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Number of items: 38.

Journal Article

Beckett, A.C., Loh, J.T., Chopra, A., Leary, S., Lin, A.S., McDonnell, W.J., Dixon, B.R.E.A., Noto, J.M., Israel, D.A., Peek Jr, R.M., Mallal, S., Algood, H.M.S. and Cover, T.L. (2018) Helicobacter pylori genetic diversification in the Mongolian gerbil model. PeerJ, 6 .

Weiskopf, D., Grifoni, A., Arlehamn, C.S.L., Angelo, M., Leary, S., Sidney, J., Frazier, A., Mack, S.J., Phillips, E., Mallal, S., Cerpas, C., Balmaseda, A., Harris, E. and Sette, A. (2018) Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 339 adults from Managua, Nicaragua. Human Immunology, 79 (1). pp. 1-2.

Moore, E., Grifoni, A., Weiskopf, D., Schulten, V., Arlehamn, C.S.L., Angelo, M., Pham, J., Leary, S., Sidney, J., Broide, D., Frazier, A., Phillips, E., Mallal, S., Mack, S.J. and Sette, A. (2018) Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA. Human Immunology, 79 (12). pp. 821-822.

Noto, J.M., Chopra, A., Loh, J., Romero-Gallo, J., Piazuelo, M.B., Watson, M.W., Leary, S., Beckett, A., Cover, T., Mallal, S., Israel, D. and Peek, R.M. (2017) Carcinogenic host microenvironments target and modify key pathogenic loci within helicobacter pylori. Gastroenterology, 152 (5). S666.

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).

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).

Noto, J.M., Chopra, A., Loh, J.T., Romero-Gallo, J., Piazuelo, M.B., Watson, M., Leary, S., Beckett, A.C., Wilson, K.T., Cover, T.L., Mallal, S., Israel, D.A. and Peek, R.M. (2017) Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments. Gut, 67 (10). pp. 1793-1804.

Arlehamn, C.S.L., Copin, R., Leary, S., Mack, S.J., Phillips, E., Mallal, S., Sette, A., Blatner, G., Siefers, H. and Ernst, J.D. (2017) Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 100 Luo infants from the Boro area of Nyanza Province, Kenya. Human Immunology, 78 (4). pp. 325-326.

Grifoni, A., Weiskopf, D., Lindestam Arlehamn, C.S., Angelo, M., Leary, S., Sidney, J., Frazier, A., Phillips, E., Mallal, S., Mack, S.J., Tippalagama, R., Goonewardana, S., Premawansa, S., Premawansa, G., Wijewickrama, A., De Silva, A.D. and Sette, A. (2017) Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka. Human Immunology, 79 (2). pp. 87-88.

Elera, J.D., Boteanu, C., Blanco, M.A.J., Gonzalez-Mendiola, R., García, I.C., Alvarez, A., Martinez, J.J.L., Garrido, J.M., Barona, C.T., Chorda, C.P., Salgueiro, R.L., Palacios, M.D., De Rojas, D.H.F., Acar, E.A., Aktas, A., Ermertcan, A.T., Temiz, C., Lin, C-Y, Hui, C-Y.R., Chang, Y-C, Yang, C-H, Chung, W-H, Carolino, F., Silva, D., De Castro, E.D., Cernadas, J.R., Ensina, L.F., Aranda, C., Nunes, I.C., Lacerda, A., Martins, A.M., Goudouris, E., Ribeiro, M., Da Silva Franco, J.F., Queiroz, L., Solé, D., Dalgiç, C.T., Sin, A.Z., Günsen, F.D., Bulut, G., Ardeniz, F.Ö., Gülbahar, O., Gökmen, E.N.M., Kokuludag, A., De Francisco, A.M.M., De Vicente Jiménez, T.M., Mendoza Parra, A.M., Burgos Pimentel, A.M., Luque, A.G., Amaral, L., Leão, L.C., Pinto, N., Belo, J., Marques, J., Carreiro-Martins, P., Leiria-Pinto, P., Chaabane, A., Romdhane, H.B., Fredj, N.B., Chadly, Z., Boughattas, N.A., Aouam, K., Uyttebroek, A.P., Bridts, C.H., Romano, A., Ebo, D.G., Sabato, V., Lopes, A., Cosme, J., Aguiar, R., Lourenço, T., Paes, M-J, Spínola-Santos, A., Pereira-Barbosa, M., Cruz, C.R., Dos Reis, R.P., Tomaz, E., Pires, A.P., Inácio, F., Benito-Garcia, F., Mota, I., Correia, M., Gaspar, Â., Chambel, M., Piedade, S., Morais-Almeida, M., Nakonechna, A., Antipkin, Y., Umanets, T., Pineda, F., Arribas, F., Lapshyn, V., Miranda, P.A., De La Cruz Hoyos, B., Blanco, A.J., Del Pozo, M., Vultaggio, A., Nencini, F., Pratesi, S., Matucci, A., Maggi, E., Cegec, I., Nahal, D.J., Turk, V.E., Aumiler, M.R., Ausperger, K.M., Kraljickovic, I., Simic, I., Yamaguchi, Y., Watanabe, T., Satoh, M., Tanegashima, T., Oda, K., Wada, H., Aihara, M., Lee, J.J., Choi, J.C., Lee, H.Y., Fernandes, R-A.R., Faria, E., Pita, J., Sousa, N., Ribeiro, C., Carrapatoso, I., Bom, A.T., Rodolfo, A., Dias-Castro, E., Voronova, M., Valle, D.K., Coronel, V.P., Chordá, C.P., Madamba, R.C.Y., Ferrer, M., Goikoetxea, M.J., D’Amelio, C., Bernad, A., Vega, O., Gastaminza, G., Bibián, B.L., Salazar, M.L., Vilà-Nadal, G., Roman, A.M.F., Ortega, J.D., Muñoz, M.G., Gancedo, S.Q., Moreno, M.R.C., Hofmeier, K.S., Barzylovych, V., Pola, B., Lluncor, M., Fiandor, A., Bellón, T., Domínguez, J., Quirce, S., Yang, M-S, Kim, S-S, Kim, S-H, Kang, H-R, Park, H-W, Cho, S-H, Min, K-U, Chang, Y-S, Delahaye, C., Flabbee, J., Waton, J., Bauvin, O., Barbaud, A., Fadhel, N.B., Gulin, S.J., Chiriac, A., Cardoso, B.K., Viseu, R., Moreira, A., Cadinha, S., Neves, A.C., Barreira, P., Malheiro, D., Da Silva, J.P., Jurakic-Toncic, R., Ljubojevic, S., Turcic, P., Gilissen, L., Huygens, S., Goossens, A., Andreu, I., Romero, A.M., Cabezas, P.G., Parejo, P.A., Del Carmen Plaza-Serón, M., Doña, I., Blanca-López, N., Flores, C., Galindo, M.L., Molina, A., Perkins, J.R., Cornejo-García, J.A., García-Agúndez, J.A., García-Martín, E., Campo, P., Canto, M.G., Blanca, M., Guéant-Rodríguez, R.M., Jurado-Escobar, R., Barrionuevo, E., Salas, M., Canto, G., Guéant, J-L, Usui, T., Tailor, A., Faulkner, L., Farrell, J., Alfirevic, A., Kevin Park, B., Naisbitt, D.J., Trelles, O., Guerrero, M.A., Upton, A., Ueta, M., Sawai, H., Sotozono, C., Tokunaga, K., Kinoshita, S., Sukasem, C., Satapornpong, P., Tempark, T., Rerknimitr, P., Pairayayutakul, K., Klaewsongkram, J., Koomdee, N., Jantararoungtong, T., Santon, S., Puangpetch, A., Intusoma, U., Tassaneeyakul, W., Theeramoke, V., Ramirez, E., Borobia, A.M., Tong, H., Castañer, J.L., De Abajo, F.J., Galvao, V.R., Pavlos, R., McKinnon, E., Williams, K., Beeghly-Fadiel, A., Phillips, E., Castells, M., Boni, E., Russello, M., Mauro, M., Ue, K.L., Rutkowski, K., Gomis, V.S., Ferre, J.F., Rodriguez, A.E., Reig, V.C., Sanchez, J.F., Breynaert, C., Van Hoeyveld, E., Schrijvers, R., Blanco, A.J., Irigoyen, R.F., Collado, D., Vida, Y., Najera, F., Perez-Inestrosa, E., Mesa-Antunez, P., Mayorga, C., Torres, M.J., Tannert, L.K., Mortz, C.G., Skov, P.S., Bindslev-Jensen, C., Pfützner, W., Dörnbach, H., Visse, J., Rauber, M., Möbs, C., Elzagallaai, A.A., Chow, L., Abuzgaia, A.M., Rieder, M.J., Trubiano, J., Woolnough, E., Cheng, C., Kato, K., Azukizawa, H., Hanafusa, T., Katayama, I., Fujiyama, T., Hashizume, H., Umayahara, T., Ito, T., Tokura, Y., Silar, M., Zidarn, M., Rupnik, H., Korosec, P., Redwood, A.J., Strautins, K., White, K., Chopra, A., Konvinse, K., Leary, S., Mallal, S., Cabañas, R., Fiandor, A.M., Sullivan, A., Whitaker, P., Peckham, D., Haw, W.Y., Polak, M.E., Mcguire, C., Ardern-Jones, M.R., Aoyama, Y., Shiohara, T., Correia, S., Gelincik, A., Demir, S., Sen, F., Bozbey, H.U., Olgac, M., Unal, D., Coskun, R., Colakoglu, B., Buyuozturk, S., Çatin-Aktas, E., Deniz, G., Laguna, J.J., Dionicio, J., Fernandez, T., Olazabal, I., Ruiz, M.D., Torres, M.J., Lafuente, A., Núñez, J., Fernández, T.D., Palomares, F., Fernández, R., Sanchez, M.I., Fernandez, T., Ruiz, A., Ariza, A., Alonso, A.B., Garófalo, C.D., Matute, O.V., Puga, M.F., Lapresa, M.J.G., Lasarte, G.G., Thinnes, A., Merk, H.F., Baron, J.M., Leverkus, M., Balakirski, G., Gibson, A., Ogese, M., Al-Attar, Z., Yaseen, F., Meng, X., Jenkins, R., Farrel, J., Alhilali, K., Xue, Y., Illing, P., Mifsud, N., Fettke, H., Lai, J., Ho, R., Kwan, P., Purcell, A., Ogese, M.O., Betts, C., Thomson, P., Alhaidari, M., Berry, N., O’Neill, P.M., Alzahrani, A., Azoury, M.E., Fili, L., Bechara, R., Scornet, N., Nhim, C., Weaver, R., Claude, N., Joseph, D., Maillere, B., Parronchi, P., Pallardy, M., Villani, A.P., Rozières, A., Bensaïd, B., Tardieu, M., Albert, F., Mutez, V., Baysal, T., Maryanski, J., Nicolas, J-F, Kanagawa, O., Vocanson, M., Hung, S-L, Harrison, C.J., Jenkins, R.E., French, N.S., Montañez, M.I., Fernandez, T.D., Martin-Serrano, A., Torres, M.J., Molina, N., Wood, S., Pirmohamed, M., Montañez, M.I., Martín-Serrano, Á., Pérez-Inestrosa, E., Pérez-Sala, D., Guzmán, A.E., Ko, T-M, Chen, Y-T, Wu, J-Y, Sánchez-Gómez, F.J., González-Morena, J.M., Torres, M.J., Arreola, A.M., Corona, J.A.B., Flores, S.M., Cherit, J.D., Figueroa, N.V.D., Flores, J.L.C., Perkins, J., Pérez-Alzate, D., Bogas, G., Torres, M.J., Marti, L.M.T., De La Losa, F.P., Poves, F.A., Lopez, J.T. and Santiago, T.L. (2016) 7th Drug hypersensitivity meeting: part two. Clinical and Translational Allergy, 6 (S3).

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).

Creaney, J., Ma, S., Sneddon, S.A., Tourigny, M.R., Dick, I.M., Leon, J.S., Khong, A., Fisher, S.A., Lake, R.A., Lesterhuis, W.J., Nowak, A.K., Leary, S., Watson, M.W. and Robinson, B.W. (2015) Strong spontaneous tumor neoantigen responses induced by a natural human carcinogen. OncoImmunology, 4 (7). e1011492.

Conference Paper

Keane, N.M., Almeida, C., Chopra, A., Leary, S., McKinnon, E., Cooper, D., Mallal, S. and John, M. (2014) Viral adaptation in autologous viral sequences of patients with acute and early HIV infection prior to full seroconversion. In: Australian Centre for HIV & Hepatitis Virology Research (ACH2) 5th National Workshop, 3 - 5 June, Terrigal, NSW, Australia

Lucas, A., Meyer-Pannwitt, V., McKinnon, E., Burrows, S., Rist, M., Leary, S., Lucas, M., Mallal, S. and Phillips, E. (2013) Abacavir impairs an HLA-B*5701-restricted CD8+ T Cell response to an immunodominant Epstein-Barr virus epitope. In: 20th Conference on Retroviruses and Opportunistic Infections (CROI 2013), 3 - 6 March 2013, Atlanta, Georgia

Conference Item

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.

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.

Strautins, K., Tschochner, M., Berry, C., James, I., Leary, S., Choo, L., Clark, H., Pedrini, M., Kermode, A., Carroll, W. and Nolan, D. (2016) Identifying novel potential cross-reactive targets in Multiple Sclerosis. In: Science on the Swan 2016, 2 - 5 May 2016, Perth, Western Australia.

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.

Symons, J., Chopra, A., Malantinkova, E., De Spiegelaere, W. and Leary, S. (2016) Integration analysis of latently infected cell lines: Evidence of ongoing replication. In: 23rd Conference on Retroviruses and Opportunistic Infections (CROI), 20-25 February 2016, Boston, MA.

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.

Redwood, A., White, K., Strautins, K., Chopra, A., Konvinse, K., Leary, S., Pavlos, R., Mallal, S. and Phillips, E. (2016) Single cell analysis of drug responsive T cells; identification of candidate drug reactive T cell receptors in abacavir and carbamazepine hypersensitivity. In: 7th Drug Hypersensitivity Meeting (DHM) 2016, 21 - 23 April 2016, Malaga, Spain.

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, 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.

Symons, J., Lewin, S., Chopra, A., Malatinkova, E., De Spiegelaere, W., Leary, S., Cooper, D., Vandekerckhove, L., Mallal, S. and Cameron, P. (2015) Integration site analysis of latently infected cell lines: evidence of ongoing replication. In: 7th International workshop on HIV Persistence during Therapy, 8 - 11 December 2015, Miami, FL.

Strautins, K., Tschochner, M., James, I., Leary, S., Choo, L., Walters, S., Pedrini, M., Dunn, D., Berry, C., Clark, H., Cooper, D., Kermode, A., Carroll, W. and Nolan, D. (2015) Investigating the role of EBV infection in multiple sclerosis pathogenesis. 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.

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.

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: 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.

Tschochner, M., Leary, S., Strautins, K., Clark, H., Chopra, A., Choo, L., Carroll, W., Kermode, A. and Nolan, D. (2013) Identifying Epstein-Barr virus EBNA-1 sequence variation using 454 FLX technology in Multiple Sclerosis patient samples. In: Keystone Symposia on Molecular and Cellular Biology: Multiple Sclerosis, 11 - 16 January 2013, Big Sky, Montana USA.

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.

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.

Tschochner, M., Leary, S. and Nolan, D. (2011) Identifying potential targets for Epstein-Barr virus-associated molecular mimicry in T cell-mediated autoimmunity of multiple sclerosis. In: 5th Joint Triennial Congress of the European and Americas Committees for Treatment and Research in Multiple Sclerosis, 19 – 22 October 2011, Amsterdam, Netherlands.

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.

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.

This list was generated on Thu Apr 18 12:27:01 2019 UTC.