Mullins Molecular Retrovirology Lab

Publications

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 chemotherapyEpub ahead of print pubmed
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 elements vaccines: Relationship between sequence conservation and replicative capacity. Journal of VirologyEpub ahead of print 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 DiseasesEpub ahead of print pubmed
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 DiseasesEpub ahead of print 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 2012 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 methodsEpub ahead of print pubmed
Wagner TA, McKernan JL, Tobin NH, Tapia KA, Mullins JI, Frenkel LM 2012 An Increasing Proportion of Monotypic HIV-1 DNA Sequences During Antiretroviral Treatment Suggests Proliferation of HIV-Infected Cells. Journal of virologyEpub ahead of print pubmed
Lingappa J, Thomas KK, Hughes JP, Baeten JM, Wald A, Farquhar C, de Bruyn G, Fife KH, Campbell MS, Kapiga S, Mullins JI, Celum C 2012 Partner characteristics predicting HIV-1 setpoint in sexually acquired HIV-1 among African seroconverters. AIDS research and human retrovirusesEpub ahead of print 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. NatureEpub ahead of print 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, Mascio MD, 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, Lint CV, Verdin E, Woolfrey A, Zaia J, Barré-Sinoussi F 2012 Towards an HIV cure: a global scientific strategy. Nature reviews. ImmunologyEpub ahead of print 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

Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD 2009 Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1. Molecular biology and evolution274819-32 pubmed
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 diseases200121825-1833 pubmed
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 One49e7122 pubmed
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. Vaccine27486678-87 pubmed
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 one49e6949 pubmed
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 one49e6915 pubmed
Liu Y, Woodward A, Zhu H, Andrus T, McNevin J, Lee J, Mullins JI, Corey L, McElrath MJ, Zhu T 2009 Pre-infection HIV-specific CTL failed to prevent HIV-1 infection from strains genetically unrelated to viruses in long-term exposed partner. Journal of Virology832010821-9 pubmed
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 diseases19991323-6 pubmed
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 ONE45e5690 pubmed
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. AIDS238923-8 pubmed
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 Pathogens54e1000365 pubmed
Bull ME, Learn GH, McElhone S, Hitti J, Lockhart D, Holte S, Dragavon J, Coombs RW, Mullins JI, Frenkel LM 2009 Monotypic HIV-1 Genotypes across the Uterine Cervix and in Blood Suggests Proliferation of Cells with Provirus. Journal of Virology836020-8 pubmed
Gottlieb GS, Badiane NMD, Hawes SE, Fortes L, Toure M, Ndour CT, Starling AK, Traore F, Sall F, Wong KG, CherneSL, AndersonDJ, Dye SA, Smith RA, Mullins JI, Kiviat NB, Sow PS, for the University of Washington-Dakar HIV-2 Study Group 2009 Emergence of Multiclass Drug-Resistance in HIV-2 in Antiretroviral-Treated Individuals in Senegal: Implications for HIV-2 Treatment in Resouce-Limited West Africa. Clinical Infectious Diseases484476-83 pubmed		Supplemental Data

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
Rousseau C, Lockhart D, Listgarten J, Kadie C, Learn G, Maley S, Nickle D, Heckerman D, Deng W, Brander C, Ndung'u T, Coovadia H, Goulder P, Korber B, Walker B, Mullins J 2009 Rare HLA Drive Additional HIV Evolution Compared to More Frequent Alleles AIDS Research and Human Retroviruses253297-303 pubmed		Supplemental Data
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. Epub 2008 Sep 24 pubmed
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 chemotherapy521329-32 pubmed
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 virology82178548-59 pubmed
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 biology41e25 pubmed
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 virology82136434-46 pubmed
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 retroviruses244561-71 pubmed
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 diseases19771011-5 pubmed
Liu Y, Curlin ME, Diem K, Zhao H, Ghosh AK, Zhu H, Woodward AS, Maenza J, Stevens CE, Stekler J, Collier AC, Genowati I, Deng W, Zioni R, Corey L, Zhu T, Mullins JI 2008 Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. Virology3742229-33 pubmed		Supplemental Data
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)224447-56 pubmed
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 retroviruses24172-82 pubmed
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 diseases1975714-20 pubmed
Mullins JI, Rolland M, Allen TM 2008 Viral evolution and escape during primary human immunodeficiency virus-1 infection: implications for vaccine design. Curr Opin HIV AIDS3160-6 pubmed
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 diseases1972309-18 pubmed

Liu Y, Mittler JE 2008 Selection dramatically reduces effective population size in HIV-1 infection. BMC evolutionary biology8133 pubmed
Rolland M, Nickle DC, Mullins JI 2007 HIV-1 group M conserved elements vaccine. PLoS pathogens311e157 pubmed		Supplemental Data
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 virology821495-502 pubmed
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 ONE31e1424 pubmed
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 ONE32e1525 pubmed
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 virology812212179-88 pubmed
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. Microbiology59C1 pubmed
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 diseases1963493-4; 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)23172334-6 pubmed
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 virology81168507-14 pubmed
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
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 ONE29e823 pubmed
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
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 : the journal of the American Medical Association2978805; author reply 806-7 pubmed
Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, Kosakovsky Pond SL 2007 HIV-specific probabilistic models of protein evolution. PLoS ONE26e503 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 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
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)17774699-708 pubmed
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 virology80199519-29 pubmed
Shriner D, Liu Y, Nickle DC, Mullins JI 2006 Evolution of intrahost HIV-1 genetic diversity during chronic infection. Evolution; international journal of organic evolution6061165-76 pubmed
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 medicine13146-53 pubmed
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 biology34e75 pubmed
Jensen MA, Coetzer M, van 't Wout AB, Morris L, Mullins JI 2006 A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. Journal of virology80104698-704 pubmed		Supplemental Data
Mullins JI, Jensen MA 2006 Evolutionary dynamics of HIV-1 and the control of AIDS. Current topics in microbiology and immunology299171-92 pubmed
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)413266-76 pubmed
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 virology8073617-23 pubmed
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. Vaccine252381-90 pubmed
Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI 2006 Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host. Journal of virology8041637-44 pubmed		Supplemental Data
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 methods1361-2118-25 pubmed
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 retroviruses2111907-14 pubmed

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
Doria-Rose NA, Learn GH, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, Hensel MT, McLaughlin S, Edmonson PF, Montefiori D, Barnett SW, Haigwood NL, Mullins JI 2005 Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope. Journal of virology791711214-24 pubmed		Supplemental Data
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
Tobin NH, Learn GH, Holte SE, Wang Y, Melvin AJ, McKernan JL, Pawluk DM, Mohan KM, Lewis PF, Mullins JI, Frenkel LM 2005 Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus. Journal of virology79159625-34 pubmed		Supplemental Data
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
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 virology79149006-18 pubmed
Gottlieb GS, Nickle DC Multidrug-resistant, dual-tropic HIV-1 and rapid progression. Lancet36594751923-4; 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)199990-3 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 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
Shriner D, Rodrigo AG, Nickle DC, Mullins JI 2004 Pervasive genomic recombination of HIV-1 in vivo. Genetics16741573-83 pubmed
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
Mullins JI, Nickle DC, Heath L, Rodrigo AG, Learn GH 2004 Immunogen sequence: the fourth tier of AIDS vaccine design. Expert review of vaccines34 SupplS151-9 pubmed
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 virology78157883-93 pubmed
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
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)184F1-9 pubmed
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. Genetics16631155-64 pubmed
Gottlieb GS, Nickle DC, Jensen MA, Wong KG, Grobler J, Li F, Liu SL, Rademeyer C, Learn GH, Karim SS, Williamson C, Corey L, Margolick JB, Mullins JI 2004 Dual HIV-1 infection associated with rapid disease progression. Lancet3639409619-22 pubmed		Supplemental Data
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
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. Virology3291101-8 pubmed

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

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