Publications: Institute for Immunology and Infectious Diseases

2013

Acikyol, B., Graham, R.M., Trinder, D., House, M.J., Olynyk, J.K., Scott, R.J., Milward, E.A. and Johnstone, D.M. (2013) Brain transcriptome perturbations in the transferrin receptor 2 mutant mouse support the case for brain changes in iron loading disorders, including effects relating to long-term depression and long-term potentiation. Neuroscience, 235 . pp. 119-128.

Apps, R., Qi, Y., Carlson, J.M., Chen, H., Gao, X., Thomas, R., Yuki, Y., Del Prete, G.Q., Goulder, P., Brumme, Z.L., Brumme, C.J., John, M., Mallal, S., Nelson, G., Bosch, R., Heckerman, D., Stein, J.L., Soderberg, K.A., Moody, M.A., Denny, T.N., Zeng, X., Fang, J., Moffett, A., Lifson, J.D., Goedert, J.J., Buchbinder, S., Kirk, G.D., Fellay, J., McLaren, P., Deeks, S.G., Pereyra, F., Walker, B., Michael, N.L., Weintrob, A., Wolinsky, S., Liao, W. and Carrington, M. (2013) Influence of HLA-C expression level on HIV control. Science, 340 (6128). pp. 87-91.

Bronke, C., Almeida, C.M., McKinnon, E., Roberts, S.G., Keane, N.M., Chopra, A., Carlson, J.M., Heckerman, D., Mallal, S. and John, M. (2013) HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes. AIDS, 27 (6). pp. 899-905.

Chopra, A. and Nanjundiah, V. (2013) The precision with which single cells of Dictyostelium discoideum can locate a source of cyclic AMP. Chaos, Solitons & Fractals, 50 . pp. 3-12.

D'Orsogna, L.J., Nguyen, T.H.O., Claas, F.H.J., Witt, C. and Mifsud, N.A. (2013) Endogenous-peptide-dependent alloreactivity: new scientific insights and clinical implications. Tissue Antigens, 81 (6). pp. 399-407.

Graham, R., Delima, R.D., Johnstone, D., Milward, E.A., Olynyk, J.K. and Trinder, D. (2013) Changes in gene expression of cholesterol metabolism pathways in mouse models of haemochromatosis. In: BioIron 2013, 14 - 18 April 2013, University College, London.

Hazeldine, S., Trinder, D. and Olynyk, J.K. (2013) Non-Hfe iron overload: Is Phlebotomy the answer? Current Hepatitis Reports, 12 (1). pp. 20-27.

Herrmann, S., McKinnon, E., Hyland, N.B., Lalanne, C., Mallal, S., Nolan, D., Chassany, O. and Duracinsky, M. (2013) HIV-related stigma and physical symptoms have a persistent influence on health-related quality of life in Australians with HIV infection. Health and Quality of Life Outcomes, 11 (1).

House, M.J., Gan, E.K., Adams, L.A., Ayonrinde, O.T., Bangma, S.J., Bhathal, P.S., Olynyk, J.K. and St. Pierre, T.G. (2013) Diagnostic performance of a rapid magnetic resonance imaging method of measuring hepatic steatosis. PLoS ONE, 8 (3). e59287.

Maker, G.L., Siva, B., Batty, K.T, Trengove, R.D., Ferrari, P. and Olynyk, J.K. (2013) Pharmacokinetics and safety of deferasirox in subjects with chronic kidney disease undergoing haemodialysis. Nephrology, 18 (3). pp. 188-193.

Oddy, W.H., Herbison, C.E., Jacoby, P., Ambrosini, G.L., O'Sullivan, T.A., Ayonrinde, O.T., Olynyk, J.K., Black, L.J., Beilin, L.J., Mori, T.A., Hands, B.P. and Adams, L.A. (2013) The western dietary pattern is prospectively associated with non-alcoholic fatty liver disease in adolescence. The American Journal of Gastroenterology, 108 (5). pp. 778-785.

Phillips, E., Bartlett, J.A., Sanne, I., Lederman, M.M., Hinkle, J., Rousseau, F., Dunn, D., Pavlos, R., James, I., Mallal, S.A. and Haas, D.W. (2013) Associations between HLA-DRB1*0102, HLA-B*5801, and hepatotoxicity during initiation of nevirapine-containing regimens in South Africa. JAIDS Journal of Acquired Immune Deficiency Syndromes, 62 (2). e55-e57.

Phillips, E.J. and Mallal, S.A. (2013) HLA-B*5701 and flucloxacillin associated drug-induced liver disease. AIDS, 27 (3). pp. 491-492.

Plauzolles, A., Lucas, M. and Gaudieri, S. (2013) Hepatitis C virus adaptation to T-cell immune pressure. The Scientific World Journal, 2013 . pp. 1-7.

Qiu, W., Pham, K., James, I., Nolan, D., Castley, A., Christiansen, F.T., Czarniak, P., Luo, Y., Wu, J., Garlepp, M., Wilton, S., Carroll, W.M., Mastaglia, F.L. and Kermode, A.G. (2013) The influence of non-HLA gene polymorphisms and interactions on disease risk in a Western Australian multiple sclerosis cohort. Journal of Neuroimmunology . In Press.

Rive, C.M., Bourke, J. and Phillips, E.J. (2013) Testing for drug hypersensitivity syndromes. Clinical Biochemist Reviews, 34 (1). pp. 15-38.

Xu, W., li, R., Dai, Y., Wu, A., Wang, H., Cheng, C., Qiu, W., Lu, Z., Zhong, X., Shu, Y., Kermode, A.G. and Hu, X. (2013) IL-22 secreting CD4+ T cells in the patients with neuromyelitis optica and multiple sclerosis. Journal of Neuroimmunology . In Press.

Yagita, Y., Kuse, N., Kuroki, K., Gatanaga, H., Carlson, J. M., Chikata, T., Brumme, Z. L., Murakoshi, H., Akahoshi, T., Pfeifer, N., Mallal, S., John, M., Ose, T., Matsubara, H., Kanda, R., Fukunaga, Y., Honda, K., Kawashima, Y., Ariumi, Y., Oka, S., Maenaka, K. and Takiguchi, M. (2013) Distinct HIV-1 Escape Patterns Selected by Cytotoxic T Cells with Identical Epitope Specificity. Journal of Virology, 87 (4). pp. 2253-2263.

2012

Brockman, M.A., Chopera, D.R., Olvera, A., Brumme, C.J., Sela, J., Markle, T.J., Martin, E., Carlson, J.M., Le, A.Q., McGovern, R., Cheung, P.K., Kelleher, A.D., Jessen, H., Markowitz, M., Rosenberg, E., Frahm, N., Sanchez, J., Mallal, S., John, M., Harrigan, P.R., Heckerman, D., Brander, C., Walker, B.D. and Brumme, Z.L. (2012) Uncommon pathways of immune escape attenuate HIV-1 integrase replication capacity. Journal of Virology, 86 (12). pp. 6913-6923.

Carlson, J.M., Brumme, C.J., Martin, E., Listgarten, J., Brockman, M.A., Le, A.Q., Chui, C.K.S., Cotton, L.A., Knapp, D.J.H.F., Riddler, S.A., Haubrich, R., Nelson, G., Pfeifer, N., DeZiel, C.E., Heckerman, D., Apps, R., Carrington, M., Mallal, S., Harrigan, P.R., John, M. and Brumme, Z.L. (2012) Correlates of protective cellular immunity revealed by analysis of population-level immune escape pathways in HIV-1. Journal of Virology, 86 (24). pp. 13202-13216.

Chalmers, K.A., Knuiman, M.W., Divitini, M.L., Bruce, D.G., Olynyk, J.K. and Milward, E.A. (2012) Long-term mortality risks associated with mild anaemia in older persons: the Busselton Health Study. Age and Ageing, 41 (6). pp. 759-764.

Cheng, Y.-C., Anderson, C.D., Bione, S., Keene, K., Maguire, J.M., Nalls, M., Rasheed, A., Zeginigg, M., Attia, J., Baker, R., Barlera, S., Biffi, A., Bookman, E., Brott, T.G., Brown, R. D., Chen, F., Chen, W.-M., Ciusani, E., Cole, J.W., Cortellini, L., Danesh, J., Doheny, K., Ferrucci, L., Grazia Franzosi, M., Frossard, P., Furie, K.L., Golledge, J., Hankey, G.J., Hernandez, D., Holliday, E.G., Hsu, F.-C., Jannes, J., Kamal, A., Khan, M.S., Kittner, S.J., Koblar, S.A., Lewis, M., Lincz, L., Lisa, A., Matarin, M., Moscato, P., Mychaleckyj, J.C., Parati, E.A., Parolo, S., Pugh, E., Rost, N.S., Schallert, M., Schmidt, H., Scott, R.J., Sturm, J.W., Yadav, S., Zaidi, M., Boncoraglio, G.B., Levi, C.R., Meschia, J.F., Rosand, J., Sale, M., Saleheen, D., Schmidt, R., Sharma, P., Worrall, B. and Mitchell, B.D. (2012) Are myocardial infarction-associated single-nucleotide polymorphisms associated with ischemic stroke? Stroke, 43 (4). pp. 980-986.

Chikata, T., Carlson, J.M., Tamura, Y., Brumme, Z.L., Naruto, T., Hashimoto, M., Borghan, M.A., John, M., Mallal, S., Gatanaga, H., Oka, S. and Yakiguchi, M. (2012) HLA-associated viral polymorphism in chronically HIV-1-infected Japanese cohort: analysis of four-digit HLA allele level. Retrovirology, 9 (Suppl 2).

Cotton, L., Chopera, D., Penney, K., Carlson, J., Martin, E., Le, A., Kuang, T., Walker, B., Fuchs, J., Buchbinder, S., Wagner, T., John, M., Mallal, S., Koblin, B., Mayer, K., Poon, A., Brockman, M. and Brumme, Z. (2012) Limited evidence for alterations in Gag-mediated HIV replication capacity over the course of the North American epidemic (1979-present). Retrovirology, 9 (Suppl 2). P157.

D'Orsogna, L.J., van den Heuvel, H., van der Meer-Prins, E.M.W., Roelen, D.L., Doxiadis, I.I.N. and Claas, F.H.J. (2012) Stimulation of human EBV-and CMV-specific cytolytic effector function using allogeneic HLA molecules. The Journal of Immunology, 189 (10). pp. 4825-4831.

Desmond, C.P., Gaudieri, S., James, I.R., Pfafferott, K., Chopra, A., Lau, G.K., Audsley, J., Day, C., Chivers, S., Gordon, A., Revill, P.A., Bowden, S., Ayres, A., Desmond, P.V., Thompson, A.J., Roberts, S. K., Locarnini, S.A., Mallal, S.A. and Lewin, S.R. (2012) Viral adaptation to host immune responses occurs in chronic hepatitis B virus (HBV) infection, and adaptation is greatest in HBV e antigen-negative disease. Journal of Virology, 86 (2). pp. 1181-1192.

Duracinsky, M., Herrmann, S., Berzins, B., Armstrong, A.R., Kohli, R., Le Coeur, S., Diouf, A., Fournier, I., Schechter, M. and Chassany, O. (2012) The development of PROQOL-HIV: An international instrument to assess the health-related quality of life of persons living with HIV/AIDS. JAIDS Journal of Acquired Immune Deficiency Syndromes, 59 (5). pp. 498-505.

Duracinsky, M., Lalanne, C., Le Coeur, S., Herrmann, S., Berzins, B., Armstrong, A.R., Fai Lau, J.T., Fournier, I. and Chassany, O. (2012) Psychometric validation of the PROQOL-HIV questionnaire, a new health-related quality of life instrument–specific to HIV disease. JAIDS Journal of Acquired Immune Deficiency Syndromes, 59 (5). pp. 506-515.

Gaudieri, S., Lucas, M., Lucas, A., McKinnon, E., Albloushi, H., Rauch, A., di Iulio, J., Martino, D., Prescott, S.L. and Tulic, M.K. (2012) Genetic variations in IL28B and allergic disease in children. PLoS ONE, 7 (1). e30607.

Gaudieri, S., Tulic, M.K., Lucas, A. and Lucas, M. (2012) IFN-λ and IgE-mediated allergic disease: A potential future role? Biomarkers in Medicine, 6 (2). pp. 151-157.

Hammond, E., McKinnon, E., Glendenning, P., Williams, R., Mallal, S. and Phillips, E. (2012) Association between 25-OH vitamin D and insulin is independent of lipoatrophy in HIV. Clinical Endocrinology, 76 (2). pp. 201-206.

Herrmann, S., Wardrop, J., John, M., Gaudieri, S., Lucas, M., Mallal, S. and Nolan, D. (2012) The impact of visa status and Medicare eligibility on people diagnosed with HIV in Western Australia: a qualitative report. Sexual Health, 9 (5). p. 407.

Keane, N., Almeida, C., Chopra, A., Cooper, D., Demaine, E., Mallal, S. and John, M. (2012) Early changes in the CD8 T Cell immunodominance hierarchy in primary HIV infection prior to seroconversion. Retrovirology, 9 (Suppl 2).

Keane, N., Almeida, C., Roberts, S., Ahmad, I., Mallal, S. and John, M. (2012) Evaluation of the dual IFNγ/IL-2 fluorospot-assay with flow cytometry for detection of HLA-restricted HIV-specific T-cell responses in HIV controllers. Retrovirology, 9 (Suppl 2). P243.

Keane, N.M., Roberts, S.G., Almeida, C.M., Krishnan, T., Chopra, A., Demaine, E., Laird, R., Tschochner, M., Carlson, J.M., Mallal, S., Heckerman, D., James, I. and John, M. (2012) High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection. Immunology and Cell Biology, 90 (2). pp. 224-234.

Kruger, P.C., Leahy, M.F. and Olynyk, J.K. (2012) Assessing iron overload: Are we there yet? Clinical Cancer Research, 18 (23). pp. 6395-6397.

Lucas, M. and Gaudieri, S. (2012) The interferon family as biomarkers of disease: renaissance of the innate immune system. Biomarkers in Medicine, 6 (2). pp. 133-135.

Nolan, D., Castley, A., Tschochner, M., James, I., Qiu, W., Sayer, D., Christiansen, F.T., Witt, C., Mastaglia, F., Carroll, W. and Kermode, A. (2012) Contributions of vitamin D response elements and HLA promoters to multiple sclerosis risk. Neurology, 79 (6). pp. 538-546.

Ostrov, D.A., Grant, B.J., Pompeu, Y.A., Sidney, J., Harndahl, M., Southwood, S., Oseroff, C., Lu, S., Jakoncic, J., de Oliveira, C.A.F., Yang, L., Mei, H., Shi, L., Shabanowitz, J., English, A.M., Wriston, A., Lucas, A., Phillips, E., Mallal, S., Grey, H.M., Sette, A., Hunt, D.F., Buus, S. and Peters, B. (2012) Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire. Proceedings of the National Academy of Sciences, 109 (25). pp. 9959-9964.

Pavlos, R., Mallal, S. and Phillips, E. (2012) HLA and pharmacogenetics of drug hypersensitivity. Pharmacogenomics, 13 (11). pp. 1285-1306.

Pavlos, R. and Phillips, E.J. (2012) Individualization of antiretroviral therapy. Pharmacogenomics and Personalized Medicine, 5 (1). pp. 1-17.

Pompeu, Y.A., Stewart, J.D., Mallal, S., Phillips, E., Peters, B. and Ostrov, D.A. (2012) The structural basis of HLA-associated drug hypersensitivity syndromes. Immunological Reviews, 250 (1). pp. 158-166.

Rojana-udomsart, A., James, I., Castley, A., Needham, M., Scott, A., Day, T., Kiers, L., Corbett, A., Sue, C., Witt, C., Martinez, P., Christiansen, F. and Mastaglia, F. (2012) High-resolution HLA-DRB1 genotyping in an Australian inclusion body myositis (s-IBM) cohort: An analysis of disease-associated alleles and diplotypes. Journal of Neuroimmunology, 250 (1-2). pp. 77-82.

Shasha, D., Meseret, Y., Chopra, A., Cooper, D., James, I., Herrmann, S., Wolday, D., Maayan, S., Mallal, S. and John, M. (2012) Unique footprints of HLA class I on clade C HIV-1 in a cohort of Ethiopian patients. In: 19th Conference on Retroviruses and Opportunistic Infections (CROI 2012), 5 - 8 March, Seattle, Washington, USA.

2011

Almeida, C.M., Bronke, C., Roberts, S.G., McKinnon, E., Keane, N.M., Chopra, A., Kadie, C., Carlson, J., Haas, D. W., Riddler, S. A., Haubrich, R., Heckerman, D., Mallal, S. and John, M. (2011) Translation of HLA-HIV associations to the cellular level: HIV adapts to inflate CD8 T cell responses against Nef and HLA-adapted variant epitopes. The Journal of Immunology, 187 (5). pp. 2502-2513.

Armstrong, A., Duracinsky, M., Lalanne, C., de Silva, M., Jamal, L., Herrmann, S., Carrieri, P., Davril, J. and Chassany, O. (2011) A new framework for understanding the impact of hepatitis C and its treatment on quality of life. In: ISPOR 14th Annual European Congress, 5 - 8 November, Madrid, Spain.

Bull, R.A., Luciani, F., McElroy, K., Gaudieri, S., Pham, S.T., Chopra, A., Cameron, B., Maher, L., Dore, G.J., White, P.A. and Lloyd, A.R. (2011) Sequential bottlenecks drive viral evolution in early acute Hepatitis C virus infection. PLoS Pathogens, 7 (9). e1002243.

Chakera, A., Lucas, A. and Lucas, M. (2011) Surrogate markers of infection: interrogation of the immune system. Biomarkers in Medicine, 5 (2). pp. 131-148.

Côté, H.C.F., Gerschenson, M., Walker, U.A., Miro, O., Garrabou, G., Hammond, E.L., Villarroya, J., Giralt, M., Villarroya, F., Cinque, P., Garcia-Arumi, E., Andreu, A.L., Pinti, M. and Cossarizza, A. (2011) Quality assessment of human mitochondrial DNA quantification: MITONAUTS, an international multicentre survey. Mitochondrion, 11 (3). pp. 520-527.

Dong, T., Zhang, Y., Xu, K. Y., Yan, H., James, I., Peng, Y., Blais, M.-E., Gaudieri, S., Chen, X., Lun, W., Wu, H., Qu, W. Y., Rostron, T., Li, N., Mao, Y., Mallal, S., Xu, X., McMichael, A., John, M. and Rowland-Jones, S. L. (2011) Extensive HLA-driven viral diversity following a narrow-source HIV-1 outbreak in rural China. Blood, 118 (1). pp. 98-106.

Gaudieri, S. (2011) Biomarkers that reflect immune activation or dysfunction will be important in the management of infectious diseases. Biomarkers in Medicine, 5 (2). pp. 109-112.

Haas, D.W., Kuritzkes, D.R., Ritchie, M.D., Amur, S., Gage, B.F., Maartens, G., Masys, D., Fellay, J., Phillips, E., Ribaudo, H.J., Freedberg, K.A., Petropoulos, C., Manolio, T.A., Gulick, R.M., Haubrich, R., Kim, P., Dehlinger, M., Abebe, R. and Telenti, A. (2011) Pharmacogenomics of HIV therapy: Summary of a workshop sponsored by the National Institute of Allergy and Infectious Diseases. HIV Clinical Trials, 12 (5). pp. 277-285.

Herrmann, S., John, M., Wardrop, J. and Nolan, D. (2011) Antiretroviral issues in temporary visa holders in Western Australia: A qualitative report on access, attitude and adherence. In: 23rd Annual Australasian Society for HIV Medicine Conference, 26 - 28 September, Canberra, Australia.

Herrmann, S., John, M., Wardrop, J. and Nolan, D. (2011) Experiences of people on temporary visas who are diagnosed with HIV in Western Australia. In: 23rd Annual Australasian Society for HIV Medicine Conference, 26 - 28 September, Canberra, Australia.

Herrmann, S., Lucas, M., John, M. and Nolan, D. (2011) Implementing medication adherence interventions into HIV clinical care: Implications for current research and other blood borne viruses. In: WA SiREN Research Symposium - Found or Lost in Translation, 6 May, Perth, Western Australia.

Hertz, T., Nolan, D., James, I., John, M., Gaudieri, S., Phillips, E.J., Huang, J.C., Riadi, G., Mallal, S. and Jojic, N. (2011) Mapping the Landscape of Host-Pathogen Coevolution: HLA Class I Binding and Its Relationship with Evolutionary Conservation in Human and Viral Proteins. Journal of Virology, 85 (3). pp. 1310-1321.

Keane, N.M. and John, M. (2011) Biomarkers of natural and vaccine immunity against HIV. Biomarkers in Medicine, 5 (2). pp. 113-116.

Kostenko, L., Kjer-Nielsen, L., Nicholson, I., Hudson, F., Lucas, A., Foley, B., Chen, K., Lynch, K., Nguyen, J., Wu, A.H.B., Tait, B.D., Holdsworth, R., Mallal, S., Rossjohn, J., Bharadwaj, M. and McCluskey, J. (2011) Rapid screening for the detection of HLA-B57 and HLA-B58 in prevention of drug hypersensitivity. Tissue Antigens, 78 (1). pp. 11-20.

Lalanne, C., Armstrong, A.R., Herrmann, S., Chassany, O. and Duracinsky, M. (2011) How does health-related quality Of life relate to symptoms experienced in HIV patients treated with highly-active antiretroviral therapy? In: ISPOR 14th Annual European Congress, 5 - 8 November, Madrid, Spain.

Merani, S., Petrovic, D., James, I., Chopra, A., Cooper, D., Freitas, E., Rauch, A., di Iulio, J., John, M., Lucas, M., Fitzmaurice, K., McKiernan, S., Norris, S., Kelleher, D., Klenerman, P. and Gaudieri, S. (2011) Effect of immune pressure on hepatitis C virus evolution: Insights from a single-source outbreak. Hepatology, 53 (2). pp. 396-405.

Pfafferott, K., Gaudieri, S., Ulsenheimer, A., James, I., Heeg, M., Nolan, D., John, M., Rauch, A., Mallal, S., Lucas, A.D., Klenerman, P., Diepolder, H.M. and Lucas, M. (2011) Constrained pattern of viral evolution in acute and early HCV infection limits viral plasticity. PLoS ONE, 6 (2). e16797.

Phillips, E.J., Chung, W-H, Mockenhaupt, M., Roujeau, J-C and Mallal, S. (2011) Drug hypersensitivity: Pharmacogenetics and clinical syndromes. Journal of Allergy and Clinical Immunology, 127 (3). S60-S66.

Phillips, E.J. and Mallal, S.A. (2011) HLA-B*1502 Screening and toxic effects of carbamazepine. New England Journal of Medicine, 365 (7). pp. 672-673.

Suppiah, V., Gaudieri, S., Armstrong, N.J., O'Connor, K.S., Berg, T., Weltman, M., Abate, M.L., Spengler, U., Bassendine, M., Dore, G.J., Irving, W.L., Powell, E., Hellard, M., Riordan, S., Matthews, G., Sheridan, D., Nattermann, J., Smedile, A., Müller, T., Hammond, E., Dunn, D.S., Negro, F., Bochud, P-Y, Mallal, S., Ahlenstiel, G., Stewart, G.J., George, J. and Booth, D.R. (2011) IL28B, HLA-C, and KIR variants additively predict response to therapy in chronic Hepatitis C virus infection in a European cohort: A cross-sectional study. PLoS Medicine, 8 (9). e1001092.

2010

Hammond, E., Lucas, A., Lucas, M., Phillips, E. and Gaudieri, S. (2010) Vaniprevir: HCV NS3/4A protease inhibitor treatment of hepatitis C. Drugs of the Future, 35 (10). pp. 803-813.

Herrmann, S., Williams, L., McKinnon, E. and Nolan, D. (2010) Vulnerable populations: Substance use in the WA HIV Cohort Study. In: 17th Western Australian Drug and Alcohol Symposium, 30 August - 1 September, Fremantle, Western Australia.

Herrmann, S.E., McKinnon, E.J., Williams, L.J., John, M., Mallal, S., Lucas, M. and Nolan, D.A. (2010) Use of alcohol, nicotine and other drugs in the Western Australian HIV Cohort study. Sexual Health, 9 (2). pp. 199-201.

John, M., Heckerman, D., James, I., Park, L.P., Carlson, J.M., Chopra, A., Gaudieri, S., Nolan, D., Haas, D.W., Riddler, S.A., Haubrich, R. and Mallal, S. (2010) Adaptive interactions between HLA and HIV-1: highly divergent selection imposed by HLA class I molecules with common supertype motifs. The Journal of Immunology, 184 (8). pp. 4368-4377.

Phillips, E.J. and Mallal, S. (2010) Pharmacogenetics of drug hypersensitivity. Pharmacogenomics, 11 (7). pp. 973-987.

Phillips, E.J. and Mallal, S.A. (2010) Abacavir. In: Wu, A.H.B. and Kiang-Teck, J.Y., (eds.) Pharmacogenomic Testing in Current Clinical Practice. Humana Press, New York, U.S.A, pp. 201-212.

Phillips, E.J. and Mallal, S.A. (2010) HLA and drug reactions. In: Mehra, N.K., Kaur, G., McCluskey, J., Christiansen, F.T. and Claas, F.H.J., (eds.) The HLA Complex in Biology and Medicine: A Resource Book. Jaypee Brothers Medical Publishers (P) Ltd, New Delhi, India, pp. 332-349.

2009

Almeida, C., Bronke, C., Roberts, S., Cooper, D., Corkery, M., McKinnon, E., Ahmad, I., Keane, N., Chopra, A., Mallal, S., John, M. and Heckerman, D. (2009) Identification of multiple novel HIV-specific T-cell epitopes using HLA-associated HIV polymorphisms. In: 39th Annual Scientific Meeting of the Australasian Society for Immunology 2009, 6 - 10 December 2009, Gold Coast, QLD.

Chaubey, S.K., Sinha, A.K., Phillips, E., Russell, D.B. and Falhammar, H. (2009) Transient cardiac arrhythmias related to lopinavir/ritonavir in two patients with HIV infection. Sexual Health, 6 (3). pp. 254-257.

Chopra, A., Watson, M., Cooper, D., Leary, S., John, M. and Mallal, S. (2009) High throughput long amplicon sequencing, assembly and reference mapping of HIV genome using the GS FLX sequencer. In: 21st Annual Conference of the Australasian Society for HIV Medicine (ASHM), 9 - 11 September, Brisbane, Australia.

Falster, K., Petoumenos, K., Chuah, J., Mijch, A., Mulhall, B., Kelly, M., Cooper, D.A. and Mallal, S. (2009) Poor baseline immune function predicts an incomplete immune response to combination antiretroviral treatment despite sustained viral suppression. JAIDS Journal of Acquired Immune Deficiency Syndromes, 50 (3). pp. 307-313.

Fellay, J., Ge, D., Shianna, K.V., Colombo, S., Ledergerber, B., Cirulli, E.T., Urban, T.J., Zhang, K., Gumbs, C.E., Smith, J. P., Castagna, A., Cozzi-Lepri, A., De Luca, A., Easterbrook, P., Günthard, H.F., Mallal, S., Mussini, C., Dalmau, J., Martinez-Picado, J., Miro, J.M., Obel, N., Wolinsky, S.M., Martinson, J.J., Detels, R., Margolick, J.B., Jacobson, L.P., Descombes, P., Antonarakis, S.E., Beckmann, J.S., O'Brien, S.J., Letvin, N.L., McMichael, A.J., Haynes, B.F., Carrington, M., Feng, S., Telenti, A., Goldstein, D.B. and McCarthy, M.I. (2009) Common genetic variation and the control of HIV-1 in humans. PLoS Genetics, 5 (12). e1000791.

Gaudieri, S., Rauch, A., James, I., Pfafferott, K., Baker, R., Cheng, W., McCaughan, G., Shackel, N., Jeffrey, G., Mollinson, L., Mallal, S., Furrer, H., Günthard, H., Hirschel, B., Klenerman, P., Nolan, D., John, M. and Lucas, M. (2009) Co-localisation of hepatitis C virus drug-resistant mutations and immune-driven adaptations: Relevance to therapy outcome. In: 19th Annual Combined Biological Sciences Meeting 2009, 28 August 2009, Perth, Western Australia.

Gaudieri, S., Rauch, A., James, I., Pfafferott, K., Cheng, W., McCaughan, G., Jeffrey, G., Mollison, L., Furrer, H., Günthard, H., Hirschel, B., Klenerman, P., Mallal, S., Nolan, D., John, M. and Lucas, M. (2009) Divergent adaptation of Hepatitis C virus genotypes to HLA-restricted immune pressure: relevance to HCV infection and vaccine design. In: 16th International Symposium on Hepatitis C Virus & Related Viruses, 3 - 7 October 2009, Nice, France.

Herrmann, S., Duracinsky, M., Lalanne, C., Acquadro, C., Mallal, S. and Nolan, D. (2009) Health-related quality of life in the WA HIV Cohort: 2008. In: 21st Annual Conference of the Australasian Society for HIV Medicine (ASHM), 9 - 11 September, Brisbane, Australia.

Herrmann, S., Williams, L., McKinnon, E. and Nolan, D. (2009) Substance use in the WA HIV Cohort: 2002-2008. In: 21st Annual Conference of the Australasian Society for HIV Medicine (ASHM), 9 - 11 September, Brisbane, Australia.

Lippert, E., Girodon, F., Hammond, E., Jelinek, J., Reading, N.S., Fehse, B., Hanlon, K., Hermans, M., Richardson, C., Swierczek, S., Ugo, V., Carillo, S., Harrivel, V., Marzac, C., Pietra, D., Sobas, M., Mounier, M., Migeon, M., Ellard, S., Kroger, N., Herrmann, R., Prchal, J.T., Skoda, R.C. and Hermouet, S. (2009) Concordance of assays designed for the quantification of JAK2V617F: a multicenter study. Haematologica, 94 (1). pp. 38-45.

Lucas, M., Pfafferott, K., Baker, R., Baccala, M., Herrmann, S. and Gaudieri, S. (2009) HCV-specific T-cell responses reflect Hepatitis C infection outcome following multiple exposures to the virus. In: Australian Centre for HIV & Hepatitis Virology Research (ACH2) 5th National Workshop, 3 - 5 June, Terrigal, NSW, Australia.

Lucas, M., Pfafferott, K., Baker, R., Cheng, W., Mollison, L., Baccala, M., Miczkova, S., Nazareth, S., Herrmann, S., Rauch, A. and Gaudieri, S. (2009) Correlates of infection outcome following multiple exposures to the Hepatitis C virus. In: 16th International Symposium on Hepatitis C Virus & Related Viruses, 3 - 7 October, Nice, France.

Mallal, S. (2009) Pharmacogenetic testing for predicting at risk patients: Genotyping and flow cytometry of HLA-B. In: Annual Meeting of the American Association of Clinical Chemistry (AACC) 2009, 19 - 23 July 2009, Chicago, IL.

Nolan, D. and Mallal, S. (2009) EBV and MS: Lessons from hepatitis and HIV. In: 10th Biennial Scientific Conferene on "Progress on MS Research" - MSRA Conference 2009, 15 - 17 October 2009, Sydney, Australia.

Phillips, E.J. and Mallal, S. (2009) HLA and drug-induced toxicity. Current Opinion in Molecular Therapeutics, 11 (3). pp. 231-242.

Phillips, E.J. and Mallal, S. (2009) Personalizing antiretroviral therapy: is it a reality? Personalized Medicine, 6 (4). pp. 393-408.

Phillips, E.J. (2009) Drugs that cause hypersensitivity reactions: Personalising medicine & Predicting the unpredictable. In: Annual Meeting of the American Association of Clinical Chemistry (AACC) 2009, 19 - 23 July 2009, Chicago, IL.

Phillips, E.J. (2009) Overcoming the barrier of clinical translation: The Abacavir example. In: Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists (ASCEPT) Conference 2009, 29 November - 2 December 2009, Sydney Convention Centre, Sydney.

Roberts , S., Almeida, C., Bronke, C., Ahmad, I., Keane, N., Chopra, A., Mallal, S., John, M., Heckerman, D. and Mallal, S. (2009) Screening for HIV responses using optimal epitopes predicted by HLA-viral sequence polymorphism associations. In: 21st Annual Conference of the Australasian Society for HIV Medicine (ASHM), 9 - 11 September, Brisbane, Australia.

Tschochner, M., James , I., Almeida, C., Keane, N., Roberts, S., Bronke, C., Chopra, A., Maiden, T., Ahmad, I., Gaudieri, S., Mallal, S., Rauch, A., John, M., Furrer, H. and Günthard, H. (2009) Effects of HIV-1 immune selection on susceptability to integrase inhibitor resistance. In: 12th European AIDS Conference (EACS) 2009, 11 - 14 November 2009, Cologne, Germany.

2008

D'Arminio Monforte, A., Abrams, D., Pradier, C., Weber, R., Reiss, P., Bonnet, F., Kirk, O., Law, M., De Wit, S., Friis-Moller, N., Phillips, A., Sabin, C., Lundgren, J. and Mallal, S. (2008) HIV-induced immunodeficiency and mortality from AIDS-defining and non-AIDS-defining malignancies. AIDS, 22 (16). pp. 2143-2153.

Flanagan, D., MacLellan, D., Gibbs, H., Baker, R. and Fletcher, J. (2008) The insidious hazard of hospitalisation: Venous thromboembolism. Medicine Today, 9 (9). pp. 16-26.

Mallal, S., Phillips, E., Carosi, G., Molina, J-M, Workman, C., Tomazic, J., Jagel-Guedes, E., Rugina, S., Kozyrev, O., Cid, J.F., Hay, P., Nolan, D., Hughes, S., Hughes, A., Ryan, S., Fitch, N., Thorborn, D. and Benbow, A. (2008) HLA-B*5701 screening for hypersensitivity to Abacavir. The New England Journal of Medicine, 358 (6). pp. 568-579.

Phillips, E., Hayden, A., Gutiérrez, S., Jahnke, N., Yip, B., Lima, V.D., Hogg, R.S., Harrigan, P.R. and Montaner, J.S.G. (2008) Is nevirapine-based therapy discontinuation in hepatitis C co-infected patients a more important mortality determinant than hypersensitivity: Authorsʼ reply. AIDS, 22 (4). pp. 548-549.

Phillips, E., Nolan, D. and Mallal, S. (2008) The Authors reply - Response to Vandekerckhove et al & Abel et al. New England Journal of Medicine, 358 (23). pp. 2515-2516.

Phillips, E.J. and Mallal, S.A. (2008) Pharmacogenetics and the potential for the individualization of antiretroviral therapy. Current Opinion in Infectious Diseases, 21 (1). pp. 16-24.

Rauch, A., Gaudieri, S., Evison, J., Nolan, D., Cavassini, M., Weber, R., James, I. and Furrer, H. (2008) Low current and nadir CD4+ T-cell counts are associated with higher hepatitis C virus RNA levels in the Swiss HIV cohort study. Antiviral Therapy, 13 (3). pp. 455-60.

Saag, M., Balu, R., Phillips, E.J., Brachman, P., Martorell, C., Burman, W., Stancil, B., Mosteller, M., Brothers, C., Wannamaker, P., Hughes, A., Sutherland‐Phillips, D., Mallal, S. and Shaefer, M. (2008) High sensitivity of human leukocyte antigen–B*5701 as a marker for immunologically confirmed abacavir hypersensitivity in white and black patients. Clinical Infectious Diseases, 46 (7). pp. 1111-1118.

Sabin, C., D'Arminio Monforte, A., Friis-Moller, N., Weber, R., El-Sadr, W., Reiss, P., Kirk, O., Mercie, P., Law, M., De Wit, S., Pradier, C., Phillips, A., Lundgren, J. and Mallal, S. (2008) Changes over time in risk factors for cardiovascular disease and use of Lipid‐lowering drugs in HIV‐Infected individuals and impact on myocardial infarction. Clinical Infectious Diseases, 46 (7). pp. 1101-1110.

Sabin, C., Worm, S., Weber, R., Reiss, P., El-Sadr, W., Dabis, F., De Wit, S., Law, M., D'Arminio Monforte, A., Friis-Moller, N., Kirk, O., Pradier, C., Weller, I., Phillips, A., Lundgren, J. and Mallal, S. (2008) Use of nucleoside reverse transcriptase inhibitors and risk of myocardial infarction in HIV-infected patients enrolled in the D:A:D study: a multi-cohort collaboration. The Lancet, 371 (9622). pp. 1417-1426.

Shear, N.H., Milpied, B., Bruynzeel, D.P. and Phillips, E.J. (2008) A review of drug patch testing and implications for HIV clinicians. AIDS, 22 (9). pp. 999-1007.

2007

Awadalla, P., Carlson, J., Kadie, C., Mallal, S. and Heckerman, D. (2007) Leveraging hierarchical population structure in discrete association studies. PloS one, 2 (7). pp. 1-13.

Bhattacharya, T., Daniels, M., Heckerman, D., Foley, B., Frahm, N., Kadie, C., Carlson, J., Yusim, K., McMahon, B., Gaschen, B., Mallal, S., Mullins, J.I., Nickle, D.C., Herbeck, J., Rousseau, C, Learn, G.H., Miura, T., Brander, C., Walker, B. and Korber, B. (2007) Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science, 315 (5818). pp. 1583-1586.

Chopra, A., Deganaar, J., Rushton, B., Maiden, T., Keller, J., Park, P.L., Gaudieri, S., John, M. and Mallal, S. (2007) High throughput sequencing of full length HIV-1 genomes. In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

Desmond, C.P., Bartholomeusz, A., Gaudieri, S., Revill, P.A. and Lewin, S.R. (2007) A systematic review of T-cell epitopes in hepatitis B virus: Identification, genotypic variation and relevance to antiviral therapeutics. Antiviral Therapy, 13 (2). pp. 161-175.

Gabutero, E., Moore, C., Mallal, S., Stewart, G. and Williamson, P. (2007) Interaction between allelic variation in IL12B and CCR5 affects the development of AIDS: IL12B/CCR5 interaction and HIV/AIDS. AIDS, 21 (1). pp. 65-69.

Hammond, E., Almeida, C., Mamotte, C., Nolan, D., Phillips, E., Schollaardt, T., Gill, M.J., Angel, J.B., Neurath, D., Li, J., Giulivi, T., McIntyre, C., Koultchitski, G., Wong, B., Reis, M., Rachlis, A., Cole, D.E., Chew, C.B., Neifer, S. and Mallal, S. (2007) Multi-centre evaluation of HLA-B*5701 allele detection by SSP-PCR typing: a quality assurance initiative. In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

Harari, A., Cellerai, C., Kostler, J., Gaudieri, S., James, I., John, M., Wagner, R., Mallal, S. and Pantaleo, G. (2007) Relationship between HLA Genotype and the functional profile of Antigen-specific CD8 T cells. In: 14th Conference on Retroviruses and Opportunistic Infections, 25 - 28 February 2007, Los Angeles, U.S.A.

Keane, N., Lucas, A., Netto, J., Almeida, C., Martin, A., Marriott, D., Kelleher, A., Phillips, E., Nolan, D. and Mallal, S. (2007) Use of the ELISpot assay to detect abacavir- and nevirapine-induced IFN-g responses in PBMC from HIV-infected patients with abacavir or nevirapine hypersensitivity reactions. In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

Kostenko, L., Lucas, A., Kjer-Nielsen, L., Foley, B., Nicholson, I., Tait, B., Holdsworth, R., Rossjohn, J., Mallal, S. and McCluskey, J. (2007) A rapid and sensitive flow-based screening test for detection of HLA-B57 to avoid abacavir hypersensitivity. In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

Mallal, S., Phillips, E., Carosi, G., Molina, J-M, Workman, C., Tomazic, J., Jagel-Guedes, E., Rugina, S., Kozyrev, O., Flores, C.J., Hay, P., Nolan, D., Hughes, S., Hughes, A., Thorborn, D. and Benbow, A. (2007) PREDICT-1: a novel randomised prospective study to determine the clinical utility of HLA-B*5701 screening to reduce abacavir hypersensitivity in HIV-1 infected subjects (study CNA106030). In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

McCluskey, J., Chessman, D., Lethborg, T., Kostenko, L., Purcell, A.W., Kjer-Nielsen, L., Mifsud, N.A., Tait, B.D., Holdsworth, R., Almeida, C., Nolan, D., Mallal, S., Bharadwaj, M. and Rossjohn, J. (2007) Abacavir hypersensitivity in HLA-B57-positive individuals with HIV infection is dependent upon the conventional MHC-I Ag presentation pathway. In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

McKenzie, E.J., Taylor, P., Stillion, R.J., Lucas, A.D., Harris, J., Gordon , S. and Martinez-Pomares, L. (2007) Mannose receptor expression and function define a new population of murine dendritic cells. Journal of Immunology, 178 (8). pp. 4975-4983.

Pfafferott, K., Ulsenheimer, A., Naidoo, K., Rauch, A., Gaudieri, S., Mallal, S., Diepolder, H.M. and Lucas, M. (2007) Genetic analysis of Hepatitis C (HCV) in acutely infected patients-evidence of limited HLA class II-driven selection pressure. In: 3rd Australian Centre for HIV & Hepatitis Research (ACH2) Workshop, 8 - 10 October 2007, Melbourne, Australia.

Phillips, E., Rauch, A., Nolan, D., Martin, A., Almeida, C., Knowles, S., Shear, N., Cavassini, M., Harrigan, R., Montaner, J., Keane, N., Laird, R., Lucas, A. and Mallal, S. (2007) Genetic characterization of patients with MHC class I mediated abacavir hypersensitivity reaction. In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

Phillips, E., Rauch, A., Nolan, D., Martin, A., Almeida, C., Laird, R., Montaner, J., Shear, N., Lucas, A. and Mallal, S. (2007) Genetic characterization of patch test negative patients reporting symptoms after initiation after abacavir. In: 8th International Workshop on Clinical Pharmacology of HIV Therapy, 16 - 18 April 2007, Budapest, Hungary.

Phillips, E.J. and Mallal, S. (2007) Drug hypersensitivity in HIV. Current Opinion in Allergy and Clinical Immunology, 7 (4). pp. 324-330.

Raboud, J., Lesosky, M., Sterling, S., Phillips, E.J., Walmsley, S. and Bayoumi, A. (2007) An Estimate of the proportion of symptoms reported in Self-administered questionnaires that are captured as adverse drug events in an observational database. HIV Clinical Trials, 8 (5). pp. 311-319.

Saag, M., Balu, R., Brachman, P., Brothers, C., Stancil, B., Mosteller, M., Wannamaker, P., Sutherland‐Phillips, D., Phillips, E., Mallal, S. and Shaefer, M. (2007) High sensitivity of HLA-B*5701 in Whites and Blacks in immunologically-confirmed cases of abacavir hypersensitivity (ABC HSR). In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

2006

Bihl, F., Frahm, N., Di Giammarino, L., Sidney, J., John, M., Yusim, K., Woodberry, T., Sango, K., Hewitt, H.S., Henry, L., Linde, C.H., Chisholm, J.V., Zaman, T.M., Pae, E., Mallal, S., Walker, B.D., Sette, A., Korber, B.T., Heckerman, D. and Brander, C. (2006) Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses. Journal of Immunology, 176 (7). pp. 4094-101.

Cherry, C.L., Nolan, D., James, I.R., McKinnon, E.J., Mallal, S.A., Gahan, M.E., Lal, L., McArthur, J.C. and Wesselingh, S.L. (2006) Tissue-specific associations between mitochondrial DNA levels and current treatment status in HIV-Infected individuals. JAIDS Journal of Acquired Immune Deficiency Syndromes, 42 (4). pp. 435-440.

Martin, A.M., Krueger, R., Almeida, C.A., Nolan, D., Phillips, E. and Mallal, S. (2006) A sensitive and rapid alternative to HLA typing as a genetic screening test for abacavir hypersensitivity syndrome. Pharmacogenetics and Genomics, 16 (5). pp. 353-357.

Pett, S.L., Wand, H., Law, M.G, Arduino, R., Lopez, J.C., Knysz, B., Pereira, L.C., Pollack, S., Reiss, P., Tambussi, G. and Mallal, S. (2006) Evaluation of subcutaneous proleukin (Interleukin-2) in a randomized international trial (ESPRIT): Geographical and gender differences in the baseline characteristics of participants. HIV Clinical Trials, 7 (2). pp. 70-85.

Rauch, A., Nolan, D., Martin, A., McKinnon, E., Almeida, C. and Mallal, S. (2006) Prospective genetic screening decreases the incidence of Abacavir hypersensitivity reactions in the Western Australian HIV cohort study. Clinical Infectious Diseases, 43 (1). pp. 99-102.

2005

Martin, A., Nolan, D., Rauch, A., Almeida, C., McKinnon, E. and Mallal, S. (2005) Genetic screening for Abacavir hypersensitivity (ABC-HSR) in the Western Australian cohort: Prospective data and novel diagnostic approaches. In: 17th Annual Conference of the Australasian Society for HIV Medicine (ASHM 2005), 24 - 27 August 2005, Hobart, Tasmania.

Martin, A.M., Almeida, C., Nolan, D., Cameron, P., Purcell, A., Chessman, D., McCluskey, J., Phillips, E. and Mallal, S. (2005) Involvement of metabolic and immune responses in the pathogenesis of Abacavir hypersensitivity reaction. In: 17th Annual Conference of the Australasian Society for HIV Medicine (ASHM 2005), 24 - 27 August 2005, Hobart, Tasmania.

2004

Mallal, S. (2004) HIV, Now a chronic disease. In: 29th Australian & New Zealand Intensive Care Society Annual Scientific Meeting on Intensive Care, 7 - 10 October 2004, Melbourne, VIC.