In silico prediction of HIV-1-host molecular interactions and their directionality. by Haiting Chai, Quan Gu, Joseph Hughes, David L Robertson

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Prediction of virus-host associations using protein language models and multiple instance learning. by Dan Liu, Francesca Young, Kieran D Lamb, David L Robertson, Ke Yuan

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Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. by Jamie I MacPherson, Jonathan E Dickerson, John W Pinney, David L Robertson

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The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach. by John Archer, Andrew Rambaut, Bruce E Taillon, P Richard Harrigan, Marilyn Lewis, David L Robertson

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. by Oscar A MacLean, Spyros Lytras, Steven Weaver, Joshua B Singer, Maciej F Boni, Philippe Lemey, Sergei L Kosakovsky Pond, David L Robertson

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Use of four next-generation sequencing platforms to determine HIV-1 coreceptor tropism. by John Archer, Jan Weber, Kenneth Henry, Dane Winner, Richard Gibson, Lawrence Lee, Ellen Paxinos, Eric J Arts, David L Robertson, Larry Mimms, Miguel E Quiñones-Mateu

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The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. by Elena Sugrue, Arthur Wickenhagen, Nardus Mollentze, Muhamad Afiq Aziz, Vattipally B Sreenu, Sven Truxa, Lily Tong, Ana da Silva Filipe, David L Robertson, Joseph Hughes, Suzannah J Rihn, Sam J Wilson

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Evaluation of risk-based travel policy for the COVID-19 epidemic in Scotland: a population-based surveillance study by Jennifer Bishop, David L Robertson, Alison Smith-Palmer, Samantha Lycett, Matthew T G Holden, Gonzalo Yebra, Christopher Redman, Joseph Hughes, Kirstin Leslie, Isobel McLachlan, Selene Huntley, Sharif Shaaban, Nicolaos Christofidis, Sema Nickbakhsh

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The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. by Andrew E Shaw, Suzannah J Rihn, Nardus Mollentze, Arthur Wickenhagen, Douglas G Stewart, Richard J Orton, Srikeerthana Kuchi, Siddharth Bakshi, Mila Rodriguez Collados, Matthew L Turnbull, Joseph Busby, Quan Gu, Katherine Smollett, Connor G G Bamford, Elena Sugrue, Paul C D Johnson, Ana Filipe Da Silva, Alfredo Castello, Daniel G Streicker, David L Robertson, Massimo Palmarini, Sam J Wilson

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Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. by Chris Davis, Nicola Logan, Grace Tyson, Richard Orton, William T Harvey, Jonathan S Perkins, Guy Mollett, Rachel M Blacow, COVID-19 Genomics UK (COG-UK) Consortium, Thomas P Peacock, Wendy S Barclay, Peter Cherepanov, Massimo Palmarini, Pablo R Murcia, Arvind H Patel, David L Robertson, John Haughney, Emma C Thomson, Brian J Willett, COVID-19 DeplOyed VaccinE (DOVE) Cohort Study investigators

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Virus species names have been standardized; virus names remain unchanged by F. Murilo Zerbini, Peter Simmonds, Evelien M. Adriaenssens, Elliot J. Lefkowitz, Hanna M. Oksanen, Poliane Alfenas-Zerbini, Frank O. Aylward, Juliana Freitas-Astúa, Holly R. Hughes, Małgorzata Łobocka, Mart Krupovic, Jens H. Kuhn, Arcady Mushegian, Judit J. Penzes, Alejandro Reyes, David L. Robertson, Simon Roux, Luisa Rubino, Sead Sabanadzovic, Donald B. Smith, Nobuhiro Suzuki, Dann Turner, Koenraad Van Doorslaer, Arvind Varsani

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The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis. by David J Pascall, Elen Vink, Rachel Blacow, Naomi Bulteel, Alasdair Campbell, Robyn Campbell, Sarah Clifford, Chris Davis, Ana da Silva Filipe, Noha El Sakka, Ludmila Fjodorova, Ruth Forrest, Emily Goldstein, Rory Gunson, John Haughney, Matthew T G Holden, Patrick Honour, Joseph Hughes, Edward James, Tim Lewis, Samantha Lycett, Oscar MacLean, Martin McHugh, Guy Mollett, Yusuke Onishi, Ben Parcell, Surajit Ray, David L Robertson, Sharif Shabaan, James G Shepherd, Katherine Smollett, Kate Templeton, Elizabeth Wastnedge, Craig Wilkie, Thomas Williams, Emma C Thomson, COVID-19 Genomics UK (COG-UK) Consortium

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Four principles to establish a universal virus taxonomy. by Peter Simmonds, Evelien M Adriaenssens, F Murilo Zerbini, Nicola G A Abrescia, Pakorn Aiewsakun, Poliane Alfenas-Zerbini, Yiming Bao, Jakub Barylski, Christian Drosten, Siobain Duffy, W Paul Duprex, Bas E Dutilh, Santiago F Elena, Maria Laura García, Sandra Junglen, Aris Katzourakis, Eugene V Koonin, Mart Krupovic, Jens H Kuhn, Amy J Lambert, Elliot J Lefkowitz, Małgorzata Łobocka, Cédric Lood, Jennifer Mahony, Jan P Meier-Kolthoff, Arcady R Mushegian, Hanna M Oksanen, Minna M Poranen, Alejandro Reyes-Muñoz, David L Robertson, Simon Roux, Luisa Rubino, Sead Sabanadzovic, Stuart Siddell, Tim Skern, Donald B Smith, Matthew B Sullivan, Nobuhiro Suzuki, Dann Turner, Koenraad Van Doorslaer, Anne-Mieke Vandamme, Arvind Varsani, Nikos Vasilakis

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A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. by Suzannah J Rihn, Andres Merits, Siddharth Bakshi, Matthew L Turnbull, Arthur Wickenhagen, Akira J T Alexander, Carla Baillie, Benjamin Brennan, Fiona Brown, Kirstyn Brunker, Steven R Bryden, Kerry A Burness, Stephen Carmichael, Sarah J Cole, Vanessa M Cowton, Paul Davies, Chris Davis, Giuditta De Lorenzo, Claire L Donald, Mark Dorward, James I Dunlop, Matthew Elliott, Mazigh Fares, Ana da Silva Filipe, Joseph R Freitas, Wilhelm Furnon, Rommel J Gestuveo, Anna Geyer, Daniel Giesel, Daniel M Goldfarb, Nicola Goodman, Rory Gunson, C James Hastie, Vanessa Herder, Joseph Hughes, Clare Johnson, Natasha Johnson, Alain Kohl, Karen Kerr, Hannah Leech, Laura Sandra Lello, Kathy Li, Gauthier Lieber, Xiang Liu, Rajendra Lingala, Colin Loney, Daniel Mair, Marion J McElwee, Steven McFarlane, Jenna Nichols, Kyriaki Nomikou, Anne Orr, Richard J Orton, Massimo Palmarini, Yasmin A Parr, Rute Maria Pinto, Samantha Raggett, Elaine Reid, David L Robertson, Jamie Royle, Natalia Cameron-Ruiz, James G Shepherd, Katherine Smollett, Douglas G Stewart, Meredith Stewart, Elena Sugrue, Agnieszka M Szemiel, Aislynn Taggart, Emma C Thomson, Lily Tong, Leah S Torrie, Rachel Toth, Margus Varjak, Sainan Wang, Stuart G Wilkinson, Paul G Wyatt, Eva Zusinaite, Dario R Alessi, Arvind H Patel, Ali Zaid, Sam J Wilson, Suresh Mahalingam

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