Mullins Molecular Retrovirology Lab

  • Department of Microbiology
  • School of Medicine
  • University of Washington
University of Washington/Fred Hutch Center for AIDS Research

Publications

2021

Raugi DN, Ba S, Cisse O, Diallo K, Tamba IT, Ndour C, Badiane NMD, Fortes L, Diallo MB, Faye D, Smith RA, Sall F, Toure M, Sall EI, Diallo Agne H, Faye K, Diatta JP, Sy MP, Chang M, Diaw B, Sambou J, Bakhoum R, Sy MD, Niang A, Malomar JJ, Coombs RW, Hawes SE, Ndoye I, Kiviat NB, Sow PS, Seydi M, Gottlieb GS, University of Washington–Senegal HIV-2 Study Group (2021). Long-term Experience and Outcomes of Programmatic Antiretroviral Therapy for Human Immunodeficiency Virus Type 2 Infection in Senegal, West Africa. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 72(3), 369-378. (pubmed) (doi)

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Santiago JC, Goldman JD, Zhao H, Pankow AP, Okuku F, Schmitt MW, Chen LH, Hill CA, Casper C, Phipps WT, Mullins JI (2021). Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma. PLoS pathogens, 17(1), e1008594. (pubmed) (doi)

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2020

Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Kirtley S, Gouws-Williams E, Ghys PD, WHO-UNAIDS Network for HIV Isolation and Characterisation (2020). Global and regional epidemiology of HIV-1 recombinants in 1990-2015: a systematic review and global survey. The lancet. HIV, 7(11), e772-e781. (pubmed) (doi)

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Aamer HA, McClure J, Ko D, Maenza J, Collier AC, Coombs RW, Mullins JI, Frenkel LM (2020). Cells producing residual viremia during antiretroviral treatment appear to contribute to rebound viremia following interruption of treatment. PLoS pathogens, 16(8), e1008791. (pubmed) (doi)

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2019

Trebelcock WL, Lama JR, Duerr A, Sanchez H, Cabello R, Gilada T, Segura P, Reisner SL, Mayer KH, Mullins J, Bender Ignacio RA (2019). HIV pretreatment drug resistance among cisgender MSM and transgender women from Lima, Peru. Journal of the International AIDS Society, 22(11), e25411. (pubmed) (doi)

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Williams-Wietzikoski CA, Campbell MS, Payant R, Lam A, Zhao H, Huang H, Wald A, Stevens W, Gray G, Farquhar C, Rees H, Celum C, Mullins JI, Lingappa JR, Frenkel LM (2019). Comparisons of Human Immunodeficiency Virus Type 1 Envelope Variants in Blood and Genital Fluids near the Time of Male-to-Female Transmission. Journal of virology (ePub ahead of print). (pubmed) (doi)

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Bull ME, McKernan JL, Styrchak S, Kraft K, Hitti J, Cohn SE, Tapia K, Deng W, Holte S, Mullins JI, Coombs RW, Frenkel LM (2019). Phylogenetic Analyses Comparing HIV Sequences from Plasma at Virologic Failure to Cervix Versus Blood Sequences from Antecedent Antiretroviral Therapy Suppression. AIDS research and human retroviruses, 35(6), 557-566. (pubmed) (doi)

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Smith RA, Raugi DN, Wu VH, Zavala CG, Song J, Diallo KM, Seydi M, Gottlieb GS, University of Washington-Dakar HIV-2 Study Group (2019). Comparison of the Antiviral Activity of Bictegravir against HIV-1 and HIV-2 Isolates and Integrase Inhibitor-Resistant HIV-2 Mutants. Antimicrobial agents and chemotherapy (ePub ahead of print). (pubmed) (doi)

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Sibley TR, Silberman EJ, Mullins JI (2019). ISDB: a database toolkit for storing and analyzing viral integration site data. Bioinformatics (Oxford, England), 35(6), 1073-1075. (pubmed) (doi)

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O'Connor MA, Munson PV, Tunggal HC, Hajari N, Lewis TB, Bratt D, Moats C, Smedley J, Bagley KC, Mullins JI, Fuller DH (2019). Mucosal T Helper 17 and T Regulatory Cell Homeostasis Correlate with Acute Simian Immunodeficiency Virus Viremia and Responsiveness to Antiretroviral Therapy in Macaques. AIDS research and human retroviruses, 35(3), 295-305. (pubmed) (doi)

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Mackelprang RD, Bamshad MJ, Chong JX, Hou X, Buckingham KJ, Shively K, deBruyn G, Mugo NR, Mullins JI, McElrath MJ, Baeten JM, Celum C, Emond MJ, Lingappa JR, Partners in Prevention HSV/HIV Transmission Study and the Partners PrEP Study Teams (2019). Correction: Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1. PLoS pathogens, 15(2), e1007588. (pubmed) (doi)

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Hemelaar J, Elangovan R, Yun J, Dickson-Tetteh L, Fleminger I, Kirtley S, Williams B, Gouws-Williams E, Ghys PD, WHO–UNAIDS Network for HIV Isolation Characterisation (2019). Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis. The Lancet. Infectious diseases, 19(2), 143-155. (pubmed) (doi)

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2018

Smith RA, Wu VH, Zavala CG, Raugi DN, Ba S, Seydi M, Gottlieb GS, University of Washington-Dakar HIV-2 Study Group (2018). In Vitro Antiviral Activity of Cabotegravir against HIV-2. Antimicrobial agents and chemotherapy (ePub ahead of print). (pubmed) (doi)

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Hu X, Valentin A, Cai Y, Dayton F, Rosati M, Ramírez-Salazar EG, Kulkarni V, Broderick KE, Sardesai NY, Wyatt LS, Earl PL, Moss B, Mullins JI, Pavlakis GN, Felber BK (2018). DNA Vaccine-Induced Long-Lasting Cytotoxic T Cells Targeting Conserved Elements of Human Immunodeficiency Virus Gag Are Boosted Upon DNA or Recombinant Modified Vaccinia Ankara Vaccination. Human gene therapy, 29(9), 1029-1043. (pubmed) (doi)

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Stekler JD, Tapia K, Maenza J, Stevens CE, Ure GA, O'Neal JD, Lane A, Mullins JI, Coombs RW, Holte S, Collier AC (2018). No Time to Delay! Fiebig Stages and Referral in Acute HIV infection: Seattle Primary Infection Program Experience. AIDS research and human retroviruses, 34(8), 657-666. (pubmed) (doi)

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Hu X, Lu Z, Valentin A, Rosati M, Broderick KE, Sardesai NY, Marx PA, Mullins JI, Pavlakis GN, Felber BK (2018). Gag and env conserved element CE DNA vaccines elicit broad cytotoxic T cell responses targeting subdominant epitopes of HIV and SIV Able to recognize virus-infected cells in macaques. Human vaccines & immunotherapeutics, 14(9), 2163-2177. (pubmed) (doi)

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Munson P, Liu Y, Bratt D, Fuller JT, Hu X, Pavlakis GN, Felber BK, Mullins JI, Fuller DH (2018). Therapeutic conserved elements (CE) DNA vaccine induces strong T-cell responses against highly conserved viral sequences during simian-human immunodeficiency virus infection. Human vaccines & immunotherapeutics, 14(7), 1820-1831. (pubmed) (doi)

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Stekler JD, Milne R, Payant R, Beck I, Herbeck J, Maust B, Deng W, Tapia K, Holte S, Maenza J, Stevens CE, Mullins JI, Collier AC, Frenkel LM (2018). Transmission of HIV-1 drug resistance mutations within partner-pairs: A cross-sectional study of a primary HIV infection cohort. PLoS medicine, 15(3), e1002537. (pubmed) (doi)

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Herbeck JT, Peebles K, Edlefsen PT, Rolland M, Murphy JT, Gottlieb GS, Abernethy N, Mullins JI, Mittler JE, Goodreau SM (2018). HIV population-level adaptation can rapidly diminish the impact of a partially effective vaccine. Vaccine, 36(4), 514-520. (pubmed) (doi)

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2017

King CC, Ellington SR, Davis NL, Coombs RW, Pyra M, Hong T, Mugo N, Patel RC, Lingappa JR, Baeten JM, Kourtis AP, Partners in Prevention HSV/HIV Transmission Study and Partners PrEP Study Teams (2017). Prevalence, Magnitude, and Correlates of HIV-1 Genital Shedding in Women on Antiretroviral Therapy. The Journal of infectious diseases, 216(12), 1534-1540. (pubmed) (doi)

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Hu X, Valentin A, Rosati M, Manocheewa S, Alicea C, Chowdhury B, Bear J, Broderick KE, Sardesai NY, Gall SL, Mullins JI, Pavlakis GN, Felber BK (2017). HIV Env conserved element DNA vaccine alters immunodominance in macaques. Human vaccines & immunotherapeutics, 13(12), 2859-2871. (pubmed) (doi)

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deCamp AC, Rolland M, Edlefsen PT, Sanders-Buell E, Hall B, Magaret CA, Fiore-Gartland AJ, Juraska M, Carpp LN, Karuna ST, Bose M, LePore S, Miller S, O'Sullivan A, Poltavee K, Bai H, Dommaraju K, Zhao H, Wong K, Chen L, Ahmed H, Goodman D, Tay MZ, Gottardo R, Koup RA, Bailer R, Mascola JR, Graham BS, Roederer M, O'Connell RJ, Michael NL, Robb ML, Adams E, D'Souza P, Kublin J, Corey L, Geraghty DE, Frahm N, Tomaras GD, McElrath MJ, Frenkel L, Styrchak S, Tovanabutra S, Sobieszczyk ME, Hammer SM, Kim JH, Mullins JI, Gilbert PB (2017). Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120. PloS one, 12(11), e0185959. (pubmed) (doi)

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Mackelprang RD, Bamshad MJ, Chong JX, Hou X, Buckingham KJ, Shively K, deBruyn G, Mugo NR, Mullins JI, McElrath MJ, Baeten JM, Celum C, Emond MJ, Lingappa JR, Partners in Prevention HSV/HIV Transmission Study and the Partners PrEP Study Teams (2017). Whole genome sequencing of extreme phenotypes identifies variants in CD101 and UBE2V1 associated with increased risk of sexually acquired HIV-1. PLoS pathogens, 13(11), e1006703. (pubmed) (doi)

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Bochner AF, Baeten JM, Rustagi AS, Nakku-Joloba E, Lingappa JR, Mugo NR, Bukusi EA, Kapiga S, Delany-Moretlwe S, Celum C, Barnabas RV, Partners in Prevention HSV/HIV Transmission Study and Partners PrEP Study Teams (2017). A cross-sectional analysis of Trichomonas vaginalis infection among heterosexual HIV-1 serodiscordant African couples. Sexually transmitted infections, 93(7), 520-529. (pubmed) (doi)

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Supplemental data

Dapp MJ, Kober KM, Chen L, Westfall DH, Wong K, Zhao H, Hall BM, Deng W, Sibley T, Ghorai S, Kim K, Chen N, McHugh S, Au L, Cohen M, Anastos K, Mullins JI (2017). Patterns and rates of viral evolution in HIV-1 subtype B infected females and males. PloS one, 12(10), e0182443. (pubmed) (doi)

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Wu VH, Smith RA, Masoum S, Raugi DN, Ba S, Seydi M, Grobler JA, Gottlieb GS, University of Washington–Dakar HIV-2 Study Group (2017). MK-8591 (4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine) Exhibits Potent Activity against HIV-2 Isolates and Drug-Resistant HIV-2 Mutants in Culture. Antimicrobial agents and chemotherapy (ePub ahead of print). (pubmed) (doi)

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Mullins JI, Frenkel LM (2017). Clonal Expansion of Human Immunodeficiency Virus-Infected Cells and Human Immunodeficiency Virus Persistence During Antiretroviral Therapy. The Journal of infectious diseases, 215(suppl_3), S119-S127. (pubmed) (doi)

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Nedellec R, Herbeck JT, Hunt PW, Deeks SG, Mullins JI, Anton ED, Reeves JD, Mosier DE (2017). High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia. AIDS research and human retroviruses, 33(3), 234-245. (pubmed) (doi)

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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. Retrovirology, 14(1), 6. (pubmed) (doi)

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2016

Hu X, Valentin A, Dayton F, Kulkarni V, Alicea C, Rosati M, Chowdhury B, Gautam R, Broderick KE, Sardesai NY, Martin MA, Mullins JI, Pavlakis GN, Felber BK (2016). DNA Prime-Boost Vaccine Regimen To Increase Breadth, Magnitude, and Cytotoxicity of the Cellular Immune Responses to Subdominant Gag Epitopes of Simian Immunodeficiency Virus and HIV. Journal of immunology (Baltimore, Md. : 1950), 197(10), 3999-4013. (pubmed)

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Goldman JD, Frenkel LM, Mullins JI (2016). HIV Transmission During Condomless Sex With a Seropositive Partner With Suppressed Infection. JAMA, 316(19), 2044-2045. (pubmed) (doi)

Smith KN, Mailliard RB, Piazza PA, Fischer W, Korber BT, Fecek RJ, Ratner D, Gupta P, Mullins JI, Rinaldo CR (2016). Erratum for Smith et al., Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8+ T Cells. mBio (ePub ahead of print). (pubmed) (doi)

Smith KN, Mailliard RB, Piazza PA, Fischer W, Korber BT, Fecek RJ, Ratner D, Gupta P, Mullins JI, Rinaldo CR (2016). Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8+ T Cells. mBio (ePub ahead of print). (pubmed) (doi)

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Smith KN, Mailliard RB, Piazza PA, Fischer W, Korber BT, Fecek RJ, Ratner D, Gupta P, Mullins JI, Rinaldo CR (2016). Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8+ T Cells. mBio (ePub ahead of print). (pubmed) (doi)

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Collier AC, Chun TW, Maenza J, Coombs RW, Tapia K, Chang M, Stevens CE, Justement JS, Murray D, Stekler JD, Mullins JI, Holte SE (2016). A Pilot Study of Raltegravir Plus Combination Antiretroviral Therapy in Early Human Immunodeficiency Virus Infection: Challenges and Lessons Learned. BioResearch open access, 5(1), 15-21. (pubmed) (doi)

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2015

Fife KH, Mugwanya K, Thomas KK, Baeten JM, Celum C, Bukusi E, de Bruyn G, Mujugira A, Vwalika B, Wald A, Lingappa JR, Partners in Prevention HSV/HIV Transmission Study Team (2016). Transient Increase in Herpes Simplex Virus Type 2 (HSV-2)-Associated Genital Ulcers Following Initiation of Antiretroviral Therapy in HIV/HSV-2-Coinfected Individuals. The Journal of infectious diseases, 213(10), 1573-8. (pubmed) (doi)

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Magaret AS, Mujugira A, Hughes JP, Lingappa J, Bukusi EA, DeBruyn G, Delany-Moretlwe S, Fife KH, Gray GE, Kapiga S, Karita E, Mugo NR, Rees H, Ronald A, Vwalika B, Were E, Celum C, Wald A, Partners in Prevention HSV/HIV Transmission Study Team (2016). Effect of Condom Use on Per-act HSV-2 Transmission Risk in HIV-1, HSV-2-discordant Couples. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 62(4), 456-61. (pubmed) (doi)

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McLaren PJ, Coulonges C, Bartha I, Lenz TL, Deutsch AJ, Bashirova A, Buchbinder S, Carrington MN, Cossarizza A, Dalmau J, De Luca A, Goedert JJ, Gurdasani D, Haas DW, Herbeck JT, Johnson EO, Kirk GD, Lambotte O, Luo M, Mallal S, van Manen D, Martinez-Picado J, Meyer L, Miro JM, Mullins JI, Obel N, Poli G, Sandhu MS, Schuitemaker H, Shea PR, Theodorou I, Walker BD, Weintrob AC, Winkler CA, Wolinsky SM, Raychaudhuri S, Goldstein DB, Telenti A, de Bakker PI, Zagury JF, Fellay J (2015). Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. Proceedings of the National Academy of Sciences of the United States of America, 112(47), 14658-63. (pubmed) (doi)

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Manocheewa S, Mittler JE, Samudrala R, Mullins JI (2015). Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development. Viruses, 7(11), 5718-35. (pubmed) (doi)

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Peterson CW, Haworth KG, Polacino P, Huang ML, Sykes C, Obenza WM, Repetto AC, Kashuba A, Bumgarner R, DeRosa SC, Woolfrey AE, Jerome KR, Mullins JI, Hu SL, Kiem HP (2015). Lack of viral control and development of combination antiretroviral therapy escape mutations in macaques after bone marrow transplantation. AIDS (London, England), 29(13), 1597-606. (pubmed) (doi)

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Janes H, Herbeck JT, Tovanabutra S, Thomas R, Frahm N, Duerr A, Hural J, Corey L, Self SG, Buchbinder SP, McElrath MJ, O'Connell RJ, Paris RM, Rerks-Ngarm S, Nitayaphan S, Pitisuttihum P, Kaewkungwal J, Robb ML, Michael NL, Mullins JI, Kim JH, Gilbert PB, Rolland M (2015). HIV-1 infections with multiple founders are associated with higher viral loads than infections with single founders. Nature medicine, 21(10), 1139-41. (pubmed) (doi)

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Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI (2015). Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection. PloS one, 10(8), e0135903. (pubmed) (doi)

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Olson SC, Ngo-Giang-Huong N, Beck I, Deng W, Britto P, Shapiro DE, Bumgarner RE, Mullins JI, Van Dyke RB, Jourdain G, Frenkel LM (2015). Resistance detected by pyrosequencing following zidovudine monotherapy for prevention of HIV-1 mother-to-child-transmission. AIDS (London, England), 29(12), 1467-71. (pubmed) (doi)

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Sunshine JE, Larsen BB, Maust B, Casey E, Deng W, Chen L, Westfall DH, Kim M, Zhao H, Ghorai S, Lanxon-Cookson E, Rolland M, Collier AC, Maenza J, Mullins JI, Frahm N (2015). Fitness-Balanced Escape Determines Resolution of Dynamic Founder Virus Escape Processes in HIV-1 Infection. Journal of virology, 89(20), 10303-18. (pubmed) (doi)

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Manocheewa S, Lanxon-Cookson EC, Liu Y, Swain JV, McClure J, Rao U, Maust B, Deng W, Sunshine JE, Kim M, Rolland M, Mullins JI (2015). Pairwise growth competition assay for determining the replication fitness of human immunodeficiency viruses. Journal of visualized experiments : JoVE, (99), e52610. (pubmed) (doi)

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Maenza J, Tapia K, Holte S, Stekler JD, Stevens CE, Mullins JI, Collier AC (2015). How often does treatment of primary HIV lead to post-treatment control? Antiviral therapy, 20(8), 855-63. (pubmed) (doi)

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Herbeck J, Ghorai S, Chen L, Rinaldo CR, Margolick JB, Detels R, Jacobson L, Wolinsky S, Mullins JI (2015). p21(WAF1/CIP1) RNA expression in highly HIV-1 exposed, uninfected individuals. PloS one, 10(3), e0119218. (pubmed) (doi)

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Mothe B, Hu X, Llano A, Rosati M, Olvera A, Kulkarni V, Valentin A, Alicea C, Pilkington GR, Sardesai NY, Rocafort M, Crespo M, Carrillo J, Marco A, Mullins JI, Dorrell L, Hanke T, Clotet B, Pavlakis GN, Felber BK, Brander C (2015). A human immune data-informed vaccine concept elicits strong and broad T-cell specificities associated with HIV-1 control in mice and macaques. Journal of translational medicine, 13, 60. (pubmed) (doi)

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Smith RA, Raugi DN, Pan C, Sow PS, Seydi M, Mullins JI, Gottlieb GS, University of Washington-Dakar HIV-2 Study Group (2015). In vitro activity of dolutegravir against wild-type and integrase inhibitor-resistant HIV-2. Retrovirology, 12, 10. (pubmed) (doi)

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Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Kijak GH, Bose M, RV144 Sequencing Team, Arroyo MA, O'Connell RJ, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, Kirys T, Georgiev IS, Kwong PD, Scheffler K, Pond SL, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB (2015). Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS computational biology, 11(2), e1003973. (pubmed) (doi)

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Ceresola ER, Nozza S, Sampaolo M, Pignataro AR, Saita D, Ferrarese R, Ripa M, Deng W, Mullins JI, Boeri E, Tambussi G, Toniolo A, Lazzarin A, Clementi M, Canducci F (2015). Performance of commonly used genotypic assays and comparison with phenotypic assays of HIV-1 coreceptor tropism in acutely HIV-1-infected patients. The Journal of antimicrobial chemotherapy, 70(5), 1391-5. (pubmed) (doi)

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Zolla-Pazner S, Edlefsen PT, Rolland M, Kong XP, deCamp A, Gottardo R, Williams C, Tovanabutra S, Sharpe-Cohen S, Mullins JI, deSouza MS, Karasavvas N, Nitayaphan S, Rerks-Ngarm S, Pitisuttihum P, Kaewkungwal J, O'Connell RJ, Robb ML, Michael NL, Kim JH, Gilbert P (2014). Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses. EBioMedicine, 1(1), 37-45. (pubmed)

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2014

Moroni M, Ghezzi S, Baroli P, Heltai S, De Battista D, Pensieroso S, Cavarelli M, Dispinseri S, Vanni I, Pastori C, Zerbi P, Tosoni A, Vicenzi E, Nebuloni M, Wong K, Zhao H, McHugh S, Poli G, Lopalco L, Scarlatti G, Biassoni R, Mullins JI, Malnati MS, Alfano M (2014). Spontaneous control of HIV-1 viremia in a subject with protective HLA-B plus HLA-C alleles and HLA-C associated single nucleotide polymorphisms. Journal of translational medicine, 12, 335. (pubmed) (doi)

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Mackelprang RD, Carrington M, Thomas KK, Hughes JP, Baeten JM, Wald A, Farquhar C, Fife K, Campbell MS, Kapiga S, Gao X, Mullins JI, Lingappa JR (2015). Host genetic and viral determinants of HIV-1 RNA set point among HIV-1 seroconverters from sub-saharan Africa. Journal of virology, 89(4), 2104-11. (pubmed) (doi)

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Mackelprang RD, Carrington M, Thomas KK, Hughes JP, Baeten JM, Wald A, Farquhar C, Fife K, Campbell MS, Kapiga S, Gao X, Mullins JI, Lingappa JR (2015). Host genetic and viral determinants of HIV-1 RNA set point among HIV-1 seroconverters from sub-saharan Africa. Journal of virology, 89(4), 2104-11. (pubmed) (doi)

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Mothe B, Hu X, Llano A, Rosati M, Olvera A, Kulkarni V, Valentin A, Alicea C, Sardesai NJ, Rocafort M, Crespo M, Carrillo J, Marco A, Mullins JI, Dorrell L, Hanke T, Clotet B, Pavlakis GN, Felber BK, Brander C 2014 A Novel T-cell Vaccine Eliciting T-cell Specificities Associated with Control of HIV-1 In Humans Is Highly Immunogenic in Mice and Macaques. AIDS research and human retroviruses30 Suppl 1A76 pubmed

Felber BK, Hu X, Kulkarni V, Valentin A, Rosati M, Alicea C, Rolland M, Le Gall S, Sardesai NY, Mothe B, Brander C, Mullins JI, Pavlakis GN 2014 Expanded Epitope Recognition by Vaccination with DNA Encoding Novel Immunogens Comprising HIV Conserved Elements. AIDS research and human retroviruses30 Suppl 1A45-6 pubmed

Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Bose M, Arroyo MA, O'Connell RJ, deSouza MS, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, McLellan JS, Georgiev IS, Kirys T, Kwong PD, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB 2014 Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial. AIDS research and human retroviruses30 Suppl 1A25-6 pubmed

Dommaraju K, Kijak G, Carlson JM, Larsen BB, Tovanabutra S, Geraghty DE, Deng W, Maust BS, Edlefsen PT, Sanders-Buell E, Ratto-Kim S, deSouza MS, Rerks-Ngarm S, Nitayaphan S, Pitisuttihum P, Kaewkungwal J, O'Connell RJ, Robb ML, Michael NL, Mullins JI, Kim JH, Rolland M (2014). CD8 and CD4 epitope predictions in RV144: no strong evidence of a T-cell driven sieve effect in HIV-1 breakthrough sequences from trial participants. PloS one, 9(10), e111334. (pubmed) (doi)

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Kulkarni V, Valentin A, Rosati M, Rolland M, Mullins JI, Pavlakis GN, Felber BK (2014). HIV-1 conserved elements p24CE DNA vaccine induces humoral immune responses with broad epitope recognition in macaques. PloS one, 9(10), e111085. (pubmed) (doi)

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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.), 345(6196), 570-3. (pubmed) (doi)

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Herbeck JT, Mittler JE, Gottlieb GS, Mullins JI (2014). An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load. PLoS computational biology, 10(6), e1003673. (pubmed) (doi)

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Smith KN, Mailliard RB, Larsen BB, Wong K, Gupta P, Mullins JI, Rinaldo CR (2014). Dendritic cells restore CD8+ T cell reactivity to autologous HIV-1. Journal of virology, 88(17), 9976-90. (pubmed) (doi)

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Castro E, Zhao H, Cavassini M, Mullins JI, Pantaleo G, Bart PA (2014). HIV-1 superinfection with a triple-class drug-resistant strain in a patient successfully controlled with antiretroviral treatment. AIDS (London, England), 28(12), 1840-4. (pubmed) (doi)

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Stekler JD, McKernan J, Milne R, Tapia KA, Mykhalchenko K, Holte S, Maenza J, Stevens CE, Buskin SE, Mullins JI, Frenkel LM, Collier AC (2015). Lack of resistance to integrase inhibitors among antiretroviral-naive subjects with primary HIV-1 infection, 2007-2013. Antiviral therapy, 20(1), 77-80. (pubmed) (doi)

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Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, Sidney J, Sette A, Zolla-Pazner S, Montefiori D, McElrath MJ, Mullins JI, Kim JH, Gilbert PB, Hertz T (2014). Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial. Journal of virology, 88(15), 8242-55. (pubmed) (doi)

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Beck IA, Deng W, Payant R, Hall R, Bumgarner RE, Mullins JI, Frenkel LM (2014). Validation of an oligonucleotide ligation assay for quantification of human immunodeficiency virus type 1 drug-resistant mutants by use of massively parallel sequencing. Journal of clinical microbiology, 52(7), 2320-7. (pubmed) (doi)

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Liu Y, Rao U, McClure J, Konopa P, Manocheewa S, Kim M, Chen L, Troyer RM, Tebit DM, Holte S, Arts EJ, Mullins JI (2014). Impact of mutations in highly conserved amino acids of the HIV-1 Gag-p24 and Env-gp120 proteins on viral replication in different genetic backgrounds. PloS one, 9(4), e94240. (pubmed) (doi)

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Bigham AW, Mackelprang RD, Celum C, De Bruyn G, Beima-Sofie K, John-Stewart G, Ronald A, Mugo NR, Buckingham K, Bamshad MJ, Mullins JI, McElrath MJ, Lingappa JR (2014). Variants in host viral replication cycle genes are associated with heterosexual HIV-1 acquisition in Africans. Journal of acquired immune deficiency syndromes (1999), 66(2), 127-34. (pubmed) (doi)

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Kulkarni V, Valentin A, Rosati M, Alicea C, Singh AK, Jalah R, Broderick KE, Sardesai NY, Le Gall S, Mothe B, Brander C, Rolland M, Mullins JI, Pavlakis GN, Felber BK (2014). Altered response hierarchy and increased T-cell breadth upon HIV-1 conserved element DNA vaccination in macaques. PloS one, 9(1), e86254. (pubmed) (doi)

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Kahle E, Campbell M, Lingappa J, Donnell D, Celum C, Ondondo R, Mujugira A, Fife K, Mugo N, Kapiga S, Mullins JI, Baeten JM, Partners in Prevention HSVHIV Transmission Study Team (2014). HIV-1 subtype C is not associated with higher risk of heterosexual HIV-1 transmission: a multinational study among HIV-1 serodiscordant couples. AIDS (London, England), 28(2), 235-43. (pubmed) (doi)

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2013

Melhem NM, Smith KN, Huang XL, Colleton BA, Jiang W, Mailliard RB, Mullins JI, Rinaldo CR (2014). The impact of viral evolution and frequency of variant epitopes on primary and memory human immunodeficiency virus type 1-specific CD8⁺ T cell responses. Virology, 450-451, 34-48. (pubmed) (doi)

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Mackelprang RD, Bigham AW, Celum C, de Bruyn G, Beima-Sofie K, John-Stewart G, Ronald A, Mugo NR, Buckingham KJ, Bamshad MJ, Mullins JI, McElrath MJ, Lingappa JR (2014). Toll-like receptor polymorphism associations with HIV-1 outcomes among sub-Saharan Africans. The Journal of infectious diseases, 209(10), 1623-7. (pubmed) (doi)

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Sunshine J, Kim M, Carlson JM, Heckerman D, Czartoski J, Migueles SA, Maenza J, McElrath MJ, Mullins JI, Frahm N (2014). Increased sequence coverage through combined targeting of variant and conserved epitopes correlates with control of HIV replication. Journal of virology, 88(2), 1354-65. (pubmed) (doi)

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Dobrowsky TM, Rabi SA, Nedellec R, Daniels BR, Mullins JI, Mosier DE, Siliciano RF, Wirtz D (2013). Adhesion and fusion efficiencies of human immunodeficiency virus type 1 (HIV-1) surface proteins. Scientific reports, 3, 3014. (pubmed) (doi)

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Larsen BB, Chen L, Maust BS, Kim M, Zhao H, Deng W, Westfall D, Beck I, Frenkel LM, Mullins JI (2013). Improved detection of rare HIV-1 variants using 454 pyrosequencing. PloS one, 8(10), e76502. (pubmed) (doi)

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Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI (2013). Quality score based identification and correction of pyrosequencing errors. PloS one, 8(9), e73015. (pubmed) (doi)

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Shankarappa R, Mullins JI (2013). Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. Journal of virological methods, 194(1-2), 169-77. (pubmed) (doi)

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Lanxon-Cookson EC, Swain JV, Manocheewa S, Smith RA, Maust B, Kim M, Westfall D, Rolland M, Mullins JI (2013). Factors affecting relative fitness measurements in pairwise competition assays of human immunodeficiency viruses. Journal of virological methods, 194(1-2), 7-13. (pubmed) (doi)

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Mailliard RB, Smith KN, Fecek RJ, Rappocciolo G, Nascimento EJ, Marques ET, Watkins SC, Mullins JI, Rinaldo CR (2013). Selective induction of CTL helper rather than killer activity by natural epitope variants promotes dendritic cell-mediated HIV-1 dissemination. Journal of immunology (Baltimore, Md. : 1950), 191(5), 2570-80. (pubmed) (doi)

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Mujugira A, Magaret AS, Celum C, Baeten JM, Lingappa JR, Morrow RA, Fife KH, Delany-Moretlwe S, de Bruyn G, Bukusi EA, Karita E, Kapiga S, Corey L, Wald A, Partners in Prevention HSV/HIV Transmission Study Team (2013). Daily acyclovir to decrease herpes simplex virus type 2 (HSV-2) transmission from HSV-2/HIV-1 coinfected persons: a randomized controlled trial. The Journal of infectious diseases, 208(9), 1366-74. (pubmed) (doi)

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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), 29(19), 2402-9. (pubmed) (doi)

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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 (2013). Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS pathogens, 9(7), e1003515. (pubmed) (doi)

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Manocheewa S, Swain JV, Lanxon-Cookson E, Rolland M, Mullins JI (2013). Fitness costs of mutations at the HIV-1 capsid hexamerization interface. PloS one, 8(6), e66065. (pubmed) (doi)

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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 one, 8(5), e64405. (pubmed) (doi)

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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, University of Washington-Dakar HIV-2 Study Group (2013). Complex patterns of protease inhibitor resistance among antiretroviral treatment-experienced HIV-2 patients from Senegal: implications for second-line therapy. Antimicrobial agents and chemotherapy, 57(6), 2751-60. (pubmed) (doi)

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Kulkarni V, Rosati M, Valentin A, Ganneru B, Singh AK, Yan J, Rolland M, Alicea C, Beach RK, Zhang GM, Le Gall S, Broderick KE, Sardesai NY, Heckerman D, Mothe B, Brander C, Weiner DB, Mullins JI, Pavlakis GN, Felber BK (2013). HIV-1 p24(gag) derived conserved element DNA vaccine increases the breadth of immune response in mice. PloS one, 8(3), e60245. (pubmed) (doi)

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Rolland M, Manocheewa S, Swain JV, Lanxon-Cookson EC, Kim M, Westfall DH, Larsen BB, Gilbert PB, Mullins JI (2013). HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity. Journal of virology, 87(10), 5461-7. (pubmed) (doi)

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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 diseases, 207(8), 1206-15. (pubmed) (doi)

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Campbell MS, Kahle EM, Celum C, Lingappa JR, Kapiga S, Mujugira A, Mugo NR, Fife KH, Mullins JI, Baeten JM, Partners in Prevention HSV/HIV Transmission Study Team (2013). Plasma viral loads during early HIV-1 infection are similar in subtype C- and non-subtype C-infected African seroconverters. The Journal of infectious diseases, 207(7), 1166-70. (pubmed) (doi)

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Nakamura KJ, Cerini C, Sobrera ER, Heath L, Sinkala M, Kankasa C, Thea DM, Mullins JI, Kuhn L, Aldrovandi GM (2013). Coverage of primary mother-to-child HIV transmission isolates by second-generation broadly neutralizing antibodies. AIDS (London, England), 27(3), 337-46. (pubmed) (doi)

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2012

Mullins J, Paler H (None). Identifying and transferring offenders with mental health needs. Nursing standard (Royal College of Nursing (Great Britain) : 1987), 27(11), 42-7; quiz 49. (pubmed)

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Murnane PM, Hughes JP, Celum C, Lingappa JR, Mugo N, Farquhar C, Kiarie J, Wald A, Baeten JM, Partners in Prevention HSV/HIV Transmission Study Team (2012). Using plasma viral load to guide antiretroviral therapy initiation to prevent HIV-1 transmission. PloS one, 7(11), e51192. (pubmed) (doi)

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CorQ: Quality score based identification and correction of pyrosequencing errors. Shyamala Iyer, Heather Bouzek, Wenjie Deng, Brendan Larsen, Eleanor Casey, James I. Mullins

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Liu Y, Holte S, Rao U, McClure J, Konopa P, Swain JV, Lanxon-Cookson E, Kim M, Chen L, Mullins JI (2013). A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture. Journal of virological methods, 189(1), 157-66. (pubmed) (doi)

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Kahle EM, Hughes JP, Lingappa JR, John-Stewart G, Celum C, Nakku-Joloba E, Njuguna S, Mugo N, Bukusi E, Manongi R, Baeten JM, Partners in Prevention HSVHIV Transmission Study and the Partners PrEP Study Teams (2013). An empiric risk scoring tool for identifying high-risk heterosexual HIV-1-serodiscordant couples for targeted HIV-1 prevention. Journal of acquired immune deficiency syndromes (1999), 62(3), 339-47. (pubmed) (doi)

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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 virology, 87(3), 1770-8. (pubmed) (doi)

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Heffron R, Mugo N, Ngure K, Celum C, Donnell D, Were E, Rees H, Kiarie J, Baeten JM, Partners in Prevention HSVHIV Transmission Study Team (2013). Hormonal contraceptive use and risk of HIV-1 disease progression. AIDS (London, England), 27(2), 261-7. (pubmed) (doi)

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Lingappa JR, Thomas KK, Hughes JP, Baeten JM, Wald A, Farquhar C, de Bruyn G, Fife KH, Campbell MS, Kapiga S, Mullins JI, Celum C, Partners in Prevention HSV/HIV Transmission Study Team (2013). Partner characteristics predicting HIV-1 set point in sexually acquired HIV-1 among African seroconverters. AIDS research and human retroviruses, 29(1), 164-71. (pubmed)

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Smith RA, Raugi DN, Pan C, Coyne M, Hernandez A, Church B, Parker K, Mullins JI, Sow PS, Gottlieb GS, University of Washington-Dakar HIV-2 Study Group (2012). Three main mutational pathways in HIV-2 lead to high-level raltegravir and elvitegravir resistance: implications for emerging HIV-2 treatment regimens. PloS one, 7(9), e45372. (pubmed) (doi)

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Kurian MV, Hamilton L, Keeven J, Mehl P, Mullins JM (2012). Enhanced cell survival and diminished apoptotic response to simulated ischemia-reperfusion in H9c2 cells by magnetic field preconditioning. Apoptosis : an international journal on programmed cell death, 17(11), 1182-96. (pubmed) (doi)

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Rolland M, Edlefsen PT, Larsen BB, Tovanabutra S, Sanders-Buell E, Hertz T, deCamp AC, Carrico C, Menis S, Magaret CA, Ahmed H, Juraska M, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, McLellan JS, Georgiev I, Kwong PD, Carlson JM, Michael NL, Schief WR, Gilbert PB, Mullins JI, Kim JH (2012). Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2. Nature, 490(7420), 417-20. (pubmed) (doi)

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Mullins J (2012). Malawi breathes new life into childhood pneumonia care. Lancet (London, England), 380(9843), 717. (pubmed)

Janes H, Frahm N, DeCamp A, Rolland M, Gabriel E, Wolfson J, Hertz T, Kallas E, Goepfert P, Friedrich DP, Corey L, Mullins JI, McElrath MJ, Gilbert P (2012). MRKAd5 HIV-1 Gag/Pol/Nef vaccine-induced T-cell responses inadequately predict distance of breakthrough HIV-1 sequences to the vaccine or viral load. PloS one, 7(8), e43396. (pubmed) (doi)

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Mullins J (2012). China registers success with TB-diabetes screening initiative. Lancet (London, England), 380(9842), 635-6. (pubmed)

Mullins J (2012). Cohort reporting improves hypertension care for refugees. Lancet (London, England), 380(9841), 552. (pubmed)

International AIDS Society Scientific Working Group on HIV Cure, Deeks SG, Autran B, Berkhout B, Benkirane M, Cairns S, Chomont N, Chun TW, Churchill M, Di Mascio M, Katlama C, Lafeuillade A, Landay A, Lederman M, Lewin SR, Maldarelli F, Margolis D, Markowitz M, Martinez-Picado J, Mullins JI, Mellors J, Moreno S, O'Doherty U, Palmer S, Penicaud MC, Peterlin M, Poli G, Routy JP, Rouzioux C, Silvestri G, Stevenson M, Telenti A, Van Lint C, Verdin E, Woolfrey A, Zaia J, Barré-Sinoussi F (2012). Towards an HIV cure: a global scientific strategy. Nature reviews. Immunology, 12(8), 607-14. (pubmed) (doi)

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Mothe B, Llano A, Ibarrondo J, Zamarreño J, Schiaulini M, Miranda C, Ruiz-Riol M, Berger CT, Herrero MJ, Palou E, Plana M, Rolland M, Khatri A, Heckerman D, Pereyra F, Walker BD, Weiner D, Paredes R, Clotet B, Felber BK, Pavlakis GN, Mullins JI, Brander C (2012). CTL responses of high functional avidity and broad variant cross-reactivity are associated with HIV control. PloS one, 7(1), e29717. (pubmed) (doi)

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2011

Ngure K, Heffron R, Mugo NR, Celum C, Cohen CR, Odoyo J, Rees H, Kiarie JN, Were E, Baeten JM, Partners in Prevention HSVHIV Transmission Study Team (2012). Contraceptive method and pregnancy incidence among women in HIV-1-serodiscordant partnerships. AIDS (London, England), 26(4), 513-8. (pubmed) (doi)

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Lingappa JR, Petrovski S, Kahle E, Fellay J, Shianna K, McElrath MJ, Thomas KK, Baeten JM, Celum C, Wald A, de Bruyn G, Mullins JI, Nakku-Joloba E, Farquhar C, Essex M, Donnell D, Kiarie J, Haynes B, Goldstein D, Partners in Prevention HSV/HIV Transmission Study Team (2011). Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure. PloS one, 6(12), e28632. (pubmed) (doi)

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Mothe B, Llano A, Ibarrondo J, Daniels M, Miranda C, Zamarreño J, Bach V, Zuniga R, Pérez-Álvarez S, Berger CT, Puertas MC, Martinez-Picado J, Rolland M, Farfan M, Szinger JJ, Hildebrand WH, Yang OO, Sanchez-Merino V, Brumme CJ, Brumme ZL, Heckerman D, Allen TM, Mullins JI, Gómez G, Goulder PJ, Walker BD, Gatell JM, Clotet B, Korber BT, Sanchez J, Brander C (2011). Definition of the viral targets of protective HIV-1-specific T cell responses. Journal of translational medicine, 9, 208. (pubmed) (doi)

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Herbeck JT, Müller V, Maust BS, Ledergerber B, Torti C, Di Giambenedetto S, Gras L, Günthard HF, Jacobson LP, Mullins JI, Gottlieb GS (2012). Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS (London, England), 26(2), 193-205. (pubmed) (doi)

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Smith RA, Raugi DN, Kiviat NB, Hawes SE, Mullins JI, Sow PS, Gottlieb GS, University of Washington-Dakar HIV-2 Study Group (2011). Phenotypic susceptibility of HIV-2 to raltegravir: integrase mutations Q148R and N155H confer raltegravir resistance. AIDS (London, England), 25(18), 2235-41. (pubmed) (doi)

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Ndase P, Celum C, Thomas K, Donnell D, Fife KH, Bukusi E, Delany-Moretlwe S, Baeten JM, Partners in Prevention HSVHIV Transmission Study Team (2012). Outside sexual partnerships and risk of HIV acquisition for HIV uninfected partners in African HIV serodiscordant partnerships. Journal of acquired immune deficiency syndromes (1999), 59(1), 65-71. (pubmed) (doi)

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Smith RA (2011). Antiviral Drug Susceptibility Patterns in Gammaretroviridae: Lessons from XMRV and Related Retroviruses. Drugs of the Future 36(6)455-464 read online

Chen RT, Hu DJ, Dunne E, Shaw M, Mullins JI, Rerks-Ngarm S (2011). Preparing for the availability of a partially effective HIV vaccine: some lessons from other licensed vaccines. Vaccine, 29(36), 6072-8. (pubmed) (doi)

Gottlieb GS, Smith RA, Dia Badiane NM, Ba S, Hawes SE, Toure M, Starling AK, Traore F, Sall F, Cherne SL, Stern J, Wong KG, Lu P, Kim M, Raugi DN, Lam A, Mullins JI, Kiviat NB, Papa Salif Sow for the UW-Dakar HIV-2 Study Group (2011). HIV-2 integrase variation in integrase inhibitor-naïve adults in Senegal, West Africa. PloS one, 6(7), e22204. (pubmed) (doi)

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Nikolova M, Carriere M, Jenabian MA, Limou S, Younas M, Kök A, Huë S, Seddiki N, Hulin A, Delaneau O, Schuitemaker H, Herbeck JT, Mullins JI, Muhtarova M, Bensussan A, Zagury JF, Lelievre JD, Lévy Y (2011). CD39/adenosine pathway is involved in AIDS progression. PLoS pathogens, 7(7), e1002110. (pubmed) (doi)

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Nikolova M, Carriere M, Jenabian MA, Limou S, Younas M, Kök A, Huë S, Seddiki N, Hulin A, Delaneau O, Schuitemaker H, Herbeck JT, Mullins JI, Muhtarova M, Bensussan A, Zagury JF, Lelievre JD, Lévy Y (2011). CD39/adenosine pathway is involved in AIDS progression. PLoS pathogens, 7(7), e1002110. (pubmed) (doi)

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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 virology, 85(15), 7523-34. (pubmed) (doi)

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Baeten JM, Kahle E, Lingappa JR, Coombs RW, Delany-Moretlwe S, Nakku-Joloba E, Mugo NR, Wald A, Corey L, Donnell D, Campbell MS, Mullins JI, Celum C, Partners in Prevention HSV/HIV Transmission Study Team (2011). Genital HIV-1 RNA predicts risk of heterosexual HIV-1 transmission. Science translational medicine, 3(77), 77ra29. (pubmed) (doi)

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Rolland M, Frahm N, Nickle DC, Jojic N, Deng W, Allen TM, Brander C, Heckerman DE, Mullins JI (2011). Increased breadth and depth of cytotoxic T lymphocytes responses against HIV-1-B Nef by inclusion of epitope variant sequences. PloS one, 6(3), e17969. (pubmed) (doi)

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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, Partners in Prevention HSV/HIV Transmission Study Team (2011). Viral linkage in HIV-1 seroconverters and their partners in an HIV-1 prevention clinical trial. PloS one, 6(3), e16986. (pubmed) (doi)

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Rolland M, Tovanabutra S, deCamp AC, Frahm N, Gilbert PB, Sanders-Buell E, Heath L, Magaret CA, Bose M, Bradfield A, O'Sullivan A, Crossler J, Jones T, Nau M, Wong K, Zhao H, Raugi DN, Sorensen S, Stoddard JN, Maust BS, Deng W, Hural J, Dubey S, Michael NL, Shiver J, Corey L, Li F, Self SG, Kim J, Buchbinder S, Casimiro DR, Robertson MN, Duerr A, McElrath MJ, McCutchan FE, Mullins JI (2011). Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial. Nature medicine, 17(3), 366-71. (pubmed) (doi)

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Liu Y, McNevin JP, Holte S, McElrath MJ, Mullins JI (2011). Dynamics of viral evolution and CTL responses in HIV-1 infection. PloS one, 6(1), e15639. (pubmed) (doi)

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Niu L, Termini JM, Kanagavelu SK, Gupta S, Rolland MM, Kulkarni V, Pavlakis GN, Felber BK, Mullins JI, Fischl MA, Stone GW (2011). Preclinical evaluation of HIV-1 therapeutic ex vivo dendritic cell vaccines expressing consensus Gag antigens and conserved Gag epitopes. Vaccine, 29(11), 2110-9. (pubmed) (doi)

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Mullins JI, Heath L, Hughes JP, Kicha J, Styrchak S, Wong KG, Rao U, Hansen A, Harris KS, Laurent JP, Li D, Simpson JH, Essigmann JM, Loeb LA, Parkins J (2011). Mutation of HIV-1 genomes in a clinical population treated with the mutagenic nucleoside KP1461. PloS one, 6(1), e15135. (pubmed) (doi)

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2010

Smith RA (2010). Contamination of clinical specimens with MLV-encoding nucleic acids: implications for XMRV and other candidate human retroviruses. Retrovirology, 7, 112. (pubmed) (doi)

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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 pathogens, 6(12), e1001228. (pubmed) (doi)

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Le Clerc S, Coulonges C, Delaneau O, Van Manen D, Herbeck JT, Limou S, An P, Martinson JJ, Spadoni JL, Therwath A, Veldink JH, van den Berg LH, Taing L, Labib T, Mellak S, Montes M, Delfraissy JF, Schächter F, Winkler C, Froguel P, Mullins JI, Schuitemaker H, Zagury JF (2011). Screening low-frequency SNPS from genome-wide association study reveals a new risk allele for progression to AIDS. Journal of acquired immune deficiency syndromes (1999), 56(3), 279-84. (pubmed) (doi)

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Boutwell CL, Rolland MM, Herbeck JT, Mullins JI, Allen TM (2010). Viral evolution and escape during acute HIV-1 infection. The Journal of infectious diseases, 202 Suppl 2, S309-14. (pubmed) (doi)

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Heath L, Frenkel LM, Foley BT, Mullins JI (2010). Comment on “The origins of sexually transmitted HIV among men who have sex with men”. Science translational medicine, 2(50), 50le1; author reply 50lr1. (pubmed) (doi)

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Huang XL, Fan Z, Borowski L, Mailliard RB, Rolland M, Mullins JI, Day RD, Rinaldo CR (2010). Dendritic cells reveal a broad range of MHC class I epitopes for HIV-1 in persons with suppressed viral load on antiretroviral therapy. PloS one, 5(9), e12936. (pubmed) (doi)

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Lingappa JR, Hughes JP, Wang RS, Baeten JM, Celum C, Gray GE, Stevens WS, Donnell D, Campbell MS, Farquhar C, Essex M, Mullins JI, Coombs RW, Rees H, Corey L, Wald A, Partners in Prevention HSV/HIV Transmission Study Team (2010). Estimating the impact of plasma HIV-1 RNA reductions on heterosexual HIV-1 transmission risk. PloS one, 5(9), e12598. (pubmed) (doi)

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Rolland M, Carlson JM, Manocheewa S, Swain JV, Lanxon-Cookson E, Deng W, Rousseau CM, Raugi DN, Learn GH, Maust BS, Coovadia H, Ndung'u T, Goulder PJ, Walker BD, Brander C, Heckerman DE, Mullins JI (2010). Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics. PloS one (ePub ahead of print). (pubmed) (doi)

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Smith RA, Gottlieb GS, Miller AD (2010). Susceptibility of the human retrovirus XMRV to antiretroviral inhibitors. Retrovirology, 7, 70. (pubmed) (doi)

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Limou S, Coulonges C, Herbeck JT, van Manen D, An P, Le Clerc S, Delaneau O, Diop G, Taing L, Montes M, van’t Wout AB, Gottlieb GS, Therwath A, Rouzioux C, Delfraissy JF, Lelièvre JD, Lévy Y, Hercberg S, Dina C, Phair J, Donfield S, Goedert JJ, Buchbinder S, Estaquier J, Schächter F, Gut I, Froguel P, Mullins JI, Schuitemaker H, Winkler C, Zagury JF (2010). Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor involved in long-term nonprogression to AIDS. The Journal of infectious diseases, 202(6), 908-15. (pubmed) (doi)

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Smith RA (2010). Random-scanning mutagenesis. Methods in molecular biology (Clifton, N.J.), 634, 387-97. (pubmed) (doi)

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Gantt S, Carlsson J, Heath L, Bull ME, Shetty AK, Mutsvangwa J, Musingwini G, Woelk G, Zijenah LS, Katzenstein DA, Mullins JI, Frenkel LM (2010). Genetic analyses of HIV-1 env sequences demonstrate limited compartmentalization in breast milk and suggest viral replication within the breast that increases with mastitis. Journal of virology, 84(20), 10812-9. (pubmed) (doi)

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Deng W, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, Kosakovsky Pond SL, Mullins JI (2010). DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites. BioTechniques, 48(5), 405-8. (pubmed) (doi)

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Donnell D, Baeten JM, Kiarie J, Thomas KK, Stevens W, Cohen CR, McIntyre J, Lingappa JR, Celum C, Partners in Prevention HSV/HIV Transmission Study Team (2010). Heterosexual HIV-1 transmission after initiation of antiretroviral therapy: a prospective cohort analysis. Lancet (London, England), 375(9731), 2092-8. (pubmed) (doi)

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Heath L, Conway S, Jones L, Semrau K, Nakamura K, Walter J, Decker WD, Hong J, Chen T, Heil M, Sinkala M, Kankasa C, Thea DM, Kuhn L, Mullins JI, Aldrovandi GM (2010). Restriction of HIV-1 genotypes in breast milk does not account for the population transmission genetic bottleneck that occurs following transmission. PloS one, 5(4), e10213. (pubmed) (doi)

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Nakamura KJ, Gach JS, Jones L, Semrau K, Walter J, Bibollet-Ruche F, Decker JM, Heath L, Decker WD, Sinkala M, Kankasa C, Thea D, Mullins J, Kuhn L, Zwick MB, Aldrovandi GM (2010). 4E10-resistant HIV-1 isolated from four subjects with rare membrane-proximal external region polymorphisms. PloS one, 5(3), e9786. (pubmed) (doi)

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Dinges WL, Richardt J, Friedrich D, Jalbert E, Liu Y, Stevens CE, Maenza J, Collier AC, Geraghty DE, Smith J, Moodie Z, Mullins JI, McElrath MJ, Horton H (2010). Virus-specific CD8+ T-cell responses better define HIV disease progression than HLA genotype. Journal of virology, 84(9), 4461-8. (pubmed) (doi)

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Celum C, Wald A, Lingappa JR, Magaret AS, Wang RS, Mugo N, Mujugira A, Baeten JM, Mullins JI, Hughes JP, Bukusi EA, Cohen CR, Katabira E, Ronald A, Kiarie J, Farquhar C, Stewart GJ, Makhema J, Essex M, Were E, Fife KH, de Bruyn G, Gray GE, McIntyre JA, Manongi R, Kapiga S, Coetzee D, Allen S, Inambao M, Kayitenkore K, Karita E, Kanweka W, Delany S, Rees H, Vwalika B, Stevens W, Campbell MS, Thomas KK, Coombs RW, Morrow R, Whittington WL, McElrath MJ, Barnes L, Ridzon R, Corey L, Partners in Prevention HSV/HIV Transmission Study Team (2010). Acyclovir and transmission of HIV-1 from persons infected with HIV-1 and HSV-2. The New England journal of medicine, 362(5), 427-39. (pubmed) (doi)

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Herbeck JT, Gottlieb GS, Winkler CA, Nelson GW, An P, Maust BS, Wong KG, Troyer JL, Goedert JJ, Kessing BD, Detels R, Wolinsky SM, Martinson J, Buchbinder S, Kirk GD, Jacobson LP, Margolick JB, Kaslow RA, O'Brien SJ, Mullins JI (2010). Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS. The Journal of infectious diseases, 201(4), 618-26. (pubmed) (doi)

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2009

Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD (2010). Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Molecular biology and evolution, 27(4), 819-32. (pubmed) (doi)

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Liu Y, McNevin J, Rolland M, Zhao H, Deng W, Maenza J, Stevens CE, Collier AC, McElrath MJ, Mullins JI (2009). Conserved HIV-1 epitopes continuously elicit subdominant cytotoxic T-lymphocyte responses. The Journal of infectious diseases, 200(12), 1825-33. (pubmed) (doi)

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Bull M, Learn G, Genowati I, McKernan J, Hitti J, Lockhart D, Tapia K, Holte S, Dragavon J, Coombs R, Mullins J, Frenkel L (2009). Compartmentalization of HIV-1 within the female genital tract is due to monotypic and low-diversity variants not distinct viral populations. PloS one, 4(9), e7122. (pubmed) (doi)

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Heath L, Fox A, McClure J, Diem K, van ’t Wout AB, Zhao H, Park DR, Schouten JT, Twigg HL, Corey L, Mullins JI, Mittler JE (2009). Evidence for limited genetic compartmentalization of HIV-1 between lung and blood. PloS one, 4(9), e6949. (pubmed) (doi)

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Malhotra U, Nolin J, Horton H, Li F, Corey L, Mullins JI, McElrath MJ (2009). Functional properties and epitope characteristics of T-cells recognizing natural HIV-1 variants. Vaccine, 27(48), 6678-87. (pubmed) (doi)

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Herbeck JT, Gottlieb GS, Wong K, Detels R, Phair JP, Rinaldo CR, Jacobson LP, Margolick JB, Mullins JI (2009). Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies. PloS one, 4(9), e6915. (pubmed) (doi)

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Liu Y, Woodward A, Zhu H, Andrus T, McNevin J, Lee J, Mullins JI, Corey L, McElrath MJ, Zhu T (2009). Preinfection human immunodeficiency virus (HIV)-specific cytotoxic T lymphocytes failed to prevent HIV type 1 infection from strains genetically unrelated to viruses in long-term exposed partners. Journal of virology, 83(20), 10821-9. (pubmed) (doi)

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Supplemental data

Curlin ME, Zioni R, Hawes SE, Liu Y, Deng W, Gottlieb GS, Zhu T, Mullins JI 2009 HIV-1 envelope subregion length variation during disease progression

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Campbell MS, Gottlieb GS, Hawes SE, Nickle DC, Wong KG, Deng W, Lampinen TM, Kiviat NB, Mullins JI (2009). HIV-1 superinfection in the antiretroviral therapy era: are seroconcordant sexual partners at risk? PloS one, 4(5), e5690. (pubmed) (doi)

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Smith RA, Anderson DJ, Pyrak CL, Preston BD, Gottlieb GS (2009). Antiretroviral drug resistance in HIV-2: three amino acid changes are sufficient for classwide nucleoside analogue resistance. The Journal of infectious diseases, 199(9), 1323-6. (pubmed) (doi)

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Wagner TA, Tobin NH, McKernan JL, Xu M, Melvin AJ, Mohan KM, Learn GH, Mullins JI, Frenkel LM (2009). Increased mutations in Env and Pol suggest greater HIV-1 replication in sputum-derived viruses compared with blood-derived viruses. AIDS (London, England), 23(8), 923-8. (pubmed) (doi)

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Troyer RM, McNevin J, Liu Y, Zhang SC, Krizan RW, Abraha A, Tebit DM, Zhao H, Avila S, Lobritz MA, McElrath MJ, Le Gall S, Mullins JI, Arts EJ (2009). Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response. PLoS pathogens, 5(4), e1000365. (pubmed) (doi)

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Bull ME, Learn GH, McElhone S, Hitti J, Lockhart D, Holte S, Dragavon J, Coombs RW, Mullins JI, Frenkel LM (2009). Monotypic human immunodeficiency virus type 1 genotypes across the uterine cervix and in blood suggest proliferation of cells with provirus. Journal of virology, 83(12), 6020-8. (pubmed) (doi)

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Supplemental data

Rousseau CM, Lockhart DW, Listgarten J, Maley SN, Kadie C, Learn GH, Nickle DC, Heckerman DE, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder PJ, Korber BT, Walker BD, Mullins JI (2009). Rare HLA drive additional HIV evolution compared to more frequent alleles. AIDS research and human retroviruses, 25(3), 297-303. (pubmed) (doi)

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Supplemental data

Gottlieb GS, Badiane NM, Hawes SE, Fortes L, Toure M, Ndour CT, Starling AK, Traore F, Sall F, Wong KG, Cherne SL, Anderson DJ, Dye SA, Smith RA, Mullins JI, Kiviat NB, Sow PS, 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 diseases : an official publication of the Infectious Diseases Society of America, 48(4), 476-83. (pubmed) (doi)

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2008

Carlson JM, Brumme ZL, Rousseau CM, Brumme CJ, Matthews P, Kadie C, Mullins JI, Walker BD, Harrigan PR, Goulder PJ, Heckerman D (2008). Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLoS computational biology, 4(11), e1000225. (pubmed) (doi)

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Coetzer M, Nedellec R, Salkowitz J, McLaughlin S, Liu Y, Heath L, Mullins JI, Mosier DE (2008). Evolution of CCR5 use before and during coreceptor switching. Journal of virology, 82(23), 11758-66. (pubmed) (doi)

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Matthews PC, Prendergast A, Leslie A, Crawford H, Payne R, Rousseau C, Rolland M, Honeyborne I, Carlson J, Kadie C, Brander C, Bishop K, Mlotshwa N, Mullins JI, Coovadia H, Ndung'u T, Walker BD, Heckerman D, Goulder PJ (2008). Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. Journal of virology, 82(17), 8548-59. (pubmed) (doi)

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Nickle DC, Jojic N, Heckerman D, Jojic V, Kirovski D, Rolland M, Kosakovsky Pond S, Mullins JI (2008). Comparison of immunogen designs that optimize peptide coverage: reply to Fischer et al. PLoS computational biology, 4(1), e25. (pubmed) (doi)

Liu Y, Mittler JE (2008). Selection dramatically reduces effective population size in HIV-1 infection. BMC evolutionary biology, 8, 133. (pubmed) (doi)

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Diem K, Nickle DC, Motoshige A, Fox A, Ross S, Mullins JI, Corey L, Coombs RW, Krieger JN (2008). Male genital tract compartmentalization of human immunodeficiency virus type 1 (HIV). AIDS research and human retroviruses, 24(4), 561-71. (pubmed) (doi)

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Rousseau CM, Daniels MG, Carlson JM, Kadie C, Crawford H, Prendergast A, Matthews P, Payne R, Rolland M, Raugi DN, Maust BS, Learn GH, Nickle DC, Coovadia H, Ndung'u T, Frahm N, Brander C, Walker BD, Goulder PJ, Bhattacharya T, Heckerman DE, Korber BT, Mullins JI (2008). HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load. Journal of virology, 82(13), 6434-46. (pubmed) (doi)

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Gottlieb GS, Heath L, Nickle DC, Wong KG, Leach SE, Jacobs B, Gezahegne S, van ’t Wout AB, Jacobson LP, Margolick JB, Mullins JI (2008). HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study. The Journal of infectious diseases, 197(7), 1011-5. (pubmed) (doi)

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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. Virology, 374(2), 229-33. (pubmed) (doi)

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Frahm N, Nickle DC, Linde CH, Cohen DE, Zuñiga R, Lucchetti A, Roach T, Walker BD, Allen TM, Korber BT, Mullins JI, Brander C (2008). Increased detection of HIV-specific T cell responses by combination of central sequences with comparable immunogenicity. AIDS (London, England), 22(4), 447-56. (pubmed) (doi)

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Ngumbela KC, Day CL, Mncube Z, Nair K, Ramduth D, Thobakgale C, Moodley E, Reddy S, de Pierres C, Mkhwanazi N, Bishop K, van der Stok M, Ismail N, Honeyborne I, Crawford H, Kavanagh DG, Rousseau C, Nickle D, Mullins J, Heckerman D, Korber B, Coovadia H, Kiepiela P, Goulder PJ, Walker BD (2008). Targeting of a CD8 T cell env epitope presented by HLA-B*5802 is associated with markers of HIV disease progression and lack of selection pressure. AIDS research and human retroviruses, 24(1), 72-82. (pubmed) (doi)

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Chun TW, Nickle DC, Justement JS, Meyers JH, Roby G, Hallahan CW, Kottilil S, Moir S, Mican JM, Mullins JI, Ward DJ, Kovacs JA, Mannon PJ, Fauci AS (2008). Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. The Journal of infectious diseases, 197(5), 714-20. (pubmed) (doi)

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Herbeck JT, Gottlieb GS, Li X, Hu Z, Detels R, Phair J, Rinaldo C, Jacobson LP, Margolick JB, Mullins JI (2008). Lack of evidence for changing virulence of HIV-1 in North America. PloS one, 3(2), e1525. (pubmed) (doi)

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Rolland M, Heckerman D, Deng W, Rousseau CM, Coovadia H, Bishop K, Goulder PJ, Walker BD, Brander C, Mullins JI (2008). Broad and Gag-biased HIV-1 epitope repertoires are associated with lower viral loads. PloS one, 3(1), e1424. (pubmed) (doi)

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Xu Y, Zhu H, Wilcox CK, van’t Wout A, Andrus T, Llewellyn N, Stamatatos L, Mullins JI, Corey L, Zhu T (2008). Blood monocytes harbor HIV type 1 strains with diversified phenotypes including macrophage-specific CCR5 virus. The Journal of infectious diseases, 197(2), 309-18. (pubmed) (doi)

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Mullins JI, Rolland M, Allen TM (2008). Viral evolution and escape during primary human immunodeficiency virus-1 infection: implications for vaccine design. Current opinion in HIV and AIDS, 3(1), 60-6. (pubmed) (doi)

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2007

Smith RA, Gottlieb GS, Anderson DJ, Pyrak CL, Preston BD (2008). Human immunodeficiency virus types 1 and 2 exhibit comparable sensitivities to Zidovudine and other nucleoside analog inhibitors in vitro. Antimicrobial agents and chemotherapy, 52(1), 329-32. (pubmed)

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Cao J, McNevin J, McSweyn M, Liu Y, Mullins JI, McElrath MJ (2008). Novel cytotoxic T-lymphocyte escape mutation by a three-amino-acid insertion in the human immunodeficiency virus type 1 p6Pol and p6Gag late domain associated with drug resistance. Journal of virology, 82(1), 495-502. (pubmed)

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Rolland M, Nickle DC, Deng W, Frahm N, Brander C, Learn GH, Heckerman D, Jojic N, Jojic V, Walker BD, Mullins JI (2007). Recognition of HIV-1 peptides by host CTL is related to HIV-1 similarity to human proteins. PloS one, 2(9), e823. (pubmed)

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Liu Y, McNevin J, Zhao H, Tebit DM, Troyer RM, McSweyn M, Ghosh AK, Shriner D, Arts EJ, McElrath MJ, Mullins JI (2007). Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escape. Journal of virology, 81(22), 12179-88. (pubmed)

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Rolland M, Brander C, Nickle DC, Herbeck JT, Gottlieb GS, Campbell MS, Maust BS, Mullins JI (2007). HIV-1 over time: fitness loss or robustness gain? Nature reviews. Microbiology, 5(9), C1. (pubmed)

Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Kaslow RA, Shepherd JC, Margolick JB, Mullins JI (2007). HIV type 1 superinfection with a dual-tropic virus and rapid progression to AIDS: a case report. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 45(4), 501-9. (pubmed)

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Bull ME, Learn GH, Mullins JI, Frenkel LM (2007). Methods used to examine compartmentalization of viral populations between the genital tract and peripheral blood. The Journal of infectious diseases, 196(3), 493-4; author reply 494-5. (pubmed)

Deng W, Nickle DC, Learn GH, Maust B, Mullins JI (2007). ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user’s datasets. Bioinformatics (Oxford, England), 23(17), 2334-6. (pubmed)

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Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, Kosakovsky Pond SL (2007). HIV-specific probabilistic models of protein evolution. PloS one, 2(6), e503. (pubmed)

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Rolland M, Jensen MA, Nickle DC, Yan J, Learn GH, Heath L, Weiner D, Mullins JI (2007). Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins. Journal of virology, 81(16), 8507-14. (pubmed)

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Herbeck JT, Lyagoba F, Moore SW, Shindo N, Biryahwaho B, Kaleebu P, Mullins JI (2007). Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda. AIDS research and human retroviruses, 23(5), 755-60. (pubmed)

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Crawford H, Prado JG, Leslie A, Hué S, Honeyborne I, Reddy S, van der Stok M, Mncube Z, Brander C, Rousseau C, Mullins JI, Kaslow R, Goepfert P, Allen S, Hunter E, Mulenga J, Kiepiela P, Walker BD, Goulder PJ (2007). Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. Journal of virology, 81(15), 8346-51. (pubmed)

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Chun TW, Justement JS, Moir S, Hallahan CW, Maenza J, Mullins JI, Collier AC, Corey L, Fauci AS (2007). Decay of the HIV reservoir in patients receiving antiretroviral therapy for extended periods: implications for eradication of virus. The Journal of infectious diseases, 195(12), 1762-4. (pubmed)

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Nickle DC, Rolland M, Jensen MA, Pond SL, Deng W, Seligman M, Heckerman D, Mullins JI, Jojic N (2007). Coping with viral diversity in HIV vaccine design. PLoS computational biology, 3(4), e75. (pubmed)

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Bhattacharya T, Daniels M, Heckerman D, Foley B, Frahm N, Kadie C, Carlson J, Yusim K, McMahon B, Gaschen B, Mallal S, Mullins JI, Nickle DC, Herbeck J, Rousseau C, Learn GH, Miura T, Brander C, Walker B, Korber B (2007). Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science (New York, N.Y.), 315(5818), 1583-6. (pubmed)

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Gottlieb GS, Hawes SE, Nickle DC, Herbeck JT, Kiviat NB, Mullins JI, Sow PS (2007). Presenting plasma HIV RNA level and rate of CD4 T-cell decline. JAMA, 297(8), 805; author reply 806-7. (pubmed)

Malhotra U, Li F, Nolin J, Allison M, Zhao H, Mullins JI, Self S, McElrath MJ (2007). Enhanced detection of human immunodeficiency virus type 1 (HIV-1) Nef-specific T cells recognizing multiple variants in early HIV-1 infection. Journal of virology, 81(10), 5225-37. (pubmed)

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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 virology, 81(9), 4492-500. (pubmed)

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Honeyborne I, Prendergast A, Pereyra F, Leslie A, Crawford H, Payne R, Reddy S, Bishop K, Moodley E, Nair K, van der Stok M, McCarthy N, Rousseau CM, Addo M, Mullins JI, Brander C, Kiepiela P, Walker BD, Goulder PJ (2007). Control of human immunodeficiency virus type 1 is associated with HLA-B*13 and targeting of multiple gag-specific CD8+ T-cell epitopes. Journal of virology, 81(7), 3667-72. (pubmed)

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2006

Kiepiela P, Ngumbela K, Thobakgale C, Ramduth D, Honeyborne I, Moodley E, Reddy S, de Pierres C, Mncube Z, Mkhwanazi N, Bishop K, van der Stok M, Nair K, Khan N, Crawford H, Payne R, Leslie A, Prado J, Prendergast A, Frater J, McCarthy N, Brander C, Learn GH, Nickle D, Rousseau C, Coovadia H, Mullins JI, Heckerman D, Walker BD, Goulder P (2007). CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nature medicine, 13(1), 46-53. (pubmed)

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Leslie A, Price DA, Mkhize P, Bishop K, Rathod A, Day C, Crawford H, Honeyborne I, Asher TE, Luzzi G, Edwards A, Rousseau CM, Rosseau CM, Mullins JI, Tudor-Williams G, Novelli V, Brander C, Douek DC, Kiepiela P, Walker BD, Goulder PJ (2006). Differential selection pressure exerted on HIV by CTL targeting identical epitopes but restricted by distinct HLA alleles from the same HLA supertype. Journal of immunology (Baltimore, Md. : 1950), 177(7), 4699-708. (pubmed)

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Liu Y, McNevin J, Cao J, Zhao H, Genowati I, Wong K, McLaughlin S, McSweyn MD, Diem K, Stevens CE, Maenza J, He H, Nickle DC, Shriner D, Holte SE, Collier AC, Corey L, McElrath MJ, Mullins JI (2006). Selection on the human immunodeficiency virus type 1 proteome following primary infection. Journal of virology, 80(19), 9519-29. (pubmed)

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Malhotra U, Nolin J, Mullins JI, McElrath MJ (2007). Comprehensive epitope analysis of cross-clade Gag-specific T-cell responses in individuals with early HIV-1 infection in the US epidemic. Vaccine, 25(2), 381-90. (pubmed)

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Shriner D, Liu Y, Nickle DC, Mullins JI (2006). Evolution of intrahost HIV-1 genetic diversity during chronic infection. Evolution; international journal of organic evolution, 60(6), 1165-76. (pubmed)

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Rousseau CM, Birditt BA, McKay AR, Stoddard JN, Lee TC, McLaughlin S, Moore SW, Shindo N, Learn GH, Korber BT, Brander C, Goulder PJ, Kiepiela P, Walker BD, Mullins JI (2006). Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. Journal of virological methods, 136(1-2), 118-25. (pubmed)

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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 virology, 80(10), 4698-704. (pubmed)

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Mullins JI, Jensen MA (2006). Evolutionary dynamics of HIV-1 and the control of AIDS. Current topics in microbiology and immunology, 299, 171-92. (pubmed)

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Holte SE, Melvin AJ, Mullins JI, Tobin NH, Frenkel LM (2006). Density-dependent decay in HIV-1 dynamics. Journal of acquired immune deficiency syndromes (1999), 41(3), 266-76. (pubmed)

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Martinez-Picado J, Prado JG, Fry EE, Pfafferott K, Leslie A, Chetty S, Thobakgale C, Honeyborne I, Crawford H, Matthews P, Pillay T, Rousseau C, Mullins JI, Brander C, Walker BD, Stuart DI, Kiepiela P, Goulder P (2006). Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. Journal of virology, 80(7), 3617-23. (pubmed)

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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 virology, 80(4), 1637-44. (pubmed)

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Liu Y, Mullins JI, Mittler JE (2006). Waiting times for the appearance of cytotoxic T-lymphocyte escape mutants in chronic HIV-1 infection. Virology, 347(1), 140-6. (pubmed)

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Shepherd BE, Rossini AJ, Soto RJ, De Rivera IL, Mullins JI (2005). Sampling designs for HIV molecular epidemiology with application to Honduras. AIDS research and human retroviruses, 21(11), 907-14. (pubmed)

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Iversen AK, Stewart-Jones G, Learn GH, Christie N, Sylvester-Hviid C, Armitage AE, Kaul R, Beattie T, Lee JK, Li Y, Chotiyarnwong P, Dong T, Xu X, Luscher MA, MacDonald K, Ullum H, Klarlund-Pedersen B, Skinhøj P, Fugger L, Buus S, Mullins JI, Jones EY, van der Merwe PA, McMichael AJ (2006). Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope. Nature immunology, 7(2), 179-89. (pubmed)

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2005

Frahm N, Kiepiela P, Adams S, Linde CH, Hewitt HS, Sango K, Feeney ME, Addo MM, Lichterfeld M, Lahaie MP, Pae E, Wurcel AG, Roach T, St John MA, Altfeld M, Marincola FM, Moore C, Mallal S, Carrington M, Heckerman D, Allen TM, Mullins JI, Korber BT, Goulder PJ, Walker BD, Brander C (2006). Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nature immunology, 7(2), 173-8. (pubmed)

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Chun TW, Nickle DC, Justement JS, Large D, Semerjian A, Curlin ME, O'Shea MA, Hallahan CW, Daucher M, Ward DJ, Moir S, Mullins JI, Kovacs C, Fauci AS (2005). HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. The Journal of clinical investigation, 115(11), 3250-5. (pubmed)

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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 virology, 79(17), 11214-24. (pubmed)

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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 virology, 79(15), 9625-34. (pubmed)

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van ’t Wout AB, Swain JV, Schindler M, Rao U, Pathmajeyan MS, Mullins JI, Kirchhoff F (2005). Nef induces multiple genes involved in cholesterol synthesis and uptake in human immunodeficiency virus type 1-infected T cells. Journal of virology, 79(15), 10053-8. (pubmed)

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Troyer RM, Collins KR, Abraha A, Fraundorf E, Moore DM, Krizan RW, Toossi Z, Colebunders RL, Jensen MA, Mullins JI, Vanham G, Arts EJ (2005). Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression. Journal of virology, 79(14), 9006-18. (pubmed)

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Gottlieb GS, Nickle DC (None). Multidrug-resistant, dual-tropic HIV-1 and rapid progression. Lancet (London, England), 365(9475), 1923-4; author reply 1924. (pubmed)

Iversen AK, Learn GH, Skinhøj P, Mullins JI, McMichael AJ, Rambaut A (2005). Preferential detection of HIV subtype C' over subtype A in cervical cells from a dually infected woman. AIDS (London, England), 19(9), 990-3. (pubmed)

Leslie A, Kavanagh D, Honeyborne I, Pfafferott K, Edwards C, Pillay T, Hilton L, Thobakgale C, Ramduth D, Draenert R, Le Gall S, Luzzi G, Edwards A, Brander C, Sewell AK, Moore S, Mullins J, Moore C, Mallal S, Bhardwaj N, Yusim K, Phillips R, Klenerman P, Korber B, Kiepiela P, Walker B, Goulder P (2005). Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. The Journal of experimental medicine, 201(6), 891-902. (pubmed)

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2004

Kiepiela P, Leslie AJ, Honeyborne I, Ramduth D, Thobakgale C, Chetty S, Rathnavalu P, Moore C, Pfafferott KJ, Hilton L, Zimbwa P, Moore S, Allen T, Brander C, Addo MM, Altfeld M, James I, Mallal S, Bunce M, Barber LD, Szinger J, Day C, Klenerman P, Mullins J, Korber B, Coovadia HM, Walker BD, Goulder PJ (2004). Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature, 432(7018), 769-75. (pubmed)

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Curlin ME, Gottlieb GS, Hawes SE, Sow PS, Ndoye I, Critchlow CW, Kiviat NB, Mullins JI (2004). No evidence for recombination between HIV type 1 and HIV type 2 within the envelope region in dually seropositive individuals from Senegal. AIDS research and human retroviruses, 20(9), 958-63. (pubmed)

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Iversen AK, Attermann J, Gerstoft J, Fugger L, Mullins JI, Skinhøj P (2004). Longitudinal and cross-sectional studies of HIV-1 RNA and DNA loads in blood and the female genital tract. European journal of obstetrics, gynecology, and reproductive biology, 117(2), 227-35. (pubmed)

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Liu Y, Nickle DC, Shriner D, Jensen MA, Learn GH, Mittler JE, Mullins JI (2004). Molecular clock-like evolution of human immunodeficiency virus type 1. Virology, 329(1), 101-8. (pubmed)

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Shriner D, Rodrigo AG, Nickle DC, Mullins JI (2004). Pervasive genomic recombination of HIV-1 in vivo. Genetics, 167(4), 1573-83. (pubmed)

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Mullins JI, Nickle DC, Heath L, Rodrigo AG, Learn GH (2004). Immunogen sequence: the fourth tier of AIDS vaccine design. Expert review of vaccines, 3(4 Suppl), S151-9. (pubmed)

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Fulcher JA, Hwangbo Y, Zioni R, Nickle D, Lin X, Heath L, Mullins JI, Corey L, Zhu T (2004). Compartmentalization of human immunodeficiency virus type 1 between blood monocytes and CD4+ T cells during infection. Journal of virology, 78(15), 7883-93. (pubmed)

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Zhu T, Hu SL, Feng F, Polacino P, Liu H, Hwangbo Y, Learn GH, Mullins JI, Corey L (2004). Persistence of low levels of simian immunodeficiency virus in macaques that were transiently viremic by conventional testing. Virology, 323(2), 208-19. (pubmed)

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Yu XG, Addo MM, Perkins BA, Wej F, Rathod A, Geer SC, Parta M, Cohen D, Stone DR, Russell CJ, Tanzi G, Mei S, Wurcel AG, Frahm N, Lichterfeld M, Heath L, Mullins JI, Marincola F, Goulder PJ, Brander C, Allen T, Cao Y, Walker BD, Altfeld M (2004). Differences in the expressed HLA class I alleles effect the differential clustering of HIV type 1-specific T cell responses in infected Chinese and caucasians. AIDS research and human retroviruses, 20(5), 557-64. (pubmed)

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Brumme ZL, Dong WW, Yip B, Wynhoven B, Hoffman NG, Swanstrom R, Jensen MA, Mullins JI, Hogg RS, Montaner JS, Harrigan PR (2004). Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS (London, England), 18(4), F1-9. (pubmed)

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Shriner D, Shankarappa R, Jensen MA, Nickle DC, Mittler JE, Margolick JB, Mullins JI (2004). Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection. Genetics, 166(3), 1155-64. (pubmed)

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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. Lancet (London, England), 363(9409), 619-22. (pubmed)

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Frahm N, Korber BT, Adams CM, Szinger JJ, Draenert R, Addo MM, Feeney ME, Yusim K, Sango K, Brown NV, SenGupta D, Piechocka-Trocha A, Simonis T, Marincola FM, Wurcel AG, Stone DR, Russell CJ, Adolf P, Cohen D, Roach T, StJohn A, Khatri A, Davis K, Mullins J, Goulder PJ, Walker BD, Brander C (2004). Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities. Journal of virology, 78(5), 2187-200. (pubmed)

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2003

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 virology, 77(24), 13376-88. (pubmed)

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Nickle DC, Shriner D, Mittler JE, Frenkel LM, Mullins JI (2003). Importance and detection of virus reservoirs and compartments of HIV infection. Current opinion in microbiology, 6(4), 410-6. (pubmed)

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Gottlieb GS, Sow PS, Hawes SE, Ndoye I, Coll-Seck AM, Curlin ME, Critchlow CW, Kiviat NB, Mullins JI (2003). Molecular epidemiology of dual HIV-1/HIV-2 seropositive adults from Senegal, West Africa. AIDS research and human retroviruses, 19(7), 575-84. (pubmed)

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Jensen MA, van ’t Wout AB (None). Predicting HIV-1 coreceptor usage with sequence analysis. AIDS reviews, 5(2), 104-12. (pubmed)

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Shriner D, Nickle DC, Jensen MA, Mullins JI (2003). Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genetical research, 81(2), 115-21. (pubmed)

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Altfeld M, Addo MM, Shankarappa R, Lee PK, Allen TM, Yu XG, Rathod A, Harlow J, O'Sullivan K, Johnston MN, Goulder PJ, Mullins JI, Rosenberg ES, Brander C, Korber B, Walker BD (2003). Enhanced detection of human immunodeficiency virus type 1-specific T-cell responses to highly variable regions by using peptides based on autologous virus sequences. Journal of virology, 77(13), 7330-40. (pubmed)

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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 evolution, 20(7), 1168-80. (pubmed)

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Zhu T, Corey L, Hwangbo Y, Lee JM, Learn GH, Mullins JI, McElrath MJ (2003). Persistence of extraordinarily low levels of genetically homogeneous human immunodeficiency virus type 1 in exposed seronegative individuals. Journal of virology, 77(11), 6108-16. (pubmed)

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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 virology, 77(10), 5721-30. (pubmed)

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Nickle DC, Jensen MA, Shriner D, Brodie SJ, Frenkel LM, Mittler JE, Mullins JI (2003). Evolutionary indicators of human immunodeficiency virus type 1 reservoirs and compartments. Journal of virology, 77(9), 5540-6. (pubmed)

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Nickle DC, Jensen MA, Gottlieb GS, Shriner D, Learn GH, Rodrigo AG, Mullins JI (2003). Consensus and ancestral state HIV vaccines. Science (New York, N.Y.), 299(5612), 1515-8; author reply 1515-8. (pubmed)

Dybul M, Daucher M, Jensen MA, Hallahan CW, Chun TW, Belson M, Hidalgo B, Nickle DC, Yoder C, Metcalf JA, Davey RT, Ehler L, Kress-Rock D, Nies-Kraske E, Liu S, Mullins JI, Fauci AS (2003). Genetic characterization of rebounding human immunodeficiency virus type 1 in plasma during multiple interruptions of highly active antiretroviral therapy. Journal of virology, 77(5), 3229-37. (pubmed)

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2002

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 virology, 77(2), 1392-402. (pubmed)

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Learn GH, Muthui D, Brodie SJ, Zhu T, Diem K, Mullins JI, Corey L (2002). Virus population homogenization following acute human immunodeficiency virus type 1 infection. Journal of virology, 76(23), 11953-9. (pubmed)

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Liu SL, Mittler JE, Nickle DC, Mulvania TM, Shriner D, Rodrigo AG, Kosloff B, He X, Corey L, Mullins JI (2002). Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS. Journal of virology, 76(21), 10674-84. (pubmed)

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Malaspina A, Moir S, Nickle DC, Donoghue ET, Ogwaro KM, Ehler LA, Liu S, Mican JA, Dybul M, Chun TW, Mullins JI, Fauci AS (2002). Human immunodeficiency virus type 1 bound to B cells: relationship to virus replicating in CD4+ T cells and circulating in plasma. Journal of virology, 76(17), 8855-63. (pubmed)

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Qanungo KR, Kundu SC, Mullins JI, Ghosh AK (2002). Molecular cloning and characterization of Antheraea mylitta cytoplasmic polyhedrosis virus genome segment 9. The Journal of general virology, 83(Pt 6), 1483-91. (pubmed)

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Gottlieb GS, Sow PS, Hawes SE, Ndoye I, Redman M, Coll-Seck AM, Faye-Niang MA, Diop A, Kuypers JM, Critchlow CW, Respess R, Mullins JI, Kiviat NB (2002). Equal plasma viral loads predict a similar rate of CD4+ T cell decline in human immunodeficiency virus (HIV) type 1- and HIV-2-infected individuals from Senegal, West Africa. The Journal of infectious diseases, 185(7), 905-14. (pubmed)

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Li F, Mullins JI (2002). Site-directed mutagenesis facilitated by DpnI selection on hemimethylated DNA. Methods in molecular biology (Clifton, N.J.), 182, 19-27. (pubmed)

2001

Zhu T, Muthui D, Holte S, Nickle D, Feng F, Brodie S, Hwangbo Y, Mullins JI, Corey L (2002). Evidence for human immunodeficiency virus type 1 replication in vivo in CD14(+) monocytes and its potential role as a source of virus in patients on highly active antiretroviral therapy. Journal of virology, 76(2), 707-16. (pubmed)

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Nickle DC, Learn GH, Rain MW, Mullins JI, Mittler JE (2002). Curiously modern DNA for a “250 million-year-old” bacterium. Journal of molecular evolution, 54(1), 134-7. (pubmed)

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Gottlieb GS, Mullins JI (2001). Re: Follow-up study of intrahost HIV type 2 variability reveals discontinuous evolution of C2V3 sequences. AIDS research and human retroviruses, 17(16), 1563-5, 1567. (pubmed)

Anderson JP, Rodrigo AG, Learn GH, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI (2001). Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region. Journal of molecular evolution, 53(1), 55-62. (pubmed)

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Shankarappa R, Chatterjee R, Learn GH, Neogi D, Ding M, Roy P, Ghosh A, Kingsley L, Harrison L, Mullins JI, Gupta P (2001). Human immunodeficiency virus type 1 env sequences from Calcutta in eastern India: identification of features that distinguish subtype C sequences in India from other subtype C sequences. Journal of virology, 75(21), 10479-87. (pubmed)

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Holterman L, Dubbes R, Mullins J, Learn G, Niphuis H, Koornstra W, Koopman G, Kuhn EM, Wade-Evans A, Rosenwirth B, Haaijman J, Heeney J (2001). Characteristics of a pathogenic molecular clone of an end-stage serum-derived variant of simian immunodeficiency virus (SIV(F359)). Journal of virology, 75(19), 9328-38. (pubmed)

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Kreisberg JF, Kwa D, Schramm B, Trautner V, Connor R, Schuitemaker H, Mullins JI, van’t Wout AB, Goldsmith MA (2001). Cytopathicity of human immunodeficiency virus type 1 primary isolates depends on coreceptor usage and not patient disease status. Journal of virology, 75(18), 8842-7. (pubmed)

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Frey SC, Hoover EA, Mullins JI (2001). Feline immunodeficiency virus cell entry. Journal of virology, 75(11), 5433-40. (pubmed)

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Frenkel LM, Mullins JI (2001). Should patients with drug-resistant HIV-1 continue to receive antiretroviral therapy? The New England journal of medicine, 344(7), 520-2. (pubmed)

Altfeld M, Rosenberg ES, Shankarappa R, Mukherjee JS, Hecht FM, Eldridge RL, Addo MM, Poon SH, Phillips MN, Robbins GK, Sax PE, Boswell S, Kahn JO, Brander C, Goulder PJ, Levy JA, Mullins JI, Walker BD (2001). Cellular immune responses and viral diversity in individuals treated during acute and early HIV-1 infection. The Journal of experimental medicine, 193(2), 169-80. (pubmed)

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2000

Anderson JP, Rodrigo AG, Learn GH, Madan A, Delahunty C, Coon M, Girard M, Osmanov S, Hood L, Mullins JI (2000). Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E. Journal of virology, 74(22), 10752-65. (pubmed)

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Russell KL, Carcamo C, Watts DM, Sanchez J, Gotuzzo E, Euler A, Blanco JC, Galeano A, Alava A, Mullins JI, Holmes KK, Carr JK (2000). Emerging genetic diversity of HIV-1 in South America. AIDS (London, England), 14(12), 1785-91. (pubmed)

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Kliks S, Contag CH, Corliss H, Learn G, Rodrigo A, Wara D, Mullins JI, Levy JA (2000). Genetic analysis of viral variants selected in transmission of human immunodeficiency viruses to newborns. AIDS research and human retroviruses, 16(13), 1223-33. (pubmed)

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Chun TW, Davey RT, Ostrowski M, Shawn Justement J, Engel D, Mullins JI, Fauci AS (2000). Relationship between pre-existing viral reservoirs and the re-emergence of plasma viremia after discontinuation of highly active anti-retroviral therapy. Nature medicine, 6(7), 757-61. (pubmed)

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Upchurch DA, Shankarappa R, Mullins JI (2000). Position and degree of mismatches and the mobility of DNA heteroduplexes. Nucleic acids research, 28(12), E69. (pubmed)

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Robertson DL, Anderson JP, Bradac JA, Carr JK, Foley B, Funkhouser RK, Gao F, Hahn BH, Kalish ML, Kuiken C, Learn GH, Leitner T, McCutchan F, Osmanov S, Peeters M, Pieniazek D, Salminen M, Sharp PM, Wolinsky S, Korber B (2000). HIV-1 nomenclature proposal. Science (New York, N.Y.), 288(5463), 55-6. (pubmed)

Panther LA, Tucker L, Xu C, Tuomala RE, Mullins JI, Anderson DJ (2000). Genital tract human immunodeficiency virus type 1 (HIV-1) shedding and inflammation and HIV-1 env diversity in perinatal HIV-1 transmission. The Journal of infectious diseases, 181(2), 555-63. (pubmed)

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Iversen AK, Learn GH, Fugger L, Gerstoft J, Mullins JI, Skinhoj P (1999). Presence of multiple HIV subtypes and a high frequency of subtype chimeric viruses in heterosexually infected women. Journal of acquired immune deficiency syndromes (1999), 22(4), 325-32. (pubmed)

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Loeb LA, Mullins JI (2000). Lethal mutagenesis of HIV by mutagenic ribonucleoside analogs. AIDS research and human retroviruses, 16(1), 1-3. (pubmed)

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1999

Mulvania T, Lynch JB, Robertson MN, Greenberg PD, Morton WR, Mullins JI (None). Antigen-specific cytokine responses in vaccinated Macaca nemestrina. Journal of medical primatology, 28(4-5), 181-9. (pubmed)

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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 virology, 73(12), 10489-502. (pubmed)

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Li F, Liu SL, Mullins JI (1999). Site-directed mutagenesis using uracil-containing double-stranded DNA templates and DpnI digestion. BioTechniques, 27(4), 734-8. (pubmed)

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Melvin AJ, Rodrigo AG, Mohan KM, Lewis PA, Manns-Arcuino L, Coombs RW, Mullins JI, Frenkel LM (1999). HIV-1 dynamics in children. Journal of acquired immune deficiency syndromes and human retrovirology : official publication of the International Retrovirology Association, 20(5), 468-73. (pubmed)

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Rodrigo AG, Shpaer EG, Delwart EL, Iversen AK, Gallo MV, Brojatsch J, Hirsch MS, Walker BD, Mullins JI (1999). Coalescent estimates of HIV-1 generation time in vivo. Proceedings of the National Academy of Sciences of the United States of America, 96(5), 2187-91. (pubmed)

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Loeb LA, Essigmann JM, Kazazi F, Zhang J, Rose KD, Mullins JI (1999). Lethal mutagenesis of HIV with mutagenic nucleoside analogs. Proceedings of the National Academy of Sciences of the United States of America, 96(4), 1492-7. (pubmed)

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Tien PC, Chiu T, Latif A, Ray S, Batra M, Contag CH, Zejena L, Mbizvo M, Delwart EL, Mullins JI, Katzenstein DA (1999). Primary subtype C HIV-1 infection in Harare, Zimbabwe. Journal of acquired immune deficiency syndromes and human retrovirology : official publication of the International Retrovirology Association, 20(2), 147-53. (pubmed)

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1998

Rinaldo CR, Gupta P, Huang XL, Fan Z, Mullins JI, Gange S, Farzadegan H, Shankarappa R, Muñoz A, Margolick JB (1998). Anti-HIV type 1 memory cytotoxic T lymphocyte responses associated with changes in CD4+ T cell numbers in progression of HIV type 1 infection. AIDS research and human retroviruses, 14(16), 1423-33. (pubmed)

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Iversen AK, Fugger L, Eugen-Olsen J, Balslev U, Jensen T, Wahl S, Gerstoft J, Mullins JI, Skinhoj P (1998). Cervical human immunodeficiency virus type 1 shedding is associated with genital beta-chemokine secretion. The Journal of infectious diseases, 178(5), 1334-42. (pubmed)

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Mulvania T, Coon E, Kuller L, Agy MB, Morton WR, Mullins JI (None). Natural history of SIVmac BK28 and H824 infection in Macaca nemestrina. Journal of medical primatology, 27(2-3), 87-93. (pubmed)

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Poss M, Rodrigo AG, Gosink JJ, Learn GH, de Vange Panteleeff D, Martin HL, Bwayo J, Kreiss JK, Overbaugh J (1998). Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. Journal of virology, 72(10), 8240-51. (pubmed)

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Ostrowski MA, Krakauer DC, Li Y, Justement SJ, Learn G, Ehler LA, Stanley SK, Nowak M, Fauci AS (1998). Effect of immune activation on the dynamics of human immunodeficiency virus replication and on the distribution of viral quasispecies. Journal of virology, 72(10), 7772-84. (pubmed)

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Dwyer DE, Herring BL, Ge YC, Bolton WV, Ellis-Pegler RB, Thomas M, Schroeder BA, Croxson MC, Cunningham AL, Mullins JI, Saksena NK (1998). Human immunodeficiency virus type 1 subtypes B and C detected in New Zealand. AIDS research and human retroviruses, 14(12), 1105-8. (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.), 280(5366), 1073-7. (pubmed)

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Iversen AK, Larsen AR, Jensen T, Fugger L, Balslev U, Wahl S, Gerstoft J, Mullins JI, Skinhøj P (1998). Distinct determinants of human immunodeficiency virus type 1 RNA and DNA loads in vaginal and cervical secretions. The Journal of infectious diseases, 177(5), 1214-20. (pubmed)

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Polyak SJ, McArdle S, Liu SL, Sullivan DG, Chung M, Hofgärtner WT, Carithers RL, McMahon BJ, Mullins JI, Corey L, Gretch DR (1998). Evolution of hepatitis C virus quasispecies in hypervariable region 1 and the putative interferon sensitivity-determining region during interferon therapy and natural infection. Journal of virology, 72(5), 4288-96. (pubmed)

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Paladin FJ, Monzon OT, Tsuchie H, Aplasca MR, Learn GH, Kurimura T (1998). Genetic subtypes of HIV-1 in the Philippines. AIDS (London, England), 12(3), 291-300. (pubmed)

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Shankarappa R, Gupta P, Learn GH, Rodrigo AG, Rinaldo CR, Gorry MC, Mullins JI, Nara PL, Ehrlich GD (1998). Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles. Virology, 241(2), 251-9. (pubmed)

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Edmonson P, Murphey-Corb M, Martin LN, Delahunty C, Heeney J, Kornfeld H, Donahue PR, Learn GH, Hood L, Mullins JI (1998). Evolution of a simian immunodeficiency virus pathogen. Journal of virology, 72(1), 405-14. (pubmed)

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Delwart EL, Mullins JI, Gupta P, Learn GH, Holodniy M, Katzenstein D, Walker BD, Singh MK (1998). Human immunodeficiency virus type 1 populations in blood and semen. Journal of virology, 72(1), 617-23. (pubmed)

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1997

Delwart EL, Pan H, Sheppard HW, Wolpert D, Neumann AU, Korber B, Mullins JI (1997). Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. Journal of virology, 71(10), 7498-508. (pubmed)

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Mullins JI (1997). Curtailing the AIDS pandemic. Science (New York, N.Y.), 276(5321), 1955-7. (pubmed)

Rodrigo AG, Goracke PC, Rowhanian K, Mullins JI (1997). Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays. AIDS research and human retroviruses, 13(9), 737-42. (pubmed)

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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 virology, 71(6), 4241-53. (pubmed)

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Liu SL, Schacker T, Musey L, Shriner D, McElrath MJ, Corey L, Mullins JI (1997). Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. Journal of virology, 71(6), 4284-95. (pubmed)

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Contag CH, Ehrnst A, Duda J, Bohlin AB, Lindgren S, Learn GH, Mullins JI (1997). Mother-to-infant transmission of human immunodeficiency virus type 1 involving five envelope sequence subtypes. Journal of virology, 71(2), 1292-300. (pubmed)

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1996

Rodrigo AG, Mullins JI (1996). Human immunodeficiency virus type 1 molecular evolution and the measure of selection. AIDS research and human retroviruses, 12(18), 1681-5. (pubmed)

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Yoshimura FK, Diem K, Learn GH, Riddell S, Corey L (1996). Intrapatient sequence variation of the gag gene of human immunodeficiency virus type 1 plasma virions. Journal of virology, 70(12), 8879-87. (pubmed)

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Sabino EC, Diaz RS, Brigido LF, Learn GH, Mullins JI, Reingold AL, Duarte AJ, Mayer A, Busch MP (1996). Distribution of HIV-1 subtypes seen in an AIDS clinic in Sao Paulo City, Brazil. AIDS (London, England), 10(13), 1579-84. (pubmed)

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Bickel PJ, Cosman PC, Olshen RA, Spector PC, Rodrigo AG, Mullins JI (1996). Covariability of V3 loop amino acids. AIDS research and human retroviruses, 12(15), 1401-11. (pubmed)

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Goulston C, Stevens E, Gallo D, Mullins JI, Hanson CV, Katzenstein D (1996). Human immunodeficiency virus in plasma and genital secretions during the menstrual cycle. The Journal of infectious diseases, 174(4), 858-61. (pubmed)

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Quackenbush SL, Dean GA, Mullins JI, Hoover EA (1996). Analysis of FeLV-FAIDS provirus burden and productive infection in lymphocyte subsets in vivo. Virology, 223(1), 1-9. (pubmed)

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Holterman L, Mullins JI, Haaijman JJ, Heeney JL (1996). Direct amplification and cloning of up to 5-kb lentivirus genomes from serum. BioTechniques, 21(2), 312-9. (pubmed)

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Learn GH, Korber BT, Foley B, Hahn BH, Wolinsky SM, Mullins JI (1996). Maintaining the integrity of human immunodeficiency virus sequence databases. Journal of virology, 70(8), 5720-30. (pubmed)

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Liu SL, Rodrigo AG, Shankarappa R, Learn GH, Hsu L, Davidov O, Zhao LP, Mullins JI (1996). HIV quasispecies and resampling. Science (New York, N.Y.), 273(5274), 415-6. (pubmed)

Quackenbush SL, Mullins JI, Hoover EA (1996). Replication kinetics and cell tropism of an immunosuppressive feline leukaemia virus. The Journal of general virology, 77 ( Pt 7), 1411-20. (pubmed)

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Lu S, Arthos J, Montefiori DC, Yasutomi Y, Manson K, Mustafa F, Johnson E, Santoro JC, Wissink J, Mullins JI, Haynes JR, Letvin NL, Wyand M, Robinson HL (1996). Simian immunodeficiency virus DNA vaccine trial in macaques. Journal of virology, 70(6), 3978-91. (pubmed)

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McElrath MJ, Corey L, Greenberg PD, Matthews TJ, Montefiori DC, Rowen L, Hood L, Mullins JI (1996). Human immunodeficiency virus type 1 infection despite prior immunization with a recombinant envelope vaccine regimen. Proceedings of the National Academy of Sciences of the United States of America, 93(9), 3972-7. (pubmed)

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Hoover EA, Mullins JI, Chu HJ, Wasmoen TL (1996). Efficacy of an inactivated feline leukemia virus vaccine. AIDS research and human retroviruses, 12(5), 379-83. (pubmed)

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Mossman SP, Bex F, Berglund P, Arthos J, O'Neil SP, Riley D, Maul DH, Bruck C, Momin P, Burny A, Fultz PN, Mullins JI, Liljeström P, Hoover EA (1996). Protection against lethal simian immunodeficiency virus SIVsmmPBj14 disease by a recombinant Semliki Forest virus gp160 vaccine and by a gp120 subunit vaccine. Journal of virology, 70(3), 1953-60. (pubmed)

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Iversen AK, Shafer RW, Wehrly K, Winters MA, Mullins JI, Chesebro B, Merigan TC (1996). Multidrug-resistant human immunodeficiency virus type 1 strains resulting from combination antiretroviral therapy. Journal of virology, 70(2), 1086-90. (pubmed)

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Yasutomi Y, Robinson HL, Lu S, Mustafa F, Lekutis C, Arthos J, Mullins JI, Voss G, Manson K, Wyand M, Letvin NL (1996). Simian immunodeficiency virus-specific cytotoxic T-lymphocyte induction through DNA vaccination of rhesus monkeys. Journal of virology, 70(1), 678-81. (pubmed)

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de Noronha CM, Reinhart TA, Mullins JI (1996). Generation and role of defective proviruses in cytopathic feline leukemia virus (FeLV-FAIDS) infections. Journal of virology, 70(1), 359-67. (pubmed)

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1995

Robinson HL, Lu S, Mustafa F, Johnson E, Santoro JC, Arthos J, Winsink J, Mullins JI, Montefiori D, Yasutomi Y (1995). Simian immunodeficiency virus DNA vaccine trial in macaques. Annals of the New York Academy of Sciences, 772, 209-11. (pubmed)

Korber BT, Learn G, Mullins JI, Hahn BH, Wolinsky S (1995). Protecting HIV databases. Nature, 378(6554), 242-4. (pubmed)

Contag CH, Contag PR, Mullins JI, Spilman SD, Stevenson DK, Benaron DA (1995). Photonic detection of bacterial pathogens in living hosts. Molecular microbiology, 18(4), 593-603. (pubmed)

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Hoover EA, Mullins JI, Chu HJ, Wasmoen TL (1995). Development and testing of an inactivated feline leukemia virus vaccine. Seminars in veterinary medicine and surgery (small animal), 10(4), 238-43. (pubmed)

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Ghosh AK, Mullins JI (1995). cDNA encoding a functional feline liver/bone/kidney-type alkaline phosphatase. Archives of biochemistry and biophysics, 322(1), 240-9. (pubmed)

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Iversen AK, Shpaer EG, Rodrigo AG, Hirsch MS, Walker BD, Sheppard HW, Merigan TC, Mullins JI (1995). Persistence of attenuated rev genes in a human immunodeficiency virus type 1-infected asymptomatic individual. Journal of virology, 69(9), 5743-53. (pubmed)

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Delwart EL, Herring B, Rodrigo AG, Mullins JI (1995). Genetic subtyping of human immunodeficiency virus using a heteroduplex mobility assay. PCR methods and applications, 4(5), S202-16. (pubmed)

Sodora DL, Courcelle J, Brojatsch J, Berson A, Wang YC, Dow SW, Hoover EA, Mullins JI (1995). Analysis of a feline immunodeficiency virus provirus reveals patterns of gene sequence conservation distinct from human immunodeficiency virus type 1. AIDS research and human retroviruses, 11(4), 531-3. (pubmed)

Wang RF, Mullins JI (1995). Mammalian cell/vaccinia virus expression vectors with increased stability of retroviral sequences in Escherichia coli: production of feline immunodeficiency virus envelope protein. Gene, 153(2), 197-202. (pubmed)

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