Publication Supplemental Data

Nakamura KJ, Heath L, Sobrera ER, Wilkinson TA, Semrau K, Kankasa C, Tobin NH, Webb NE, Lee B, Thea DM, Kuhn L, Mullins JI, Aldrovandi GM 2017 Breast milk and in utero transmission of HIV-1 select for envelope variants with unique molecular signatures. Retrovirology1416 pubmed Supplemental Data
Wagner TA, McLaughlin S, Garg K, Cheung CY, Larsen BB, Styrchak S, Huang HC, Edlefsen PT, Mullins JI, Frenkel LM 2014 HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science (New York, N.Y.)3456196570-3 pubmed Supplemental Data
Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI 2013 Quality score based identification and correction of pyrosequencing errors. PloS one89e73015 pubmed Supplemental Data
Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI 2013 Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. Bioinformatics (Oxford, England)29192402-9 pubmed Supplemental Data
Manocheewa S, Swain JV, Lanxon-Cookson E, Rolland M, Mullins JI 2013 Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface. PloS one86e66065 pubmed Supplemental Data
Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA, Stevens CE, Maenza J, Collier AC, Mullins JI, Hertz T, Yu X, Horton H 2013 Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design. PloS one85e64405 pubmed Supplemental Data
Raugi DN, Smith RA, Ba S, Toure M, Traore F, Sall F, Pan C, Blankenship L, Montano A, Olson J, Dia Badiane NM, Mullins JI, Kiviat NB, Hawes SE, Sow PS, Gottlieb GS, 2013 Complex patterns of protease inhibitor resistance among antiretroviral treatment-experienced HIV-2 patients from Senegal: implications for second-line therapy. Antimicrobial agents and chemotherapy5762751-60 pubmed Supplemental Data
Bull ME, Heath LM, McKernan-Mullin JL, Kraft KM, Acevedo L, Hitti JE, Cohn SE, Tapia KA, Holte SE, Dragavon JA, Coombs RW, Mullins JI, Frenkel LM 2013 Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time. The Journal of infectious diseases20781206-15 pubmed Supplemental Data
Wagner TA, McKernan JL, Tobin NH, Tapia KA, Mullins JI, Frenkel LM 2013 An increasing proportion of monotypic HIV-1 DNA sequences during antiretroviral treatment suggests proliferation of HIV-infected cells. Journal of virology8731770-8 pubmed Supplemental Data
Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI. 2011 Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of Virology85157523-34 pubmed Supplemental Data
Campbell MS, Mullins JI, Hughes JP, Celum C, Wong KG, Raugi DN, Sorensen S, Stoddard JN, Zhao H, Deng W, Kahle E, Panteleeff D, Baeten JM, McCutchan FE, Albert J, Leitner T, Wald A, Corey L, Lingappa JR, 2011 Viral Linkage in HIV-1 Seroconverters and Their Partners in an HIV-1 Prevention Clinical Trial. PloS one63e16986 pubmed Supplemental Data
Curlin ME, Zioni R, Hawes SE, Liu Y, Deng W, Gottlieb GS, Zhu T, Mullins JI 2010 HIV-1 Envelope Subregion Length Variation during Disease Progression. PLoS Pathogens612 e1001228 pubmed Supplemental Data
Gottlieb GS, Badiane NMD, Hawes SE, Fortes L, Toure M, Ndour CT, Starling AK, Traore F, Sall F, Wong KG, CherneSL, AndersonDJ, Dye SA, Smith RA, Mullins JI, Kiviat NB, Sow PS, for the University of Washington-Dakar HIV-2 Study Group 2009 Emergence of Multiclass Drug-Resistance in HIV-2 in Antiretroviral-Treated Individuals in Senegal: Implications for HIV-2 Treatment in Resouce-Limited West Africa. Clinical Infectious Diseases484476-83 pubmed Supplemental Data
Rousseau C, Lockhart D, Listgarten J, Kadie C, Learn G, Maley S, Nickle D, Heckerman D, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder P, Korber B, Walker B, Mullins J 2009 Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles AIDS Research and Human Retroviruses253297-303 pubmed Supplemental Data
Liu Y, Curlin ME, Diem K, Zhao H, Ghosh AK, Zhu H, Woodward AS, Maenza J, Stevens CE, Stekler J, Collier AC, Genowati I, Deng W, Zioni R, Corey L, Zhu T, Mullins JI 2008 Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. Virology3742229-33 pubmed Supplemental Data
Rolland M, Nickle DC, Mullins JI 2007 HIV-1 group M conserved elements vaccine. PLoS pathogens311e157 pubmed Supplemental Data
Rousseau CM, Learn GH, Bhattacharya T, Nickle DC, Heckerman D, Chetty S, Brander C, Goulder PJ, Walker BD, Kiepiela P, Korber BT, Mullins JI 2007 Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. Journal of virology8194492-500 pubmed Supplemental Data
Jensen MA, Coetzer M, van 't Wout AB, Morris L, Mullins JI 2006 A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. Journal of virology80104698-704 pubmed Supplemental Data
Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI 2006 Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. Journal of virology8041637-44 pubmed Supplemental Data
Doria-Rose NA, Learn GH, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, Hensel MT, McLaughlin S, Edmonson PF, Montefiori D, Barnett SW, Haigwood NL, Mullins JI 2005 Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope. Journal of virology791711214-24 pubmed Supplemental Data
Tobin NH, Learn GH, Holte SE, Wang Y, Melvin AJ, McKernan JL, Pawluk DM, Mohan KM, Lewis PF, Mullins JI, Frenkel LM 2005 Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus. Journal of virology79159625-34 pubmed Supplemental Data
Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Grobler J, Li F, Liu SL, Rademeyer C, Learn GH, Karim SS, Williamson C, Corey L, Margolick JB, Mullins JI 2004 Dual HIV-1 infection associated with rapid disease progression. Lancet3639409619-22 pubmed Supplemental Data
Jensen MA, Li FS, van 't Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI 2003 Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. Journal of virology772413376-88 pubmed Supplemental Data
Anderson JP, Learn GH, Rodrigo AG, He X, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI 2003 Predicting demographic group structures based on DNA sequence data. Molecular biology and evolution2071168-80 pubmed Supplemental Data
Frenkel LM, Wang Y, Learn GH, McKernan JL, Ellis GM, Mohan KM, Holte SE, De Vange SM, Pawluk DM, Melvin AJ, Lewis PF, Heath LM, Beck IA, Mahalanabis M, Naugler WE, Tobin NH, Mullins JI 2003 Multiple viral genetic analyses detect low-level human immunodeficiency virus type 1 replication during effective highly active antiretroviral therapy. Journal of virology77105721-30 pubmed Supplemental Data
van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI 2003 Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. Journal of virology7721392-402 pubmed Supplemental Data
Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI 1999 Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. Journal of virology731210489-502 pubmed Supplemental Data
Frenkel LM, Mullins JI, Learn GH, Manns-Arcuino L, Herring BL, Kalish ML, Steketee RW, Thea DM, Nichols JE, Liu SL, Harmache A, He X, Muthui D, Madan A, Hood L, Haase AT, Zupancic M, Staskus K, Wolinsky S, Krogstad P, Zhao J, Chen I, Koup R, Ho D, Korber B, Apple RJ, Coombs RW, Pahwa S, Roberts NJ 1998 Genetic evaluation of suspected cases of transient HIV-1 infection of infants. Science (New York, N.Y.)28053661073-7 pubmed Supplemental Data
Bachmann MH, Mathiason-Dubard C, Learn GH, Rodrigo AG, Sodora DL, Mazzetti P, Hoover EA, Mullins JI 1997 Genetic diversity of feline immunodeficiency virus: dual infection, recombination, and distinct evolutionary rates among envelope sequence clades. Journal of virology7164241-53 pubmed Supplemental Data
Department of Microbiology
School of Medicine
University of Washington
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