2008 and previous

Herpes simplex virus as a tool to define the role of complement in the immune response to peripheral infection. Brockman MA, Knipe DM. Vaccine. 2008 Dec 30;26 Suppl 8(Suppl 8):I94-9. doi: 10.1016/j.vaccine.2008.11.062.

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. Carlson JM, Brumme ZL, Rousseau CM, Brumme CJ, Matthews P, Kadie C, Mullins JI, Walker BD, Harrigan PR, Goulder PJ, Heckerman D. PLoS Comput Biol. 2008 Nov;4(11):e1000225. doi: 10.1371/journal.pcbi.1000225. Epub 2008 Nov 21.

Type 2 Bias of T cells expanded from the blood of melanoma patients switched to type 1 by IL-12p70 mRNA-transfected dendritic cells. Minkis K, Kavanagh DG, Alter G, Bogunovic D, O'Neill D, Adams S, Pavlick A, Walker BD, Brockman MA, Gandhi RT, Bhardwaj N. Cancer Res. 2008 Nov 15;68(22):9441-50. doi: 10.1158/0008-5472.CAN-08-0900.

Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. Brumme ZL, Brumme CJ, Carlson J, Streeck H, John M, Eichbaum Q, Block BL, Baker B, Kadie C, Markowitz M, Jessen H, Kelleher AD, Rosenberg E, Kaldor J, Yuki Y, Carrington M, Allen TM, Mallal S, Altfeld M, Heckerman D, Walker BD. J Virol. 2008 Sep;82(18):9216-27. doi: 10.1128/JVI.01041-08. Epub 2008 Jul 9.

Human leukocyte antigen-specific polymorphisms in HIV-1 Gag and their association with viral load in chronic untreated infection. Brumme ZL, Tao I, Szeto S, Brumme CJ, Carlson JM, Chan D, Kadie C, Frahm N, Brander C, Walker B, Heckerman D, Harrigan PR. AIDS. 2008 Jul 11;22(11):1277-86. doi: 10.1097/QAD.0b013e3283021a8c.

Genetic characterization of human immunodeficiency virus type 1 in elite controllers: lack of gross genetic defects or common amino acid changes. Miura T, Brockman MA, Brumme CJ, Brumme ZL, Carlson JM, Pereyra F, Trocha A, Addo MM, Block BL, Rothchild AC, Baker BM, Flynn T, Schneidewind A, Li B, Wang YE, Heckerman D, Allen TM, Walker BD. J Virol. 2008 Sep;82(17):8422-30. doi: 10.1128/JVI.00535-08. Epub 2008 Jun 18.

Quantitative effect of suboptimal codon usage on translational efficiency of mRNA encoding HIV-1 gag in intact T cells. Ngumbela KC, Ryan KP, Sivamurthy R, Brockman MA, Gandhi RT, Bhardwaj N, Kavanagh DG. PLoS One. 2008 Jun 4;3(6):e2356. doi: 10.1371/journal.pone.0002356.

Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid. Schneidewind A, Brockman MA, Sidney J, Wang YE, Chen H, Suscovich TJ, Li B, Adam RI, Allgaier RL, Mothé BR, Kuntzen T, Oniangue-Ndza C, Trocha A, Yu XG, Brander C, Sette A, Walker BD, Allen TM. J Virol. 2008 Jun;82(11):5594-605. doi: 10.1128/JVI.02356-07. Epub 2008 Apr 2.

Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells. Streeck H, Brumme ZL, Anastario M, Cohen KW, Jolin JS, Meier A, Brumme CJ, Rosenberg ES, Alter G, Allen TM, Walker BD, Altfeld M. PLoS Med. 2008 May 6;5(5):e100. doi: 10.1371/journal.pmed.0050100.

Rapid ex vivo isolation and long-term culture of human Th17 cells. Streeck H, Cohen KW, Jolin JS, Brockman MA, Meier A, Power KA, Waring MT, Alter G, Altfeld M. J Immunol Methods. 2008 Apr 20;333(1-2):115-25. doi: 10.1016/j.jim.2008.01.018. Epub 2008 Feb 15.

Upregulation of PD-L1 on monocytes and dendritic cells by HIV-1 derived TLR ligands. Meier A, Bagchi A, Sidhu HK, Alter G, Suscovich TJ, Kavanagh DG, Streeck H, Brockman MA, LeGall S, Hellman J, Altfeld M. AIDS. 2008 Mar 12;22(5):655-8. doi: 10.1097/QAD.0b013e3282f4de23.

HIV evolution in response to HLA-restricted CTL selection pressures: a population-based perspective. Carlson JM, Brumme ZL. Microbes Infect. 2008 Apr;10(5):455-61. doi: 10.1016/j.micinf.2008.01.013. Epub 2008 Feb 1.

HIV increases HCV replication in a TGF-beta1-dependent manner. Lin W, Weinberg EM, Tai AW, Peng LF, Brockman MA, Kim KA, Kim SS, Borges CB, Shao RX, Chung RT. Gastroenterology. 2008 Mar;134(3):803-11. doi: 10.1053/j.gastro.2008.01.005. Epub 2008 Jan 10.

Statistical resolution of ambiguous HLA typing data. Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, Carrington M, Goulder P, Heckerman D. PLoS Comput Biol. 2008 Feb 29;4(2):e1000016. doi: 10.1371/journal.pcbi.1000016.

CD4-dependent characteristics of coreceptor use and HIV type 1 V3 sequence in a large population of therapy-naive individuals. Low AJ, Marchant D, Brumme CJ, Brumme ZL, Dong W, Sing T, Hogg RS, Montaner JS, Gill V, Cheung PK, Harrigan PR. AIDS Res Hum Retroviruses. 2008 Feb;24(2):219-28. doi: 10.1089/aid.2007.0140.

Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. Schneidewind A, Brockman MA, Yang R, Adam RI, Li B, Le Gall S, Rinaldo CR, Craggs SL, Allgaier RL, Power KA, Kuntzen T, Tung CS, LaBute MX, Mueller SM, Harrer T, McMichael AJ, Goulder PJ, Aiken C, Brander C, Kelleher AD, Allen TM. J Virol. 2007 Nov;81(22):12382-93. doi: 10.1128/JVI.01543-07. Epub 2007 Sep 5.

Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A. Brockman MA, Schneidewind A, Lahaie M, Schmidt A, Miura T, Desouza I, Ryvkin F, Derdeyn CA, Allen S, Hunter E, Mulenga J, Goepfert PA, Walker BD, Allen TM. J Virol. 2007 Nov;81(22):12608-18. doi: 10.1128/JVI.01369-07. Epub 2007 Aug 29.

A 21-base pair insertion/duplication at codon 69 of the HIV type 1 reverse transcriptase in a patient undergoing multiple nucleoside therapy. Harrigan PR, Mo T, Hirsch J, Brumme ZL, McKenna P, Bacheler L. AIDS Res Hum Retroviruses. 2007 Jul;23(7):895-9. doi: 10.1089/aid.2006.0198.

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. Brumme ZL, Brumme CJ, Heckerman D, Korber BT, Daniels M, Carlson J, Kadie C, Bhattacharya T, Chui C, Szinger J, Mo T, Hogg RS, Montaner JS, Frahm N, Brander C, Walker BD, Harrigan PR. PLoS Pathog. 2007 Jul;3(7):e94. doi: 10.1371/journal.ppat.0030094.

A simple screening approach to reduce B*5701-associated abacavir hypersensitivity on the basis of sequence variation in HIV reverse transcriptase. Chui CK, Brumme ZL, Brumme CJ, Yip B, Phillips EJ, Montaner JS, Harrigan PR. Clin Infect Dis. 2007 Jun 1;44(11):1503-8. doi: 10.1086/517499. Epub 2007 Apr 18.

Effects of human leukocyte antigen class I genetic parameters on clinical outcomes and survival after initiation of highly active antiretroviral therapy. Brumme ZL, Brumme CJ, Chui C, Mo T, Wynhoven B, Woods CK, Henrick BM, Hogg RS, Montaner JS, Harrigan PR. J Infect Dis. 2007 Jun 1;195(11):1694-704. doi: 10.1086/516789. Epub 2007 Apr 24. PMID: 17471440

Assay of HIV gp41 amino acid sequence to identify baseline variation and mutation development in patients with virologic failure on enfuvirtide. Loutfy MR, Raboud JM, Montaner JS, Antoniou T, Wynhoven B, Smaill F, Rouleau D, Gill J, Schlech W, Brumme ZL, Mo T, Gough K, Rachlis A, Harrigan PR, Walmsley SL. Antiviral Res. 2007 Jul;75(1):58-63. doi: 10.1016/j.antiviral.2006.11.011. Epub 2006 Dec 18.

Selective depletion of high-avidity human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T cells after early HIV-1 infection. Lichterfeld M, Yu XG, Mui SK, Williams KL, Trocha A, Brockman MA, Allgaier RL, Waring MT, Koibuchi T, Johnston MN, Cohen D, Allen TM, Rosenberg ES, Walker BD, Altfeld M. J Virol. 2007 Apr;81(8):4199-214. doi: 10.1128/JVI.01388-06. Epub 2007 Feb 7.

Properties of a herpes simplex virus multiple immediate-early gene-deleted recombinant as a vaccine vector. Watanabe D, Brockman MA, Ndung'u T, Mathews L, Lucas WT, Murphy CG, Felber BK, Pavlakis GN, Deluca NA, Knipe DM. Virology. 2007 Jan 20;357(2):186-98. doi: 10.1016/j.virol.2006.08.015. Epub 2006 Sep 22.

The impact of human genetic variation on HIV disease in the era of HAART. Brumme ZL, Harrigan PR. AIDS Rev. 2006 Apr-Jun;8(2):78-87.

HIV VprR77Q mutation does not influence clinical response of individuals initiating highly active antiretroviral therapy. Chui C, Cheung PK, Brumme CJ, Mo T, Brumme ZL, Montaner JS, Badley AD, Harrigan PR. AIDS Res Hum Retroviruses. 2006 Jul;22(7):615-8. doi: 10.1089/aid.2006.22.615.

Optimal long-term humoral responses to replication-defective herpes simplex virus require CD21/CD35 complement receptor expression on stromal cells. Brockman MA, Verschoor A, Zhu J, Carroll MC, Knipe DM. J Virol. 2006 Jul;80(14):7111-7. doi: 10.1128/JVI.01421-05.

HIV therapy, hepatitis C virus infection, antibiotics and obesity, a mitochondria killer mix? Côté HC, Brumme ZL, Chan JW, Guillemi S, Montaner JS, Harrigan PR. AIDS. 2006 Jun 12;20(9):1343-5. doi: 10.1097/01.aids.0000232250.89404.00.

Use of a novel GFP reporter cell line to examine replication capacity of CXCR4- and CCR5-tropic HIV-1 by flow cytometry. Brockman MA, Tanzi GO, Walker BD, Allen TM. J Virol Methods. 2006 Feb;131(2):134-42. doi: 10.1016/j.jviromet.2005.08.003. Epub 2005 Sep 22.

Short communication. Association of the CCR5delta32 mutation with clinical response and >5-year survival following initiation of first triple antiretroviral regimen. Brumme ZL, Henrick BM, Brumme CJ, Hogg RS, Montaner JS, Harrigan PR. Antivir Ther. 2005;10(7):849-53.

Treatment interruption of highly active antiretroviral therapy in patients with nadir CD4 cell counts >200 cells/mm3. Toulson AR, Harrigan R, Heath K, Yip B, Brumme ZL, Harris M, Hogg RS, Montaner JS. J Infect Dis. 2005 Nov 15;192(10):1787-93. doi: 10.1086/491738. Epub 2005 Oct 5.

Molecular and clinical epidemiology of CXCR4-using HIV-1 in a large population of antiretroviral-naive individuals. Brumme ZL, Goodrich J, Mayer HB, Brumme CJ, Henrick BM, Wynhoven B, Asselin JJ, Cheung PK, Hogg RS, Montaner JS, Harrigan PR. J Infect Dis. 2005 Aug 1;192(3):466-74. doi: 10.1086/431519. Epub 2005 Jun 23.

Rare mutations at codon 103 of HIV-1 reverse transcriptase can confer resistance to non-nucleoside reverse transcriptase inhibitors. Harrigan PR, Mo T, Wynhoven B, Hirsch J, Brumme Z, McKenna P, Pattery T, Vingerhoets J, Bacheler LT. AIDS. 2005 Mar 24;19(6):549-54. doi: 10.1097/01.aids.0000163930.68907.37.

HIV-1 drug resistance: degree of underestimation by a cross-sectional versus a longitudinal testing approach. Harrigan PR, Wynhoven B, Brumme ZL, Brumme CJ, Sattha B, Major JC, de la Rosa R, Montaner JS. J Infect Dis. 2005 Apr 15;191(8):1325-30. doi: 10.1086/428852. Epub 2005 Mar 16.

Predictors of HIV drug-resistance mutations in a large antiretroviral-naive cohort initiating triple antiretroviral therapy. Harrigan PR, Hogg RS, Dong WW, Yip B, Wynhoven B, Woodward J, Brumme CJ, Brumme ZL, Mo T, Alexander CS, Montaner JS. J Infect Dis. 2005 Feb 1;191(3):339-47. doi: 10.1086/427192. Epub 2004 Dec 22.

Antiretroviral resistance among HIV-infected persons who have died in British Columbia, in the era of modern antiretroviral therapy. Recsky MA, Brumme ZL, Chan KJ, Wynhoven B, Yip B, Dong WW, Heath KV, Montaner JS, Levy AR, Hogg RS, Harrigan PR. J Infect Dis. 2004 Jul 15;190(2):285-92. doi: 10.1086/422007. Epub 2004 Jun 11.

Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. Brumme ZL, Dong WW, Yip B, Wynhoven B, Hoffman NG, Swanstrom R, Jensen MA, Mullins JI, Hogg RS, Montaner JS, Harrigan PR. AIDS. 2004 Mar 5;18(4):F1-9. doi: 10.1097/00002030-200403050-00001.

Myeloid C3 determines induction of humoral responses to peripheral herpes simplex virus infection. Verschoor A, Brockman MA, Gadjeva M, Knipe DM, Carroll MC. J Immunol. 2003 Nov 15;171(10):5363-71. doi: 10.4049/jimmunol.171.10.5363.

Modest decreases in NNRTI susceptibility do not influence virological outcome in patients receiving initial NNRTI-containing triple therapy. Harrigan PR, Hertogs K, Verbiest W, Larder B, Yip B, Brumme ZL, Alexander C, Tilley J, O'Shaughnessy MV, Montaner JS. Antivir Ther. 2003 Oct;8(5):395-402.

Insulin-like growth factor-1 protects ischemic murine myocardium from ischemia/reperfusion associated injury. Davani EY, Brumme Z, Singhera GK, Côté HC, Harrigan PR, Dorscheid DR. Crit Care. 2003 Dec;7(6):R176-83. doi: 10.1186/cc2375. Epub 2003 Oct 10.

Prevalence and clinical implications of insertions in the HIV-1 p6Gag N-terminal region in drug-naive individuals initiating antiretroviral therapy. Brumme ZL, Chan KJ, Dong WW, Wynhoven B, Mo T, Hogg RS, Montaner JS, O'Shaughnessy MV, Harrigan PR. Antivir Ther. 2003 Apr;8(2):91-6.

Influence of polymorphisms within the CX3CR1 and MDR-1 genes on initial antiretroviral therapy response. Brumme ZL, Dong WW, Chan KJ, Hogg RS, Montaner JS, O'Shaughnessy MV, Harrigan PR. AIDS. 2003 Jan 24;17(2):201-8. doi: 10.1097/00002030-200301240-00010.

Macrophage-derived complement component C4 can restore humoral immunity in C4-deficient mice. Gadjeva M, Verschoor A, Brockman MA, Jezak H, Shen LM, Knipe DM, Carroll MC. J Immunol. 2002 Nov 15;169(10):5489-95. doi: 10.4049/jimmunol.169.10.5489.

No association between GB virus-C viremia and virological or immunological failure after starting initial antiretroviral therapy. Brumme ZL, Chan KJ, Dong WW, Mo T, Wynhoven B, Hogg RS, Montaner JS, O'Shaughnessy MV, Harrigan PR. AIDS. 2002 Sep 27;16(14):1929-33. doi: 10.1097/00002030-200209270-00010.

A mutation in the 3' region of the human immunodeficiency virus type 1 reverse transcriptase (Y318F) associated with nonnucleoside reverse transcriptase inhibitor resistance. Harrigan PR, Salim M, Stammers DK, Wynhoven B, Brumme ZL, McKenna P, Larder B, Kemp SD. J Virol. 2002 Jul;76(13):6836-40. doi: 10.1128/jvi.76.13.6836-6840.2002.

Phenotypic susceptibilities to tenofovir in a large panel of clinically derived human immunodeficiency virus type 1 isolates. Harrigan PR, Miller MD, McKenna P, Brumme ZL, Larder BA. Antimicrob Agents Chemother. 2002 Apr;46(4):1067-72. doi: 10.1128/AAC.46.4.1067-1072.2002.

Herpes simplex virus vectors elicit durable immune responses in the presence of preexisting host immunity. Brockman MA, Knipe DM. J Virol. 2002 Apr;76(8):3678-87. doi: 10.1128/jvi.76.8.3678-3687.2002.

Herpes simplex virus. Taylor TJ, Brockman MA, McNamee EE, Knipe DM. Front Biosci. 2002 Mar 1;7:d752-64. doi: 10.2741/taylor.

Changes in mitochondrial DNA as a marker of nucleoside toxicity in HIV-infected patients. Côté HC, Brumme ZL, Craib KJ, Alexander CS, Wynhoven B, Ting L, Wong H, Harris M, Harrigan PR, O'Shaughnessy MV, Montaner JS. N Engl J Med. 2002 Mar 14;346(11):811-20. doi: 10.1056/NEJMoa012035.

CCR5Delta32 and promoter polymorphisms are not correlated with initial virological or immunological treatment response. Brumme ZL, Chan KJ, Dong W, Hogg R, O'Shaughnessy MV, Montaner JS, Harrigan PR. AIDS. 2001 Nov 23;15(17):2259-66. doi: 10.1097/00002030-200111230-00007.

Cutting edge: myeloid complement C3 enhances the humoral response to peripheral viral infection. Verschoor A, Brockman MA, Knipe DM, Carroll MC. J Immunol. 2001 Sep 1;167(5):2446-51. doi: 10.4049/jimmunol.167.5.2446.

Human immunodeficiency virus type 1 protease cleavage site mutations associated with protease inhibitor cross-resistance selected by indinavir, ritonavir, and/or saquinavir. Côté HC, Brumme ZL, Harrigan PR. J Virol. 2001 Jan;75(2):589-94. doi: 10.1128/JVI.75.2.589-594.2001.

Construction, phenotypic analysis, and immunogenicity of a UL5/UL29 double deletion mutant of herpes simplex virus 2. Da Costa X, Kramer MF, Zhu J, Brockman MA, Knipe DM. J Virol. 2000 Sep;74(17):7963-71. doi: 10.1128/jvi.74.17.7963-7971.2000.

Humoral response to herpes simplex virus is complement-dependent. Da Costa XJ, Brockman MA, Alicot E, Ma M, Fischer MB, Zhou X, Knipe DM, Carroll MC. Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12708-12. doi: 10.1073/pnas.96.22.12708.