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Publications: Cooper, Donald

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Number of items: 33.

2017

Symons, J., Chopra, A., Malatinkova, E., De Spiegelaere, W., Leary, S., Cooper, D., Abana, C.O., Rhodes, A., Rezaei, S.D., Vandekerckhove, L., Mallal, S., Lewin, S.R. and Cameron, P.U. (2017) Erratum to: HIV integration sites in latently infected cell lines: evidence of ongoing replication. Retrovirology, 14 (1).

Symons, J., Chopra, A., Malantinkova, E., De Spiegelaere, W., Leary, S., Cooper, D., Abana, C.O., Rhodes, A., Rezaei, S.D., Vandekerckhove, L., Mallal, S., Lewin, S.R. and Cameron, P.U. (2017) HIV integration sites in latently infected cell lines: evidence of ongoing replication. Retrovirology, 14 (1).

2016

Leary, S., Cooper, D., Chopra, A., Watson, M. and Mallal, S. (2016) Analysis and visualisation tools for NGS sequence data. In: Science on the Swan 2016, 2 - 5 May 2016, Perth, Western Australia.

Tschochner, M., Strautins, K., James, I., Leary, S., Choo, L., Clark, H., Dunn, D., Chopra, A., Cooper, D., Kermode, A., Carroll, W. and Nolan, D. (2016) Contribution of EBV infection to Multiple Sclerosis Pathogenesis: Human leukocyte antigen restricted, EBV epitope-specific T cell responses in Multiple Sclerosis. In: Science on the Swan 2016, 2 - 5 May 2016, Perth, Western Australia.

Chopra, A., Gaudieri, S., Pilkington, M., Blinco, J., Leary, S., Cooper, D., Abana, C., Watson, M., 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.

Murphy, N.M., Burton, M., Powell, D.R., Rossello, F.J., Cooper, D., Chopra, A., Hsieh, M.J., Sayer, D.C., Gordon, L., Pertile, M.D., Tait, B.D., Irving, H.R. and Pouton, C.W. (2016) Haplotyping the human leukocyte antigen system from single chromosomes. Scientific Reports, 6 . p. 30381.

Tschochner, M., Leary, S., Cooper, D., Strautins, K., Chopra, A., Clark, H., Choo, L., Dunn, D., James, I., Carroll, W.M., Kermode, A.G. and Nolan, D. (2016) Identifying Patient-Specific Epstein-Barr nuclear antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis. PloS one, 11 (2).

Symons, J., Lewin, S.R., Chopra, A., Malantinkova, E., De Spiegelaere, W., Leary, S., Cooper, D., Vandekerckhove, L., Mallal, S. and Cameron, P. (2016) Integration site analysis of latently infected cell lines: evidence of ongoing replication. In: Science on the Swan 2016, 2 - 5 May 2016, Perth, Western Australia.

2015

Chopra, A., Gaudieri, S., Clark, H., Blinco, J., Cooper, D., Leary, S., Watson, M. 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.

Cooper, Donald (2015) High resolution HLA typing from second generation sequencing data. PhD thesis, Murdoch University.

Cooper, D., Chopra, A., Blinco, J., Leary, S., Watson, M. and Mallal, S. (2015) Hybridization based enrichment for genotyping HLA and KIR genes using Next Generation Sequencing. In: Science on the Swan, 21 - 23 April 2015, Perth, Western Australia.

Bernard, R., Chopra, A., James, I., Cooper, D., Blinco, J., Watson, M., 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.

2013

Keane, N., Almeida, C., Chopra, A., Leary, S., Cooper, D., McKinnon, E., Mallal, S. and John, M. (2013) Analysis of HLA-restricted HIV-specific CD8 T cell responses and viral adaptation in patients with acute HIV infection prior to full seroconversion. In: 9th Annual Scientific Workshop Australian Centre for HIV and Hepatitis Virology Research, (ACH²), 5 - 7 June 2013, Katoomba, NSW.

Cooper, D., Chopra, A., Blinco, J., Watson, M., 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.

Leary, S., Cooper, D., Chopra, A., Watson, M. and Mallal, S. (2013) IIID VGAS: A visual genome analysis studio incorporating high performance next generation sequence analysis. In: Great Lakes Bioinformatics Conference (GLBIO) 2013, 14 - 16 May 2013, Pittsburgh, PA.

Chopra, A., Cooper, D., Sharma, L., Plauzolles, A., Watson, M.W., 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.

Tschochner, M., Leary, S., Strautins, K., Clark, H., Cooper, D., Chopra, A., Choo, L., Carroll, W., Kermode, A. and Nolan, D. (2013) Multiple Sclerosis Patient Sequence Variation In Epstein-Barr Virus Nuclear Antigen 1. In: Pan-Asian Committee for Treatment and Research in Multiple Sclerosis (PACTRIMS) 2013, 6 - 8 November 2013, Kyoto, Japan.

2012

Cooper, D., Chopra, A., Blinco, J., Jabara, C., Lemon, S., Barnard, R., Gaudieri, S., Watson, M. 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.

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

Keane, N.M., Almeida, C., Chopra, A., Cooper, D., Demaine, E., Mallal, S. and John, M. (2012) Early changes in the CD8 T cell immunodominance hierarchy in primary HIV infection prior to seroconversion. In: AIDS Vaccine 2012, 9 - 12 September 2012, Boston, U.S.A.

Chopra, A., Cooper, D., Sharma, L., Choo, L., Blinco, J., Dunn, D., Leary, S., Watson, M. and Mallal, S. (2012) High throughput HLA sequence-based typing using Next Generation Sequencing. In: 22nd Annual Combined Biological Sciences Meeting, 24 August 2012, University of Western Australia, Perth.

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

2011

Cooper, D., Patsopoulos, N., Chopra, A., Watson, M., de Bakker, P. and Mallal, S. (2011) HLA Class I typing based on FLX 454 sequencing. In: 21st Annual Combined Biological Sciences Meeting, 26 August 2011, Perth, Western Australia.

Keane, N.M., Pfafferott, K., Cooper, D., Chopra, A., Roberts, S.G., Sterrett, S., Leary, S., Demaine, E., Krishnan, T., Mallal, S., Bar, K., Shaw, G. and John, M. (2011) Limited acute CTL escape among three founder viruses in a case of acute heterosexual transmission of HIV-1 infections. In: 6th IAS Conference on HIV Pathogenesis, Treatment and Prevention., 17 - 20 July, 2011, Rome, Italy.

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.

Chopra, A., Cooper, D., Demaine, E., Rive, C., Keane, N., Watson, M., Bar, K.J., Shaw, G.M., John, M. and Mallal, S. (2011) Importance of Primer selection and PCR amplification in Estimating HIV viral variation using traditional and 454 FLX sequencing. In: 23rd Australasian HIV/AIDS Conference, 26-28 September 2011, Canberra, ACT, Australia.

2010

Keane, N.M., Pfafferott, K., Cooper, D., Roberts, S.G., Chopra, A., Demaine, E., Krishan, T., Mallal, S. and John, M. (2010) FLX 454 deep sequencing of HLA-restricted viral epitope sequences in acute HIV infection identifies sites of selection. In: 40th Annual Scientific Meeting for the Australasian Society for Immunology, 5 - 9 December 2010, Perth, 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.

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

Keane, N.M., Pfafferott, K., Cooper, D., Roberts, S.G., Chopra, A., Demaine, E., Krishnan, T., Mallal, S. and John, M. (2010) HIV-1 adaptation to early HLA restricted immune responses in acute heterosexual transmission. In: 22nd Annual Conference of the Australasian Society for HIV Medicine, 20 - 22 October 2010, Sydney, Australia

2009

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

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

2005

Mallon, P., Sedwell, R., Rogers, G., Nolan, D., Unemore, P., Wand, H., Samaras, K., Kelleher, A., Emery, S., Cooper, D. and Carr, A. (2005) The effect of rosiglitazone on PPAR gamma expression in human adipose tissue is limited by continued exposure to thymidine NRTI. In: 12th Conference on Retroviruses and Opportunistic Infections, 22 - 25 February 2005, Hynes Convention Center, Boston, MA.

This list was generated on Thu Jul 27 09:55:08 2017 UTC.