Mullins Molecular Retrovirology Lab

Publications

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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