PubMed

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1.

Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD.

Mol Biol Evol. 2009 Dec 2. [Epub ahead of print]PMID: 19955476 [PubMed - as supplied by publisher]Related articles

HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins.

Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, Swenson LC, Tao I, Szeto S, Rosato P, Sela J, Kadie CM, Frahm N, Brander C, Haas DW, Riddler SA, Haubrich R, Walker BD, Harrigan PR, Heckerman D, Mallal S.

PLoS One. 2009 Aug 19;4(8):e6687.PMID: 19690614 [PubMed - in process]Related articlesFree article

Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study.

Avila-Rios S, Ormsby CE, Carlson JM, Valenzuela-Ponce H, Blanco-Heredia J, Garrido-Rodriguez D, Garcia-Morales C, Heckerman D, Brumme ZL, Mallal S, John M, Espinosa E, Reyes-Teran G.

Retrovirology. 2009 Aug 10;6:72.PMID: 19664284 [PubMed - indexed for MEDLINE]Related articlesFree article

Impact of select immunologic and virologic biomarkers on CD4 cell count decrease in patients with chronic HIV-1 subtype C infection: results from Sinikithemba Cohort, Durban, South Africa.

Brumme Z, Wang B, Nair K, Brumme C, de Pierres C, Reddy S, Julg B, Moodley E, Thobakgale C, Lu Z, van der Stok M, Bishop K, Mncube Z, Chonco F, Yuki Y, Frahm N, Brander C, Carrington M, Freedberg K, Kiepiela P, Goulder P, Walker B, Ndung'u T, Losina E.

Clin Infect Dis. 2009 Sep 15;49(6):956-64.PMID: 19663693 [PubMed - indexed for MEDLINE]Related articles

Tracking the culprit: HIV-1 evolution and immune selection revealed by single-genome amplification.

Brumme ZL, Walker BD.

J Exp Med. 2009 Jun 8;206(6):1215-8. Epub 2009 Jun 1.PMID: 19487418 [PubMed - indexed for MEDLINE]Related articles

Adaptation of HIV-1 to human leukocyte antigen class I.

Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A, Koizumi H, Kuse N, Oka S, Duda A, Prendergast A, Crawford H, Leslie A, Brumme Z, Brumme C, Allen T, Brander C, Kaslow R, Tang J, Hunter E, Allen S, Mulenga J, Branch S, Roach T, John M, Mallal S, Ogwu A, Shapiro R, Prado JG, Fidler S, Weber J, Pybus OG, Klenerman P, Ndung'u T, Phillips R, Heckerman D, Harrigan PR, Walker BD, Takiguchi M, Goulder P.

Nature. 2009 Apr 2;458(7238):641-5. Epub 2009 Feb 25.PMID: 19242411 [PubMed - indexed for MEDLINE]Related articles

HLA-associated viral mutations are common in human immunodeficiency virus type 1 elite controllers.

Miura T, Brumme CJ, Brockman MA, Brumme ZL, Pereyra F, Block BL, Trocha A, John M, Mallal S, Harrigan PR, Walker BD.

J Virol. 2009 Apr;83(7):3407-12. Epub 2009 Jan 19.PMID: 19153230 [PubMed - indexed for MEDLINE]Related articlesFree article

HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition.

Miura T, Brockman MA, Schneidewind A, Lobritz M, Pereyra F, Rathod A, Block BL, Brumme ZL, Brumme CJ, Baker B, Rothchild AC, Li B, Trocha A, Cutrell E, Frahm N, Brander C, Toth I, Arts EJ, Allen TM, Walker BD.

J Virol. 2009 Mar;83(6):2743-55. Epub 2008 Dec 30. Erratum in: J Virol. 2009 Jun;83(11):5961. PMID: 19116253 [PubMed - indexed for MEDLINE]Related articlesFree article

Transmission and long-term stability of compensated CD8 escape mutations.

Schneidewind A, Brumme ZL, Brumme CJ, Power KA, Reyor LL, O'Sullivan K, Gladden A, Hempel U, Kuntzen T, Wang YE, Oniangue-Ndza C, Jessen H, Markowitz M, Rosenberg ES, Sékaly RP, Kelleher AD, Walker BD, Allen TM.

J Virol. 2009 Apr;83(8):3993-7. Epub 2008 Dec 17.PMID: 19091871 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Nov 21.PMID: 19023406 [PubMed - indexed for MEDLINE]Related articlesFree article

HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1.

Miura T, Brockman MA, Brumme ZL, Brumme CJ, Pereyra F, Trocha A, Block BL, Schneidewind A, Allen TM, Heckerman D, Walker BD.

J Virol. 2009 Jan;83(1):140-9. Epub 2008 Oct 29.PMID: 18971283 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Jul 9.PMID: 18614631 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18580606 [PubMed - indexed for MEDLINE]Related articles

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. Epub 2008 Jun 18.PMID: 18562530 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18462013 [PubMed - indexed for MEDLINE]Related articlesFree article

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. Epub 2008 Feb 1. Review.PMID: 18407775 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 18392148 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18240966 [PubMed - indexed for MEDLINE]Related articles

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.PMID: 17678473 [PubMed - indexed for MEDLINE]Related articles

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. Erratum in: PLoS Pathog. 2007 Aug 10;3(8):e121. PMID: 17616974 [PubMed - indexed for MEDLINE]Related articlesFree article