Joseph Hughes

Publication Activity (10 Years)

Years Active: 2018-2023
Publications (10 Years): 42

Top Topics

Antimicrobial Resistance

Hepatitis C Virus

Machine Learning

Top Venues

Virus evolution

Nature reviews. Microbiology

This page only lists publications with an associated author ORCID identifier.

Publications

Maria-Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir R Abi-Said, Stéphane Hué, Joseph Hughes, Anna Gatseva, Robert James Gifford
Emergence and pandemic spread of small ruminant lentiviruses. Virus evolution 9 (1) (2023)
Jonathan E Pekar, Spyros Lytras, Mahan Ghafari, Andrew F Magee, Edyth Parker, Jennifer L Havens, Aris Katzourakis, Tetyana I Vasylyeva, Marc A Suchard, Alice C Hughes, Joseph Hughes, David L Robertson, Simon Dellicour, Michael Worobey, Joel O Wertheim, Philippe Lemey
The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2. bioRxiv : the preprint server for biology (2023)
Alessandro M Carabelli, Thomas P Peacock, Lucy G Thorne, William T Harvey, Joseph Hughes, null null, Sharon J Peacock, Wendy S Barclay, Thushan I de Silva, Greg J Towers, David L Robertson
SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature reviews. Microbiology 21 (3) (2023)
Rute Maria Pinto, Siddharth Bakshi, Spyros Lytras, Mohammad Khalid Zakaria, Simon Swingler, Julie C Worrell, Vanessa Herder, Kerrie E Hargrave, Margus Varjak, Natalia Cameron-Ruiz, Mila Collados Rodriguez, Mariana Varela, Arthur Wickenhagen, Colin Loney, Yanlong Pei, Joseph Hughes, Elise Valette, Matthew L Turnbull, Wilhelm Furnon, Quan Gu, Lauren Orr, Aislynn Taggart, Ola Diebold, Christopher A Davis, Chris Boutell, Finn Grey, Edward Hutchinson, Paul Digard, Isabella Monne, Sarah K Wootton, Megan K L MacLeod, Sam J Wilson, Massimo Palmarini
BTN3A3 evasion promotes the zoonotic potential of influenza A viruses. Nature (2023)
Alessandro M Carabelli, Thomas P Peacock, Lucy G Thorne, William T Harvey, Joseph Hughes, null null, Sharon J Peacock, Wendy S Barclay, Thushan I de Silva, Greg J Towers, David L Robertson
SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature reviews. Microbiology 21 (3) (2023)
Alessandro M Carabelli, Thomas P Peacock, Lucy G Thorne, William T Harvey, Joseph Hughes, null null, Sharon J Peacock, Wendy S Barclay, Thushan I de Silva, Greg J Towers, David L Robertson
SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature reviews. Microbiology 21 (3) (2023)
Maria-Luisa Carrozza, Anna-Maria Niewiadomska, Maurizio Mazzei, Mounir R Abi-Said, Stéphane Hué, Joseph Hughes, Anna Gatseva, Robert James Gifford
Emergence and pandemic spread of small ruminant lentiviruses. Virus evolution 9 (1) (2023)
Alessandro M Carabelli, Thomas P Peacock, Lucy G Thorne, William T Harvey, Joseph Hughes, null null, Sharon J Peacock, Wendy S Barclay, Thushan I de Silva, Greg J Towers, David L Robertson
SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature reviews. Microbiology (2023)
Alessandro M Carabelli, Thomas P Peacock, Lucy G Thorne, William T Harvey, Joseph Hughes, null null, Sharon J Peacock, Wendy S Barclay, Thushan I de Silva, Greg J Towers, David L Robertson
SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature reviews. Microbiology 21 (3) (2023)
Sarah Iannucci, William T Harvey, Joseph Hughes, David L Robertson, Matthieu Poyade, Edward C Hutchinson
The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern. Journal of visual communication in medicine (2023)
Alessandro M Carabelli, Thomas P Peacock, Lucy G Thorne, William T Harvey, Joseph Hughes, null null, Sharon J Peacock, Wendy S Barclay, Thushan I de Silva, Greg J Towers, David L Robertson
SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature reviews. Microbiology 21 (3) (2023)
Alessandro M Carabelli, Thomas P Peacock, Lucy G Thorne, William T Harvey, Joseph Hughes, null null, Sharon J Peacock, Wendy S Barclay, Thushan I de Silva, Greg J Towers, David L Robertson
SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nature reviews. Microbiology (2023)
Thomas B Waltzek, Kuttichantran Subramaniam, Andor Doszpoly, Joseph Hughes, Matej Vučak, Andrew J Davison
Genome sequence of white sturgeon herpesvirus 1 isolated from farmed white sturgeon ( Acipenser transmontanus ). Microbiology resource announcements (2023)
Virginia-Maria Vlachava, Sepehr Seirafian, Ceri Alan Fielding, Simon Kollnberger, Rebecca J Aicheler, Joseph Hughes, Alexander Baker, Michael P Weekes, Simone Forbes, Gavin W G Wilkinson, Eddie C Y Wang, Richard James Stanton
HCMV-secreted glycoprotein gpUL4 inhibits TRAIL-mediated apoptosis and NK cell activation. Proceedings of the National Academy of Sciences of the United States of America 120 (49) (2023)
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 J Lycett, Oscar MacLean, Martin P 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, null null
The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis. PloS one 18 (4) (2023)
Derek W Wright, William T Harvey, Joseph Hughes, MacGregor Cox, Thomas P Peacock, Rachel Colquhoun, Benjamin C Jackson, Richard J Orton, Morten Nielsen, Nienyun Sharon Hsu, null null, Ewan M Harrison, Thushan I de Silva, Andrew Rambaut, Sharon J Peacock, David L Robertson, Alessandro M Carabelli
Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer. Virus evolution 8 (1) (2022)
Yao-Tsun Li, Francisco Gerardo M Polotan, Gerald Ivan S Sotelo, Anne Pauline A Alpino, Ardiane Ysabelle M Dolor, Ma Angelica A Tujan, Ma Ricci R Gomez, Othoniel Jan T Onza, Angela Kae T Chang, Criselda T Bautista, June C Carandang, Maria Sofia L Yangzon, Elcid Aaron R Pangilinan, Renato Jacinto Mantaring, Alyssa Joyce E Telles, John Michael C Egana, Joshua Jose S Endozo, Rianna Patricia S Cruz, Francis A Tablizo, Jan Michael C Yap, Benedict A Maralit, Marc Edsel C Ayes, Eva Marie C de la Paz, Cynthia P Saloma, Dodge R Lim, Lei Lanna M Dancel, Mayan Uy-Lumandas, Inez Andrea P Medado, Timothy John R Dizon, Katie Hampson, Simon Daldry, Joseph Hughes, Kirstyn Brunker
Lineage BA.2 dominated the Omicron SARS-CoV-2 epidemic wave in the Philippines. Virus evolution 8 (2) (2022)
Diego Cantoni, Gabriel Siracusano, Martin Mayora Neto, Claudia Pastori, Tobia Fantoni, Spyros Lytras, Cecilia Di Genova, Joseph Hughes, null On Behalf Of The Ambulatorio Medico San Luca Villanuova Group, Lopalco Lucia, Nigel J Temperton
Analysis of Antibody Neutralisation Activity against SARS-CoV-2 Variants and Seasonal Human Coronaviruses NL63, HKU1, and 229E Induced by Three Different COVID-19 Vaccine Platforms. Vaccines 11 (1) (2022)
Ru Xu, Xia Rong, Elihu Aranday-Cortes, Vattipally B Sreenu, Joseph Hughes, John McLauchlan, Yongshui Fu
The Transmission Route and Selection Pressure in HCV Subtype 3a and 3b Chinese Infections: Evolutionary Kinetics and Selective Force Analysis. Viruses 14 (7) (2022)
Salvatore Camiolo, Joseph Hughes, Fausto Baldanti, Milena Furione, Daniele Lilleri, Giuseppina Lombardi, Micol Angelini, Giuseppe Gerna, Maurizio Zavattoni, Andrew J Davison, Nicolás M Suárez
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus evolution 8 (2) (2022)
Diego Cantoni, Gabriel Siracusano, Martin Mayora Neto, Claudia Pastori, Tobia Fantoni, Spyros Lytras, Cecilia Di Genova, Joseph Hughes, null On Behalf Of The Ambulatorio Medico San Luca Villanuova Group, Lopalco Lucia, Nigel J Temperton
Analysis of Antibody Neutralisation Activity against SARS-CoV-2 Variants and Seasonal Human Coronaviruses NL63, HKU1, and 229E Induced by Three Different COVID-19 Vaccine Platforms. Vaccines 11 (1) (2022)
Salvatore Camiolo, Joseph Hughes, Fausto Baldanti, Milena Furione, Daniele Lilleri, Giuseppina Lombardi, Micol Angelini, Giuseppe Gerna, Maurizio Zavattoni, Andrew J Davison, Nicolás M Suárez
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus evolution 8 (2) (2022)
Salvatore Camiolo, Joseph Hughes, Fausto Baldanti, Milena Furione, Daniele Lilleri, Giuseppina Lombardi, Micol Angelini, Giuseppe Gerna, Maurizio Zavattoni, Andrew J Davison, Nicolás M Suárez
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus evolution 8 (2) (2022)
Ru Xu, Elihu Aranday-Cortes, E Carol McWilliam Leitch, Joseph Hughes, Joshua B Singer, Vattipally Sreenu, Lily Tong, Ana da Silva Filipe, Connor G G Bamford, Xia Rong, Jieting Huang, Min Wang, Yongshui Fu, John McLauchlan
The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China. Virus evolution 8 (1) (2022)
Diego Cantoni, Gabriel Siracusano, Martin Mayora Neto, Claudia Pastori, Tobia Fantoni, Spyros Lytras, Cecilia Di Genova, Joseph Hughes, null On Behalf Of The Ambulatorio Medico San Luca Villanuova Group, Lopalco Lucia, Nigel J Temperton
Analysis of Antibody Neutralisation Activity against SARS-CoV-2 Variants and Seasonal Human Coronaviruses NL63, HKU1, and 229E Induced by Three Different COVID-19 Vaccine Platforms. Vaccines 11 (1) (2022)
MacGregor Cox, Thomas P Peacock, William T Harvey, Joseph Hughes, Derek W Wright, null null, Brian J Willett, Emma C Thomson, Ravindra K Gupta, Sharon J Peacock, David L Robertson, Alessandro M Carabelli
SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature reviews. Microbiology (2022)
Sejal Modha, David L Robertson, Joseph Hughes, Richard J Orton
Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. mSystems 7 (2) (2022)
Haiting Chai, Quan Gu, David L Robertson, Joseph Hughes
Defining the characteristics of interferon-alpha-stimulated human genes: insight from expression data and machine learning. GigaScience 11 (2022)
Haiting Chai, Quan Gu, Joseph Hughes, David L Robertson
In silico prediction of HIV-1-host molecular interactions and their directionality. PLoS computational biology 18 (2) (2022)
Diego Cantoni, Gabriel Siracusano, Martin Mayora Neto, Claudia Pastori, Tobia Fantoni, Spyros Lytras, Cecilia Di Genova, Joseph Hughes, null On Behalf Of The Ambulatorio Medico San Luca Villanuova Group, Lopalco Lucia, Nigel J Temperton
Analysis of Antibody Neutralisation Activity against SARS-CoV-2 Variants and Seasonal Human Coronaviruses NL63, HKU1, and 229E Induced by Three Different COVID-19 Vaccine Platforms. Vaccines 11 (1) (2022)
Salvatore Camiolo, Joseph Hughes, Fausto Baldanti, Milena Furione, Daniele Lilleri, Giuseppina Lombardi, Micol Angelini, Giuseppe Gerna, Maurizio Zavattoni, Andrew J Davison, Nicolás M Suárez
Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples. Virus evolution 8 (2) (2022)
Spyros Lytras, Joseph Hughes, Darren P Martin, Phillip Swanepoel, Arné de Klerk, Rentia Lourens, Sergei L Kosakovsky Pond, Wei Xia, Xiaowei Jiang, David L Robertson
Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination. Genome biology and evolution 14 (2) (2022)
Brian J Willett, Joe Grove, Oscar A MacLean, Craig Wilkie, Giuditta De Lorenzo, Wilhelm Furnon, Diego Cantoni, Sam Scott, Nicola Logan, Shirin Ashraf, Maria Manali, Agnieszka Szemiel, Vanessa M Cowton, Elen Vink, William T Harvey, Chris Davis, Patawee Asamaphan, Katherine Smollett, Lily Tong, Richard Orton, Joseph Hughes, Poppy Holland, Vanessa Silva, David J Pascall, Kathryn Puxty, Ana da Silva Filipe, Gonzalo Yebra, Sharif Shaaban, Matthew T G Holden, Rute Maria Pinto, Rory Gunson, Kate Templeton, Pablo Ramiro Murcia, Arvind H Patel, Paul Klenerman, Susanna J Dunachie, null null, null null, John Haughney, David L Robertson, Massimo Palmarini, Surajit Ray, Emma C Thomson
SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature microbiology 7 (8) (2022)
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 Max 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 Amy 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 E 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
A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS biology 19 (2) (2021)
Arthur Wickenhagen, Elena Sugrue, Spyros Lytras, Srikeerthana Kuchi, Marko Noerenberg, Matthew L Turnbull, Colin Loney, Vanessa Herder, Jay Allan, Innes Jarmson, Natalia Cameron-Ruiz, Margus Varjak, Rute Maria Pinto, Jeffrey Y Lee, Louisa Iselin, Natasha Johnson, Douglas G Stewart, Simon Swingler, Edward J D Greenwood, Thomas W M Crozier, Quan Gu, Emma L Davies, Sara Clohisey Hendry, Bo Wang, Fabio Trindade Maranhão Costa, Monique Freire Santana, Luiz Carlos de Lima Ferreira, Lee Murphy, Angie Fawkes, Alison M Meynert, Graeme Grimes, null null, Joao Luiz Da Silva Filho, Matthias Marti, Joseph Hughes, Richard James Stanton, Eddie C Y Wang, Antonia Ho, Ilan Davis, Ruth F Jarrett, Alfredo Castello, David L Robertson, Malcolm Gracie Semple, Peter J M Openshaw, Massimo Palmarini, Paul J Lehner, John Kenneth Baillie, Suzannah J Rihn, Sam J Wilson
A prenylated dsRNA sensor protects against severe COVID-19. Science (New York, N.Y.) 374 (6567) (2021)
Spyros Lytras, Joseph Hughes
Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses. Viruses 12 (4) (2020)
Ana da Silva Filipe, James G Shepherd, Thomas C Williams, Joseph Hughes, Elihu Aranday-Cortes, Patawee Asamaphan, Shirin Ashraf, Carlos Balcazar, Kirstyn Brunker, Alasdair Campbell, Stephen Carmichael, Chris Davis, Rebecca Dewar, Michael D Gallagher, Rory Gunson, Verity Hill, Antonia Ho, Ben Jackson, Edward James, Natasha Jesudason, Natasha Johnson, E Carol McWilliam Leitch, Kathy Li, Alasdair MacLean, Daniel Mair, David A McAllister, John T McCrone, Sarah E McDonald, Martin P McHugh, A Keith Morris, Jenna Nichols, Marc Niebel, Kyriaki Nomikou, Richard J Orton, Áine Niamh O'Toole, Massimo Palmarini, Benjamin J Parcell, Yasmin Amy Parr, Andrew Rambaut, Stefan Rooke, Sharif Shabaan, Rajiv Shah, Joshua B Singer, Katherine Smollett, Igor Starinskij, Lily Tong, Vattipally B Sreenu, Elizabeth Wastnedge, null null, Matthew T G Holden, David L Robertson, Kate Templeton, Emma C Thomson
Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature microbiology 6 (1) (2020)
Sejal Modha, Joseph Hughes, Giovanni Bianco, Heather M Ferguson, Barbara Helm, Lily Tong, Gavin S Wilkie, Alain Kohl, Esther Schnettler
Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus. Viruses 11 (9) (2019)
Joshua B Singer, Emma C Thomson, Joseph Hughes, Elihu Aranday-Cortes, John McLauchlan, Ana da Silva Filipe, Lily Tong, Carmen F Manso, Robert James Gifford, David L Robertson, Eleanor Barnes, M Azim Ansari, Jean L Mbisa, David F Bibby, Daniel Bradshaw, David Anthony Smith
Interpreting Viral Deep Sequencing Data with GLUE. Viruses 11 (4) (2019)
Henan Zhu, Batchuluun Damdinjav, Gaelle Gonzalez, Livia Victoria Patrono, Humberto Ramírez-Mendoza, Julien A R Amat, Joanna Crispell, Yasmin Amy Parr, Toni-Ann Hammond, Enkhtuvshin Shiilegdamba, Y H Connie Leung, Malik Peiris, John F Marshall, Joseph Hughes, Martin Gilbert, Pablo Ramiro Murcia
Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds. PLoS pathogens 15 (2) (2019)
Maha Maabar, Andrew J Davison, Matej Vučak, Fiona Thorburn, Pablo R Murcia, Rory Gunson, Massimo Palmarini, Joseph Hughes
DisCVR: Rapid viral diagnosis from high-throughput sequencing data. Virus evolution 5 (2) (2019)
Bernardo Saucedo, Joseph Hughes, Annemarieke Spitzen-van der Sluijs, Natasja Kruithof, Marc Schills, Jolianne M Rijks, Mónica Jacinto-Maldonado, Nicolás M Suárez, Olga L M Haenen, Michal Voorbergen-Laarman, Jan van den Broek, Maarten Gilbert, Andrea Gröne, Steven J van Beurden, Monique H Verheije
Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.). Emerging microbes & infections 7 (1) (2018)