, Deeks SG, Hunt P, Yiannoutsos CT, Spudich S, Price RW. Antiretroviral treatment effect on immune activation reduces cerebrospinal fluid HIV-1 infection. J Acquir Immune Defic Syndr. 2008 Apr 15; 47(5):544-52.
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      219. Ahuja SK, Kulkarni H, Catano G, Agan BK, Camargo JF, He W, O'Connell RJ, Marconi VC, Delmar J, Eron J, Clark RA, Frost S, Martin J, Ahuja SS, Deeks SG, Little S, Richman D, Hecht FM, Dolan MJ. CCL3L1-CCR5 genotype influences durability of immune recovery during antiretroviral therapy of HIV-1-infected individuals. Nat Med. 2008 Apr; 14(4):413-20.
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      220. Emu B, Sinclair E, Hatano H, Ferre A, Shacklett B, Martin JN, McCune JM, Deeks SG. HLA class I-restricted T-cell responses may contribute to the control of human immunodeficiency virus infection, but such responses are not always necessary for long-term virus control. J Virol. 2008 Jun; 82(11):5398-407.
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      221. Price RW, Parham R, Kroll JL, Wring SA, Baker B, Sailstad J, Hoh R, Liegler T, Spudich S, Kuritzkes DR, Deeks SG. Enfuvirtide cerebrospinal fluid (CSF) pharmacokinetics and potential use in defining CSF HIV-1 origin. Antivir Ther. 2008; 13(3):369-74.
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      222. Hunt PW, Brenchley J, Sinclair E, McCune JM, Roland M, Page-Shafer K, Hsue P, Emu B, Krone M, Lampiris H, Douek D, Martin JN, Deeks SG. Relationship between T cell activation and CD4+ T cell count in HIV-seropositive individuals with undetectable plasma HIV RNA levels in the absence of therapy. J Infect Dis. 2008 Jan 1; 197(1):126-33.
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      223. Barker E, Martinson J, Brooks C, Landay A, Deeks S. Dysfunctional natural killer cells, in vivo, are governed by HIV viremia regardless of whether the infected individual is on antiretroviral therapy. AIDS. 2007 Nov 12; 21(17):2363-5.
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      224. Petersen ML, Deeks SG, van der Laan MJ. Individualized treatment rules: generating candidate clinical trials. Stat Med. 2007 Nov 10; 26(25):4578-601.
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      225. Dolan MJ, Kulkarni H, Camargo JF, He W, Smith A, Anaya JM, Miura T, Hecht FM, Mamtani M, Pereyra F, Marconi V, Mangano A, Sen L, Bologna R, Clark RA, Anderson SA, Delmar J, O'Connell RJ, Lloyd A, Martin J, Ahuja SS, Agan BK, Walker BD, Deeks SG, Ahuja SK. CCL3L1 and CCR5 influence cell-mediated immunity and affect HIV-AIDS pathogenesis via viral entry-independent mechanisms. Nat Immunol. 2007 Dec; 8(12):1324-36.
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      226. Petersen ML, Deeks SG, Martin JN, van der Laan MJ. History-adjusted marginal structural models for estimating time-varying effect modification. Am J Epidemiol. 2007 Nov 1; 166(9):985-93.
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      227. Deeks SG. Protease inhibitors as immunomodulatory drugs for HIV infection. Clin Pharmacol Ther. 2007 Sep; 82(3):248-50.
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      228. Deeks SG, Walker BD. Human immunodeficiency virus controllers: mechanisms of durable virus control in the absence of antiretroviral therapy. Immunity. 2007 Sep; 27(3):406-16.
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      229. Owen RE, Sinclair E, Emu B, Heitman JW, Hirschkorn DF, Epling CL, Tan QX, Custer B, Harris JM, Jacobson MA, McCune JM, Martin JN, Hecht FM, Deeks SG, Norris PJ. Loss of T cell responses following long-term cryopreservation. J Immunol Methods. 2007 Sep 30; 326(1-2):93-115.
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      230. Karlsson AC, Chapman JM, Heiken BD, Hoh R, Kallas EG, Martin JN, Hecht FM, Deeks SG, Nixon DF. Antiretroviral drug therapy alters the profile of human immunodeficiency virus type 1-specific T-cell responses and shifts the immunodominant cytotoxic T-lymphocyte response from Gag to Pol. J Virol. 2007 Oct; 81(20):11543-8.
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      231. Lederman MM, Miller V, Weller I, Deeks SG. A new approach for 'deep salvage' trials in advanced HIV infection. AIDS. 2007 Jul 31; 21(12):1503-6.
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      232. Hatano H, Deeks SG. Drug resistant HIV. BMJ. 2007 Jun 2; 334(7604):1124-5.
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      233. Martin MP, Qi Y, Gao X, Yamada E, Martin JN, Pereyra F, Colombo S, Brown EE, Shupert WL, Phair J, Goedert JJ, Buchbinder S, Kirk GD, Telenti A, Connors M, O'Brien SJ, Walker BD, Parham P, Deeks SG, McVicar DW, Carrington M. Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1. Nat Genet. 2007 Jun; 39(6):733-40.
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      234. Bangsberg DR, Kroetz DL, Deeks SG. Adherence-resistance relationships to combination HIV antiretroviral therapy. Curr HIV/AIDS Rep. 2007 May; 4(2):65-72.
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      235. Ray N, Harrison JE, Blackburn LA, Martin JN, Deeks SG, Doms RW. Clinical resistance to enfuvirtide does not affect susceptibility of human immunodeficiency virus type 1 to other classes of entry inhibitors. J Virol. 2007 Apr; 81(7):3240-50.
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      236. Luetkemeyer AF, Charlebois ED, Flores LL, Bangsberg DR, Deeks SG, Martin JN, Havlir DV. Comparison of an interferon-gamma release assay with tuberculin skin testing in HIV-infected individuals. Am J Respir Crit Care Med. 2007 Apr 1; 175(7):737-42.
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      237. Gange SJ, Kitahata MM, Saag MS, Bangsberg DR, Bosch RJ, Brooks JT, Calzavara L, Deeks SG, Eron JJ, Gebo KA, Gill MJ, Haas DW, Hogg RS, Horberg MA, Jacobson LP, Justice AC, Kirk GD, Klein MB, Martin JN, McKaig RG, Rodriguez B, Rourke SB, Sterling TR, Freeman AM, Moore RD. Cohort profile: the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD). Int J Epidemiol. 2007 Apr; 36(2):294-301.
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      238. Riddler SA, Jiang H, Tenorio A, Huang H, Kuritzkes DR, Acosta EP, Landay A, Bastow B, Haas DW, Tashima KT, Jain MK, Deeks SG, Bartlett JA. A randomized study of antiviral medication switch at lower- versus higher-switch thresholds: AIDS Clinical Trials Group Study A5115. Antivir Ther. 2007; 12(4):531-41.
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      239. Deeks SG, Martin JN. Partial treatment interruptions. Curr Opin HIV AIDS. 2007 Jan; 2(1):46-55.
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      240. Deeks SG, Lu J, Hoh R, Neilands TB, Beatty G, Huang W, Liegler T, Hunt P, Martin JN, Kuritzkes DR. Interruption of enfuvirtide in HIV-1 infected adults with incomplete viral suppression on an enfuvirtide-based regimen. J Infect Dis. 2007 Feb 1; 195(3):387-91.
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      241. Kitchen CM, Lu J, Suchard MA, Hoh R, Martin JN, Kuritzkes DR, Deeks SG. Continued evolution in gp41 after interruption of enfuvirtide in subjects with advanced HIV type 1 disease. AIDS Res Hum Retroviruses. 2006 Dec; 22(12):1260-6.
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      242. Hsue PY, Hunt PW, Sinclair E, Bredt B, Franklin A, Killian M, Hoh R, Martin JN, McCune JM, Waters DD, Deeks SG. Increased carotid intima-media thickness in HIV patients is associated with increased cytomegalovirus-specific T-cell responses. AIDS. 2006 Nov 28; 20(18):2275-83.
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      243. Brenchley JM, Price DA, Schacker TW, Asher TE, Silvestri G, Rao S, Kazzaz Z, Bornstein E, Lambotte O, Altmann D, Blazar BR, Rodriguez B, Teixeira-Johnson L, Landay A, Martin JN, Hecht FM, Picker LJ, Lederman MM, Deeks SG, Douek DC. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat Med. 2006 Dec; 12(12):1365-71.
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      244. Spudich S, Lollo N, Liegler T, Deeks SG, Price RW. Treatment benefit on cerebrospinal fluid HIV-1 levels in the setting of systemic virological suppression and failure. J Infect Dis. 2006 Dec 15; 194(12):1686-96.
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      245. Hunt PW, Deeks SG. Immune-based therapy for HIV infection: are acute and chronic HIV infection different diseases? J Infect Dis. 2006 Dec 15; 194(12):1632-4.
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      246. Ahuja SK, Aiuti F, Berkhout B, Biberfeld P, Burton DR, Colizzi V, Deeks SG, Desrosiers RC, Dierich MP, Doms RW, Emerman M, Gallo RC, Girard M, Greene WC, Hoxie JA, Hunter E, Klein G, Korber B, Kuritzkes DR, Lederman MM, Malim MH, Marx PA, McCune JM, McMichael A, Miller C, Miller V, Montagnier L, Montefiori DC, Moore JP, Nixon DF, Overbaugh J, Pauza CD, Richman DD, Saag MS, Sattentau Q, Schooley RT, Shattock R, Shaw GM, Stevenson M, Trkola A, Wainberg MA, Weiss RA, Wolinsky S, Zack JA. A plea for justice for jailed medical workers. Science. 2006 Nov 10; 314(5801):924-5.
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      247. Hatano H, Hunt P, Weidler J, Coakley E, Hoh R, Liegler T, Martin JN, Deeks SG. Rate of viral evolution and risk of losing future drug options in heavily pretreated, HIV-infected patients who continue to receive a stable, partially suppressive treatment regimen. Clin Infect Dis. 2006 Nov 15; 43(10):1329-36.
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      248. Rodríguez B, Sethi AK, Cheruvu VK, Mackay W, Bosch RJ, Kitahata M, Boswell SL, Mathews WC, Bangsberg DR, Martin J, Whalen CC, Sieg S, Yadavalli S, Deeks SG, Lederman MM. Predictive value of plasma HIV RNA level on rate of CD4 T-cell decline in untreated HIV infection. JAMA. 2006 Sep 27; 296(12):1498-506.
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      249. Lu J, Deeks SG, Hoh R, Beatty G, Kuritzkes BA, Martin JN, Kuritzkes DR. Rapid emergence of enfuvirtide resistance in HIV-1-infected patients: results of a clonal analysis. J Acquir Immune Defic Syndr. 2006 Sep; 43(1):60-4.
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      250. Marcial M, Lu J, Deeks SG, Ziermann R, Kuritzkes DR. Performance of human immunodeficiency virus type 1 gp41 assays for detecting enfuvirtide (T-20) resistance mutations. J Clin Microbiol. 2006 Sep; 44(9):3384-7.
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      251. Hunt PW, Harrigan PR, Huang W, Bates M, Williamson DW, McCune JM, Price RW, Spudich SS, Lampiris H, Hoh R, Leigler T, Martin JN, Deeks SG. Prevalence of CXCR4 tropism among antiretroviral-treated HIV-1-infected patients with detectable viremia. J Infect Dis. 2006 Oct 1; 194(7):926-30.
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      252. Nomura LE, Emu B, Hoh R, Haaland P, Deeks SG, Martin JN, McCune JM, Nixon DF, Maecker HT. IL-2 production correlates with effector cell differentiation in HIV-specific CD8+ T cells. AIDS Res Ther. 2006; 3:18.
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      253. Deeks SG. Antiretroviral treatment of HIV infected adults. BMJ. 2006 Jun 24; 332(7556):1489.
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      254. Deeks SG. The risk of treatment versus the risk of HIV replication. Lancet. 2006 Jun 17; 367(9527):1955-6.
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      255. Deeks SG, Schweighardt B, Wrin T, Galovich J, Hoh R, Sinclair E, Hunt P, McCune JM, Martin JN, Petropoulos CJ, Hecht FM. Neutralizing antibody responses against autologous and heterologous viruses in acute versus chronic human immunodeficiency virus (HIV) infection: evidence for a constraint on the ability of HIV to completely evade neutralizing antibody responses. J Virol. 2006 Jun; 80(12):6155-64.
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      256. Wilson-Clark SD, Squires S, Deeks S. Bacterial meningitis among cochlear implant recipients--Canada, 2002. MMWR Morb Mortal Wkly Rep. 2006 Apr 28; 55 Suppl 1:20-4.
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      257. Hunt PW, Deeks SG, Bangsberg DR, Moss A, Sinclair E, Liegler T, Bates M, Tsao G, Lampiris H, Hoh R, Martin JN. The independent effect of drug resistance on T cell activation in HIV infection. AIDS. 2006 Mar 21; 20(5):691-9.
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      258. Deeks SG. Challenges of developing R5 inhibitors in antiretroviral naive HIV-infected patients. Lancet. 2006 Mar 4; 367(9512):711-3.
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      259. Bangsberg DR, Acosta EP, Gupta R, Guzman D, Riley ED, Harrigan PR, Parkin N, Deeks SG. Adherence-resistance relationships for protease and non-nucleoside reverse transcriptase inhibitors explained by virological fitness. AIDS. 2006 Jan 9; 20(2):223-31.
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      260. Jordan KA, Furlan SN, Gonzalez VD, Karlsson AC, Quigley MF, Deeks SG, Rosenberg MG, Nixon DF, Sandberg JK. CD8 T cell effector maturation in HIV-1-infected children. Virology. 2006 Mar 30; 347(1):117-26.
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      261. Beatty G, Hunt P, Smith A, Hoh R, Huang W, Martin J, Deeks SG. A randomized pilot study comparing combination therapy plus enfuvirtide versus a treatment interruption followed by combination therapy plus enfuvirtide. Antivir Ther. 2006; 11(3):315-9.
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      262. Chin-Hong PV, Deeks SG, Liegler T, Hagos E, Krone MR, Grant RM, Martin JN. High-risk sexual behavior in adults with genotypically proven antiretroviral-resistant HIV infection. J Acquir Immune Defic Syndr. 2005 Dec 1; 40(4):463-71.
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      263. Spudich SS, Nilsson AC, Lollo ND, Liegler TJ, Petropoulos CJ, Deeks SG, Paxinos EE, Price RW. Cerebrospinal fluid HIV infection and pleocytosis: relation to systemic infection and antiretroviral treatment. BMC Infect Dis. 2005; 5:98.
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      264. Emu B, Sinclair E, Favre D, Moretto WJ, Hsue P, Hoh R, Martin JN, Nixon DF, McCune JM, Deeks SG. Phenotypic, functional, and kinetic parameters associated with apparent T-cell control of human immunodeficiency virus replication in individuals with and without antiretroviral treatment. J Virol. 2005 Nov; 79(22):14169-78.
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      265. Legrand FA, Abadi J, Jordan KA, Davenport MP, Deeks SG, Fennelly GJ, Wiznia AA, Nixon DF, Rosenberg MG. Partial treatment interruption of protease inhibitors augments HIV-specific immune responses in vertically infected pediatric patients. AIDS. 2005 Oct 14; 19(15):1575-85.
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      266. Lo JC, Kazemi MR, Hsue PY, Martin JN, Deeks SG, Schambelan M, Mulligan K. The relationship between nucleoside analogue treatment duration, insulin resistance, and fasting arterialized lactate level in patients with HIV infection. Clin Infect Dis. 2005 Nov 1; 41(9):1335-40.
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      267. Deeks SG, Hoh R, Neilands TB, Liegler T, Aweeka F, Petropoulos CJ, Grant RM, Martin JN. Interruption of treatment with individual therapeutic drug classes in adults with multidrug-resistant HIV-1 infection. J Infect Dis. 2005 Nov 1; 192(9):1537-44.
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      268. Gisslén M, Rosengren L, Hagberg L, Deeks SG, Price RW. Cerebrospinal fluid signs of neuronal damage after antiretroviral treatment interruption in HIV-1 infection. AIDS Res Ther. 2005 Aug 18; 2:6.
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      269. Cohan D, Feakins C, Wara D, Petru A, McNicholl I, Schillinger D, Lu J, Kuritzkes D, Deeks SG. Perinatal transmission of multidrug-resistant HIV-1 despite viral suppression on an enfuvirtide-based treatment regimen. AIDS. 2005 Jun 10; 19(9):989-90.
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      270. Nixon DF, Deeks SG, Shacklett BL, Karlsson AC. Multidrug-resistant, dual-tropic HIV-1 and rapid progression. Lancet. 2005 Jun 4-10; 365(9475):1924-5.
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      271. McEvers K, Elrefaei M, Norris P, Deeks S, Martin J, Lu Y, Cao H. Modified anthrax fusion proteins deliver HIV antigens through MHC Class I and II pathways. Vaccine. 2005 Jul 14; 23(32):4128-35.
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      272. Friend J, Parkin N, Liegler T, Martin JN, Deeks SG. Isolated lopinavir resistance after virological rebound of a ritonavir/lopinavir-based regimen. AIDS. 2004 Sep 24; 18(14):1965-6.
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      273. Critchfield JM, Deeks SG. Treating the latent reservoir of HIV. AIDS Read. 2004 Sep; 14(9):485-6.
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      274. Aandahl EM, Quigley MF, Moretto WJ, Moll M, Gonzalez VD, Sönnerborg A, Lindbäck S, Hecht FM, Deeks SG, Rosenberg MG, Nixon DF, Sandberg JK. Expansion of CD7(low) and CD7(negative) CD8 T-cell effector subsets in HIV-1 infection: correlation with antigenic load and reversion by antiretroviral treatment. Blood. 2004 Dec 1; 104(12):3672-8.
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      275. Elrefaei M, McElroy MD, Preas CP, Hoh R, Deeks S, Martin J, Cao H. Central memory CD4+ T cell responses in chronic HIV infection are not restored by antiretroviral therapy. J Immunol. 2004 Aug 1; 173(3):2184-9.
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      276. Bangsberg DR, Porco TC, Kagay C, Charlebois ED, Deeks SG, Guzman D, Clark R, Moss A. Modeling the HIV protease inhibitor adherence-resistance curve by use of empirically derived estimates. J Infect Dis. 2004 Jul 1; 190(1):162-5.
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      277. Karlsson AC, Younger SR, Martin JN, Grossman Z, Sinclair E, Hunt PW, Hagos E, Nixon DF, Deeks SG. Immunologic and virologic evolution during periods of intermittent and persistent low-level viremia. AIDS. 2004 Apr 30; 18(7):981-9.
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      278. Deeks SG, Kitchen CM, Liu L, Guo H, Gascon R, Narváez AB, Hunt P, Martin JN, Kahn JO, Levy J, McGrath MS, Hecht FM. Immune activation set point during early HIV infection predicts subsequent CD4+ T-cell changes independent of viral load. Blood. 2004 Aug 15; 104(4):942-7.
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      279. Bangsberg DR, Moss AR, Deeks SG. Paradoxes of adherence and drug resistance to HIV antiretroviral therapy. J Antimicrob Chemother. 2004 May; 53(5):696-9.
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      280. Hsue PY, Lo JC, Franklin A, Bolger AF, Martin JN, Deeks SG, Waters DD. Progression of atherosclerosis as assessed by carotid intima-media thickness in patients with HIV infection. Circulation. 2004 Apr 6; 109(13):1603-8.
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      281. Deeks SG, Walker BD. The immune response to AIDS virus infection: good, bad, or both? J Clin Invest. 2004 Mar; 113(6):808-10.
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      282. Deeks SG, Martin JN, Sinclair E, Harris J, Neilands TB, Maecker HT, Hagos E, Wrin T, Petropoulos CJ, Bredt B, McCune JM. Strong cell-mediated immune responses are associated with the maintenance of low-level viremia in antiretroviral-treated individuals with drug-resistant human immunodeficiency virus type 1. J Infect Dis. 2004 Jan 15; 189(2):312-21.
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      283. Price RW, Deeks SG. Antiretroviral drug treatment interruption in human immunodeficiency virus-infected adults: Clinical and pathogenetic implications for the central nervous system. J Neurovirol. 2004; 10 Suppl 1:44-51.
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      284. Deeks SG. Treatment of antiretroviral-drug-resistant HIV-1 infection. Lancet. 2003 Dec 13; 362(9400):2002-11.
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      285. Karlsson AC, Martin JN, Younger SR, Bredt BM, Epling L, Ronquillo R, Varma A, Deeks SG, McCune JM, Nixon DF, Sinclair E. Comparison of the ELISPOT and cytokine flow cytometry assays for the enumeration of antigen-specific T cells. J Immunol Methods. 2003 Dec; 283(1-2):141-53.
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      286. Jiang H, Deeks SG, Kuritzkes DR, Lallemant M, Katzenstein D, Albrecht M, DeGruttola V. Assessing resistance costs of antiretroviral therapies via measures of future drug options. J Infect Dis. 2003 Oct 1; 188(7):1001-8.
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      287. Hunt PW, Deeks SG, Rodriguez B, Valdez H, Shade SB, Abrams DI, Kitahata MM, Krone M, Neilands TB, Brand RJ, Lederman MM, Martin JN. Continued CD4 cell count increases in HIV-infected adults experiencing 4 years of viral suppression on antiretroviral therapy. AIDS. 2003 Sep 5; 17(13):1907-15.
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      288. Bangsberg DR, Charlebois ED, Grant RM, Holodniy M, Deeks SG, Perry S, Conroy KN, Clark R, Guzman D, Zolopa A, Moss A. High levels of adherence do not prevent accumulation of HIV drug resistance mutations. AIDS. 2003 Sep 5; 17(13):1925-32.
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      289. Abrams DI, Hilton JF, Leiser RJ, Shade SB, Elbeik TA, Aweeka FT, Benowitz NL, Bredt BM, Kosel B, Aberg JA, Deeks SG, Mitchell TF, Mulligan K, Bacchetti P, McCune JM, Schambelan M. Short-term effects of cannabinoids in patients with HIV-1 infection: a randomized, placebo-controlled clinical trial. Ann Intern Med. 2003 Aug 19; 139(4):258-66.
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      290. Karlsson AC, Deeks SG, Barbour JD, Heiken BD, Younger SR, Hoh R, Lane M, Sällberg M, Ortiz GM, Demarest JF, Liegler T, Grant RM, Martin JN, Nixon DF. Dual pressure from antiretroviral therapy and cell-mediated immune response on the human immunodeficiency virus type 1 protease gene. J Virol. 2003 Jun; 77(12):6743-52.
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      291. Hunt PW, Martin JN, Sinclair E, Bredt B, Hagos E, Lampiris H, Deeks SG. T cell activation is associated with lower CD4+ T cell gains in human immunodeficiency virus-infected patients with sustained viral suppression during antiretroviral therapy. J Infect Dis. 2003 May 15; 187(10):1534-43.
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      292. Jacobson MA, Liu L, Khayam-Bashi H, Deeks SG, Hecht FM, Kahn J. Absolute or total lymphocyte count as a marker for the CD4 T lymphocyte criterion for initiating antiretroviral therapy. AIDS. 2003 Apr 11; 17(6):917-9.
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      293. Deeks SG, Grant RM, Wrin T, Paxinos EE, Liegler T, Hoh R, Martin JN, Petropoulos CJ. Persistence of drug-resistant HIV-1 after a structured treatment interruption and its impact on treatment response. AIDS. 2003 Feb 14; 17(3):361-70.
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      294. Anton PA, Mitsuyasu RT, Deeks SG, Scadden DT, Wagner B, Huang C, Macken C, Richman DD, Christopherson C, Borellini F, Lazar R, Hege KM. Multiple measures of HIV burden in blood and tissue are correlated with each other but not with clinical parameters in aviremic subjects. AIDS. 2003 Jan 3; 17(1):53-63.
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      295. Barbour JD, Wrin T, Grant RM, Martin JN, Segal MR, Petropoulos CJ, Deeks SG. Evolution of phenotypic drug susceptibility and viral replication capacity during long-term virologic failure of protease inhibitor therapy in human immunodeficiency virus-infected adults. J Virol. 2002 Nov; 76(21):11104-12.
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      296. Whitcomb JM, Huang W, Limoli K, Paxinos E, Wrin T, Skowron G, Deeks SG, Bates M, Hellmann NS, Petropoulos CJ. Hypersusceptibility to non-nucleoside reverse transcriptase inhibitors in HIV-1: clinical, phenotypic and genotypic correlates. AIDS. 2002 Oct 18; 16(15):F41-7.
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      297. Bangsberg DR, Deeks SG. Is average adherence to HIV antiretroviral therapy enough? J Gen Intern Med. 2002 Oct; 17(10):812-3.
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      298. Tebas P, Henry K, Mondy K, Deeks S, Valdez H, Cohen C, Powderly WG. Effect of prolonged discontinuation of successful antiretroviral therapy on CD4+ T cell decline in human immunodeficiency virus-infected patients: implications for intermittent therapeutic strategies. J Infect Dis. 2002 Sep 15; 186(6):851-4.
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      299. Castelli JC, Deeks SG, Shiboski S, Levy JA. Relationship of CD8(+) T cell noncytotoxic anti-HIV response to CD4(+) T cell number in untreated asymptomatic HIV-infected individuals. Blood. 2002 Jun 1; 99(11):4225-7.
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      300. Deeks SG, Wagner B, Anton PA, Mitsuyasu RT, Scadden DT, Huang C, Macken C, Richman DD, Christopherson C, June CH, Lazar R, Broad DF, Jalali S, Hege KM. A phase II randomized study of HIV-specific T-cell gene therapy in subjects with undetectable plasma viremia on combination antiretroviral therapy. Mol Ther. 2002 Jun; 5(6):788-97.
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      301. Benson CA, Deeks SG, Brun SC, Gulick RM, Eron JJ, Kessler HA, Murphy RL, Hicks C, King M, Wheeler D, Feinberg J, Stryker R, Sax PE, Riddler S, Thompson M, Real K, Hsu A, Kempf D, Japour AJ, Sun E. Safety and antiviral activity at 48 weeks of lopinavir/ritonavir plus nevirapine and 2 nucleoside reverse-transcriptase inhibitors in human immunodeficiency virus type 1-infected protease inhibitor-experienced patients. J Infect Dis. 2002 Mar 1; 185(5):599-607.
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      302. Deeks SG, Barbour JD, Grant RM, Martin JN. Duration and predictors of CD4 T-cell gains in patients who continue combination therapy despite detectable plasma viremia. AIDS. 2002 Jan 25; 16(2):201-7.
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      303. Deeks SG, Hoh R, Grant RM, Wrin T, Barbour JD, Narvaez A, Cesar D, Abe K, Hanley MB, Hellmann NS, Petropoulos CJ, McCune JM, Hellerstein MK. CD4+ T cell kinetics and activation in human immunodeficiency virus-infected patients who remain viremic despite long-term treatment with protease inhibitor-based therapy. J Infect Dis. 2002 Feb 1; 185(3):315-23.
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      304. Deeks SG, Hirschel B. Supervised interruptions of antiretroviral therapy. AIDS. 2002; 16 Suppl 4:S157-69.
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      305. Deeks SG, Barditch-Crovo P, Collier A, Smith A, Miller M, McGowan I, Coakley DF. Hydroxyurea does not enhance the anti-HIV activity of low-dose tenofovir disoproxil fumarate. J Acquir Immune Defic Syndr. 2001 Dec 1; 28(4):336-9.
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      306. Barditch-Crovo P, Deeks SG, Collier A, Safrin S, Coakley DF, Miller M, Kearney BP, Coleman RL, Lamy PD, Kahn JO, McGowan I, Lietman PS. Phase i/ii trial of the pharmacokinetics, safety, and antiretroviral activity of tenofovir disoproxil fumarate in human immunodeficiency virus-infected adults. Antimicrob Agents Chemother. 2001 Oct; 45(10):2733-9.
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      307. Teixeira L, Valdez H, McCune JM, Koup RA, Badley AD, Hellerstein MK, Napolitano LA, Douek DC, Mbisa G, Deeks S, Harris JM, Barbour JD, Gross BH, Francis IR, Halvorsen R, Asaad R, Lederman MM. Poor CD4 T cell restoration after suppression of HIV-1 replication may reflect lower thymic function. AIDS. 2001 Sep 28; 15(14):1749-56.
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      308. Deeks SG. Durable HIV treatment benefit despite low-level viremia: reassessing definitions of success or failure. JAMA. 2001 Jul 11; 286(2):224-6.
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      309. Price RW, Paxinos EE, Grant RM, Drews B, Nilsson A, Hoh R, Hellmann NS, Petropoulos CJ, Deeks SG. Cerebrospinal fluid response to structured treatment interruption after virological failure. AIDS. 2001 Jul 6; 15(10):1251-9.
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      310. Sabin CA, Olmscheid B, Moyle G, Carr A, Boyle B, Cohen C, Cooper D, Deeks S, Gulick T, Saag M. Selected topics from the 8th Conference on Retroviruses and Opportunistic Infections. February 4-8, 2001. Chicago, Illinois. HIV Clin Trials. 2001 Jul-Aug; 2(4):366-86.
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      311. Stoddart CA, Liegler TJ, Mammano F, Linquist-Stepps VD, Hayden MS, Deeks SG, Grant RM, Clavel F, McCune JM. Impaired replication of protease inhibitor-resistant HIV-1 in human thymus. Nat Med. 2001 Jun; 7(6):712-8.
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      312. Penn ML, Myers M, Eckstein DA, Liegler TJ, Hayden M, Mammano F, Clavel F, Deeks SG, Grant RM, Goldsmith MA. Primary and recombinant HIV type 1 strains resistant to protease inhibitors are pathogenic in mature human lymphoid tissues. AIDS Res Hum Retroviruses. 2001 Apr 10; 17(6):517-23.
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      313. Deeks SG. International perspectives on antiretroviral resistance. Nonnucleoside reverse transcriptase inhibitor resistance. J Acquir Immune Defic Syndr. 2001 Mar 1; 26 Suppl 1:S25-33.
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      314. Deeks SG, Wrin T, Liegler T, Hoh R, Hayden M, Barbour JD, Hellmann NS, Petropoulos CJ, McCune JM, Hellerstein MK, Grant RM. Virologic and immunologic consequences of discontinuing combination antiretroviral-drug therapy in HIV-infected patients with detectable viremia. N Engl J Med. 2001 Feb 15; 344(7):472-80.
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      315. Nijhuis M, Deeks S, Boucher C. Implications of antiretroviral resistance on viral fitness. Curr Opin Infect Dis. 2001 Feb; 14(1):23-8.
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      316. Liegler TJ, Hayden MS, Lee KH, Hoh R, Deeks SG, Granta RM. Protease inhibitor-resistant HIV-1 from patients with preserved CD4 cell counts is cytopathic in activated CD4 T lymphocytes. AIDS. 2001 Jan 26; 15(2):179-84.
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      317. Deeks SG, Martin JN. Reassessing the goal of antiretroviral therapy in the heavily pre-treated HIV-infected patient. AIDS. 2001 Jan 5; 15(1):117-9.
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      318. Napolitano LA, Grant RM, Deeks SG, Schmidt D, De Rosa SC, Herzenberg LA, Herndier BG, Andersson J, McCune JM. Increased production of IL-7 accompanies HIV-1-mediated T-cell depletion: implications for T-cell homeostasis. Nat Med. 2001 Jan; 7(1):73-9.
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      319. Parkin NT, Deeks SG, Wrin MT, Yap J, Grant RM, Lee KH, Heeren D, Hellmanna NS, Petropoulos CJ. Loss of antiretroviral drug susceptibility at low viral load during early virological failure in treatment-experienced patients. AIDS. 2000 Dec 22; 14(18):2877-87.
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      320. Mitsuyasu RT, Anton PA, Deeks SG, Scadden DT, Connick E, Downs MT, Bakker A, Roberts MR, June CH, Jalali S, Lin AA, Pennathur-Das R, Hege KM. Prolonged survival and tissue trafficking following adoptive transfer of CD4zeta gene-modified autologous CD4(+) and CD8(+) T cells in human immunodeficiency virus-infected subjects. Blood. 2000 Aug 1; 96(3):785-93.
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      321. Deeks SG. Determinants of virological response to antiretroviral therapy: implications for long-term strategies. Clin Infect Dis. 2000 Jun; 30 Suppl 2:S177-84.
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      322. Deeks SG, Barbour JD, Martin JN, Swanson MS, Grant RM. Sustained CD4+ T cell response after virologic failure of protease inhibitor-based regimens in patients with human immunodeficiency virus infection. J Infect Dis. 2000 Mar; 181(3):946-53.
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      323. Huang SS, Barbour JD, Deeks SG, Huang JS, Grant RM, Ng VL, McCune JM. Reversal of human immunodeficiency virus type 1-associated hematosuppression by effective antiretroviral therapy. Clin Infect Dis. 2000 Mar; 30(3):504-10.
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      324. McCune JM, Hanley MB, Cesar D, Halvorsen R, Hoh R, Schmidt D, Wieder E, Deeks S, Siler S, Neese R, Hellerstein M. Factors influencing T-cell turnover in HIV-1-seropositive patients. J Clin Invest. 2000 Mar; 105(5):R1-8.
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      325. Kahn J, Lagakos S, Wulfsohn M, Cherng D, Miller M, Cherrington J, Hardy D, Beall G, Cooper R, Murphy R, Basgoz N, Ng E, Deeks S, Winslow D, Toole JJ, Coakley D. Efficacy and safety of adefovir dipivoxil with antiretroviral therapy: a randomized controlled trial. JAMA. 1999 Dec 22-29; 282(24):2305-12.
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      326. Buxton J, Fyfe M, King A, Deeks S, Dore K, Ahmed R, Khakhria R, Paccagnella A, Hockin J. Salmonella typhimurium definitive type 104 isolates in British Columbia, 1997-1998. Can Commun Dis Rep. 1999 Aug 1; 25(15):129-33.
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      327. Spika JS, Keresz D, Deeks S, Talbot JA. Pneumococcal immunization and public health: the Canadian experience. Vaccine. 1999 Jul 30; 17 Suppl 1:S105-8.
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      328. Staprans S, Marlowe N, Glidden D, Novakovic-Agopian T, Grant RM, Heyes M, Aweeka F, Deeks S, Price RW. Time course of cerebrospinal fluid responses to antiretroviral therapy: evidence for variable compartmentalization of infection. AIDS. 1999 Jun 18; 13(9):1051-61.
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      329. Deeks SG, Hellmann NS, Grant RM, Parkin NT, Petropoulos CJ, Becker M, Symonds W, Chesney M, Volberding PA. Novel four-drug salvage treatment regimens after failure of a human immunodeficiency virus type 1 protease inhibitor-containing regimen: antiviral activity and correlation of baseline phenotypic drug susceptibility with virologic outcome. J Infect Dis. 1999 Jun; 179(6):1375-81.
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      330. Deeks SG, Hecht FM, Swanson M, Elbeik T, Loftus R, Cohen PT, Grant RM. HIV RNA and CD4 cell count response to protease inhibitor therapy in an urban AIDS clinic: response to both initial and salvage therapy. AIDS. 1999 Apr 16; 13(6):F35-43.
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      331. Deeks S, De Serres G, Boulianne N, Duval B, Rochette L, Déry P, Halperin S. Failure of physicians to consider the diagnosis of pertussis in children. Clin Infect Dis. 1999 Apr; 28(4):840-6.
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      332. Deeks SG. Failure of HIV-1 protease inhibitors to fully suppress viral replication. Implications for salvage therapy. Adv Exp Med Biol. 1999; 458:175-82.
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      333. Hellerstein M, Hanley MB, Cesar D, Siler S, Papageorgopoulos C, Wieder E, Schmidt D, Hoh R, Neese R, Macallan D, Deeks S, McCune JM. Directly measured kinetics of circulating T lymphocytes in normal and HIV-1-infected humans. Nat Med. 1999 Jan; 5(1):83-9.
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      334. Deeks SG, Grant RM. Sustained CD4 responses after virological failure of protease inhibitor-containing therapy. Antivir Ther. 1999; 4 Suppl 3:7-11.
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      335. Deeks SG, Barditch-Crovo P, Lietman PS, Hwang F, Cundy KC, Rooney JF, Hellmann NS, Safrin S, Kahn JO. Safety, pharmacokinetics, and antiretroviral activity of intravenous 9-[2-(R)-(Phosphonomethoxy)propyl]adenine, a novel anti-human immunodeficiency virus (HIV) therapy, in HIV-infected adults. Antimicrob Agents Chemother. 1998 Sep; 42(9):2380-4.
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      336. Deeks SG, Sax PE. Should we argue with success? AIDS Clin Care. 1998 Sep; 10(9):68, 72.
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      337. Deeks SG, Grant RM, Beatty GW, Horton C, Detmer J, Eastman S. Activity of a ritonavir plus saquinavir-containing regimen in patients with virologic evidence of indinavir or ritonavir failure. AIDS. 1998 Jul 9; 12(10):F97-102.
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      338. Volberding PA, Deeks SG. Antiretroviral therapy for HIV infection: promises and problems. JAMA. 1998 May 6; 279(17):1343-4.
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      339. Deeks SG. Antiretroviral agents: the next generation. AIDS Clin Care. 1998 May; 10(5):33-6, 39-40.
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      340. Follansbee S, Deeks S, Bartnoff H. Fifth Conference on Retroviruses & Opportunistic Infections. Interview by Ron Baker. Newsline People AIDS Coalit N Y. 1998 Mar; 7-14.
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      341. Deeks S. Clinical implications of virological "failure": interview with Steven Deeks, M.D., San Francisco General Hospital. Interview by John S. James. AIDS Treat News. 1998 Feb 20; (No 289):1-6.
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      342. Deeks SG. Practical issues regarding the use of antiretroviral therapy for HIV infection. West J Med. 1998 Feb; 168(2):133-9.
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      343. Deeks SG, Collier A, Lalezari J, Pavia A, Rodrigue D, Drew WL, Toole J, Jaffe HS, Mulato AS, Lamy PD, Li W, Cherrington JM, Hellmann N, Kahn J. The safety and efficacy of adefovir dipivoxil, a novel anti-human immunodeficiency virus (HIV) therapy, in HIV-infected adults: a randomized, double-blind, placebo-controlled trial. J Infect Dis. 1997 Dec; 176(6):1517-23.
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      344. Deeks S, Kertesz D, Ryan A, Johnson W, Ashton F. Surveillance of invasive meningococcal disease in Canada, 1995-1996. Can Commun Dis Rep. 1997 Aug 15; 23(16):121-5.
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      345. Deeks SG, Coleman RL, White R, Pachl C, Schambelan M, Chernoff DN, Feinberg MB. Variance of plasma human immunodeficiency virus type 1 RNA levels measured by branched DNA within and between days. J Infect Dis. 1997 Aug; 176(2):514-7.
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      346. Deeks SG, Abrams DI. Genotypic-resistance assays and antiretroviral therapy. Lancet. 1997 May 24; 349(9064):1489-90.
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      347. Deeks SG. New principles of HIV-related medical care. Focus. 1997 Apr; 12(5):5-7.
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      348. Deeks SG, Smith M, Holodniy M, Kahn JO. HIV-1 protease inhibitors. A review for clinicians. JAMA. 1997 Jan 8; 277(2):145-53.
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      349. Deeks SG, Volberding PA. HIV-1 protease inhibitors. AIDS Clin Rev. 1997-1998; 145-85.
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      350. Gordon M, Deeks S, De Marzo C, Goodgame J, Guralnik M, Lang W, Mimura T, Pearce D, Kaneko Y. Curdlan sulfate (CRDS) in a 21-day intravenous tolerance study in human immunodeficiency virus (HIV) and cytomegalovirus (CMV) infected patients: indication of anti-CMV activity with low toxicity. J Med. 1997; 28(1-2):108-28.
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