Publications: Centre for Clinical Immunology and Biomedical Statistics

2013

Rojana-udomsart, A., Mitrpant, C., James, I., Witt, C., Needham, M., Day, T., Kiers, L., Corbett, A., Martinez, P., Wilton, S.D. and Mastaglia, F.L. (2013) Analysis of HLA-DRB3 alleles and supertypical genotypes in the MHC Class II region in sporadic inclusion body myositis. Journal of Neuroimmunology, 254 (1-2). pp. 174-177.

2012

Achhra, A.C., Amin, J., Hoy, J., Tanuma, J., Sirisanthana, T., Nolan, D., Merati, T. and Giles, M. (2012) Differences in lipid measurements by antiretroviral regimen exposure in cohorts from Asia and Australia. AIDS Research and Treatment, 2012 . pp. 1-9.

Blais, M.-E., Zhang, Y., Rostron, T., Griffin, H., Taylor, S., Xu, K., Yan, H., Wu, H., James, I., John, M., Dong, T. and Rowland-Jones, S. L. (2012) High frequency of HIV mutations associated with HLA-C suggests enhanced HLA-C - Restricted CTL selective pressure associated with an AIDS-protective polymorphism. The Journal of Immunology, 188 (9). pp. 4663-4670.

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.

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.

Loh, N.K., Lucas, M., Fernandez, S. and Prentice, D. (2012) Successful treatment of macrophage activation syndrome complicating adult Still disease with anakinra. Internal Medicine Journal, 42 (12). pp. 1358-1362.

Rajasuriar, R., Booth, D.R., Gouillou, M., Spelman, T., James, I., Solomon, A., Chua, K., Stewart, G., Deeks, S., Bangsberg, D.R., Muzoora, C., Cameron, P.U., Hunt, P., Martin, J. and Lewin, S.R. (2012) The role of SNPs in the α-chain of the IL-7R gene in CD4+ T-cell recovery in HIV-infected African patients receiving suppressive cART. Genes and Immunity, 13 (1). pp. 83-93.

Rojana-udomsart, A., Bundell, C., James, I., Castley, A., Martinez, P., Christiansen, F., Hollingsworth, P. and Mastaglia, F. (2012) Frequency of autoantibodies and correlation with HLA-DRB1 genotype in sporadic inclusion body myositis (s-IBM): A population control study. Journal of Neuroimmunology, 249 (1-2). pp. 66-70.

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.

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.

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.

Fitzmaurice, K., Petrovic, D., Ramamurthy, N., Simmons, R., Merani, S., Gaudieri, S., Sims, S., Dempsey, E., Freitas, E., Lea, S., McKiernan, S., Norris, S., Long, A., Kelleher, D. and Klenerman, P. (2011) Molecular footprints reveal the impact of the protective HLA-A*03 allele in hepatitis C virus infection. Gut, 60 (11). pp. 1563-1571.

Lucas, M., Nicol, P., McKinnon, E., Whidborne, R., Lucas, A.D., Thambiran, A., Burgner, D., Waring, J. and French, M. (2011) The potential danger of a solely interferon-gamma release assay-based approach to testing for latent Mycobacterium tuberculosis infection in children. Thorax, 66 (3). p. 265.

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.

Morahan, G., Mehta, M., James, I., Chen, W.-M., Akolkar, B., Erlich, H. A., Hilner, J. E., Julier, C., Nerup, J., Nierras, C., Pociot, F., Todd, J. A. and Rich, S. S. (2011) Tests for genetic interactions in Type 1 Diabetes: Linkage and stratification analyses of 4,422 affected Sib-Pairs. Diabetes, 60 (3). pp. 1030-1040.

Olcaydu, D., Rumi, E., Harutyunyan, A., Passamonti, F., Pietra, D., Pascutto, C., Berg, T., Jager, R., Hammond, E.L., Cazzola, M. and Kralovics, R. (2011) The role of the JAK2 GGCC haplotype and the TET2 gene in familial myeloproliferative neoplasms. Haematologica, 96 (3). pp. 367-374.

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.

Pirmohamed, M., Friedmann, P.S., Molokhia, M., Loke, Y.K., Smith, C., Phillips, E., La Grenade, L., Carleton, B., Papaluca-Amati, M., Demoly, P. and Shear, N.H. (2011) Phenotype Standardization for Immune-Mediated Drug-Induced Skin Injury. Clinical Pharmacology & Therapeutics, 89 (6). pp. 896-901.

Qiu, W., James, I., Carroll, W.M., Mastaglia, F.L. and Kermode, A.G. (2011) HLA-DR allele polymorphism and multiple sclerosis in Chinese populations: a meta-analysis. Multiple Sclerosis, 17 (4). pp. 382-388.

Qiu, W., Raven, S., James, I., Luo, Y., Wu, J., Castley, A., Christiansen, F.T., Carroll, W.M., Mastaglia, F.L. and Kermode, A.G. (2011) Spinal cord involvement in multiple sclerosis: A correlative MRI and high-resolution HLA-DRB1 genotyping study. Journal of the Neurological Sciences, 300 (1-2). pp. 114-119.

Zhang, Y., Peng, Y., Yan, H., Xu, K., Saito, M., Wu, H., Chen, X., Ranasinghe, S., Kuse, N., Powell, T., Zhao, Y., Li, W., Zhang, X., Feng, X., Li, N., Leligdowicz, A., Xu, X., John, M., Takiguchi, M., McMichael, A., Rowland-Jones, S. and Dong, T. (2011) Multilayered defense in HLA-B51-associated HIV viral control. The Journal of Immunology, 187 (2). pp. 684-691.

2010

Almeida, C.M., Roberts, S.G., Laird, R., McKinnon, E., Ahmad, I., Keane, N.M., Chopra, A., Kadie, C., Heckerman, D., Mallal, S. and John, M. (2010) Exploiting knowledge of immune selection in HIV-1 to detect HIV-specific CD8 T-cell responses. Vaccine, 28 (37). pp. 6052-6057.

Breen, J., Li, D., Dunn, D.S., Bekes, F., Kong, X., Zhang, J., Jia, J., Wicker, T., Mago, R., Ma, W., Bellgard, M. and Appels, R. (2010) Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain. BMC Plant Biology, 10 (1). p. 99.

Falster, K., Wand, H., Donovan, B., Anderson, J., Nolan, D., Watson, K., Watson, J. and Law, M.G (2010) Hospitalizations in a cohort of HIV patients in Australia, 1999–2007. AIDS, 24 (9). pp. 1329-1339.

Friis-Møller, N., Thiébaut, R., Reiss, P., Weber, R., Monforte, A.D., De Wit, S., El-Sadr, W., Fontas, E., Worm, S., Kirk, O., Phillips, A., Sabin, C.A., Lundgren, J.D., Law, M.G. and Mallal, S. (2010) Predicting the risk of cardiovascular disease in HIV-infected patients: The Data collection on Adverse Effects of Anti-HIV Drugs Study. European Journal of Cardiovascular Prevention & Rehabilitation, 17 (5). pp. 491-501.

Hammond, E.L., McKinnon, E. and Nolan, D. (2010) Human immunodeficiency virus treatment-induced adipose tissue pathology and lipoatrophy: Prevalence and metabolic consequences. Clinical Infectious Diseases, 51 (5). pp. 591-599.

Iwabu, Y., Kinomoto, M., Tatsumi, M., Fujita, H., Shimura, M., Tanaka, Y., Ishizaka, Y., Nolan, D., Mallal, S., Sata, T. and Tokunaga, K. (2010) Differential anti-APOBEC3G activity of HIV-1 Vif proteins derived from different subtypes. Journal of Biological Chemistry, 285 (46). pp. 35350-35358.

James, I. (2010) Correlation estimation with bivariate censored data via alternating regressions. In: ASC 2010 Australian Statistical Conference Statistics in the West: Understanding our World., 6 - 10 December, Fremantle, Western Australia.

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.

Lucas, M., Nicol, P., McKinnon, E., Whidborne, R., Lucas, A.D., Thambiran, A., Burgner, D., Waring, J. and French, M. (2010) A prospective large-scale study of methods for the detection of latent Mycobacterium tuberculosis infection in refugee children. Thorax, 65 (5). pp. 442-448.

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

Qiu, W., Wu, J-S, Castley, A., James, I., Joseph, J., Christiansen, F.T., Carroll, W.M., Mastaglia, F.L. and Kermode, A.G. (2010) Clinical profile and HLA-DRB1 genotype of late onset multiple sclerosis in Western Australia. Journal of Clinical Neuroscience, 17 (8). pp. 1009-1013.

Qiu, W., Bundell, C., Wu, J.-S., Castley, A., James, I., Hollingsworth, P., Christiansen, F., Carroll, W.M., Mastaglia, F.L and Kermode, A.G (2010) Low level of systemic autoimmunity in Western Australian multiple sclerosis patients. Multiple Sclerosis, 16 (3). pp. 351-354.

Rohrbach, J., Robinson, N., Harcourt, G., Hammond, E.L., Gaudieri, S., Gorgievski, M., Telenti, A., Keiser, O., Gunthard, H. F., Hirschel, B., Hoffmann, M., Bernasconi, E., Battegay, M., Furrer, H., Klenerman, P., Rauch, A. and Swiss HIV Cohort Study, . (2010) Cellular immune responses to HCV core increase and HCV RNA levels decrease during successful antiretroviral therapy. Gut, 59 (9). pp. 1252-1258.

Smyth, R.P., Schlub, T.E., Grimm, A., Venturi, V., Chopra, A., Mallal, S., Davenport, M.P. and Mak, J. (2010) Reducing chimera formation during PCR amplification to ensure accurate genotyping. Gene, 469 (1-2). pp. 45-51.

Worm, S.W., Friis-Møller, N., Bruyand, M., Monforte, A.D., Rickenbach, M., Reiss, P., El-Sadr, W., Phillips, A., Lundgren, J., Sabin, C. and Mallal, S. (2010) High prevalence of the metabolic syndrome in HIV-infected patients: impact of different definitions of the metabolic syndrome. AIDS, 24 (3). pp. 427-435.

Wu, J-S, Qiu, W., Castley, A., James, I., Joseph, J., Christiansen, F.T., Carroll, W.M., Mastaglia, F.L. and Kermode, A.G. (2010) Presence of CSF oligoclonal bands (OCB) is associated with the HLA-DRB1 genotype in a West Australian multiple sclerosis cohort. Journal of the Neurological Sciences, 288 (1-2). pp. 63-67.

Wu, J-S, Qiu, W., Castley, A., James, I., Mastaglia, F.L, Christiansen, F.T, Carroll, W.M, Joseph, J. and Kermode, A.G (2010) Modifying effects of HLA-DRB1 allele interactions on age at onset of multiple sclerosis in Western Australia. Multiple Sclerosis, 16 (1). pp. 15-20.

Wu, J.S., James, I., Wei, Q., Castley, A., Christiansen, F.T., Carroll, W.M., Mastaglia, F.L. and Kermode, A.G. (2010) Influence of HLA-DRB1 allele heterogeneity on disease risk and clinical course in a West Australian MS cohort: a high-resolution genotyping study. Multiple Sclerosis, 16 (5). pp. 526-532.

2009

Almeida, C.M., Roberts, S.G., Laird, R., McKinnon, E., Ahmad, I., Pfafferott, K., Turley, J., Keane, N.M., Lucas, A.D., Rushton, B.C., Chopra, A., Mallal, S. and John, M. (2009) Automation of the ELISpot assay for high-throughput detection of antigen-specific T-cell responses. Journal of Immunological Methods, 344 (1). pp. 1-5.

Avila-Rios, S., Ormsby, C.E., Carlson, J.M., Valenzuela-Ponce, H., Blanco-Heredia, J., Garrido-Rodriguez, D., Garcia-Morales, C., Heckerman, D., Brumme, Z.L., Mallal, S., John, M., Espinosa, E. and Reyes-Teran, G. (2009) Unique features of HLA-mediated HIV evolution in a Mexican cohort: a comparative study. Retrovirology, 6 . p. 72.

Brumme, Z.L., John, M., Carlson, J.M., Brumme, C.J., Chan, D., Brockman, M.A., Swenson, L.C., Tao, I., Szeto, S., Rosato, P., Sela, J., Kadie, C.M., Frahm, N., Brander, C., Haas, D.W., Riddler, S.A., Haubrich, R., Walker, B.D., Harrigan, P.R., Heckerman, D., Mallal, S. and Nixon, D.F. (2009) HLA-Associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins. PLoS ONE, 4 (8). e6687.

D'Orsogna, L.J., Wright, M.P., Krueger, R.G., McKinnon, E.J., Buffery, S.I., Witt, C.S., Staples, N., Loh, R., Cannell, P.K., Christiansen, F.T. and French, M.A. (2009) Allogeneic hematopoietic stem cell transplantation recipients have defects of both switched and IgM memory B cells. Biology of Blood and Marrow Transplantation, 15 (7). pp. 795-803.

Egger, S., Petoumenos, K., Kamarulzaman, A., Hoy, J., Sungkanuparph, S., Chuah, J., Falster, K., Zhou, J., Law, M.G. and Mallal, S. (2009) Long-term patterns in CD4 response are determined by an interaction between baseline CD4 cell count, viral load, and time: The Asia Pacific HIV Observational Database (APHOD). JAIDS Journal of Acquired Immune Deficiency Syndromes, 50 (5). pp. 513-520.

Falster, K., Choi, J.Y., Donovan, B., Duncombe, C., Mulhall, B., Sowden, D., Zhou, J., Law, M.G. and Mallal, S. (2009) AIDS-related and non-AIDS-related mortality in the Asia-Pacific region in the era of combination antiretroviral treatment. AIDS, 23 (17). pp. 2323-2336.

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., Pfafferott, K., Barnes, E., Cheng, W., McCaughan, G., Shackel, N., Jeffrey, G.P., Mollison, L., Baker, R., Furrer, H., Günthard, H.F., Freitas, E., Humphreys, I., Klenerman, P., Mallal, S., James, I., Roberts, S., Nolan, D. and Lucas, M. (2009) Hepatitis C virus drug resistance and immune-driven adaptations: Relevance to new antiviral therapy. Hepatology, 49 (4). pp. 1069-1082.

James, I., McKinnon, E., Gaudieri, S. and Morahan, G. (2009) Missingness in the T1DGC MHC fine-mapping SNP data: association with HLA genotype and potential influence on genetic association studies. Diabetes, Obesity and Metabolism, 11 (Supp. 1). pp. 101-107.

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, J.G., Fidler, S., Weber, J., Pybus, O.G., Klenerman, P., Ndung’u, T., Phillips, R., Heckerman, D., Harrigan, P.R., Walker, Bruce D., Takiguchi, M. and Goulder, P. (2009) Adaptation of HIV-1 to human leukocyte antigen class I. Nature, 458 (7238). pp. 641-645.

Keane, N., Roberts, S., Laird, R., Chopra, A., Krishnan, T., Almeida, C., Bronke, C., Mallal, S., James, I. and John, M. (2009) P09-15. Selection of higher avidity HLA-restricted T cell responses as a viral adaptation strategy. In: AIDS Vaccine 2009, 19 - 22 October 2009, Paris, France.

Keane, N.M., Roberts, S.G., Laird, R., Chopra, A., Krishnan, T., Almeida, C.M., Bronke, C., Mallal, S., James, I. and John, M. (2009) P09-15. Selection of higher avidity HLA-restricted T cell responses as a viral adaptation strategy. Retrovirology, 6 (Suppl 3, 22 October 2009). P128.

Mastaglia, F.L., Needham, M., Scott, A., James, I., Zilko, P., Day, T., Kiers, L., Corbett, A., Witt, C.S., Allcock, R., Laing, N., Garlepp, M. and Christiansen, F.T. (2009) Sporadic inclusion body myositis: HLA-DRB1 allele interactions influence disease risk and clinical phenotype. Neuromuscular Disorders, 19 (11). pp. 763-765.

McKinnon, E., Morahan, G., Nolan, D. and James, I. (2009) Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach. Diabetes, Obesity and Metabolism, 11 (Supp. 1). pp. 92-100.

Miura, T., Brumme, C. J., Brockman, M. A., Brumme, Z. L., Pereyra, F., Block, B. L., Trocha, A., John, M., Mallal, S., Harrigan, P. R. and Walker, B. D. (2009) HLA-Associated viral mutations are common in human immunodeficiency virus type 1 elite controllers. Journal of Virology, 83 (7). pp. 3407-3412.

Morahan, G., Mehta, M., McKinnon, E. and James, I. (2009) Effect of linkage status of affected sib-pairs on the search for novel type 1 diabetes susceptibility genes in the HLA complex. Diabetes, Obesity and Metabolism, 11 (Supp. 1). pp. 67-73.

Nolan, D. (2009) HLA-B*5701 screening prior to abacavir prescription: Clinical and laboratory aspects. Critical Reviews in Clinical Laboratory Sciences, 46 (3). pp. 153-165.

Phillips, E.J. and Mallal, S. (2009) Successful translation of pharmacogenetics into the clinic: The abacavir example. Molecular Diagnosis and Therapy, 13 (1). pp. 1-9.

Phillips, E.J. (2009) Pharmacogenetic of drug hypersensitivity: Personalising medicine and predicting the unpredictable. In: WAMSG 5th Annual Medication Safety Symposium: ADRs ain'y just ADRs: Action on Adverse Drug Reactions for Medication Safety, 14 July 2009, University Club, University of Western Australia, Crawley.

Price, P. and James, I. (2009) IL1A alleles associate with a virological response to antiretroviral therapy in HIV patients beginning therapy with advanced disease. AIDS, 23 (9). pp. 1173-1176.

Rauch, A., James, I., Pfafferott, K., Nolan, D., Klenerman, P., Cheng, W., Mollison, L., McCaughan, G., Shackel, N., Jeffrey, G.P., Baker, R., Freitas, E., Humphreys, I., Furrer, H., Günthard, H.F., Hirschel, B., Mallal, S., John, M., Lucas, M., Barnes, E. and Gaudieri, S. (2009) Divergent adaptation of hepatitis C virus genotypes 1 and 3 to human leukocyte antigen-restricted immune pressure. Hepatology, 50 (4). pp. 1017-1029.

Rauch, A., Gaudieri, S., Thio, C. and Bochud, P-Y (2009) Host genetic determinants of spontaneous hepatitis C clearance. Pharmacogenomics, 10 (11). pp. 1819-1837.

Tschochner, M., Chopra, A., Maiden, T.M., Ahmad, I.F., James, I., Furrer, H., Günthard, H., Mallal, S., Rauch, A. and John, M. (2009) Effects of HIV type-1 immune selection on susceptability to integrase inhibitor resistance. Antiviral Therapy, 14 (7). pp. 953-964.

2008

Almeida, C.M., Martin, A.M., Nolan, D., Lucas, A., Cameron, P.U., James, I., Phillips, E. and Mallal, S. (2008) Cytokine profiling in abacavir hypersensitivity patients. Antiviral Therapy, 13 (2). pp. 281-288.

Brumme, Z. L., Brumme, C. J., Carlson, J., Streeck, H., John, M., Eichbaum, Q., Block, B. L., Baker, B., Kadie, C., Markowitz, M., Jessen, H., Kelleher, A. D., Rosenberg, E., Kaldor, J., Yuki, Y., Carrington, M., Allen, T. M., Mallal, S., Altfeld, M., Heckerman, D. and Walker, B. D. (2008) Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute/early HIV-1 infection. Journal of Virology, 82 (18). pp. 9216-9227.

Chessman, D., Kostenko, L., Lethborg, T., Purcell, A.W., Williamson, N.A., Chen, Z., Kjer-Nielsen, L., Mifsud, N.A., Tait, B.D., Holdsworth, R., Almeida, C.M., Nolan, D., Macdonald, W.A., Archbold, J.K., Kellerher, A.D., Marriott, D., Mallal, S., Bharadwaj, M., Rossjohn, J. and McCluskey, J. (2008) Human leukocyte Antigen Class I-restricted activation of CD8+ T Cells provides the immunogenetic basis of a systemic drug hypersensitivity. Immunity, 28 (6). pp. 822-832.

Duracinsky, M., Acquadro, C., Herrmann, S., Berzins, B., Le Coeur, S., Kohli, R., Ban, B., Ferro do Lago, R. and Chassany, O. (2008) International development of a new health-related quality of life questionnaire specific to HIV/AIDS – item banking. In: XVII International AIDS Conference, 3 - 8 August, Mexico City, Mexico.

Duracinsky, M., Herrmann, S., Acquadro, C., Berzins, B., Le Coeur, S., Hyland, N., Fournier, I., McKinnon, E., Nolan, D., Mallal, S. and Chassany, O. (2008) Development of a new health-related quality of life questionnaire specific to HIV/AIDS: an international and cross cultural initiative. In: 20th Annual Australasian Society for HIV Medicine Conference, 17 - 20 September, Perth, Western Australia.

Guallar, J.P., Gallego-Escuredo, J.M., Domingo, J.C., Alegre, M., Fontdevila, J., Martínez, E., Hammond, E.L., Domingo, P., Giralt, M. and Villarroya, F. (2008) Differential gene expression indicates that ‘buffalo hump’ is a distinct adipose tissue disturbance in HIV-1-associated lipodystrophy. AIDS, 22 (5). pp. 575-584.

Hammond, E.L., Martin, A., Nolan, D., Metcalf, C. and Mallal, S. (2008) Eruptive haemangioma associated with HIV therapy and mitochondrial pathology. Pathology, 40 (4). pp. 425-429.

Hammond, E.L., McKinnon, E., Mallal, S. and Nolan, D. (2008) Longitudinal evaluation of cardiovascular disease-associated biomarkers in relation to abacavir therapy. AIDS, 22 (18). pp. 2540-2543.

Herrmann, S., McKinnon, E., John, M., Nolan, D., Martinez, O.P., Phillips, E. and Mallal, S. (2008) Side effects, dosing schedules, pill burden and perceived stress: interaction and influence on medication. In: 20th Annual Australasian Society for HIV Medicine Conference, 17 - 20 September, Perth, Western Australia.

Kulski, J.K., Shigenari, A., Shiina, T., Ota, M., Hosomichi, K., James, I. and Inoko, H. (2008) Human endogenous retrovirus (HERVK9) structural polymorphism with haplotypic HLA-A allelic associations. Genetics, 180 (1). pp. 445-457.

Lo, G., Herrmann, S., Cheng, W., Kontorinis, N., Phillips, E., Nolan, D. and Lucas, M. (2008) Screening for hepatocellular carcinoma (HCC) in hepatitis/HIV co-infection using ultrasound imaging and alfa-feto protein levels. In: 20th Annual Australasian Society for HIV Medicine Conference, 17 - 20 September, Perth, Western Australia.

Needham, M., Hooper, A., James, I., van Bockxmeer, F., Corbett, A., Day, T., Garlepp, M.J. and Mastaglia, F.L. (2008) Apolipoprotein ε alleles in sporadic inclusion body myositis: A reappraisal. Neuromuscular Disorders, 18 (2). pp. 150-152.

Needham, M., James, I., Corbett, A., Day, T., Christiansen, F., Phillips, B. and Mastaglia, F.L. (2008) Sporadic inclusion body myositis: Phenotypic variability and influence of HLA-DR3 in a cohort of 57 Australian cases. Journal of Neurology, Neurosurgery & Psychiatry, 79 (9). pp. 1056-1060.

Rauch, A., Nolan, D., Furrer, H., McKinnon, E., John, M., Mallal, S., Gaudieri, S., Günthard, H.F., Schmid, P., Battegay, M., Hirschel, B., Telenti, A., James, I. and Swiss HIV Cohort Study, . (2008) HLA‐Bw4 homozygosity is associated with an impaired CD4 T cell recovery after initiation of antiretroviral therapy. Clinical Infectious Diseases, 46 (12). pp. 1921-1925.

Rauch, A., Nolan, D., Thurnheer, C., Fux, C.A., Cavassini, M., Chave, J-P, Opravil, M., Phillips, E., Mallal, S. and Furrer, H. (2008) Refining abacavir hypersensitivity diagnoses using a structured clinical assessment and genetic testing in the Swiss HIV Cohort Study. Antiviral Therapy, 13 (8). pp. 1019-1028.

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.

Tan, D.B.A., Yong, Y.K., Tan, H.Y., Kamarulzaman, A., Tan, L.H., Lim, A., James, I., French, M. and Price, P. (2008) Immunological profiles of immune restoration disease presenting as mycobacterial lymphadenitis and cryptococcal meningitis. HIV Medicine, 9 (5). pp. 307-316.

2007

Bowyer, S., Ulsenheimer, A., Lucas, M., Pfafferott, K., Heeg, M., Gaudieri, S., Grüner, N., Rauch, A., Gerlach, J.T., Jung, M.C., Zachoval, R., Pape, G.R., Schraut, W., Santantonio, T., Nitschko, H., Obermeier, M., Phillips, R., Scriba, T.J., Semmo, N., Day, C., Weber, J.N., Fidler, S., Thimme, R., Haberstroh, A., Baumert, T.F., Klenerman, P. and Diepolder, H.M. (2007) Tracking Virus-Specific CD4+ T Cells during and after Acute Hepatitis C Virus Infection. PLoS ONE, 2 (7). e649.

D'Orsogna, L.J., Krueger, R.G., McKinnon, E.J. and French, M.A. (2007) Circulating memory B-cell subpopulations are affected differently by HIV infection and antiretroviral therapy. AIDS, 21 (13). pp. 1747-1752.

Fellay, J., Shianna, K.V., Ge, D., Colombo, S., Ledergerber, B., Weale, M., Zhang, K., Gumbs, C., Castagna, A., Cossarizza, A., Cozzi-Lepri, A., De Luca, A., Easterbrook, P., Francioli, P., Mallal, S., Martinez-Picado, J., Miro, J.M., Obel, N., Smith, J. P., Wyniger, J., Descombes, P., Antonarakis, S.E., Letvin, N.L., McMichael, A.J., Haynes, B.F., Telenti, A. and Goldstein, D.B. (2007) A Whole-Genome Association Study of Major Determinants for Host Control of HIV-1. Science, 317 (5840). pp. 944-947.

Frahm, N., Yusim, K., Suscovich, T.J., Adams, S., Sidney, J., Hraber, P., Hewitt, H.S., Linde, C.H., Kavanagh, D.G., Woodberry, T., Henry, L.M., Faircloth, K., Listgarten, J., Kadie, C., Jojic, N., Sango, K., Brown, N.V., Pae, E., Zaman, M.T., Bihl, F., Khatri, A., John, M., Mallal, S., Marincola, F.M., Walker, B.D., Sette, A., Heckerman, D., Korber, B.T.M. and Brander, C. (2007) Extensive HLA class I allele promiscuity among viral CTL epitopes. European Journal of Immunology, 37 (9). pp. 2419-2433.

Gaudieri, S., Rauch, A., Park, L.P., Freitas, E., Herrmann, S., Jeffrey, G., Cheng, W., Pfafferott, K., Naidoo, K., Chapman, R., Battegay, M., Weber, R., Telenti, A., Furrer, H., James, I., Lucas, M., Mallal, S.A. and Swiss HIV Cohort Study, (2007) Erratum: Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection (Journal of Virology (2006) 80, 22, (11094-11104)). Journal of Virology, 81 (16). pp. 8846-8848.

Hammond, E., Almeida, C.M., Mamotte, C., Nolan, D., Phillips, E.J., Schollaardt, T.A., Gill, M.J., Angel, J.B., Neurath, D., Li, J., Giulivi, T., McIntyre, C., Koultchitski, G., Wong, B., Reis, M., Rachlis, A., Cole, D., Chew, C.B., Neifer, S., Lalonde, R., Roger, M., Jeanneau, A. and Mallal, S. (2007) External quality assessment of HLA-B*5701 reporting: an international multicentre survey. Antiviral Therapy, 12 (7). pp. 1027-1032.

Hammond, E., Mamotte, C., Nolan, D. and Mallal, S. (2007) HLA-B*5701 typing: evaluation of an allele-specific polymerase chain reaction melting assay. Tissue Antigens, 70 (1). pp. 58-61.

Hammond, E. and Nolan, D. (2007) Adipose tissue inflammation and altered adipokine and cytokine production in antiretroviral therapy-associated lipodystrophy (Review). Current Opinion in HIV and AIDS, 2 (4). pp. 274-281.

Hammond, E., Shaw, K. and Herrmann, R. (2007) The JAK2 V617F mutation is detectable in granulocyte populations at greater than two copies per cell among individuals with myeloproliferative disorders [3] (letter). Leukemia, 21 (4). pp. 815-816.

Hammond, E., Shaw, K. and Herrmann, R. (2007) “The JAK2 V617F mutation is detectable in granulocyte populations at greater than two copies per cell among individuals with myeloproliferative disorders”, by El Housni et al.[5] (letter). Leukemia, 21 (4). pp. 817-818.

Harari, A., Cellerai, C., Enders, F.B., Kostler, J., Codarri, L., Tapia, G., Boyman, O., Castro, E., Gaudieri, S., James, I., John, M., Wagner, R., Mallal, S. and Pantaleo, G. (2007) Skewed association of polyfunctional antigen-specific CD8 T cell populations with HLA-B genotype. Proceedings of the National Academy of Sciences, 104 (41). pp. 16233-16238.

Herrmann, S., McKinnon, E., John, M., Hyland, N., Martinez, O.P., Cain, A., Turner, K., Coombs, A., Manolikos, C. and Mallal, S. (2007) Evidence-based, multifactorial approach to addressing non-adherence to antiretroviral therapy and improving standards of care. Internal Medicine Journal, 38 (1). pp. 8-15.

Herrmann, S.E., McKinnon, E., John, M. and Mallal, S. (2007) Influence of dosing regimen on adherence to antiretroviral therapy within PI and NNRTI regimens. In: 4th International AIDS Conference on HIV Pathogenesis, Treatment and Prevention, 22 - 25 July, Sydney, Australia.

Langan, L.L., Park, L.P., Hughes, T.L., Irish, A., Luxton, G., Witt, C.S. and Christiansen, F.T. (2007) Post-Transplant HLA class II Antibodies and High Soluble CD30 Levels are Independently Associated with Poor Kidney Graft Survival. American Journal of Transplantation, 7 (4). pp. 847-856.

Lim, A., Tan, D.B.A., Price, P., Kamarulzaman, A., Tan, H.Y., James, I. and French, M.A. (2007) Proportions of circulating T cells with a regulatory cell phenotype increase with HIV-associated immune activation and remain high on antiretroviral therapy. AIDS, 21 (12). pp. 1525-1534.

Lucas, A., Nolan, D. and Mallal, S. (2007) HLA-B*5701 screening for susceptibility to abacavir hypersensitivity. Journal of Antimicrobial Chemotherapy, 59 (4). pp. 591-593.

Mallal, S. and Phillips, E. (2007) Introduction of pharmacogenetic screening to HIV clinical practice: Potential benefits and challenges. European Infectious Diseases (2). pp. 13-18.

Martin, A., Almeida, C.M., Cameron, P.U., Purcell, Anthony W, Nolan, D., James, I., McCluskey, J., Phillips, E.J., Landay, Alan and Mallal, S. (2007) Immune responses to abacavir in antigen-presenting cells from hypersensitive patients. AIDS, 21 (10). pp. 1233-1244.

McKinnon, E., John, M., Herrmann, S.E. and James, I. (2007) Models and analysis of point-inflated data in a study of markers of HAART efficacy. In: 11th International Workshop on HIV Observational Databases, 22 - 25 March, Monte Carlo.

Nolan, D. (2007) The view from Sydney: 9th International Lipodystrophy Workshop. Nutrition and Metabolic Disorders in HIV Infection, 6 (3). pp. 1161-11643.

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

Pocathikorn, A., Taylor, R.R., James, I. and Mamotte, C.D.S. (2007) LDL-receptor mRNA expression in men is downregulated within an hour of an acute fat load and is influenced by genetic polymorphism. Journal of Nutrition, 137 (9). pp. 2062-2067.

Rauch, A., Laird, R., McKinnon, E., Telenti, A., Furrer, H., Weber, R., Smillie, D. and Gaudieri, S. (2007) Influence of inhibitory killer immunoglobulin-like receptors and their HLA-C ligands on resolving hepatitis C virus infection. Tissue Antigens, 69 (SUPPL. 1). pp. 237-240.

Wu, J.H.Y., Ward, N.C., Indrawan, A.P., Almeida, C.M., Hodgson, J.M., Proudfoot, J.M., Puddey, I.B. and Croft, K.D. (2007) Effects of -Tocopherol and Mixed Tocopherol Supplementation on Markers of Oxidative Stress and Inflammation in Type 2 Diabetes. Clinical Chemistry, 53 (3). pp. 511-519.

2006

Burgess, K., Price, P., James, I.R., Stone, S.F., Keane, N.M., Lim, A.Y.F., Warmington, J.R. and French, M.A. (2006) Interferon-Gamma responses to candida recover slowly or remain low in immunodeficient HIV patients responding to ART. Journal of Clinical Immunology, 26 (2). pp. 160-167.

Fernandez, S., Price, P., McKinnon, E.J., Nolan, R.C. and French, M.A. (2006) Low CD4+ T-cell counts in HIV patients receiving effective antiretroviral therapy are associated with CD4+ T-cell activation and senescence but not with lower effector memory T-cell function. Clinical Immunology, 120 (2). pp. 163-170.

Fernandez, S., Rosenow, A.A., James, I.R., Roberts, S.G., Nolan, R.C., French, M.A. and Price, P. (2006) Recovery of CD4+ T Cells in HIV Patients With a Stable Virologic Response to Antiretroviral Therapy Is Associated With Polymorphisms of Interleukin-6 and Central Major Histocompatibility Complex Genes. JAIDS Journal of Acquired Immune Deficiency Syndromes, 41 (1). pp. 1-5.

Frahm, N., Kiepiela, P., Adams, S., Linde, C.H., Hewitt, H.S., Sango, K., Feeney, M.E., Addo, M.M., Lichterfeld, M., Lahaie, M.P., Pae, E., Wurcel, A.G., Roach, T., St John, M.A., Altfeld, M., Marincola, F.M., Moore, C., Mallal, S., Carrington, M., Heckerman, D., Allen, T.M., Mullins, J.I., Korber, B.T., Goulder, P.J.R., Walker, B.D. and Brander, C. (2006) Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nature Immunology, 7 (2). pp. 173-178.

Gaudieri, S., Rauch, A., Naidoo, K., Park, P., Freitas, E., Herrmann, S., Jeffrey, G., Cheng, W., Pfafferott, K., Chapman, R., Battegay, M., Weber, R., Telenti, A., Furrer, H., James, I., Lucas, M., Mallal, S.A. and Swiss HIV Cohort Study, (2006) Evidence of viral adaptation to HLA Class I-restricted immune pressure in chronic Hepatitis C virus infection. In: 13th International Meeting on Hepatitis C Virus & Related Viruses, 27 - 31 August, Cairns, Australia.

Gaudieri, S., Rauch, A., Park, L.P., Freitas, E., Herrmann, S., Jeffrey, G., Cheng, W., Pfafferott, K., Naidoo, K., Chapman, R., Battegay, M., Weber, R., Telenti, A., Furrer, H., James, I., Lucas, M., Mallal, S.A. and Swiss HIV Cohort Study, (2006) Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection. Journal of Virology, 80 (22). pp. 11094-11104.

Hammond, E. (2006) Review of the 7th International Workshop on adverse reactions and lipodystrophy in HIV. Dublin 2005 (Review). Nutrition and Metabolic Disorders in HIV Infection, 5 (1). pp. 899-908.

Mallal, S. (2006) Host genetics unplugged: Removing the camouflage of viral adaptation. Current Opinion in HIV and AIDS, 1 (3). pp. 218-219.

Martin, A., Nolan, D., Almeida, C., Rauch, A. and Mallal, S. (2006) Predicting and diagnosing abacavir and nevirapine drug hypersensitivity: from bedside to bench and back again. Pharmacogenomics, 7 (1). pp. 15-23.

Martins, I.J., Hone, E., Foster, J.K., S, S.I., Gnjec, A., Fuller, S.J., Nolan, D., Gandy, S.E. and Martins, R.N. (2006) Apolipoprotein E, cholesterol metabolism, diabetes, and the convergence of risk factors for Alzheimer's disease and cardiovascular disease. Molecular Psychiatry, 11 (8). pp. 721-736.

Nolan, D., Gaudieri, S. and Mallal, S. (2006) Host genetics and viral infections: Immunology taught by viruses, virology taught by the immune system. Current Opinion in Immunology, 18 (4). pp. 413-421.

Nolan, D., Phillips, E. and Mallal, S. (2006) Efavirenz and CYP2B6 polymorphism: Implications for drug toxicity and resistance. Clinical Infectious Diseases, 42 (3). pp. 408-410.

Pace, C., Keller, J., Nolan, D., James, I., Gaudieri, S., Moore, C. and Mallal, S. (2006) Population level analysis of human immunodeficiency virus type 1 hypermutation and its relationship with APOBEC3G and vif genetic variation. Journal of Virology, 80 (18). pp. 9259-9269.

Price, P., Keane, N.M., Lee, S., Lim, A.F.Y., McKinnon, E.J. and French, M.A. (2006) A T2 cytokine environment may not limit T1 responses in human immunodeficiency virus patients with a favourable response to antiretroviral therapy. Immunology, 119 (1). pp. 74-82.

2005

Allen, T.M., Altfeld, M., Geer, S.C., Kalife, E.T., Moore, C., O'Sullivan, K.M., DeSouza, I., Feeney, M.E., Eldridge, R.L., Maier, E.L., Kaufmann, D.E., Lahaie, M.P., Reyor, L., Tanzi, G., Johnston, M.N., Brander, C., Draenert, R., Rockstroh, J.K., Jessen, H., Rosenberg, E.S., Mallal, S.A. and Walker, B.D. (2005) Selective escape from CD8+ T-Cell responses represents a major driving force of Human Immunodeficiency Virus Type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution. Journal of Virology, 79 (21). pp. 13239-13249.

Allen, T.M., Yu, X.G., Kalife, E.T., Reyor, L.L., Lichterfeld, M., John, M., Cheng, M., Allgaier, R.L., Mui, S., Frahm, N., Alter, G., Brown, N.V., Johnston, M.N., Rosenberg, E.S., Mallal, S.A., Brander, C., Walker, B.D. and Altfeld, M. (2005) De Novo generation of escape Variant-specific CD8+ T-Cell responses following Cytotoxic T-Lymphocyte escape in chronic Human Immunodeficiency Virus Type 1 Infection. Journal of Virology, 79 (20). pp. 12952-12960.

Feeney, M.E., Tang, Y., Pfafferott, K., Roosevelt, K.A., Draenert, R., Trocha, A., Yu, X.G., Verrill, C., Allen, T., Moore, C., Mallal, S., Burchett, S., McIntosh, K., Pelton, S.I., St. John, M.A., Hazra, R., Klenerman, P., Altfeld, M., Walker, B.D. and Goulder, P.J.R. (2005) HIV-1 viral escape in infancy followed by emergence of a variant-specific CTL response. Journal of Immunology, 174 (12). pp. 7524-7530.

Gaudieri, S., DeSantis, D., McKinnon, E., Moore, C., Nolan, D., Witt, C.S., Mallal, S.A. and Christiansen, F.T. (2005) Killer immunoglobulin-like receptors and HLA act both independently and synergistically to modify HIV disease progression. Genes and Immunity, 6 (8). pp. 683-690.

Gaudieri, S., Lucas, M., Freitas, E., Naidoo, K., Park, L., Pfafferott, K., Moore, C., Jeffrey, G., Cheng, W., Rauch, A., Herrmann, S. and Mallal, S. (2005) Adaptation of Hepatitis C virus to HLA-restricted responses in an Australian host population. In: 12th International Symposium on Hepatitis C and Related Viruses, 2 - 6 October, Montreal, Canada.

Gaudieri, S., Nolan, D., McKinnon, E., Witt, C.S., Mallal, S. and Christiansen, F.T. (2005) Associations between KIR epitope combinations expressed by HLA-B/-C haplotypes found in an HIV-1 infected study population may influence NK mediated immune responses. Molecular Immunology, 42 (4). pp. 557-560.

Gillett, M.J., Cameron, P.U., Nguyen, H.V., Hurley, D.M. and Mallal, S.A. (2005) Iatrogenic Cushingʼs syndrome in an HIV-infected patient treated with ritonavir and inhaled fluticasone. AIDS, 19 (7). pp. 740-741.

John, M. and Mallal, S. (2005) CTL responses to HIV and SIV: wrestling with smoke. Nature Immunology, 6 (3). pp. 232-234.

John, M., Moore, C.B., James, I.R. and Mallal, S.A. (2005) Interactive selective pressures of HLA-restricted immune responses and antiretroviral drugs on HIV-1. Antiviral Therapy, 10 . pp. 551-555.

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, A.K., Moore, S., Mullins, J., Moore, C., Mallal, S., Bhardwaj, N., Yusim, K., Phillips, R., Klenerman, P., Korber, B., Kiepiela, P., Walker, B. and Goulder, P. (2005) Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. Journal of Experimental Medicine, 201 (6). pp. 891-902.

Lucas, A.D., Gaudieri, S., Rauch, A., Nolan, D. and Mallal, S. (2005) Cellular tropism of HIV-1 mediated and contrained by coreceptor dependencies. Journal of Viral Entry, 1 (1). pp. 17-27.

Martin, A.M., Nolan, D., James, I., Cameron, P., Keller, J., Moore, C., Phillips, E., Christiansen, F.T. and Mallal, S. (2005) Predisposition to nevirapine hypersensitivity associated with HLA-DRB1*0101 and abrogated by low CD4 T-cell counts. AIDS, 19 (1). pp. 97-99.

Martin, A.M., Nolan, D. and Mallal, S. (2005) HLA-B*5701 typing by sequence-specific amplification: validation and comparison with sequence-based typing. Tissue Antigens, 65 (6). pp. 571-574.

Nolan, D. (2005) Do non-nucleoside reverse transcriptase inhibitors contribute to lipodystrophy? Drug Safety, 28 (12). pp. 1069-1074.

Nolan, D., James, I. and Mallal, S. (2005) HIV/AIDS: HIV: Experiencing the pressures of modern life. Science, 307 (5714). pp. 1422-1424.

Nolan, D. and Mallal, S. (2005) Antiretroviral-therapy-associated lipoatrophy: current status and future directions. Sexual Health, 2 (3). pp. 153-163.

Nolan, D., Reiss, P. and Mallal, S. (2005) Adverse effects of antiretroviral therapy for HIV infection: a review of selected topics. Expert Opinion on Drug Safety, 4 (2). pp. 201-218.

Petoumenos, K., Ringland, C., Goodman, R., Gotowski, M., Couldwell, D., Lewis, L., Austin, D., Block, M., Quan, D., Gowers, A., Brown, K.R., Skobalj, N. and Mallal, S. (2005) Antiretroviral treatment change among HIV, hepatitis B virus and hepatitis C virus co-infected patients in the Australian HIV Observational Database. HIV Medicine, 6 (3). pp. 155-163.

Phillips, E.J., Wong, G., Kaul, R., Shahabi, K., Nolan, D., Knowles, S.R., Martin, A.M., Mallal, S. and Shear, N.H. (2005) Clinical and immunogenetic correlates of abacavir hypersensitivity. AIDS, 19 (9). pp. 979-981.

Vidal, F., Peraire, J., Domingo, P., Broch, M., Knobel, H., Pedrol, E., Dalmau, D., Viladés, C., Sambeat, M.A., Gutiérrez, C., Richart, C. and Mallal, S. (2005) Lack of association of SDF-1 3'A variant allele with long-term nonprogressive HIV-1 infection is extended beyond 16 years. JAIDS Journal of Acquired Immune Deficiency Syndromes, 40 (3). pp. 276-279.

Vidal, F., Viladés, C., Domingo, P., Broch, M., Pedrol, E., Dalmau, D., Knobel, H., Peraire, J., Gutiérrez, C., Sambeat, M., Fontanet, À., Deig, E., Cairó, M., Montero, M., Richart, C. and Mallal, S. (2005) Spanish HIV-1-infected long-term nonprogressors of more than 15 years have an increased frequency of the CX3CR1 249I variant allele. JAIDS Journal of Acquired Immune Deficiency Syndromes, 40 (5). pp. 527-531.

2004

Allen, T.M., Altfeld, M., Yu, X.G., O'Sullivan, K.M., Lichterfeld, M., Le Gall, S., John, M., Mothe, B.R., Lee, P.K., Kalife, E.T., Cohen, D.E., Freedberg, K.A., Strick, D.A., Johnston, M.N., Sette, A., Rosenberg, E.S., Mallal, S.A., Goulder, P.J.R., Brander, C. and Walker, B.D. (2004) Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in Human Immunodeficiency Virus Type 1 infection. Journal of Virology, 78 (13). pp. 7069-7078.

Hammond, E., Nolan, D., James, I., Metcalf, C. and Mallal, S. (2004) Reduction of mitochondrial DNA content and respiratory chain activity occurs in adipocytes within 6-12 months of commencing nucleoside reverse transcriptase inhibitor therapy. AIDS, 18 (5). pp. 815-817.

Herrmann, S., McKinnon, E. and Mallal, S. (2004) Combining adherence monitoring with patient education in the Royal Perth Hospital Immunology Outpatient Clinic. In: 16th Annual Conference of the Australasian Society for HIV Medicine, 2 - 4 September, Canberra, Australia.

Kiepiela, P., Leslie, A.J., Honeyborne, I., Ramduth, D., Thobakgale, C., Chetty, S., Rathnavalu, P., Moore, C.B., Pfafferott, K.J., Hilton, L., Zimbwa, P., Moore, S., Allen, T., Brander, C., Addo, M.M., Altfeld, M., James, I., Mallal, S., Bunce, M., Barber, L.D., Szinger, J., Day, C., Klenerman, P., Mullins, J., Korber, B., Coovadia, H.M., Walker, B.D. and Goulder, P.J.R. (2004) Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature, 432 (7018). pp. 769-775.

Martin, A.M., Nolan, D., Gaudieri, S., Almeida, C., James, I., Phillips, E. and Mallal, S. (2004) Predisposition to abacavir hypersensitivity conferred by HLA-B*5701 and a haplotypic Hsp70-Hom variant. Proceedings of the National Academy of Sciences, 101 (12). pp. 4180-4185.

Martin, A.M., Nolan, D., Gaudieri, S., Phillips, E. and Mallal, S. (2004) Pharmacogenetics of antiretroviral therapy: genetic variation of response and toxicity. Pharmacogenomics, 5 (6). pp. 643-655.

Martin, A.M., Smith, D., Carr, A., Hoy, J., Chuah, J., Mallal, S., Law, M., Clements, M. and Cooper , D.A. (2004) Progression of Lipodystrophy (LD) with continued thymidine analogue usage: Long-term Follow-Up from a randomized clinical trial (The PIILR Study). HIV Clinical Trials, 5 (4). pp. 192-200.

Nolan, D., Gaudieri, S., John, M. and Mallal, S. (2004) Impact of host genetics on HIV disease progression and treatment: New conflicts on an ancient battleground. AIDS, 18 (9). pp. 1231-1240.

Nolan, D. and Mallal, S. (2004) Complications associated with NRTI therapy: Update on clinical features and possible pathogenic mechanisms. Antiviral Therapy, 9 . pp. 849-863.

Nolan, D. and Mallal, S. (2004) The role of nucleoside reverse transcriptase inhibitors in the fat redistribution syndrome. Journal of HIV Therapy, 9 (2). pp. 34-40.

2003

Amin, J., Moore, A., Carr, A., French, M.A., Law, M., Emery, S., Cooper, D.A., Kotsiou, G., Norrito, L., Dwyer, D., Packham, D., Fordham, M., Garsia, R., Baker, D., Doong, N.C., Quan, D., Beveridge, A., Genn, W., Quin, J., Mulholland, J., Sowden, D., Rawlinsen, M., Rebic, D., Street, A., De Graaf, B., Roney, J., Bryant, M., McCormack, C., Hoy, J.N., Shaw, D.V., Ferguson, W., Waddell, R., Papanaoum, K., French, M.R., Scull, N., Todhunter, L., Mallal, S., James, R. and Foreman, E. (2003) Combined analysis of Two-Year Follow-up from two open-label randomized trials comparing efficacy of three nucleoside reverse transcriptase inhibitor backbones for previously untreated HIV-1 nfection: OzCombo 1 and 2. HIV Clinical Trials, 4 (4). pp. 252-261.

Christiansen, F.T., Gaudieri, S., Santis, D.D., Moore, C.B., Witt, C.S., James, I.R. and Mallal, S.A. (2003) NK receptor genes are predictors of HIV progression. Human Immunology, 64 (10). S12.

Hammond, E.L., Sayer, D., Nolan, D., Walker, U.A., de Ronde, A., Montaner, J.S.G., Côté, H.C.F., Gahan, M.E., Cherry, C.L., Wesselingh, S.L., Reiss, P. and Mallal, S. (2003) Assessment of precision and concordance of quantitative mitochondrial DNA assays: A collaborative international quality assurance study. Journal of Clinical Virology, 27 (1). pp. 97-110.

Herrmann, S., Hyland, N., Coombs, A., Turner, K., Duncan, F., McKinnon, E., James, I., Martinez, O.P., French, M. and Mallal, S. (2003) Adherence to antiretroviral therapy in the WA HIV Cohort. In: 15th Annual Conference of the Australian Society for HIV Medicine, 22 - 25 October, Cairns, Australia.

John, M., McKinnon, E.J., James, I.R., Nolan, D., Herrmann, S.E., Moore, C.B., White, A.J. and Mallal, S.A. (2003) Randomised, controlled, 48-week study of switching stavudine and/or protease inhibitors to Combavir/abacavir to prevent or reverse lipoatrophy in HIV-infected patients. JAIDS Journal of Acquired Immune Deficiency Syndromes, 33 (1). pp. 29-34.

Lincoln, D., Petoumenos, K., Dore, G.J., Finlayson, R., Clemons, J., Ellis, D., Baker, D., Kidd, J., McFarlane, R., Law, M., Smith, D., Huffam, D., Savage, J., Morgan, S., Knibbs, P., Rogers, G., Ree, H., Magon, H., Sowden, D., Walker, A., Orth, D., Lister, G.A., Chuah, J., James, R., Fankhauser, W., Dickson, B., Bradford, D., Wilson, C., Fairley, K., Roth, N., Eu, B., Strecker, S., Russell, D., Wood, H., Maijch, A., Hoy, J., Pierce, A., McCormack, C., Watson, K., Anderson, J.S., Moore, R., McGovern, G., McNair, R., Medland, N., Daye, J. and Mallal, S. (2003) HIV/HBV and HIV/HCV coinfection, and outcomes following highly active antiretroviral therapy. HIV Medicine, 4 (3). pp. 241-249.

Martin, A., Nolan, D., Gaudieri, S., Almeida, C., Carvalho, F., Witt, C., Sayer, D., Nolan, R., Herrmann, S., Christiansen, F. and Mallal, S. (2003) Updated experience of abacavir hypersensitivity genetic testing within the major histocompatibility complex (MHC): addressing diagnostic precision and predictive value. In: 5th International Workshop on Adverse Drug Reactions and Lipodystrophy in HIV, 8 - 11 July, Paris, France.

Martin, A.M., Hammond, E., Nolan, D., Pace, C., den Boer, M., Taylor, L., Moore, H., Martinez, O.P., Christiansen, F.T. and Mallal, S. (2003) Accumulation of mitochondrial DNA mutations in Human Immunodeficiency Virus–infected patients treated with Nucleoside-analogue Reverse-transcriptase inhibitors. American Journal of Human Genetics, 72 (3). pp. 549-560.

McKinnon, E.J., James, I.R., John, M. and Mallal, S.A. (2003) Viral load detectability profiles for HIV infection. Statistics in Medicine, 22 (3). pp. 385-396.

Miller, J., Carr, A., Emery, S., Law, M., Mallal, S., Baker, D., Smith, D., Kaldor, J. and Cooper, D.A. (2003) HIV lipodystrophy: Prevalence, severity and correlates of risk in Australia. HIV Medicine, 4 (3). pp. 293-301.

Nolan, D., Gaudieri, S. and Mallal, S. (2003) Pharmacogenetics: A practical role in predicting antiretroviral drug toxicity? Journal of HIV therapy, 8 (2). pp. 36-41.

Nolan, D., Hammond, E., James, I., McKinnon, E. and Mallal, S. (2003) Contribution of nucleoside-analogue reverse transcriptase inhibitor therapy to lipoatrophy from the population to the cellular level. Antiviral Therapy, 8 . pp. 617-626.

Nolan, D., Hammond, E., Martin, A., Taylor, L., Herrmann, S., McKinnon, E., Metcalf, C., Latham, B. and Mallal, S. (2003) Mitochondrial DNA depletion and morphologic changes in adipocytes associated with nucleoside reverse transcriptase inhibitor therapy. AIDS, 17 (9). pp. 1329-1338.

Nolan, D. and Mallal, S. (2003) Thymidine analogue-sparing highly active antiretroviral therapy (HAART). Journal of HIV therapy, 8 (1). pp. 1-5.

Nolan, D., Moore, C., Castley, A., Sayer, D., Marmotte, C., John, M., James, I. and Mallal, S. (2003) Tumour necrosis factor-alpha gene -238G/A promoter polymorphism associated with a more rapid onset of lipodystrophy. AIDS, 17 (1). pp. 121-123.

Nolan, D., Watts, G.F., Herrmann, S.E., French, M.A., John, M. and Mallal, S. (2003) Endothelial function in HIV-infected patients receiving protease inhibitor therapy: does immune competence affect cardiovascular risk? QJM, 96 (11). pp. 825-832.

Nolan, R., Martin, A.M., Nolan, D., Gaudieri, S., Almeida, C., Carvalho, F., Witt, C., Sayer, D., Herrmann, S., Christiansen, F.T. and Mallal, S. (2003) Abacavir Hypersensitivity Syndrome: Clarifying genetic associations by including the presence of an abacavir specific immune response in diagnostic criteria. In: 15th Annual Conference of the Australian Society for HIV Medicine, 22 - 25 October, Cairns, Australia.

Pace, C.S., Martin, A.M., Hammond, E.L., Mamotte, C.D.S., Nolan, D.A. and Mallal, S.A. (2003) Mitochondrial proliferation, DNA depletion and adipocyte differentiation in subcutaneous adipose tissue of HIV-positive HAART recipients. Antiviral Therapy, 8 . pp. 323-331.

Telenti, A., Beckmann, J.S. and Mallal, S. (2003) HLA and HIV: Modeling adaptation to moving targets. The Pharmacogenomics Journal, 3 (5). pp. 254-256.

2002

Christiansen, F.T., John, M., James, I.R., Witt, C.S. and Mallal, S.A. (2002) Immune escape mutations in HIV-1 sequence: the influence of HLA class I and II alleles in a host population on viral evolution. Human Immunology, 63 (10). S35.

John, M. and Mallal, S. (2002) Hyperlactatemia syndromes in people with HIV infection. Current Opinion in Infectious Diseases, 15 (1). pp. 23-29.

Mallal, S., Nolan, D., Witt, C., Masel, G., Martin, A.M., Moore, C., Sayer, D., Castley, A., Mamotte, C., Maxwell, D., James, I. and Christiansen, F.T. (2002) Association between presence of HLA-B*5701, HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. The Lancet, 359 (9308). pp. 727-732.

Moore, C.B., John, M., James, I.R., Christiansen, F.T., Witt, C.S. and Mallal, S. (2002) Evidence of HIV-1 Adaptation to HLA-Restricted Immune Responses at a Population Level. Science, 296 (5572). pp. 1439-1443.

Petoumenos, K., Austin, D., Baker, D., Block, M., Brown, K., Carr, A., Cooper, D., Couldwell, D., Ellis, D., Finlayson, R., Gorton, C., Gowers, A., Keeffe, N., Kidd, J., Law, M., Liang, M.T., McFarlane, R., Mutimer, K., Miller, J., O'Connor, C., Quan, D., Rooney, P., Taylor, S., Smith, D., Wheatley, D., Knibbs, P., Huffam, S., Morgan, S., Savage, J., Bradford, D., Chuah, J., Dickson, B., Fankhauser, W., Lister, G., Magon, H., Orth, D., Rawlinson, M., Ree, H., Sowden, D., Walker, A., Wilson, C., Anderson, J., Bal, J., Daye, J., Eu, B., Fairely, C.K., Hoy, J., McCormack, C., McGovern, G., McNair, R., Medland, N., Mijch, A., Moore, R., Pierce, A., Roth, N., Russell, D., Strecker, S., Watson, K., Wood, H., Cain, A., French, M., Mallal, S., Maxwell, D., Moore, C. and Skett, J. (2002) Rates of combination antiretroviral treatment change in Australia, 1997-2000. HIV Medicine, 3 (1). pp. 28-36.

2001

Carr, A., Hudson, J., Chuah, J., Mallal, S., Law, M., Hoy, J., Doong, N., French, M., Smith, D. and Cooper, D.A. (2001) HIV protease inhibitor substitution in patients with lipodystrophy: A randomized, controlled, open-label, multicentre study. AIDS, 15 (14). pp. 1811-1822.

Ioannidis, J.P.A., Rosenberg, P.S., Goedert, J.J., Ashton, L.J., Benfield, T.L., Buchbinder, S.P., Coutinho, R.A., Eugen-Olsen, J., Gallart, T., Katzenstein, T.L., Kostrikis, L.G., Kuipers, H., Louie, L.G., Mallal, S.A., Margolick, J.B., Martinez, O.P., Meyer, L., Michael, N.L., Operskalski, E., Pantaleo, G., Rizzardi, G.P., Schuitemaker, H., Sheppard, H.W., Stewart, G.J., Theodorou, I.D., Ullum, H., Vicenzi, E., Vlahov, D., Wilkinson, D., Workman, C., Zagury, J-F and O'Brien, T.R. (2001) Effects of CCR5-Δ 32, CCR2-64I, and SDF-1 3′A Alleles on HIV-1 Disease Progression: An International Meta-Analysis of Individual-Patient Data. Annals of Internal Medicine, 135 (9). pp. 782-795.

John, M., Moore, C.B., James, I.R., Nolan, D., Upton, R.P., McKinnon, E.J. and Mallal, S.A. (2001) Chronic hyperlactatemia in HIV-infected patients taking antiretroviral therapy. AIDS, 15 (6). pp. 717-723.

John, M., Nolan, D. and Mallal, S. (2001) Antiretroviral therapy and the lipodystrophy syndrome. Antiviral Therapy, 6 . pp. 9-20.

Murray, R., Mallal, S., Heath, C. and French, M. (2001) Cerebral mycobacterium avium infection in an HIV-Infected patient following immune reconstitution and cessation of therapy for disseminated mycobacterium avium complex infection. European Journal of Clinical Microbiology and Infectious Diseases, 20 (3). pp. 199-201.

Nolan, D., John, M. and Mallal, S. (2001) Antiretoviral therapy and the lipodystrophy syndrome, part 2: Concepts in aetiopathogenesis. Antiviral Therapy, 6 . pp. 145-160.

Nolan, D. and Mallal, S. (2001) Effects of sex and race on lipodstrophy pathogenesis. Journal of HIV therapy, 6 (1). pp. 32-36.

Nolan, D. and Mallal, S. (2001) Getting to the HAART of insulin resistance. AIDS, 15 (15). pp. 2037-2041.

Nolan, D., Upton, R., McKinnon, E., John, M., James, I., Adler, B., Roff, G., Vasikaran, S. and Mallal, S. (2001) Stable or increasing bone mineral density in HIV-infected patients treated with nelfinavir or indinavir. AIDS, 15 (10). pp. 1275-1280.

Rooney, P., Taylor, S., Couldwell, D., Austin, D., Block, M., Quan, D., Gowers, A., O'Conner, C., Gorton, C., Allen, D., Mulhall, B., Mutimer, K., Smith, D., Keeffe, N., Cooper, D., Carr, A., Miller, J., Finlayson, R., Wheatley, D., Ellis, D., Baker, D., Kidd, J., McFarlane, R., Liang, M.T., Brown, K., Petoumenos, K., Law, M., Huffam, S., Savage, J., Morgan, S., Knibbs, P., Sowden, D., Rawlinson, M., Walker, A., Orth, D., Lister, G., Chuah, J., Fankhauser, W., Dickson, B., Bradford, D., Wilson, C., Ree, H., Magon, H., Fairley, C.K., Roth, N., Eu, B., Strecker, S., Russel, D., Wood, H., Mijch, A., Hoy, J., Pierce, A., McCormack, C., Watson, K., Anderson, J., Moore, R., Russell, D., McGovern, G., McNair, R., Bal, J., Medland, N., Daye, J., Mallal, S., French, M., Skett, J., Moore, C., Maxwell, D. and Cain, A. (2001) Time trends in antiretroviral treatment use in Australia, 1997-2000. Venereology, 14 (4). pp. 162-168.