By Emeritus Professor Rodney Phillips

Book Chapters

Klenerman P; Lalloo D; Phillips R; McMichael A, 1996, 'Immune escape through T cell antagonism?', in Gene Technology, Springer Berlin Heidelberg, pp. 361 - 368, http://dx.doi.org/10.1007/978-3-642-61122-3_26

Journal articles

Granger LA; Huettner I; Debeljak F; Kaleebu P; Schechter M; Tambussi G; Weber J; Miro JM; Phillips R; Babiker A; Cooper DA; Fisher M; Ramjee G; Fidler S; Frater J; Fox J; Doores KJ, 2021, 'Broadly neutralizing antibody responses in the longitudinal primary HIV-1 infection Short Pulse Anti-Retroviral Therapy at Seroconversion cohort', AIDS, 35, pp. 2073 - 2084, http://dx.doi.org/10.1097/QAD.0000000000002988

Palmer DS; Turner I; Fidler S; Frater J; Goedhals D; Goulder P; Huang KHG; Oxenius A; Phillips R; Shapiro R; Vuuren CV; McLean AR; McVean G, 2019, 'Mapping the drivers of within-host pathogen evolution using massive data sets', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-10724-w

Murray LW; Satti I; Meyerowitz J; Jones M; Willberg CB; Ussher JE; Goedhals D; Hurst J; Phillips RE; McShane H; van Vuuren C; Frater J, 2018, 'Human immunodeficiency virus infection impairs Th1 and Th17 mycobacterium tuberculosis–specific T-Cell responses', Journal of Infectious Diseases, 217, pp. 1782 - 1792, http://dx.doi.org/10.1093/infdis/jiy052

Hoffmann M; Pantazis N; Martin GE; Hickling S; Hurst J; Meyerowitz J; Willberg CB; Robinson N; Brown H; Fisher M; Kinloch S; Babiker A; Weber J; Nwokolo N; Fox J; Fidler S; Phillips R; Frater J, 2016, 'Exhaustion of Activated CD8 T Cells Predicts Disease Progression in Primary HIV-1 Infection', PLoS Pathogens, 12, http://dx.doi.org/10.1371/journal.ppat.1005661

Llibre A; López-Macías C; Marafioti T; Mehta H; Partridge A; Kanzig C; Rivellese F; Galson JD; Walker LJ; Milne P; Phillips RE; Kelly DF; Freeman GJ; El Shikh ME; Klenerman P; Willberg CB, 2016, 'LLT1 and CD161 Expression in Human Germinal Centers Promotes B Cell Activation and CXCR4 Downregulation.', J Immunol, 196, pp. 2085 - 2094, http://dx.doi.org/10.4049/jimmunol.1502462

Hurst T; Pace M; Katzourakis A; Phillips R; Klenerman P; Frater J; Magiorkinis G, 2016, 'Human endogenous retrovirus (HERV) expression is not induced by treatment with the histone deacetylase (HDAC) inhibitors in cellular models of HIV-1 latency.', Retrovirology, 13, pp. 10, http://dx.doi.org/10.1186/s12977-016-0242-4

Ussher JE; van Wilgenburg B; Hannaway RF; Ruustal K; Phalora P; Kurioka A; Hansen TH; Willberg CB; Phillips RE; Klenerman P, 2016, 'TLR signaling in human antigen-presenting cells regulates MR1-dependent activation of MAIT cells.', Eur J Immunol, 46, pp. 1600 - 1614, http://dx.doi.org/10.1002/eji.201545969

Hurst J; Hoffmann M; Pace M; Williams JP; Thornhill J; Hamlyn E; Meyerowitz J; Willberg C; Koelsch KK; Robinson N; Brown H; Fisher M; Kinloch S; Cooper DA; Schechter M; Tambussi G; Fidler S; Babiker A; Weber J; Kelleher AD; Phillips RE; Frater J, 2015, 'Immunological biomarkers predict HIV-1 viral rebound after treatment interruption', Nature Communications, 6, pp. 8495, http://dx.doi.org/10.1038/ncomms9495

Roberts HE; Hurst J; Robinson N; Brown H; Flanagan P; Vass L; Fidler S; Weber J; Babiker A; Phillips RE; McLean AR; Frater J; Cooper D, 2015, 'Structured Observations Reveal Slow HIV-1 CTL Escape', PLoS Genetics, 11, pp. 1 - 22, http://dx.doi.org/10.1371/journal.pgen.1004914

Ussher JE; Phalora P; Cosgrove C; Hannaway RF; Rauch A; Günthard HF; Goulder P; Phillips RE; Willberg CB; Klenerman P, 2015, 'Molecular Analyses Define Vα7.2-Jα33+ MAIT Cell Depletion in HIV Infection: A Case-Control Study.', Medicine (Baltimore), 94, pp. e1134, http://dx.doi.org/10.1097/MD.0000000000001134

Jones M; Williams J; Gärtner K; Phillips R; Hurst J; Frater J, 2014, 'Low copy target detection by Droplet Digital PCR through application of a novel open access bioinformatic pipeline, 'definetherain'', Journal of Virological Methods, 202, pp. 46 - 53, http://dx.doi.org/10.1016/j.jviromet.2014.02.020

Frater J; Ewings F; Hurst J; Brown H; Robinson N; Fidler S; Babiker A; Weber J; Porter K; Phillips RE, 2014, 'HIV-1-specific CD4⁺ responses in primary HIV-1 infection predict disease progression', AIDS, 28, pp. 699 - 708, http://dx.doi.org/10.1097/QAD.0000000000000130

Williams JP; Hurst J; Stöhr W; Robinson N; Brown H; Fisher M; Kinloch S; Cooper D; Schechter M; Tambussi G; Fidler S; Carrington M; Babiker A; Weber J; Koelsch KK; Kelleher AD; Phillips RE; Frater J, 2014, 'HIV-1 DNA predicts disease progression and post-treatment virological control', eLife, 3, pp. e03821, http://dx.doi.org/10.7554/eLife.03821

Stöhr W; Fidler S; McClure M; Weber J; Cooper D; Ramjee G; Kaleebu P; Tambussi G; Schechter M; Babiker A; Phillips RE; Porter K; Frater J, 2013, 'Duration of HIV-1 Viral Suppression on Cessation of Antiretroviral Therapy in Primary Infection Correlates with Time on Therapy', PLoS ONE, 8, http://dx.doi.org/10.1371/journal.pone.0078287

Palmer D; Frater J; Phillips R; McLean AR; McVean G, 2013, 'Integrating genealogical and dynamical modelling to infer escape and reversion rates in HIV epitopes', Proceedings of the Royal Society B: Biological Sciences, 280, http://dx.doi.org/10.1098/rspb.2013.0696

Cosgrove C; Ussher JE; Rauch A; Gärtner K; Kurioka A; Hühn MH; Adelmann K; Kang YH; Fergusson JR; Simmonds P; Goulder P; Hansen TH; Fox J; Günthard HF; Khanna N; Powrie F; Steel A; Gazzard B; Phillips RE; Frater J; Uhlig H; Klenerman P, 2013, 'Early and nonreversible decrease of CD161⁺⁺/MAIT cells in HIV infection', Blood, 121, pp. 951 - 961, http://dx.doi.org/10.1182/blood-2012-06-436436

Yager N; Robinson N; Brown H; Flanagan P; Frater J; Fidler S; Weber J; Phillips R, 2013, 'Longitudinal analysis of an HLA-B*51-restricted epitope in integrase reveals immune escape in early HIV-1 infection', AIDS, 27, pp. 313 - 323, http://dx.doi.org/10.1097/QAD.0b013e32835b8cf5

Williams JP; Southern P; Lissina A; Christian HC; Sewell AK; Phillips R; Pankhurst Q; Frater J, 2013, 'Application of magnetic field hyperthermia and superparamagnetic iron oxide nanoparticles to HIV-1-specific T-cell cytotoxicity.', International journal of nanomedicine, 8, pp. 2543 - 2554, http://dx.doi.org/10.2147/ijn.s44013

Porter K; Ewings FM; Ramjee G; Cooper DA; Fisher M; Schechter MT; Tambussi G; Kinloch-De Loes S; Miro J; Kelleher AD; Mcclure MO; Gabriel M; Phillips R; Weber J; Babiker AG, 2013, 'Short-course antiretroviral therapy in primary HIV infection', New England Journal of Medicine, 368, pp. 207 - 217, http://dx.doi.org/10.1056/NEJMoa1110039

Fryer HR; Frater J; Duda A; Palmer D; McLean REP, 2012, 'Cytotoxic T-Lymphocyte escape mutations identified by HLA association favor those which escape and revert rapidly', Journal of Virology, 86, pp. 8568 - 8580, http://dx.doi.org/10.1128/JVI.07020-11

Wood BR; Klein JP; Lyons JL; Milner DA; Phillips RE; Schutten M; Folkerth RD; Ciarlini P; Henrich TJ; Johnson JA, 2012, 'HIV-2 encephalitis: Case report and literature review', AIDS Patient Care and STDs, 26, pp. 383 - 387, http://dx.doi.org/10.1089/apc.2012.0048

Hamlyn E; Hickling S; Porter K; Frater J; Phillips R; Robinson M; MacKie NE; Kaye S; McClure M; Fidler S, 2012, 'Increased levels of CD4 T-cell activation in individuals with CXCR4 using viruses in primary HIV-1 infection', AIDS, 26, pp. 887 - 890, http://dx.doi.org/10.1097/QAD.0b013e328351e721

Frater J; Hurst J; Phillips RE, 2011, 'Beating atomic swords into immunological ploughshares', Immunity, 35, pp. 10 - 12, http://dx.doi.org/10.1016/j.immuni.2011.07.005

English S; Katzourakis A; Bonsall D; Flanagan P; Duda A; Fidler S; Weber J; McClure M; Phillips R; Frater J, 2011, 'Phylogenetic analysis consistent with a clinical history of sexual transmission of HIV-1 from a single donor reveals transmission of highly distinct variants', Retrovirology, 8, http://dx.doi.org/10.1186/1742-4690-8-54

Huang KHG; Goedhals D; Carlson JM; Brockman MA; Mishra S; Brumme ZL; Hickling S; Tang CSW; Miura T; Seebregts C; Heckerman D; Ndung'u T; Walker B; Klenerman P; Steyn D; Goulder P; Phillips R; van Vuuren C; Frater J, 2011, 'Progression to AIDS in south africa is associated with both reverting and compensatory viral mutations', PLoS ONE, 6, http://dx.doi.org/10.1371/journal.pone.0019018

Barnes E; Flanagan P; Brown A; Robinson N; Brown H; McClure M; Oxenius A; Collier J; Weber J; Günthard HF; Hirschel B; Fidler S; Phillips R; Frater J, 2010, 'Failure to detect xenotropic murine leukemia virus-related virus in blood of individuals at high risk of blood-borne viral infections', Journal of Infectious Diseases, 202, pp. 1482 - 1485, http://dx.doi.org/10.1086/657167

Fryer HR; Frater J; Duda A; Roberts MG; Phillips RE; McLean AR, 2010, 'Modelling the evolution and spread of HIV immune escape mutants', PLoS Pathogens, 6, http://dx.doi.org/10.1371/journal.ppat.1001196

Payne RP; Kløverpris H; Sacha JB; Brumme Z; Brumme C; Buus S; Sims S; Hickling S; Riddell L; Chen F; Luzzi G; Edwards A; Phillips R; Prado JG; Goulder PJR, 2010, 'Efficacious early antiviral activity of HIV Gag- and Pol-specific HLA-B*2705-restricted CD8⁺ T cells', Journal of Virology, 84, pp. 10543 - 10557, http://dx.doi.org/10.1128/JVI.00793-10

Huang KHG; Bonsall D; Katzourakis A; Thomson EC; Fidler SJ; Main J; Muir D; Weber JN; Frater AJ; Phillips RE; Pybus OG; Goulder PJR; McClure MO; Cooke GS; Klenerman P, 2010, 'B-cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection', Nature Communications, 1, http://dx.doi.org/10.1038/ncomms1100

Huang KHG; Goedhals D; Fryer H; Van Vuuren C; Katzourakis A; De Oliveira T; Brown H; Cassol S; Seebregts C; McLean A; Klenerman P; Phillips R; Frater J, 2009, 'Prevalence of HIV type-1 drug-associated mutations in pre-therapy patients in the Free State, South Africa', Antiviral Therapy, 14, pp. 975 - 984, http://dx.doi.org/10.3851/IMP1416

Fryer HR; Scherer A; Oxenius A; Phillips R; McLean AR, 2009, 'No evidence for competition between cytotoxic T-lymphocyte responses in HIV-1 infection', Proceedings of the Royal Society B: Biological Sciences, 276, pp. 4389 - 4397, http://dx.doi.org/10.1098/rspb.2009.1232

Kawashima Y; Pfafferott K; Frater J; Matthews P; Payne R; Addo M; Gatanaga H; Fujiwara M; Hachiya A; Koizumi H; Kuse N; Oka S; Duda A; Prendergast A; Crawford H; Leslie A; Brumme Z; Brumme C; Allen T; Brander C; Kaslow R; Tang J; Hunter E; Allen S; Mulenga J; Branch S; Roach T; John M; Mallal S; Ogwu A; Shapiro R; Prado JG; Fidler S; Weber J; Pybus OG; Klenerman P; Ndungu T; Phillips R; Heckerman D; Harrigan PR; Walker BD; Takiguchi M; Goulder P, 2009, 'Adaptation of HIV-1 to human leukocyte antigen class I', Nature, 458, pp. 641 - 645, http://dx.doi.org/10.1038/nature07746

Duda A; Lee-Turner L; Fox J; Robinson N; Dustan S; Kaye S; Fryer H; Carrington M; McClure M; Mclean AR; Fidler S; Weber J; Phillips RE; Frater AJ; Breckenridge A; Conlon C; Cooper D; Conradie F; Kaldor J; Schechter M; Claydon P; Kaleebu P; Ramjee G; Ssali F; Tambussi G, 2009, 'HLA-associated clinical progression correlates with epitope reversion rates in early human immunodeficiency virus infection', Journal of Virology, 83, pp. 1228 - 1239, http://dx.doi.org/10.1128/JVI.01545-08

Varela-Rohena A; Molloy PE; Dunn SM; Li Y; Suhoski MM; Carroll RG; Milicic A; Mahon T; Sutton DH; Laugel B; Moysey R; Cameron BJ; Vuidepot A; Purbhoo MA; Cole DK; Phillips RE; June CH; Jakobsen BK; Sewell AK; Riley JL, 2008, 'Control of HIV-1 immune escape by CD8 T cells expressing enhanced T-cell receptor', Nature Medicine, 14, pp. 1390 - 1395, http://dx.doi.org/10.1038/nm.1779

Fox J; Scriba TJ; Robinson N; Weber JN; Phillips RE; Fidler S, 2008, 'Human immunodeficiency virus (HIV)-specific T helper responses fail to predict CD4⁺ T cell decline following short-course treatment at primary HIV-1 infection', Clinical and Experimental Immunology, 152, pp. 532 - 537, http://dx.doi.org/10.1111/j.1365-2249.2008.03653.x

Scriba TJ; Sierro S; Brown EL; Phillips RE; Sewell AK; Massey RC, 2008, 'The Staphyloccous aureus eap protein activates expression of proinflammatory cytokines', Infection and Immunity, 76, pp. 2164 - 2168, http://dx.doi.org/10.1128/IAI.01699-07

Northfield JW; Kasprowicz V; Lucas M; Kersting N; Bengsh B; Kim A; Phillips RE; Walker BD; Thimme R; Lauer G; Klenerman P, 2008, 'CD161 expression on hepatitis C virus-specific CD8+ T cells suggests a distinct pathway of T cell differentiation', Hepatology, 47, pp. 396 - 406, http://dx.doi.org/10.1002/hep.22040

Mattes FM; Vargas A; Kopycinski J; Hainsworth EG; Sweny P; Nebbia G; Bazeos A; Lowdell M; Klenerman P; Phillips RE; Griffiths PD; Emery VC, 2008, 'Functional impairment of cytomegalovirus specific CD8 T cells predicts high-level replication after renal transplantation', American Journal of Transplantation, 8, pp. 990 - 999, http://dx.doi.org/10.1111/j.1600-6143.2008.02191.x

Massey RC; Scriba TJ; Brown EL; Phillips RE; Sewell AK, 2007, 'Use of peptide-major histocompatibility complex tetramer technology to study interactions between Staphylococcus aureus proteins and human cells', Infection and Immunity, 75, pp. 5711 - 5715, http://dx.doi.org/10.1128/IAI.00875-07

Lucas M; Ulsenheimer A; Pfafferot K; Heeg MHJ; Gaudieri S; Grüner N; Rauch A; Gerlach JT; Jung MC; Zachoval R; Pape GR; Schraut W; Santantonio T; Nitschko H; Obermeier M; Phillips R; Scriba TJ; Semmo N; Day C; Weber JN; Fidler S; Thimme R; Haberstroh A; Baumert TF; Klenerman P; Diepolder HM, 2007, 'Tracking virus-specific CD4+ T cells during and after acute hepatitis C virus infection', PLoS ONE, 2, http://dx.doi.org/10.1371/journal.pone.0000649

Frater AJ; Brown H; Oxenius A; Günthard HF; Hirschel B; Robinson N; Leslie AJ; Payne R; Crawford H; Prendergast A; Brander C; Kiepiela P; Walker BD; Goulder PJR; McLean A; Phillips RE; Battegay M; Bernasconi E; Böni J; Bucher H; Bürgisser P; Cattacin S; Cavassini M; Dubs R; Egger M; Elzi L; Erb P; Fischer M; Flepp M; Fontana A; Francioli P; Furrer H; Gorgievski M; Günthard H; Hirsch H; Hirschel B; Hösli I; Kahlert C; Kaiser L; Karrer U; Kind C; Klimkait T; Ledergerber B; Martinetti G; Martinez B; Müller N; Nadal D; Opravil M; Paccaud F; Pantaleo G; Rickenbach M; Rudin C; Schmid P; Schultze D; Schüpbach J; Speck R; Taffé P; Tarr P; Telenti A; Trkola A; Vernazza P; Weber R; Yerly S, 2007, 'Effective T-cell responses select human immunodeficiency virus mutants and slow disease progression', Journal of Virology, 81, pp. 6742 - 6751, http://dx.doi.org/10.1128/JVI.00022-07

Zimbwa P; Milicic A; Frater J; Scriba TJ; Willis A; Goulder PJR; Pillay T; Gunthard H; Weber JN; Zhang HT; Phillips RE, 2007, 'Precise identification of a human immunodeficiency virus type 1 antigen processing mutant', Journal of Virology, 81, pp. 2031 - 2038, http://dx.doi.org/10.1128/JVI.00968-06

Ulsenheimer A; Lucas M; Pfafferot K; Heeg M; Gaudieri S; Grüner N; Rauch A; Gerlach T; Jung MC; Zachoval R; Pape G; Santantonio T; Nitschko H; Obermeier M; Phillips R; Scriba T; Semmo N; Day C; Weber J; Fidler S; Thimme R; Haberstroh A; Baumert T; Klenerman P; Diepolder H, 2007, 'Erschöpfung der Virus spezifischen CD4+ T-Zellantwort bei der akuten Hepatitis C Infektion', Zeitschrift für Gastroenterologie, 45, http://dx.doi.org/10.1055/s-2007-988473

Edwards CTT; Holmes EC; Pybus OG; Wilson DJ; Viscidi RP; Abrams EJ; Phillips RE; Drummond AJ, 2006, 'Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection', Genetics, 174, pp. 1441 - 1453, http://dx.doi.org/10.1534/genetics.105.052019

Wooldridge L; Scriba TJ; Milicic A; Laugel B; Gostick E; Price DA; Phillips RE; Sewell AK, 2006, 'Anti-coreceptor antibodies profoundly affect staining with peptide-MHC class I and class II tetramers', European Journal of Immunology, 36, pp. 1847 - 1855, http://dx.doi.org/10.1002/eji.200635886

Frater AJ; Edwards CTT; McCarthy N; Fox J; Brown H; Milicic A; Mackie N; Pillay T; Drijfhout JW; Dustan S; Clarke JR; Holmes EC; Zhang HT; Pfafferott K; Goulder PJ; McClure MO; Weber J; Phillips RE; Fidler S, 2006, 'Passive sexual transmission of human immunodeficiency virus type 1 variants and adaptation in new hosts', Journal of Virology, 80, pp. 7226 - 7234, http://dx.doi.org/10.1128/JVI.02014-05

Edwards CTT; Holmes EC; Wilson DJ; Viscidi RP; Abrams EJ; Phillips RE; Drummond AJ, 2006, 'Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1', BMC Evolutionary Biology, 6, http://dx.doi.org/10.1186/1471-2148-6-28

Scriba TJ; Purbhoo M; Day CL; Robinson N; Fidler S; Fox J; Weber JN; Klenerman P; Sewell AK; Phillips RE, 2005, 'Ultrasensitive detection and phenotyping of CD4⁺ T cells with optimized HLA class II tetramer staining', Journal of Immunology, 175, pp. 6334 - 6343, http://dx.doi.org/10.4049/jimmunol.175.10.6334

Milicic A; Edwards CTT; Hué S; Fox J; Brown H; Pillay T; Drijfhout JW; Weber JN; Holmes EC; Fidler SJ; Zhang HT; Phillips RE, 2005, 'Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants', Journal of Virology, 79, pp. 13953 - 13962, http://dx.doi.org/10.1128/JVI.79.22.13953-13962.2005

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