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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 one910e111334 pubmed
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 one910e111085 pubmed
Wagner TA, McLaughlin S, Garg K, Cheung CY, Larsen BB, Styrchak S, Huang HC, Edlefsen PT, Mullins JI, Frenkel LM 2014 HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science (New York, N.Y.)3456196570-3 pubmed Supplemental Data
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)28121840-4 pubmed
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 virology88179976-90 pubmed
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 biology106e1003673 pubmed
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 virology88158242-8255 pubmed
Stekler JD, McKernan J, Milne R, Tapia KA, Mykhalchenko K, Holte S, Maenza J, Stevens CE, Buskin SE, Mullins JI, Frenkel LM, Collier AC 2014 Lack of resistance to integrase inhibitors among antiretroviral-naive subjects with primary HIV-1 infection, 2007-2013. Antiviral therapyEpub ahead of print pubmed
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 one94e94240 pubmed
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 microbiology5272320-7 pubmed
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. Virology450-45134-48 pubmed
Kahle E, Campbell M, Lingappa J, Donnell D, Celum C, Ondondo R, Mujugira A, Fife K, Mugo N, Kapiga S, Mullins JI, Baeten JM, 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)282235-43 pubmed
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)662127-34 pubmed
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 one91e86254 pubmed


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 diseases209101623-7 pubmed
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 virology8821354-65 pubmed
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 reports33014 pubmed
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 one810e76502 pubmed
Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI 2013 Quality score based identification and correction of pyrosequencing errors. PloS one89e73015 pubmed Supplemental Data
Shankarappa R, Mullins JI 2013 Inferring viral population structures using heteroduplex mobility and DNA sequence analyses. Journal of virological methods1941-2169-177 pubmed
Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI 2013 Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. Bioinformatics (Oxford, England)29192402-9 pubmed Supplemental Data
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)19152570-80 pubmed
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 methods1941-27-13 pubmed
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 pathogens97e1003515 pubmed
Manocheewa S, Swain JV, Lanxon-Cookson E, Rolland M, Mullins JI 2013 Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface. PloS one86e66065 pubmed Supplemental Data
Kunwar P, Hawkins N, Dinges WL, Liu Y, Gabriel EE, Swan DA, Stevens CE, Maenza J, Collier AC, Mullins JI, Hertz T, Yu X, Horton H 2013 Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design. PloS one85e64405 pubmed Supplemental Data
Raugi DN, Smith RA, Ba S, Toure M, Traore F, Sall F, Pan C, Blankenship L, Montano A, Olson J, Dia Badiane NM, Mullins JI, Kiviat NB, Hawes SE, Sow PS, Gottlieb GS, 2013 Complex patterns of protease inhibitor resistance among antiretroviral treatment-experienced HIV-2 patients from Senegal: implications for second-line therapy. Antimicrobial agents and chemotherapy5762751-60 pubmed Supplemental Data
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 one83e60245 pubmed
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 virology87105461-7 pubmed
Bull ME, Heath LM, McKernan-Mullin JL, Kraft KM, Acevedo L, Hitti JE, Cohn SE, Tapia KA, Holte SE, Dragavon JA, Coombs RW, Mullins JI, Frenkel LM 2013 Human immunodeficiency viruses appear compartmentalized to the female genital tract in cross-sectional analyses but genital lineages do not persist over time. The Journal of infectious diseases20781206-15 pubmed Supplemental Data
Campbell MS, Kahle EM, Celum C, Lingappa JR, Kapiga S, Mujugira A, Mugo NR, Fife KH, Mullins JI, Baeten JM, 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 diseases20771166-70 pubmed
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. AIDS273337-46 pubmed


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 methods1891157-66 pubmed
Wagner TA, McKernan JL, Tobin NH, Tapia KA, Mullins JI, Frenkel LM 2013 An increasing proportion of monotypic HIV-1 DNA sequences during antiretroviral treatment suggests proliferation of HIV-infected cells. Journal of virology8731770-8 pubmed Supplemental Data
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, 2013 Partner characteristics predicting HIV-1 set point in sexually acquired HIV-1 among African seroconverters. AIDS research and human retroviruses291164-71 pubmed
Smith RA, Raugi DN, Pan C, Coyne M, Hernandez A, Church B, Parker K, Mullins JI, Sow PS, Gottlieb GS 2012 Three Main Mutational Pathways in HIV-2 Lead to High-Level Raltegravir and Elvitegravir Resistance: Implications for Emerging HIV-2 Treatment Regimens. PloS one79e45372 pubmed
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. Nature4907420417-20 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 one78e43396 pubmed
, 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. Immunology128607-14 pubmed
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 one71e29717 pubmed
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. AIDS1426193-205 pubmed


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 pathogens77e1002110 pubmed
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, 2011 Genomewide Association Study for Determinants of HIV-1 Acquisition and Viral Set Point in HIV-1 Serodiscordant Couples with Quantified Virus Exposure. PloS one612e28632 pubmed
Mothe B, Llano A, Ibarrondo J, Daniels M, Miranda C, Zamarreno J, Bach V, Zuniga R, Perez-Alvarez 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, Gomez 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 medicine91208 pubmed
Smith RA, Raugi DN, Kiviat NB, Hawes SE, Mullins JI, Sow PS, Gottlieb GS, 2011 Phenotypic Susceptibility of HIV-2 to Raltegravir: Integrase Mutations Q148R and N155H Confer Raltegravir Resistance. AIDS25182235-41 pubmed
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, 2011 HIV-2 Integrase Variation in Integrase Inhibitor-Naïve Adults in Senegal, West Africa. PloS one67e22204 pubmed
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 pathogens77e1002110 pubmed
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. Vaccine29366072-8 pubmed
Smith RA 2011 Antiviral Drug Susceptibility Patterns in Gammaretroviridae: Lessons from XMRV and Related Retroviruses. Drugs of the Future 366455-464 read online
Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI. 2011 Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. Journal of Virology85157523-34 pubmed Supplemental Data
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 one63e17969 pubmed
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 2011 Genital HIV-1 RNA Predicts Risk of Heterosexual HIV-1 Transmission. Science translational medicine37777ra29 pubmed
Campbell MS, Mullins JI, Hughes JP, Celum C, Wong KG, Raugi DN, Sorensen S, Stoddard JN, Zhao H, Deng W, Kahle E, Panteleeff D, Baeten JM, McCutchan FE, Albert J, Leitner T, Wald A, Corey L, Lingappa JR, 2011 Viral Linkage in HIV-1 Seroconverters and Their Partners in an HIV-1 Prevention Clinical Trial. PloS one63e16986 pubmed Supplemental Data
Rolland M, Tovanabutra S, deCamp AC, Frahm NF, 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, Hrual 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 Medicine173366-71 pubmed
Liu Y, McNevin JP, Holte S, McElrath MJ, Mullins JI 2011 Dynamics of Viral Evolution and CTL Responses in HIV-1 Infection. PloS one61e15639 pubmed
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 one61e15135 pubmed
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. Vaccine29112110-9 pubmed


Smith RA 2010 Contamination of clinical specimens with MLV-encoding nucleic acids: implications for XMRV and other candidate human retroviruses. Retrovirology7112 pubmed
Curlin ME, Zioni R, Hawes SE, Liu Y, Deng W, Gottlieb GS, Zhu T, Mullins JI 2010 HIV-1 Envelope Subregion Length Variation during Disease Progression. PLoS Pathogens612 e1001228 pubmed Supplemental Data
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 2010 Screening Low Frequency SNPS From Genome Wide Association Study Reveals A New Risk Allele for Progression to Aids. Journal of acquired immune deficiency syndromes563279-84 pubmed
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 one59e12936 pubmed
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 medicine25050le1 pubmed
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, 2010 Estimating the impact of plasma HIV-1 RNA reductions on heterosexual HIV-1 transmission risk. PloS one59e12598 pubmed
Boutwell CL, Rolland MM, Herbeck JT, Mullins JI, Allen TM 2010 Viral evolution and escape during acute HIV-1 infection. The Journal of infectious diseases202 Suppl 2S309-14 pubmed
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 one59 pubmed
Smith RA, Gottlieb GS, Miller AD 2010 Susceptibility of the human retrovirus XMRV to antiretroviral inhibitors. Retrovirology770 pubmed
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 diseases2026908-15 pubmed
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 virology842010812-9 pubmed
Donnell D, Baeten JM, Kiarie J, Thomas KK, Stevens W, Cohen CR, McIntyre J, Lingappa JR, Celum C, 2010 Heterosexual HIV-1 transmission after initiation of antiretroviral therapy: a prospective cohort analysis. Lancet37597312092-8 pubmed
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. BioTechniques485405-8 pubmed
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 one54e10213 pubmed
Smith RA 2010 Random-scanning Mutagenesis. In: Methods in Molecular Biology #634: In Vitro Mutagenesis Protocolsch 27387-397 Jeff Braman (ed.), Humana Press, NY.pubmed
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 one53e9786 pubmed
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 virology8494461-8 pubmed
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 2010 Acyclovir and Transmission of HIV-1 from Persons Infected with HIV-1 and HSV-2. The New England journal of medicine3625427-39 pubmed
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 diseases2014618-626 pubmed


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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 Comput Biol411e1000225 pubmed
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Liu Y, Mittler JE 2008 Selection dramatically reduces effective population size in HIV-1 infection. BMC evolutionary biology8133 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 retroviruses235755-60 pubmed
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 virology81158346-51 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.)31558181583-6 pubmed
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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 virology81105225-37 pubmed
Rousseau CM, Learn GH, Bhattacharya T, Nickle DC, Heckerman D, Chetty S, Brander C, Goulder PJ, Walker BD, Kiepiela P, Korber BT, Mullins JI 2007 Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections. Journal of virology8194492-500 pubmed Supplemental Data
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 virology8173667-72 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 America454501-9 pubmed


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 diseases195121762-4 pubmed
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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 immunology72173-8 pubmed
Liu Y, Mullins JI, Mittler JE 2006 Waiting times for the appearance of cytotoxic T-lymphocyte escape mutants in chronic HIV-1 infection. Virology3471140-6 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 immunology72179-89 pubmed
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 virology791510053-8 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 investigation115113250-5 pubmed
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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 medicine2016891-902 pubmed


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 retroviruses209958-63 pubmed
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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. Nature4327018769-75 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. Virology3232208-19 pubmed
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 retroviruses205557-64 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 virology7852187-200 pubmed
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Jensen MA, Li FS, van 't Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI 2003 Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. Journal of virology772413376-88 pubmed Supplemental Data
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 biology1172227-35 pubmed
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 microbiology64410-6 pubmed
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 retroviruses197575-84 pubmed
Jensen MA, van 't Wout AB Predicting HIV-1 coreceptor usage with sequence analysis. AIDS reviews52104-12 pubmed
Shriner D, Nickle DC, Jensen MA, Mullins JI 2003 Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genetical research812115-21 pubmed
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 virology77137330-40 pubmed
Anderson JP, Learn GH, Rodrigo AG, He X, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI 2003 Predicting demographic group structures based on DNA sequence data. Molecular biology and evolution2071168-80 pubmed Supplemental Data
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 virology77116108-16 pubmed
Frenkel LM, Wang Y, Learn GH, McKernan JL, Ellis GM, Mohan KM, Holte SE, De Vange SM, Pawluk DM, Melvin AJ, Lewis PF, Heath LM, Beck IA, Mahalanabis M, Naugler WE, Tobin NH, Mullins JI 2003 Multiple viral genetic analyses detect low-level human immunodeficiency virus type 1 replication during effective highly active antiretroviral therapy. Journal of virology77105721-30 pubmed Supplemental Data
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 virology7795540-6 pubmed
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.)29956121515-8; 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 virology7753229-37 pubmed


van 't Wout AB, Lehrman GK, Mikheeva SA, O'Keeffe GC, Katze MG, Bumgarner RE, Geiss GK, Mullins JI 2003 Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. Journal of virology7721392-402 pubmed Supplemental Data
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 virology762311953-9 pubmed
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 virology762110674-84 pubmed
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 virology76178855-63 pubmed
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 virology83Pt 61483-91 pubmed
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 diseases1857905-14 pubmed
Li F, Mullins JI 2002 Site-directed mutagenesis facilitated by DpnI selection on hemimethylated DNA. Methods in molecular biology (Clifton, N.J.)18219-27 pubmed


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 virology762707-16 pubmed
Nickle DC, Learn GH, Rain MW, Mullins JI, Mittler JE 2002 Curiously modern DNA for a "250 million-year-old" bacterium. Journal of molecular evolution541134-7 pubmed
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 retroviruses17161563-5, 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 evolution53155-62 pubmed
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 virology752110479-87 pubmed
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 virology75199328-38 pubmed
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 virology75188842-7 pubmed
Frey SC, Hoover EA, Mullins JI 2001 Feline immunodeficiency virus cell entry. Journal of virology75115433-40 pubmed
Frenkel LM, Mullins JI 2001 Should patients with drug-resistant HIV-1 continue to receive antiretroviral therapy? The New England journal of medicine3447520-2 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 medicine1932169-80 pubmed


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 virology742210752-65 pubmed
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)14121785-91 pubmed
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 retroviruses16131223-33 pubmed
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 medicine67757-61 pubmed
Upchurch DA, Shankarappa R, Mullins JI 2000 Position and degree of mismatches and the mobility of DNA heteroduplexes. Nucleic acids research2812E69 pubmed
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.)288546355-6 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 diseases1812555-63 pubmed
Iversen AK, Learn GH, Fugger L, Gerstoft J, Mullins JI, Skinhøj 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)224325-32 pubmed
Loeb LA, Mullins JI 2000 Lethal mutagenesis of HIV by mutagenic ribonucleoside analogs. AIDS research and human retroviruses1611-3 pubmed


Mulvania T, Lynch JB, Robertson MN, Greenberg PD, Morton WR, Mullins JI Antigen-specific cytokine responses in vaccinated Macaca nemestrina. Journal of medical primatology284-5181-9 pubmed
Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI 1999 Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. Journal of virology731210489-502 pubmed Supplemental Data
Li F, Liu SL, Mullins JI 1999 Site-directed mutagenesis using uracil-containing double-stranded DNA templates and DpnI digestion. BioTechniques274734-8 pubmed
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 Association205468-73 pubmed
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 America9652187-91 pubmed
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 America9641492-7 pubmed
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 Association202147-53 pubmed


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 retroviruses14161423-33 pubmed
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 diseases17851334-42 pubmed
Mulvania T, Coon E, Kuller L, Agy MB, Morton WR, Mullins JI Natural history of SIVmac BK28 and H824 infection in Macaca nemestrina. Journal of medical primatology272-387-93 pubmed
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 virology72108240-51 pubmed
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 virology72107772-84 pubmed
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 retroviruses14121105-8 pubmed
Frenkel LM, Mullins JI, Learn GH, Manns-Arcuino L, Herring BL, Kalish ML, Steketee RW, Thea DM, Nichols JE, Liu SL, Harmache A, He X, Muthui D, Madan A, Hood L, Haase AT, Zupancic M, Staskus K, Wolinsky S, Krogstad P, Zhao J, Chen I, Koup R, Ho D, Korber B, Apple RJ, Coombs RW, Pahwa S, Roberts NJ 1998 Genetic evaluation of suspected cases of transient HIV-1 infection of infants. Science (New York, N.Y.)28053661073-7 pubmed Supplemental Data
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 diseases17751214-20 pubmed
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 virology7254288-96 pubmed
Paladin FJ, Monzon OT, Tsuchie H, Aplasca MR, Learn GH, Kurimura T 1998 Genetic subtypes of HIV-1 in the Philippines. AIDS (London, England)123291-300 pubmed
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. Virology2412251-9 pubmed
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 virology721617-23 pubmed
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 virology721405-14 pubmed


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 virology71107498-508 pubmed
Mullins JI 1997 Curtailing the AIDS pandemic. Science (New York, N.Y.)27653211955-7 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 retroviruses139737-42 pubmed
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 virology7164284-95 pubmed
Bachmann MH, Mathiason-Dubard C, Learn GH, Rodrigo AG, Sodora DL, Mazzetti P, Hoover EA, Mullins JI 1997 Genetic diversity of feline immunodeficiency virus: dual infection, recombination, and distinct evolutionary rates among envelope sequence clades. Journal of virology7164241-53 pubmed Supplemental Data
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 virology7121292-300 pubmed


Rodrigo AG, Mullins JI 1996 Human immunodeficiency virus type 1 molecular evolution and the measure of selection. AIDS research and human retroviruses12181681-5 pubmed
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 virology70128879-87 pubmed
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)10131579-84 pubmed
Bickel PJ, Cosman PC, Olshen RA, Spector PC, Rodrigo AG, Mullins JI 1996 Covariability of V3 loop amino acids. AIDS research and human retroviruses12151401-11 pubmed
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 diseases1744858-61 pubmed
Quackenbush SL, Dean GA, Mullins JI, Hoover EA 1996 Analysis of FeLV-FAIDS provirus burden and productive infection in lymphocyte subsets in vivo. Virology22311-9 pubmed
Holterman L, Mullins JI, Haaijman JJ, Heeney JL 1996 Direct amplification and cloning of up to 5-kb lentivirus genomes from serum. BioTechniques212312-9 pubmed
Learn GH, Korber BT, Foley B, Hahn BH, Wolinsky SM, Mullins JI 1996 Maintaining the integrity of human immunodeficiency virus sequence databases. Journal of virology7085720-30 pubmed
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.)2735274415-6 pubmed
Quackenbush SL, Mullins JI, Hoover EA 1996 Replication kinetics and cell tropism of an immunosuppressive feline leukaemia virus. The Journal of general virology77 ( Pt 7)1411-20 pubmed
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 virology7063978-91 pubmed
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 America9393972-7 pubmed
Hoover EA, Mullins JI, Chu HJ, Wasmoen TL 1996 Efficacy of an inactivated feline leukemia virus vaccine. AIDS research and human retroviruses125379-83 pubmed
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 virology7031953-60 pubmed
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 virology7021086-90 pubmed
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 virology701678-81 pubmed
de Noronha CM, Reinhart TA, Mullins JI 1996 Generation and role of defective proviruses in cytopathic feline leukemia virus (FeLV-FAIDS) infections. Journal of virology701359-67 pubmed


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 Sciences772209-11 pubmed
Korber BT, Learn G, Mullins JI, Hahn BH, Wolinsky S 1995 Protecting HIV databases. Nature3786554242-4 pubmed
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)104238-43 pubmed
Contag CH, Contag PR, Mullins JI, Spilman SD, Stevenson DK, Benaron DA 1995 Photonic detection of bacterial pathogens in living hosts. Molecular microbiology184593-603 pubmed
Ghosh AK, Mullins JI 1995 cDNA encoding a functional feline liver/bone/kidney-type alkaline phosphatase. Archives of biochemistry and biophysics3221240-9 pubmed
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 virology6995743-53 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 retroviruses114531-3 pubmed
Delwart EL, Herring B, Rodrigo AG, Mullins JI 1995 Genetic subtyping of human immunodeficiency virus using a heteroduplex mobility assay. PCR methods and applications45S202-16 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. Gene1532197-202 pubmed
Department of Microbiology
School of Medicine
University of Washington
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