Publications: Gaudieri, Silvana

Journal Article

Waters, S., Lee, S., Ariyanto, I., Kresoje, N., Leary, S., Munyard, K., Gaudieri, S., Irish, A., Keil, A.D., Allcock, R.J.N. and Price, P. (2022) Sequencing of the viral UL111a gene directly from clinical specimens reveals variants of HCMV-encoded IL-10 that are associated with altered immune responses to HCMV. International Journal of Molecular Sciences, 23 (9). Article 4644.

Waters, S., Lee, S., Ariyanto, I., Leary, S., Munyard, K., Gaudieri, S., Irish, A., Allcock, R.J.N. and Price, P. (2022) Variants of HCMV UL18 sequenced directly from clinical specimens associate with antibody and T-cell responses to HCMV. International Journal of Molecular Sciences, 23 (21). Article 12911.

Currenti, J., Law, B.M.P., Qin, K., John, M., Pilkinton, M.A., Bansal, A., Leary, S., Ram, R., Chopra, A., Gangula, R., Yue, L., Warren, C., Barnett, L., Alves, E., McDonnell, W.J., Sooda, A., Heath, S.L., Mallal, S., Goepfert, P., Kalams, S.A. and Gaudieri, S. (2021) Cross-Reactivity to mutated viral immune targets can influence CD8+ T cell functionality: An alternative viral adaptation strategy. Frontiers in Immunology, 12 . Art. 746986.

Leary, S., Gaudieri, S., Parker, M.D., Chopra, A., James, I., Pakala, S., Alves, E., John, M., Lindsey, B.B., Keeley, A.J., Rowland-Jones, S.L., Swanson, M.S., Ostrov, D.A., Bubenik, J.L., Das, S.R., Sidney, J., Sette, A., de Silva, T.I., Phillips, E. and Mallal, S. (2021) Generation of a novel SARS-CoV-2 Sub-genomic RNA due to the R203K/G204R variant in Nucleocapsid: Homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level. Pathogens and Immunity, 6 (2). pp. 27-49.

Pilkinton, M.A., McDonnell, W.J., Barnett, L., Chopra, A., Gangula, R., White, K.D., Leary, S., Currenti, J., Gaudieri, S., Mallal, S.A., Kalams, S.A. and Silvestri, G. (2021) In chronic infection, HIV Gag-Specific CD4+ T cell receptor diversity is higher than CD8+ T cell receptor diversity and is associated with Less HIV quasispecies diversity. Journal of Virology, 95 (8). Art. e02380-20.

Alves, E., McLeish, E., Blancafort, P., Coudert, J.D. and Gaudieri, S. (2021) Manipulating the NKG2D receptor-ligand axis using CRISPR: Novel technologies for improved host immunity. Frontiers in Immunology, 12 . Article 712722.

Alves, E., Taifour, S., Dolcetti, R., Chee, J., Nowak, A.K., Gaudieri, S. and Blancafort, P. (2021) Reprogramming the anti-tumor immune response via CRISPR genetic and epigenetic editing. Molecular Therapy - Methods & Clinical Development, 21 (11). pp. 592-606.

Waters, S., Agostino, M., Lee, S., Ariyanto, I., Kresoje, N., Leary, S., Munyard, K., Gaudieri, S., Gaff, J., Irish, A., Keil, A.D., Price, P., Allcock, R.J.N. and Campos, S.K. (2021) Sequencing directly from clinical specimens reveals genetic variations in HCMV-Encoded Chemokine Receptor US28 that may influence antibody levels and interactions with human chemokines. Microbiology Spectrum, 9 (2). Art. e00020-21.

Parker, M.D., Lindsey, B.B., Leary, S., Gaudieri, S., Chopra, A., Wyles, M., Angyal, A., Green, L.R., Parsons, P., Tucker, R.M., Brown, R., Groves, D., Johnson, K., Carrilero, L., Heffer, J., Partridge, D.G., Evans, C., Raza, M., Keeley, A.J., Smith, N., Filipe, A.D., Shepherd, J.G., Davis, C., Bennett, S., Sreenu, V.B., Kohl, A., Aranday-Cortes, E., Tong, L., Nichols, J., Thomson, E.C., Wang, D., Mallal, S. and de Silva, T.I. (2021) Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31 (4). pp. 645-658.

Ruknarong, L., Boonthongkaew, C., Chuangchot, N., Jumnainsong, A., Leelayuwat, N., Jusakul, A., Gaudieri, S. and Leelayuwat, C. (2021) Vitamin C supplementation reduces expression of circulating miR-451a in subjects with poorly controlled type 2 diabetes mellitus and high oxidative stress. PeerJ, 9 . Art. e10776.

Deshpande, P., Bundell, C., McKinnon, E., Hellard, M., Ffrench, R., Wilkinson, A.L., Drummer, H., Gaudieri, S. and Lucas, M. (2020) Frequent occurrence of low-level positive autoantibodies in chronic hepatitis C. Pathology, 52 (5). pp. 576-583.

Pavlos, R., Deshpande, P., Chopra, A., Leary, S., Strautins, K., Nolan, D., Thorborn, D., Shaefer, M., Rauch, A., Dunn, D., Montaner, J., Rachlis, A., Almeida, C.M., Choo, L., James, I., Redwood, A.J., Li, Y., Gaudieri, S., Mallal, S.A. and Phillips, E.J. (2020) New genetic predictors for abacavir tolerance in HLA-B*57:01 positive individuals. Human Immunology, 81 (6). pp. 300-304.

Currenti, J., Chopra, A., John, M., Leary, S., McKinnon, E., Alves, E., Pilkinton, M., Smith, R., Barnett, L., McDonnell, W.J., Lucas, M., Noel, F., Mallal, S., Conrad, J.A., Kalams, S.A. and Gaudieri, S. (2019) Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV. PLoS Pathogens, 15 (12).

Gaudieri, S., Currenti, J., John, M., McKinnon, E., Leary, S., Chopra, A., Pilkington, M., Smith, R., Barnett, L., McDonnell, W., Lucas, M., Mallal, S., Conrad, J. and Kalams, S. (2019) Deep sequence analysis of HIV adaptation following vertical transmission: Importance of human leucocyte antigen-driven selection on the evolution of HIV. Journal of the International AIDS Society, 22 (S5). p. 39.

Nutalai, R., Gaudieri, S., Jumnainsong, A. and Leelayuwat, C. (2019) Regulation of KIR3DL3 Expression via miRNA. Genes, 10 (8). p. 603.

Gu, J., Hardy, J., Boo, I., Vietheer, P., McCaffrey, K., Alhammad, Y., Chopra, A., Gaudieri, S., Poumbourios, P., Coulibaly, F., Drummer, H.E. and Diamond, M.S. (2018) Escape of Hepatitis C virus from Epitope I neutralization increases sensitivity of other neutralization epitopes. Journal of Virology, 92 (9). e02066-17.

Lucas, M., Deshpande, P., James, I., Rauch, A., Pfafferott, K., Gaylard, E., Merani, S., Plauzolles, A., Lucas, A., McDonnell, W., Kalams, S., Pilkinton, M., Chastain, C., Barnett, L., Prosser, A., Mallal, S., Fitzmaurice, K., Drummer, H., Ansari, M.A., Pedergnana, V., Barnes, E., John, M., Kelleher, D., Klenerman, P. and Gaudieri, S. (2018) Evidence of CD4+ T cell-mediated immune pressure on the Hepatitis C virus genome. Scientific Reports, 8 . Article number: 7224.

Karnes, J.H., Shaffer, C.M., Bastarache, L., Gaudieri, S., Glazer, A.M., Steiner, H.E., Mosley, J.D., Mallal, S., Denny, J.C., Phillips, E.J. and Roden, D.M. (2017) Comparison of HLA allelic imputation programs. PLoS ONE, 12 (2).

Abana, C.O., Pilkinton, M.A., Gaudieri, S., Chopra, A., McDonnell, W.J., Wanjalla, C., Barnett, L., Gangula, R., Hager, C., Jung, D.K., Engelhardt, B.G., Jagasia, M.H., Klenerman, P., Phillips, E.J., Koelle, D.M., Kalams, S.A. and Mallal, S.A. (2017) Cytomegalovirus (CMV) Epitope–Specific CD4 + T Cells Are Inflated in HIV + CMV + Subjects. The Journal of Immunology, 199 (9). pp. 3187-3201.

Karnes, J.H., Shaffer, C.M., Cronin, R., Bastarache, L., Gaudieri, S., James, I., Pavlos, R., Steiner, H., Mosley, J.D., Mallal, S., Denny, J.C., Phillips, E.J. and Roden, D.M. (2017) Influence of human leukocyte antigen (HLA) alleles and killer cell immunoglobulin-like receptors (KIR) types on heparin-induced thrombocytopenia (HIT). Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy, 37 (9). pp. 1164-1171.

Merani, S., Lucas, M., Deshpande, P., Pfafferott, K., Chopra, A., Cooper, D., Leary, S., Luciani, F. and Gaudieri, S. (2017) Influence of transmitted virus on the host's immune response: A case study. Viral Immunology, 30 (7).

Gaudieri, S. and Lucas, M. (2017) Innate and adaptive immunity shape circulating HCV strains. Nature Genetics, 49 (5). pp. 657-658.

Karnes, J.H., Bastarache, L., Shaffer, C.M., Gaudieri, S., Xu, Y., Glazer, A.M., Mosley, J.D., Zhao, S., Raychaudhuri, S., Mallal, S., Ye, Z., Mayer, J.G., Brilliant, M.H., Hebbring, S.J., Roden, D.M., Phillips, E.J. and Denny, J.C. (2017) Phenome-wide scanning identifies multiple diseases and disease severity phenotypes associated with HLA variants. Science Translational Medicine, 9 (389). eaai8708.

Styles, C.E., Seed, C.R., Hoad, V.C., Gaudieri, S. and Keller, A.J. (2017) Reconsideration of blood donation testing strategy for human T-cell lymphotropic virus in Australia. Vox Sanguinis, 112 (8). pp. 723-732.

Pavlos, R., McKinnon, E.J., Ostrov, D.A., Peters, B., Buus, S., Koelle, D., Chopra, A., Schutte, R., Rive, C., Redwood, A., Restrepo, S., Bracey, A., Kaever, T., Myers, P., Speers, E., Malaker, S.A., Shabanowitz, J., Jing, Y., Gaudieri, S., Hunt, D.F., Carrington, M., Haas, D.W., Mallal, S. and Phillips, E.J. (2017) Shared peptide binding of HLA Class I and II alleles associate with cutaneous nevirapine hypersensitivity and identify novel risk alleles. Scientific Reports, 7 (1).

Magaret, A., Dong, L., John, M., Mallal, S.A., James, I., Warren, T., Gaudieri, S., Koelle, D.M. and Wald, A. (2016) HLA Class I and II alleles, heterozygosity and HLA-KIR interactions are associated with rates of genital HSV shedding and lesions. Genes and Immunity, 17 (7). pp. 412-418.

Castley, A.S.L., Gaudieri, S., James, I., Gizzarelli, L.S., Guelfi, G., John, M. and Nolan, D. (2016) Longitudinal Trends in Western Australian HIV-1 Sequence Diversity and Viral Transmission Networks and Their Influence on Clinical Parameters: 2000–2014. AIDS Research and Human Retroviruses, 32 (3). pp. 211-219.

Barnard, R., Chopra, A., James, I., Blinco, J., Watson, M.W.ORCID: 0000-0002-6438-9225, Jabara, C.B., Hazuda, D., Lemon, S.M., Mallal, S. and Gaudieri, S. (2016) Primer ID ultra-deep sequencing reveals dynamics of drug resistance-associated variants in breakthrough hepatitis C viruses: Relevance to treatment outcome and resistance screening. Antiviral Therapy, 21 . pp. 567-577.

von Delft, A., Humphreys, I.S., Brown, A., Pfafferott, K., Lucas, M., Klenerman, P., Lauer, G.M., Cox, A.L., Gaudieri, S. and Barnes, E. (2016) The broad assessment of HCV genotypes 1 and 3 antigenic targets reveals limited cross-reactivity with implications for vaccine design. Gut, 65 (1). pp. 112-123.

Shoukry, N.H., Lucas, A., Lucas, M., Strhyn, A., Keane, N.M., McKinnon, E., Pavlos, R., Moran, E.M., Meyer-Pannwitt, V., Gaudieri, S., D’Orsogna, L., Kalams, S., Ostrov, D.A., Buus, S., Peters, B., Mallal, S. and Phillips, E. (2015) Abacavir-Reactive memory T Cells are present in drug naïve individuals. PLoS ONE, 10 (2). e0117160.

Shin, E-C, Pfafferott, K., Deshpande, P., McKinnon, E., Merani, S., Lucas, A., Heckerman, D., Mallal, S., John, M., Gaudieri, S. and Lucas, M. (2015) Anti-Hepatitis C virus T-Cell immunity in the context of multiple exposures to the virus. PloS one, 10 (6). e0130420.

Strock, S.B., Gaudieri, S., Mallal, S., Yu, C., Mitchell, D., Cogan, J., Mason, W., Crowe, D. and Loyd, J.E. (2015) Fibrosing mediastinitis complicating prior histoplasmosis is associated with human leukocyte antigen DQB1*04:02 − a case control study. BMC Infectious Diseases, 15 (1).

Loh, J.T., Gaddy, J.A., Algood, H.M.S., Gaudieri, S., Mallal, S. and Cover, T.L. (2015) Helicobacter pylori adaptation in vivoin response to a high salt diet. Infection and Immunity .

Gaudieri, S., Plauzolles, A. and Lucas, M. (2015) Influence of host resistance on viral adaptation: hepatitis C virus as a case study. Infection and Drug Resistance, 8 . pp. 63-74.

Bull, R.A., Leung, P., Gaudieri, S., Deshpande, P., Cameron, B., Walker, M., Chopra, A., Lloyd, A.R. and Luciani, F. (2015) Transmitted/founder viruses rapidly escape from CD8+T cell responses in acute hepatitis C virus infection. Journal of Virology, 89 (10). pp. 5478-5490.

John, M. and Gaudieri, S. (2014) Influence of HIV and HCV on T cell antigen presentation and challenges in the development of vaccines. Frontiers in Microbiology, 5 (art. 514). pp. 1-6.

Applegate, T.L., Gaudieri, S., Plauzolles, A., Chopra, A., Grebely, J., Lucas, M., Hellard, M., Luciani, F., Dore, G.J. and Matthews, G.V. (2014) Naturally occurring dominant drug resistance mutations occur infrequently in the setting of recently acquired hepatitis C. Antiviral Therapy, 20 (2). pp. 199-208.

White, K. and Gaudieri, S. (2014) New hope for biomarkers in the practice of infectious diseases medicine. Biomarkers in Medicine, 8 (9). pp. 1049-1051.

Nitschke, K., Barriga, A., Schmidt, J., Timm, J., Viazov, S., Kuntzen, T., Kim, A.Y., Lauer, G.M., Allen, T.M., Gaudieri, S., Rauch, A., Lange, C.M., Sarrazin, C., Eiermann, T., Sidney, J., Sette, A., Thimme, R., López, D. and Neumann-Haefelin, C. (2013) HLA-B∗27 subtype specificity determines targeting and viral evolution of a hepatitis C virus-specific CD8+ T cell epitope. Journal of Hepatology, 60 (1). pp. 22-29.

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.

Lucas, M. and Gaudieri, S. (2013) The role of biomarkers in the prevention of globally important diseases. Biomarkers in Medicine, 7 (3). pp. 331-332.

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.

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.

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). pp. 407-413.

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.

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.

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.

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.

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.

Suppiah, V., Gaudieri, S., Armstrong, N.J.ORCID: 0000-0002-4477-293X, 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.

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.

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.

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.

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.

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.

Hilner, J. E., Perdue, L. H., Sides, E. G., Pierce, J. J., Wagner, A. M., Aldrich, A., Loth, A., Albret, L., Wagenknecht, L. E., Nierras, C., Akolkar, B., Gaudieri, S., James, I., McKinnon, E. and Nolan, D. (2010) Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC). Clinical Trials, 7 (1 Suppl). S5-S32.

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.

Liu, S., Floess, S., Hamann, A., Gaudieri, S., Lucas, A., Hellard, M., Roberts, S., Paukovic, G., Plebanski, M., Loveland, B.E., Aitken, C., Barry, S., Schofield, L. and Gowans, E.J. (2009) Analysis of FOXP3+ Regulatory T Cells That Display Apparent Viral Antigen Specificity during Chronic Hepatitis C Virus Infection. PLoS Pathogens, 5 (12). e1000707.

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.

Humphreys, I., Fleming, V., Fabris, P., Parker, J., Schulenberg, B., Brown, A., Demetriou, C., Gaudieri, S., Pfafferott, K., Lucas, M., Collier, J., Huang, K.-H. G., Pybus, O. G., Klenerman, P. and Barnes, E. (2009) Full-Length Characterization of Hepatitis C Virus Subtype 3a Reveals Novel Hypervariable Regions under Positive Selection during Acute Infection. Journal of Virology, 83 (22). pp. 11456-11466.

Barrett, J.C., Clayton, D.G., Concannon, P., Akolkar, B., Cooper, J.D., Erlich, H.A., Julier, C., Morahan, G., Nerup, J., Nierras, C., Plagnol, V., Pociot, F., Schuilenburg, H., Smyth, D.J., Stevens, H., Todd, J.A., Walker, N.M., Rich, S.S., Gaudieri, S., James, I., McKinnon, E. and Nolan, D. (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics, 41 (6). pp. 703-707.

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.

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.

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.

Dong, T., Zhang, Y., Xu, K., Yan, H., James, I., Peng, Y., Blais, M., Gaudieri, S., Chen, X., Lun, W., Wu, H., Qu, W., Zhao, C., Li, N., Mao, Y., Rostron, T., Mallal, S., Xu, X., McMichael, A., John, M. and Rowland-Jones, S. (2009) P20-19 LB. Extensive HLA-driven viral diversity following a single-source HIV-1 outbreak in rural China. Retrovirology, 6 (Suppl 3). P423.

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., 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.

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.

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.

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.

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.

Pace, C., Keller, J., Nolan, D., James, I., Gaudieri, S., Moore, C. and Mallal, S. (2007) Erratum: Population level analysis of human immunodeficiency virus type 1 hypermutation and its relationship with APOBEC3G and vif genetic variation (Journal of Virology (2006) 80, 18, (9259-9269)). Journal of Virology, 81 (16). pp. 8843-8845.

Laird, R., Schneider, P.M. and Gaudieri, S. (2007) Forensic STRs as potential disease markers: A study of VWA and von Willebrand's Disease. Forensic Science International: Genetics, 1 (3-4). pp. 253-261.

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.

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.

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.

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.

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.

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

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.

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.

Ogasawara, M., Imanishi, T., Moriwaki, K., Gaudieri, S., Tsuda, H., Hashimoto, H., Shiroishi, T., Gojobori, T. and Koide, T. (2005) Length variation of CAG/CAA triplet repeats in 50 genes among 16 inbred mouse strains. Gene, 349 . pp. 107-119.

Laird, R., Dawkins, R.L. and Gaudieri, S. (2005) Use of the genomic matching technique to complement multiplex STR profiling reduces DNA profiling costs in high volume crimes and intelligence led screens. Forensic Science International: Genetics, 151 (2-3). pp. 249-257.

McLure, C.A., Dawkins, R.L., Williamson, J.F., Davies, R.A, Berry, J., Longman-Jacobsen, N., Laird, R. and Gaudieri, S. (2004) Amino Acid Patterns Within Short Consensus Repeats Define Conserved Duplicons Shared by Genes of the RCA Complex. Journal of Molecular Evolution, 59 (2). pp. 143-157.

Martin, A.M., Kulski, J.K., Gaudieri, S., Witt, C.S., Freitas, E.M., Trowsdale, J. and Christiansen, F.T. (2004) Comparative genomic analysis, diversity and evolution of two KIR haplotypes A and B. Gene, 335 . pp. 121-131.

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.

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., 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.

Christiansen, F., Moore, C.B., De Santis, D., Gaudieri, S., Witt, C.S., James, I.R. and Mallal, S.A. (2003) HLA and NK receptor genes in HIV progression. Genes and Immunity, 4 (S1). S6.

Meyer, M., Gaudieri, S., Rhodes, D.A. and Trowsdale, J. (2003) Cluster of TRIM genes in the human MHC class I region sharing the B30.2 domain. Tissue Antigens, 61 (1). pp. 63-71.

Longman-Jacobsen, N., Williamson, J.F., Dawkins, R.L. and Gaudieri, S. (2003) In polymorphic genomic regions indels cluster with nucleotide polymorphism: Quantum Genomics. Gene, 312 . pp. 257-261.

Harvey, M.L., Dadour, I.R. and Gaudieri, S. (2003) Mitochondrial DNA cytochrome oxidase I gene: potential for distinction between immature stages of some forensically important fly species (Diptera) in western Australia. Forensic Science International: Genetics, 131 (2-3). pp. 134-139.

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.

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.

Kulski, J.K., Dunn, D.S., Gaudieri, S., Shiina, T. and Inoko, H. (2001) Genomic and phylogenetic analysis of the human CD1 and HLA class I multicopy genes. Journal of Molecular Evolution, 53 (6). pp. 642-650.

Kok, C.C., Boyt, A., Gaudieri, S., Martins, R., Askanas, V., Dalakas, M., Kiers, L., Mastaglia, F. and Garleep, M. (2000) Mitochondrial DNA variants in inclusion body myositis. Neuromuscular Disorders, 10 (8). pp. 604-611.

Kulski, J.K., Gaudieri, S., Bellgard, M., Balmer, L., Giles, K., Inoko, H. and Dawkins, R.L. (1997) The evolution of MHC diversity by segmental duplication and transposition of retroelements. Journal of Molecular Evolution, 45 (6). pp. 599-609.

Non-refereed Article

Leary, S., Gaudieri, S., Parker, M.D., Chopra, A., James, I., Pakala, S., Alves, E., John, M., Lindsey, B.B., Keeley, A.J., Rowland-Jones, S.L., Swanson, M.S., Ostrov, D.A., Bubenik, J.L., Das, S., Sidney, J., Sette, A., de Silva, T.I., Phillips, E. and Mallal, S. (2021) Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and RNA level. bioRxiv: The preprint server for Biology .

Conference Paper

Chopra, A., Cooper, D., Sharma, L., Plauzolles, A., Watson, M.ORCID: 0000-0002-6438-9225, Rauch, A., Gaudieri, S. and Mallal, S. (2013) KIR Genotyping using a real time assay and FLX 454. In: 23rd Annual Combined Biological Sciences Meeting (CBSM) 2013, 30 August 2013, University of Western Australia, Perth

Tschochner, M., Rohrbach, J., Cooper, D., Merani, S., Chopra, A., Witteck, A., Battegay, M., Furrer, H., Günthard, H., Mallal, S., Rauch, A. and Gaudieri, S. (2010) Characterisation of hepatitis C virus evolution in HIV/HCV coinfected individuals using deep sequencing technology: Relevance for new antiviral drugs and disease outcome. In: 22nd Annual Conference of the Australasian Society for HIV Medicine, 20 - 22 October 2010, Sydney, Australia

John, M., Heckerman, D., Park, L., Gaudieri, S., Chopra, A., Carlson, J.M., James, I., Nolan, D., Haubrich, R. and Mallal, S. (2008) Genome-wide HLA-associated-selection in HIV-1 and protein-specific correlations with viral load: An ACTG5142 study. In: 15th Conference on Retroviruses and Opportunistic Infections (CROI), 3 - 6 February 2008, Boston, U.S.A

Christiansen, F.T., Gaudieri, S., De Santis, D., Witt, C.S., James, I.R. and Mallal, S. (2002) NK receptor genes are predictors of HIV progression. In: 28th Annual Meeting of the American Society for Histocompatibility and Immunogenetics, 19 - 23 October 2002, Nashville, TN

Conference Item

Chopra, A., Gaudieri, S., Pilkington, M., Blinco, J., Leary, S., Cooper, D., Abana, C., Watson, M.ORCID: 0000-0002-6438-9225, Kalams, S. and Mallal, S. (2016) Cutting edge tools for phenotyping and characterising T-Cell subsets. In: Science on the Swan 2016, 2 - 5 May 2016, Perth, Western Australia.

John, M., Gaudieri, S., Chopra, A., Leary, S., Jorritsma, J., Mallal, S., Baraki, B., Brockman, M.A. and Brumme, Z.L. (2016) HIV-1 residues under strong functional constraint are predicted by measures of evolutionary rather than population-level genetic conservation. In: 25th Conference of the Canadian Association for HIV Research (CAHR) 2016, 12-15 May 2016, Winnipeg, Manitoba, Canada.

Gaudieri, S., Chopra, A., Leary, S., Clark, H., Mallal, S., Baraki, B., Brockman, M., Brumme, Z.L. and John, M. (2016) Identifying sites of “Deep Conservation" in HIV-1 for vaccine immunogen design. In: Science on the Swan 2016, 2 - 5 May 2016, Perth, Western Australia.

Pavlos, R., McKinnon, E., Ostrov, D., Peters, B., Buus, S., Koelle, D., Chopra, A., Rive, C., Redwood, A., Restrepo, S., Bracey, A., Yuan, J., Gaudieri, S., Carrington, M., Haas, D., Mallal, S. and Phillips, E. (2016) Specific binding characteristics Of HLA Alleles associated with nevirapine hypersensitivity. In: 7th Drug Hypersensitivity Meeting (DHM) 2016, 21 - 23 April 2016, Malaga, Spain.

Gaudieri, S. (2016) T cells: TCR sequencing, transcriptomics and transfectomas. In: Science on the Swan Post Conference Workshop: Cutting Edge tools: from populations to signal cell., 6 May 2016, Perth, WA.

Chopra, A., Gaudieri, S., Clark, H., Blinco, J., Cooper, D., Leary, S., Watson, M.ORCID: 0000-0002-6438-9225 and Mallal, S. (2015) Cutting edge tools for Phenotyping and characterising T-Cell subsets. In: Science on the Swan, 21 - 23 April 2015, Perth, Western Australia.

Chopra, A., Mpunga, T. and Gaudieri, S. (2015) Differential gene expression profiling of NK cells. In: Science on the Swan, 21 - 23 April 2015, Perth, Western Australia.

Pavlos, R., Rive, C., McKinnon, E., Ostrov, D., Plascensia, P.C., Peters, B., Yuan, J., Gaudieri, S., Haas, D., Mallal, S. and Phillips, E.J. (2015) Specific binding characteristics of HLA alleles associate with nevirapine hypersensitivity. In: Science on the Swan, 21 - 23 April 2015, Perth, Western Australia.

John, M., Gaudieri, S., Chopra, A., Leary, S., Jorritsma, J., Mallal, S., Baraki, B., Brockman, M. and Brumme, Z. (2015) Strong functional constraint at residues in HIV-1 Gag are predicted by measures of evolutionary rather than population-level genetic conservation. In: 8th AIS Conference on HIV Pathogenesis, Treatment & Prevention, 19 - 22 July 2015, Vancouver, Canada.

Bernard, R., Chopra, A., James, I., Cooper, D., Blinco, J., Watson, M.ORCID: 0000-0002-6438-9225, Jabara, C., Lemon, S., Mallal, S. and Gaudieri, S. (2015) Ultra-deep sequencing reveals dynamics of drug Resistance-Associated variants in Hepatitis C viruses: Relevance to treatment outcome and resistance screening. In: Science on the Swan, 21 - 23 April 2015, Perth, Western Australia.

Prosser, A., Pfafferott, K., Deshpande, P., Eule, U., McKinnon, E., Chopra, A., Lucas, A., Gaudieri, S. and Lucas, M. (2015) Using a population based reverse genomics approach to predict HCV vaccine T cell responses. In: Science on the Swan, 21 - 23 April 2015, Perth, Western Australia.

Mpunga, T., Chopra, A. and Gaudieri, S. (2014) Differential expression levels of activating and inhibitory receptors on NK cell subsets: Relevance to NK cell function. In: 24th Annual Combined Biological Sciences Meeting 2014, 29 August 2014, University of Western Australia, Perth.

Gaylard, E., Lucas, A., Deshpande, P., Lucas, M. and Gaudieri, S. (2014) Identification of new CD4+ T Cell Hepatitis C virus targets: Relevance to infection outcome. In: 24th Annual Combined Biological Sciences Meeting 2014, 29 August 2014, University of Western Australia, Perth.

Gaudieri, S. (2014) Naturally occurring dominant drug resistance mutations occur infrequently in the setting of recently acquired hepatitis C. In: 9th Australasian Viral Hepatitis Conference 2014, 17 - 19 September 2014, Alice Springs, Australia.

Pavlos, R., Rive, C., McKinnon, E., Ostrov, D., Peters, B., Yuan, J., Gaudieri, S., Haas, D., Mallal, S. and Phillips, E. (2014) Specific binding characteristics of HLA alleles associate with Nevirapine hypersensitivity. In: Conference on Retroviruses and Opportunistic Infections (CROI) 2014, 3 - 6 March 2014, Boston, MA.

Cooper, D., Chopra, A., Blinco, J., Jabara, C., Lemon, S., Barnard, R., Gaudieri, S., Watson, M.ORCID: 0000-0002-6438-9225 and Mallal, S. (2013) Accurate identification of HCV sequence variants using deep sequencing with a primer ID. In: 9th Annual Scientific Workshop Australian Centre for HIV and Hepatitis Virology Research (ACH2), 5 - 7 June 2013, Katoomba, NSW.

Deshpande, P., Pfafferott, K., Lucas, M. and Gaudieri, S. (2013) Cross-genotype immunity in individuals with high-risk HCV exposure. In: 20th International Symposium on Hepatitis C Virus and Related Viruses, 6 - 10 October 2013, Melbourne, VIC.

Cooper, D., Chopra, A., Blinco, J., Watson, M.ORCID: 0000-0002-6438-9225, Gaudieri, S. and Mallal, S. (2013) Forensic analysis of mitochondrial DNA mixtures by 454 FLX sequencing. In: 23rd Annual Combined Biological Sciences Meeting (CBSM) 2013, 30 August 2013, University of Western Australia, Perth.

Chopra, A., Cooper, D., Sharma, L., Plauzolles, A., Watson, M.W.ORCID: 0000-0002-6438-9225, Rauch, A., Gaudieri, S. and Mallal, S. (2013) KIR genotyping using a real time assay and FLX454. In: 23rd Annual Combined Biological Sciences Meeting (CBSM) 2013, 30 August 2013, University of Western Australia, Perth.

Castley, A., Gaudieri, S., Gizzarelli, L., Guelfi, G., John, M. and Nolan, D. (2013) The changing face of HIV-1 diversity in Western Australia - a 12 year analysis. In: 25th Annual Conference of the Australasian Society for HIV Medicine (ASHM) 2013, 21 - 23 October 2013, Darwin, Australia.

Cooper, D., Chopra, A., Blinco, J., Jabara, C., Lemon, S., Barnard, R., Gaudieri, S., Watson, M.ORCID: 0000-0002-6438-9225 and Mallal, S. (2012) Accurate identification of HCV sequence variants using deep sequencing with a primer ID. In: 22nd Annual Combined Biological Sciences Meeting, 24 August 2012, University of Western Australia, Perth.

Hertz, T., Nolan, D., James, I., John, M., Gaudieri, S., Phillips, E., Huang, J., Riadi, G., Mallal, S. and Jojic, N. (2011) HLA class I binding and its relationship with evolutionary conservation in human proteins and viral proteomes. In: Keystone HIV Evolution Genomics & Pathogenesis, 20 - 25 March 2011, Whistler, British Columbia, Canada.

Tschochner, M., rohrbach, J., Cooper, D., Merani, S., Chopra, A., Witteck, A., Battegay, M., Furrer, H., Günthard, H., Mallal, S., Rauch, A. and Gaudieri, S. (2010) Characterization of hepatitis C virus evolution in HIV-HCV coinfected individuals using deep sequencing technology: relevance for new antiviral drugs and disease outcome. In: Australasian HIV/AIDS Conference 2010 – 22nd Annual Conference of the Australasian Society for HIV Medicine, 20 - 22 October 2010, Sydney, Australia.

Gaudieri, S., Tschochner, M., Cooper, D., Chopra, A., Merani, S., Witteck, A., Battegay, M., Günthard, H., Furrer, H., Rohrbach, J. and Rauch, A. (2010) Identification of HCV minority species in HIV/HCV coinfected individuals using deep sequencing technology: relevance for new anti-HCV drugs and host immune responses to HCV. In: The 17th International Meeting on Hepatitis C Virus and Related Diseases., 10 - 14 September 2010, Yokohama, Japan.

Pfafferott, K., Merani, S., Rauch, A., Baccala, M., Mallal, S., Baker, R., Gaudieri, S. and Lucas, M. (2010) One step closer to a CTL-based HCV vaccine. In: The Australian Centre for HIV and Hepatitis Virology Research (ACH2) 6th National Workshop, 23 - 25 June 2010, Yarra Valley, Australia.

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

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

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.

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.

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.

Pfafferott, K., Gaudieri, S., Ulsenheimer, A., John, M., James, I., Heeg, M., Nolan, D., Rauch, A., Lucas, A., Klenerman, P., Diepolder, H.M. and Lucas, M. (2009) Divergent pattern of viral evolution and escape dynamics in acute and early HCV and HIV infection. In: Australasian Virology Group Meeting, 13 - 17 December 2009, Mantra Erskine Resort, Lorne, VIC.

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.

Dong, T., Zhang, Y., Xu, K., Yan, H., James, I., Peng, Y., Blais, M., Gaudieri, S., Chen, X., Lun, W., Wu, H., Qu, W., Zhoo, C., Li, N., Mao, Y., Rostron, T., Mallal, S., Xu, X., McMichael, A., John, M. and Rowland-Jones, S. (2009) Extensive HLA-driven viral diversity following a single-source HIV-1 outbreak in rural China. In: AIDS Vaccine 2009, 19 - 22 October 2009, Paris, France.

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.

Desmond, C.P., Gaudieri, S., James, I., Pfafferott, K., Chopra, A., Lau, G.K., Locarnini, S.A., Revill, P.A., Day, C.F., Chivers, S., Gordon, A., Bowden, S., Ayres, A., Desmond, P.V., Thompson, A.J., Roberts, S.K., Mallal, S. and Lewin, S.R. (2009) Identification of novel hepatitis B virus (HBV) T-cell epitopes and escape mutations in Asian individuals with chronic HBV infection using a population based approach. In: 60th Annual Meeting of the American Association for the Study of Liver Diseases: The Liver Meeting 2009, 30 October - 3 November 2009, Boston, U.S.A.

Mallal, S., Hertz, T., John, M., Gaudieri, S., James, I., Phillips, E., Nolan, D. and Jojic, N. (2008) Co-evolution of HLA and viruses: implications and applications. In: Australasian Society for Immunology Meeting, 7 - 11 December 2008, Canberra, ACT, Australia.

Merani, S., Freitas, E., Gaudieri, S., Klenerman, P. and Petrovic, D. (2008) Human Leukocyte Antigen (HLA) associated viral polymorphisms in individuals infected by a single HCV source. In: Australian Centre for HIV and Hepatitis Virology Research (ACH2) 4th Annual Workshop, 4 - 6 June 2008, Novotel Barossa Valley Resort, South Australia.

Pfafferott, K., Ulsenheimer, A., Naidoo, K., Rauch, A., Gaudieri, S., Mallal, S., Diepolder, H.M. and Lucas, M. (2008) Changes in HCV dynamics due to immune pressure during early and late infection. In: Australian Centre for HIV and Hepatitis Virology Research (ACH2) 4th Annual Workshop, 4 - 6 June 2008, Novotel Barossa Valley Resort, South Australia.

Mallal, S., Hertz, T., John, M., Gaudieri, S. and James, I. (2008) Co-evolution of viruses and their human host: What it might teach us? In: Perth Immunology Group Meeting, 9 - 10 October 2008, Perth Western Australia.

Gaudieri, S., Rauch, A., Pfafferott, K., Mallal, S. and Roberts, S. (2008) Co-localisation of HCV drug resistant mutations and immune-driven adaptations for Genotype 1 and 3: Relevance to therapy outcome. In: Australasian Viral Hepatitis Meeting 2008, 20 - 22 October 2008, Brisbane, Australia.

Mallal, S., John, M., Gaudieri, S., Phillips, E. and Nolan, D. (2008) How might understanding of the co-evolution of HLA and viruses inform contemporary clinical issues. In: 20th Annual Australasian Society for HIV Medicine Conference, 17 - 20 September, Perth, Western Australia.

Gaudieri, S., Rauch, A., Mallal, S., Roberts, S., Nolan, D. and Lucas, M. (2008) Overlapping selection of hepatitis C virus drug-resistant mutations and immune-driven adaptations. In: Australian Centre for HIV and Hepatitis Virology Research (ACH2) 4th Annual Workshop, 4 - 6 June 2008, Novotel Barossa Valley Resort, South Australia.

Pfafferott, K., Gaudieri, S., Naidoo, K., Rauch, A., Baccala, M., Baker, R., Mallal, S. and Lucas, M. (2008) Population based genetic approach identifies novel hepatitis C targets of the immune response. In: 20th Annual Australasian Society for HIV Medicine Conference, 17 - 20 September, Perth, Western Australia.

Desmond, C.P., Gaudieri, S., Pfafferott, K., Chopra, A., Mallal, S. and Lewin, S.R. (2008) The impact of HLA on hepatitis B virus (HBV) sequence polymorphism in Asian individuals with chronic HBV infection. In: The European Association for Study of the Liver (EASL)Monothematic Conference: Immune Mediated Liver Injury, 4 - 6 December 2008, Hamburg, Germany.

Gaudieri, S. (2007) Evidence of viral adaptation to host immune pressure in hepatitis C virus infection. In: 31st Annual Scientific Meeting of the Australasian and South East Asian Tissue Typing Association (ASEATTA) 2007, 14 - 16 November 2007, Fremantle, WA.

KcKinnon, E., James, I., Nolan, D., Gaudieri, S. and Morahan, G. (2007) Application of survival techniques to assessment of Type I Diabetes susceptibility regions across the MHC. In: Type I Diabetes Genetics Consortium: MHC Fine Mapping Results Workshop, 27 - 28 August 2007, Washington, USA.

Gaudieri, S. (2007) Viral adaptation to the host’s immune responses to HIV and Hepatitis C. In: Annual Scientific Meeting of the Australian Society of Microbiology., 9 - 13 July 2007, Adelaide, South Australia.

Rauch, A., Gaudieri, S., Cavassini, M., Wever, R., Nolan, D., James, I. and Hurrer, H. (2007) Low CD4 cell counts are associated with higher hepatitis C viral loads in the Swiss HIV Cohort Study (SHCS). In: 14th Conference on Retroviruses and Opportunistic Infections, 25 - 28 February 2007, Los Angeles, U.S.A.

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.

Patterson, A., Sutton, K., Laird, R., Choo, L., Denholm, S., Chopra, A., Lucas, A., Nolan, D., John, M., Gaudieri, S. and Mallal, S. (2007) HLA genotyping for Population-based pathogen and disease associations research. In: 31st Annual Scientific Meeting of the Australasian and South East Asian Tissue Typing Association (ASEATTA) 2007, 14 - 16 November 2007, Fremantle, WA.

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.

Gaudieri, S., Rauch, A., Pfafferott, K., Park, L. and Mallal, S. (2007) Limited overlap in HLA-associated viral diversity between hepatitis C virus genotypes 1 and 3. In: 4th Australian Virology Group Meeting, 9 - 13 December 2007, Fraser Island, Queensland.

Pfafferott, K., Ulsenheimer, A., Naidoo, K., Rauch, A., Gaudieri, S., Mallal, S., Diepolder, H. and Lucas, M. (2007) Longitudinal analysis of HLA Class I -driven adaptation of HCV: New insights into HCV escape dynamics. In: 4th Australian Virology Group Meeting, 9 - 13 December 2007, Fraser Island, Queensland.

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.

John, M., Heckerman, D., Park, L., Gaudieri, S., James, I., Nolan, D., Chopra, A., Riddler, S., Haubrich, R. and Mallal, S. (2007) Strong genome-wide HLA associated selection in HIV-1. In: 31st Annual Scientific Meeting of the Australasian and South East Asian Tissue Typing Association (ASEATTA) 2007, 14 - 16 November 2007, Fremantle, WA.

Gaudieri, S. (2006) Host interaction in hepatitis C infection. In: 14th International HLA and Immunogenetics Workshop, 29 November - 3 December 2005, Melbourne, Australia.

Pfafferott, K., Ulsenheimer, A., Naidoo, V., Gaudieri, S., Rauch, A., Diepolder, H. and Lucas, M. (2006) HLA-driven HCV evolution in acutely infected patients. In: 13th International Meeting on Hepatitis C Virus & Related Viruses, 27 - 31 August, Cairns, Australia.

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., 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., Lucas, M., Freitas, E., Moore, C., Jeffrey, G., John, M., Cheng, W., Herrmann, S., Naidoo, V. and Mallal, S. (2005) Adaptation of Hepatitis C virus to HLA-restricted responses in an Australian host population. In: 2nd National Scientific Workshop 2005, Australian Centre for Hepatitis Virology & HIV Virology Interest Group, 4 - 6 May 2005, Terrigal, N.S.W.

Mallal, S., Pace, C., Nolan, D., Keller, J., Moore, C., Carvalho, F., Patterson, A., Sutton, K. and Gaudieri, S. (2005) Analysis of HIV-1 hypermutation and its relationship with APOBEC3G and vif genetic variation in vivo. In: 12th Conference on Retroviruses and Opportunistic Infections, 22 - 25 February 2005, Hynes Convention Center, Boston, MA.

Christiansen, F.T., Martin, A.M., Nolan, D.A., Gaudieri, S., Almeida, C., Phillips, E., Cameron, P.U., Moore, C.B., James, I. and Mallal, S.A. (2005) Host MHC influences susceptibility to hypersensitivity reactions to two drugs commonly used in HIV therapy. In: XIX European Immunogenetics & Histocompatibility Conference, 23 - 26 April 2005, Istanbul, Turkey.

Gaudieri, S., Freitas, E., Moore, C., Lucas, M., Jeffrey, G., Cheng, W., John, M. and Mallal, S. (2004) Adaptation of Hepatitis C virus to HLA-restricted responses in HLA diverse populations. In: 11th International Symposium on Hepatitis C and Related Diseases, 3 - 7 October 2004, Heidelberg, Germany.

Gaudieri, S., Freitas, E., Moore, C., Jeffrey, G., Lucas, M., John, M., Cheng, W., Herrmann, S., D'Aquila, R. and Mallal, S. (2004) Adaptation of hepatitis C virus to HLA-restricted responses in HLA diverse populations. In: 4th Australasian Hepatitis C Conference, 31 August - 2 September 2004, Canberra, Australia.

Martin, A.M., Almeida, C., Nolan, D., Gaudieri, S., James, I., Christiansen, F.T., Purcell, A., McCluskey, J. and Mallal, S. (2004) Carriage of HLA-B*5701 and a haplotypic Hsp70-Hom variant is associated with a Class I MHC-restricted hypersensitivity response to abacavir. In: 11th Conference on Retroviruses and Opportunistic Infections, 8 - 11 February 2004, Washington DC, U.S.A.

Christiansen, F.T., Gaudieri, S., De Santis, D., McKinnon, E., Moore, C., Nolan, D. and Mallal, S. (2004) NK receptor haplotypes and HLA as predictors of HIV-1 progression. In: NK2004 Workshop, 24 - 28 April 2004, Noordwijkerhout, The Netherlands.

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.

Gaudieri, S., Moore, C., D'Aquilla, R., Dietrich, D., Lucas, M., Klenerman, P. and John, M. (2003) CTL hepatitis C virus escape mutants in HLA-diverse populations. In: 10th International Meeting on Hepatitis C Virus and Related Viruses, 2 - 6 December 2003, Kyoto, Japan.

Martin, A., Gaudieri, S., Witt, C., Nolan, D., Christiansen, F.T. and Mallal, S. (2003) Mapping of genetic susceptibility to abacavir hypersensitivity. In: 10th Conference on Retroviruses and Opportunistic Infections, 10 - 14 February 2003, Boston, U.S.A.

Christiansen, F.T., Gaudieri, S., De Santis, D., Moore, C.B., Witt, C.S., James, I.R. and Mallal, S. (2003) NK receptor genes are predictors of HIV progression. In: 29th Annual Meeting of the American Society for Histocompatibility and Immunogenetics, 28 October - 1 November 2003, Miami Beach, Florida.

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.

Christiansen, F.T., Gaudieri, S., Moore, C.B., Martin, A., Nolan, D., James, I.R., McKinnon, E., DeSantis, D., Witt, C.S. and Mallal, S. (2003) The immune response to HIV: The interplay between virus and host genetic factors. In: British Society for Immunology Annual Congress, 2 - 5 December 2003, Harrogate, England.

Kulski, J.K., Gaudieri, S., Bellgard, M.I., Balmer, L. and Dawkins, R.L. (1997) Segmental duplication and transposition of retroelements in the evolution of MHC class I genes. In: International Conference on Molecular Biology and Evolution (5th SMBE), 1 - 4 June 1997, Bavaria, Germany.

Book Chapter

Gaudieri, S. and John, M. (2017) Evolution of the Human Leukocyte Antigen System. In: Tibayrenc, M. and Ayala, F.J., (eds.) On Human Nature. Elsevier Inc., pp. 211-219.

John, M., Gaudieri, S. and Mallal, S. (2017) Immunogenetics and vaccination. In: Modjarrad, K. and Koff, W.C., (eds.) Human Vaccines: Emerging Technologies in Design and Development. Academic Press.

White, K., Gaudieri, S. and Phillips, E. (2014) HLA and pharmacogenetics of drug hypersensitivity. In: Padmanabhan, S., (ed.) Handbook of Pharmacogenomics and Stratified Medicine. Academic Press, pp. 437-459.

White, K.D., Gaudieri, S. and Phillips, E.J. (2014) HLA and the Pharmacogenomics of Drug Hypersensitivity. In: Padmanabhan, S., (ed.) Handbook of Pharmacogenomics and Stratified Medicine. Elsevier, pp. 437-465.

Deshpande, P., Lucas, M. and Gaudieri, S. (2012) Genetic variation of host immune response genes and their effect on Hepatitis C infection and treatment outcome. In: Caliskan, M., (ed.) Analysis of Genetic Variation in Animals. INTECHOpen, pp. 167-186.

Lucas, M., Lucas, A. and Gaudieri, S. (2012) New Diagnostics for Mycobacterium tuberculosis. In: Understanding Tuberculosis - Global Experiences and Innovative Approaches to the Diagnosis. InTech OPEN, pp. 239-256.

Martin, A.M., Gaudieri, S., Witt, C., Sayer, D., Castley, A., Mamotte, C., Nolan, D., James, I., Christiansen, F. and Mallal, S. (2004) Association of tumour necrosis factor promoter polymorphisms with abacavir hypersensitivity. In: Hansen, John A. and Dupont, Bo, (eds.) HLA 2004: Immunobiology of the human MHC : proceedings of the 13th International Hisotcompatibility Workshop and Conference and the XIII International Congress of Histocompatibility and Immunogenetics. International Histocompatibility Working Group Press : Fred Hutchinson Cancer Research Center.