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Number of items: 90.

White, Rhys T., Bull, Matthew J., Barker, Clare R., Arnott, Julie M., Wootton, Mandy, Jones, Lim S., Howe, Robin A., Morgan, Mari, Ashcroft, Melinda M., Forde, Brian M., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 and Beatson, Scott A. 2024. Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales. Nature Communications 15 (1) , 1371. 10.1038/s41467-024-45608-1
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Mack, Andrew H., Menzies, Georgina ORCID: https://orcid.org/0000-0002-6600-6507, Southgate, Alex, Jones, D. Dafydd ORCID: https://orcid.org/0000-0001-7709-3995, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 and Leitner, Thomas 2023. A proofreading mutation with an allosteric effect allows a cluster of SARS-CoV-2 viruses to rapidly evolve. Molecular Biology and Evolution 40 (10) , msad209. 10.1093/molbev/msad209
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Morris, Arthur V., Price, Anna and Connor, Tom ORCID: https://orcid.org/0000-0003-2394-6504 2023. Afanc: a metagenomics tool for variant level disambiguation of NGS datasets. [Online]. bioRXiv. Available at: https://doi.org/10.1101/2023.10.05.560444
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Parfitt, Kasia M., Green, Angharad E., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Neill, Daniel R. and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2023. Identification of two distinct phylogenomic lineages and model strains for the understudied cystic fibrosis lung pathogen Burkholderia multivorans. Microbiology 169 (8) , 001366. 10.1099/mic.0.001366
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Tsui, Joseph L.-H., McCrone, John T., Lambert, Ben, Bajaj, Sumali, Inward, Rhys P. D., Bosetti, Paolo, Pena, Rosario Evans, Tegally, Houriiyah, Hill, Verity, Zarebski, Alexander E., Peacock, Thomas P., Liu, Luyang, Wu, Neo, Davis, Megan, Bogoch, Isaac I., Khan, Kamran, Kall, Meaghan, Abdul Aziz, Nurin Iwani Binti, Colquhoun, Rachel, O'Toole, Áine, Jackson, Ben, Dasgupta, Abhishek, Wilkinson, Eduan, de Oliveira, Tulio, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Loman, Nicholas J., Colizza, Vittoria, Fraser, Christophe, Volz, Erik, Ji, Xiang, Gutierrez, Bernardo, Chand, Meera, Dellicour, Simon, Cauchemez, Simon, Raghwani, Jayna, Suchard, Marc A., Lemey, Philippe, Rambaut, Andrew, Pybus, Oliver G. and Kraemer, Moritz U. G. 2023. Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1. Science 381 (6655) , pp. 336-343. 10.1126/science.adg6605
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Pacchiarini, Nicole ORCID: https://orcid.org/0000-0001-5383-6053, Cronin, Michelle, Sawyer, Clare, Williams, Catie, Beazer, Andrew, Cottrell, Simon, Morgan, Mari, Saunders, Vince, Moore, Catherine, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 and Williams, Christopher 2023. Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK. Microbial Genomics 9 (4) , 000984. 10.1099/mgen.0.000984
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Cotton, S., McHugh, M.P., Dewar, R., Haas, J.G., Templeton, K., Robson, Samuel C., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Loman, Nicholas J., Golubchik, Tanya, Martinez Nunez, Rocio T., Bonsall, David, Rambaut, Andrew, Snell, Luke B., Livett, Rich, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Johnston, Ian, Prieto, Jacqui A., Saeed, Kordo, Jackson, David K., Houlihan, Catherine, Frampton, Dan, Hamilton, William L., Witney, Adam A., Bucca, Giselda, Pope, Cassie F., Moore, Catherine, Thomson, Emma C., Cutino-Moguel, Teresa, Harrison, Ewan M., Smith, Colin P., Rogan, Fiona, Beckwith, Shaun M., Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A., Randell, Paul, Jackson, Leigh M., Ariani, Cristina V., Gonçalves, Sónia, Fairley, Derek J., Loose, Matthew W., Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Amato, Roberto, Smith, Darren L., Aanensen, David M., Barrett, Jeffrey C., Kele, Beatrix, Aggarwal, Dinesh, Shepherd, James G., Curran, Martin D., Parmar, Surendra, Parker, Matthew D., Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P., Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F., Byott, Matthew, Carabelli, Alessandro M., Templeton, Kate E., Peacock, Sharon J., de Silva, Thushan I., Wang, Dennis, Langford, Cordelia F., Sillitoe, John, Gunson, Rory N., Cottrell, Simon, O'Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J., Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J., Mahungu, Tabitha W., Liggett, Steven, Beckett, Angela H., Holden, Matthew TG., Levett, Lisa J., Osman, Husam, Hassan-Ibrahim, Mohammed O., Simpson, David A., Chand, Meera, Gupta, Ravi K., Darby, Alistair C., Paterson, Steve, Pybus, Oliver G., Volz, Erik M., de Angelis, Daniela, Robertson, David L., Page, Andrew J., Martincorena, Inigo, Aigrain, Louise, Bassett, Andrew R., Wong, Nick, Taha, Yusri, Erkiert, Michelle J., Spencer Chapman, Michael H., Dewar, Rebecca, McHugh, Martin P., Mookerjee, Siddharth, Aplin, Stephen, Harvey, Matthew, Sass, Thea, Umpleby, Helen, Wheeler, Helen, McKenna, James P., Warne, Ben, Taylor, Joshua F., Chaudhry, Yasmin, Izuagbe, Rhys, Jahun, Aminu S., Young, Gregory R., McMurray, Claire, McCann, Clare M., Nelson, Andrew, Elliott, Scott, Lowe, Hannah, Price, Anna, Crown, Matthew R., Rey, Sara, Roy, Sunando, Temperton, Ben, Shaaban, Sharif, Hesketh, Andrew R., Laing, Kenneth G., Monahan, Irene M., Heaney, Judith, Pelosi, Emanuela, Silviera, Siona, Wilson-Davies, Eleri, Fryer, Helen, Adams, Helen, du Plessis, Louis, Johnson, Rob, Harvey, William T., Hughes, Joseph, Orton, Richard J., Spurgin, Lewis G., Bourgeois, Yann, Ruis, Chris, O'Toole, Áine, Gourtovaia, Marina, Sanderson, Theo, Fraser, Christophe, Edgeworth, Jonathan, Breuer, Judith, Michell, Stephen L., Todd, John A., John, Michaela, Buck, David, Gajee, Kavitha, Kay, Gemma L., Heyburn, David, Charalampous, Themoula, Alcolea-Medina, Adela, Kitchman, Katie, McNal, Alan, Pritch, David T., Dervisevic, Samir, Muir, Peter, Robinson, Esther, Vipond, Barry B., Ramadan, Newara A., Jeanes, Christopher, Weldon, Danni, Catalan, Jana, Jones, Neil, da Silva Filipe, Ana, Williams, Chris, Fuchs, Marc, Miskelly, Julia, Jeffries, Aaron R., Oliver, Karen, Park, Naomi R., Ash, Amy, Koshy, Cherian, Barrow, Magdalena, Buchan, Sarah L., Mantzouratou, Anna, Clark, Gemma, Holmes, Christopher W., Campbell, Sharon, Davis, Thomas, Tan, Ngee Keong, Brown, Julianne R., Harris, Kathryn A., Kidd, Stephen P., Grant, Paul R., Xu-McCrae, Li, Cox, Alison, Madona, Pinglawathee, Pond, Marcus, Randell, Paul A., Withell, Karen T., Williams, Cheryl, Graham, Clive, Denton-Smith, Rebecca, Swindells, Emma, Turnbull, Robyn, Sloan, Tim J., Bosworth, Andrew, Hutchings, Stephanie, Pymont, Hannah M., Casey, Anna, Ratcliffe, Liz, Jones, Christopher R., Knight, Bridget A., Haque, Tanzina, Hart, Jennifer, Irish-Tavares, Dianne, Witele, Eric, Mower, Craig, Watson DipHE, Louisa K., Collins, Jennifer, Eltringham, Gary, Crudgington, Dorian, Macklin, Ben, Iturriza-Gomara, Miren, Lucaci, Anita O., McClure, Patrick C., Carlile, Matthew, Holmes, Nadine, Moore, Christopher, Storey, Nathaniel, Rooke, Stefan, Yebra, Gonzalo, Craine, Noel, Perry, Malorie, Alikhan, Nabil-Fareed, Bridgett, Stephen, Cook, Kate F., Fearn, Christopher, Goudarzi, Salman, Lyons, Ronan A., Williams, Thomas, Haldenby, Sam T., Durham, Jillian, Leonard, Steven, Davies, Robert M., Batra, Rahul, Blane, Beth, Spyer, Moira J., Smith, Perminder, Yavus, Mehmet, Williams, Rachel J., Mahanama, Adhyana IK., Samaraweera, Buddhini, Girgis, Sophia T., Hansford, Samantha E., Green, Angie, Beaver, Charlotte, Bellis, Katherine L., Dorman, Matthew J., Kay, Sally, Prestwood, Liam, Rajatileka, Shavanthi, Quick, Joshua, Poplawski, Radoslaw, Reynolds, Nicola, Mack, Andrew, Morris, Arthur, Whalley, Thomas, Patel, Bindi, Georgana, Iliana, Hosmillo, Myra, Pinckert, Malte L., Stockton, Joanne, Henderson, John H., Hollis, Amy, Stanley, William, Yew, Wen C., Myers, Richard, Thornton, Alicia, Adams, Alexander, Annett, Tara, Asad, Hibo, Birchley, Alec, Coombes, Jason, Evans, Johnathan M., Fina, Laia, Gatica-Wilcox, Bree, Gilbert, Lauren, Graham, Lee, Hey, Jessica, Hilvers, Ember, Jones, Sophie, Jones, Hannah, Kumziene-Summerhayes, Sara, McKerr, Caoimhe, Powell, Jessica, Pugh, Georgia, Taylor, Sarah, Trotter, Alexander J., Williams, Charlotte A., Kermack, Leanne M., Foulkes, Benjamin H., Gallis, Marta, Hornsby, Hailey R., Louka, Stavroula F., Pohare, Manoj, Wolverson, Paige, Zhang, Peijun, MacIntyre-Cockett, George, Trebes, Amy, Moll, Robin J., Ferguson, Lynne, Goldstein, Emily J., Maclean, Alasdair, Tomb, Rachael, Starinskij, Igor, Thomson, Laura, Southgate, Joel, Kraemer, Moritz UG., Raghwani, Jayna, Zarebski, Alex E., Boyd, Olivia, Geidelberg, Lily, Illingworth, Chris J., Jackson, Chris, Pascall, David, Vattipally, Sreenu, Freeman, Timothy M., Hsu, Sharon N., Lindsey, Benjamin B., James, Keith, Lewis, Kevin, Tonkin-Hill, Gerry, Tovar-Corona, Jaime M., Cox, MacGregor, Abudahab, Khalil, Menegazzo, Mirko, Taylor, Ben EW., Yeats, Corin A., Mukaddas, Afrida, Wright, Derek W., de Oliveira Martins, Leonardo, Colquhoun, Rachel, Hill, Verity, Jackson, Ben, McCrone, J.T., Medd, Nathan, Scher, Emily, Keatley, Jon-Paul, Curran, Tanya, Morgan, Sian, Maxwell, Patrick, Smith, Ken, Eldirdiri, Sahar, Kenyon, Anita, Holmes, Alison H., Price, James R., Wyatt, Tim, Mather, Alison E., Skvortsov, Timofey, Hartley, John A., Guest, Martyn, Kitchen, Christine, Merrick, Ian, Munn, Robert, Bertolusso, Beatrice, Lynch, Jessica, Vernet, Gabrielle, Kirk, Stuart, Wastnedge, Elizabeth, Stanley, Rachael, Idle, Giles, Bradley, Declan T., Killough, Nicholas F., Poyner, Jennifer, Mori, Matilde, Jones, Owen, Wright, Victoria, Brooks, Ellena, Churcher, Carol M., Delgado Callico, Laia, Fragakis, Mireille, Galai, Katerina, Jermy, Andrew, Judges, Sarah, Markov, Anna, McManus, Georgina M., Smith, Kim S., Thomas-McEwen, Peter MD., Westwick, Elaine, Attwood, Stephen W., Bolt, Frances, Davies, Alisha, De Lacy, Elen, Downing, Fatima, Edwards, Sue, Meadows, Lizzie, Jeremiah, Sarah, Smith, Nikki, Foulser, Luke, Patel, Amita, Berry, Louise, Boswell, Tim, Fleming, Vicki M., Howson-Wells, Hannah C., Joseph, Amelia, Khakh, Manjinder, Lister, Michelle M., Bird, Paul W., Fallon, Karlie, Helmer, Thomas, McMurray, Claire L., Odedra, Mina, Shaw, Jessica, Tang, Julian W., Willford, Nicholas J., Blakey, Victoria, Raviprakash, Veena, Sheriff, Nicola, Williams, Lesley-Anne, Feltwell, Theresa, Bedford, Luke, Cargill, James S., Hughes, Warwick, Moore, Jonathan, Stonehouse, Susanne, Atkinson, Laura, Lee, Jack CD., Shah, Divya, Ohemeng-Kumi, Natasha, Ramble, John, Sehmi, Jasveen, Williams, Rebecca, Chatterton, Wendy, Pusok, Monika, Everson, William, Castigador, Anibolina, Macnaughton, Emily, El Bouzidi, Kate, Lampejo, Temi, Sudhanva, Malur, Breen, Cassie, Sluga, Graciela, Ahmad, Shazaad SY., George, Ryan P., Machin, Nicholas W., Binns, Debbie, James, Victoria, Blacow, Rachel, Coupland, Lindsay, Smith, Louise, Barton, Edward, Padgett, Debra, Scott, Garren, Cross, Aidan, Mirfenderesky, Mariyam, Greenaway, Jane, Cole, Kevin, Clarke, Phillip, Duckworth, Nichola, Walsh, Sarah, Bicknell, Kelly, Impey, Robert, Wyllie, Sarah, Hopes, Richard, Bishop, Chloe, Chalker, Vicki, Harrison, Ian, Gifford, Laura, Molnar, Zoltan, Auckland, Cressida, Evans, Cariad, Johnson, Kate, Partridge, David G., Raza, Mohammad, Baker, Paul, Bonner, Stephen, Essex, Sarah, Murray, Leanne J., Lawton, Andrew I., Burton-Fanning, Shirelle, Payne, Brendan AI., Waugh, Sheila, Gomes, Andrea N., Kimuli, Maimuna, Murray, Darren R., Ashfield, Paula, Dobie, Donald, Ashford, Fiona, Best, Angus, Crawford, Liam, Cumley, Nicola, Mayhew, Megan, Megram, Oliver, Mirza, Jeremy, Moles-Garcia, Emma, Percival, Benita, Driscoll, Megan, Ensell, Leah, Lowe, Helen L., Maftei, Laurentiu, Mondani, Matteo, Chaloner, Nicola J., Cogger, Benjamin J., Easton, Lisa J., Huckson, Hannah, Lewis, Jonathan, Lowdon, Sarah, Malone, Cassandra S., Munemo, Florence, Mutingwende, Manasa, Nicodemi, Roberto, Podplomyk FD, Olga, Somassa, Thomas, Beggs, Andrew, Richter, Alex, Cormie, Claire, Dias, Joana, Forrest, Sally, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Davidson, Rose K., Jackson, Kathryn A., Keeley, Alexander J., Ball, Jonathan, Byaruhanga, Timothy, Chappell, Joseph G., Dey, Jayasree, Hill, Jack D., Park, Emily J., Fanaie, Arezou, Hilson, Rachel A., Yaze, Geraldine, Lo, Stephanie, Afifi, Safiah, Beer, Robert, Maksimovic, Joshua, McCluggage, Kathryn, Spellman, Karla, Bresner, Catherine, Fuller, William, Marchbank, Angela, Workma, Trudy, Shelest, Ekaterina, Debebe, Johnny, Sang, Fei, Francois, Sarah, Gutierrez, Bernardo, Vasylyeva, Tetyana I., Flaviani, Flavia, Ragonnet-Cronin, Manon, Smollett, Katherine L., Broos, Alice, Mair, Daniel, Nichols, Jenna, Nomikou, Kyriaki, Tong, Lily, Tsatsani, Ioulia, O'Brien, Sarah, Rushton, Steven, Sanderson, Roy, Perkins, Jon, Cotton, Seb, Gallagher, Abbie, Allara, Elias, Pearson, Clare, Bibby, David, Dabrer, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Hubb, Jonathan, Lackenby, Angie, Lee, David, Manesis, Nikos, Mbisa, Tamyo, Platt, Steven, Twohig, Katherine A., Morgan, Mari, Aydin, Alp, Baker, David J., Foster-Nyarko, Ebenezer, Prosolek, Sophie J., Rudder, Steven, Baxter, Chris, Carvalho, Sílvia F., Lavin, Deborah, Mariappan, Arun, Radulescu, Clara, Singh, Aditi, Tang, Miao, Morcrette, Helen, Bayzid, Nadua, Cotic, Marius, Balcazar, Carlos E., Gallagher, Michael D., Maloney, Daniel, Stanton, Thomas D., Williamson, Kathleen A., Manley, Robin, Michelsen, Michelle L., Sambles, Christine M., Studholme, David J., Warwick-Dugdale, Joanna, Eccles, Richard, Gemmell, Matthew, Gregory, Richard, Hughes, Margaret, Nelson, Charlotte, Rainbow, Lucille, Vamos, Edith E., Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Angyal, Adrienn, Green, Luke R., Whiteley, Max, Betteridge, Emma, Bronner, Iraad F., Farr, Ben W., Goodwin, Scott, Lensing, Stefanie V., McCarthy, Shane A., Quail, Michael A., Rajan, Diana, Redshaw, Nicholas M., Scott, Carol, Shirley, Lesley, Thurston, Scott AJ., Rowe, Will, Gaskin, Amy, Le-Viet, Thanh, Bonfield, James, Liddle, Jennifier and Whitwham, Andrew 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection 135 , pp. 28-36. 10.1016/j.jhin.2023.02.010
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O'Connell, L., Asad, H., Hall, G., Jones, T., Walters, J., Manchipp-Taylor, L., Barry, J., Keighan, D., Jones, H., Williams, C., Cronin, M., Hughes, H., Morgan, M., Connor, T.R. ORCID: https://orcid.org/0000-0003-2394-6504 and Healy, B. 2023. Detailed analysis of in-hospital transmission of SARS-CoV-2 using whole genome sequencing. Journal of Hospital Infection 131 , pp. 23-33. 10.1016/j.jhin.2022.09.023

Cunningham-Oakes, Edward, Pointon, Tom, Murphy, Barry, Connor, Thomas R ORCID: https://orcid.org/0000-0003-2394-6504 and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2022. Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products – a 2 retrospective, real-time analysis. Microbial Genomics 8 (11) , 000884. 10.1099/mgen.0.000884
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McCrone, John T., Hill, Verity, Bajaj, Sumali, Evans Pena, Rosario, Lambert, Ben C., Inward, Rhys, Bhatt, Samir and Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504 2022. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature 610 , pp. 154-160. 10.1038/s41586-022-05200-3
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Attwood, Stephen W., Hill, Sarah C., Aanensen, David M., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 and Pybus, Oliver G. 2022. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nature Reviews Genetics 23 , pp. 547-562. 10.1038/s41576-022-00483-8
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Willett, Brian J., Grove, Joe, MacLean, Oscar A., Wilkie, Craig, De Lorenzo, Giuditta, Furnon, Wilhelm, Cantoni, Diego, Scott, Sam, Logan, Nicola, Ashraf, Shirin, Manali, Maria, Szemiel, Agnieszka, Cowton, Vanessa, Vink, Elen, Harvey, William T., Davis, Chris, Asamaphan, Patawee, Smollett, Katherine, Tong, Lily, Orton, Richard, Hughes, Joseph, Holland, Poppy, Silva, Vanessa, Pascall, David J., Puxty, Kathryn, da Silva Filipe, Ana, Yebra, Gonzalo, Shaaban, Sharif, Holden, Matthew T. G., Pinto, Rute Maria, Gunson, Rory, Templeton, Kate, Murcia, Pablo R., Patel, Arvind H., Klenerman, Paul, Dunachie, Susanna, Dunachie, Susanna, Klenerman, Paul, Barnes, Eleanor, Brown, Anthony, Adele, Sandra, Kronsteiner, Barbara, Murray, Sam M., Abraham, Priyanka, Deeks, Alexandra, Ansari, M. Azim, de Silva, Thushan, Turtle, Lance, Moore, Shona, Austin, James, Richter, Alex, Duncan, Christopher, Payne, Rebecca, Ash, Amy, Koshy, Cherian, Kele, Beatrix, Cutino-Moguel, Teresa, Fairley, Derek J., McKenna, James P., Curran, Tanya, Adams, Helen, Fraser, Christophe, Bonsall, David, Fryer, Helen, Lythgoe, Katrina, Thomson, Laura, Golubchik, Tanya, Murray, Abigail, Singleton, Dawn, Beckwith, Shaun M., Mantzouratou, Anna, Barrow, Magdalena, Buchan, Sarah L., Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Mack, Andrew, Marchbank, Angela, Price, Anna, Morris, Arthur, Bresner, Catherine, Kitchen, Christine, Merrick, Ian, Southgate, Joel, Guest, Martyn, Jones, Owen, Munn, Robert, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Whalley, Thomas, Workman, Trudy, Fuller, William, Patel, Amita, Patel, Bindi, Nebbia, Gaia, Edgeworth, Jonathan, Snell, Luke B., Batra, Rahul, Charalampous, Themoula, Beckett, Angela H., Shelest, Ekaterina, Robson, Samuel C., Underwood, Anthony P., Taylor, Ben E. W., Yeats, Corin A., Aanensen, David M., Abudahab, Khalil, Menegazzo, Mirko, Joseph, Amelia, Clark, Gemma, Howson-Wells, Hannah C., Berry, Louise, Khakh, Manjinder, Lister, Michelle M., Boswell, Tim, Fleming, Vicki M., Holmes, Christopher W., McMurray, Claire L., Shaw, Jessica, Tang, Julian W., Fallon, Karlie, Odedra, Mina, Willford, Nicholas J., Bird, Paul W., Helmer, Thomas, Williams, Lesley-Anne, Sheriff, Nicola, Campbell, Sharon, Raviprakash, Veena, Blakey, Victoria, Moore, Christopher, Sang, Fei, Debebe, Johnny, Carlile, Matthew, Loose, Matthew W., Holmes, Nadine, Wright, Victoria, Torok, M. Estee, Hamilton, William L., Carabelli, Alessandro M., Jermy, Andrew, Blane, Beth, Churcher, Carol M., Ludden, Catherine, Aggarwal, Dinesh, Westwick, Elaine, Brooks, Ellena, McManus, Georgina M., Galai, Katerina, Smith, Ken, Smith, Kim S., Cox, MacGregor, Fragakis, Mireille, Maxwell, Patrick, Judges, Sarah, Peacock, Sharon J., Feltwell, Theresa, Kenyon, Anita, Eldirdiri, Sahar, Davis, Thomas, Taylor, Joshua F., Tan, Ngee Keong, Zarebski, Alex E., Gutierrez, Bernardo, Raghwani, Jayna, du Plessis, Louis, Kraemer, Moritz U. G., Pybus, Oliver G., Francois, Sarah, Attwood, Stephen W., Vasylyeva, Tetyana I., Jahun, Aminu S., Goodfellow, Ian G., Georgana, Iliana, Pinckert, Malte L., Hosmillo, Myra, Izuagbe, Rhys, Chaudhry, Yasmin, Ryan, Felicity, Lowe, Hannah, Moses, Samuel, Bedford, Luke, Cargill, James S., Hughes, Warwick, Moore, Jonathan, Stonehouse, Susanne, Shah, Divya, Lee, Jack C. D., Brown, Julianne R., Harris, Kathryn A., Atkinson, Laura, Storey, Nathaniel, Spyer, Moira J., Flaviani, Flavia, Alcolea-Medina, Adela, Sehmi, Jasveen, Ramble, John, Ohemeng-Kumi, Natasha, Smith, Perminder, Bertolusso, Beatrice, Thomas, Claire, Vernet, Gabrielle, Lynch, Jessica, Moore, Nathan, Cortes, Nicholas, Williams, Rebecca, Kidd, Stephen P., Levett, Lisa J., Pusok, Monika, Grant, Paul R., Kirk, Stuart, Chatterton, Wendy, Xu-McCrae, Li, Smith, Darren L., Young, Gregory R., Bashton, Matthew, Kitchman, Katie, Gajee, Kavitha, Eastick, Kirstine, Lillie, Patrick J., Burns, Phillipa J., Everson, William, Cox, Alison, Holmes, Alison H., Bolt, Frances, Price, James R., Pond, Marcus, Randell, Paul A., Madona, Pinglawathee, Mookerjee, Siddharth, Volz, Erik M., Geidelberg, Lily, Ragonnet-Cronin, Manon, Boyd, Olivia, Johnson, Rob, Pope, Cassie F., Witney, Adam A., Monahan, Irene M., Laing, Kenneth G., Smollett, Katherine L., McNally, Alan, McMurray, Claire, Stockton, Joanne, Quick, Joshua, Loman, Nicholas J., Poplawski, Radoslaw, Nicholls, Sam, Rowe, Will, Castigador, Anibolina, Macnaughton, Emily, Bouzidi, Kate El, Sudhanva, Malur, Lampejo, Temi, Martinez Nunez, Rocio T., Breen, Cassie, Sluga, Graciela, Withell, Karen T., Machin, Nicholas W., George, Ryan P., Ahmad, Shazaad S. Y., Pritchard, David T., Binns, Debbie, Wong, Nick, James, Victoria, Williams, Cheryl, Illingworth, Chris J., Jackson, Chris, de Angelis, Daniela, Pascall, David, Mukaddas, Afrida, Broos, Alice, da Silva Filipe, Ana, Mair, Daniel, Robertson, David L., Wright, Derek W., Thomson, Emma C., Starinskij, Igor, Tsatsani, Ioulia, Shepherd, James G., Nichols, Jenna, Hughes, Joseph, Nomikou, Kyriaki, Tong, Lily, Orton, Richard J., Vattipally, Sreenu, Harvey, William T., Sanderson, Roy, O'Brien, Sarah, Rushton, Steven, Perkins, Jon, Blacow, Rachel, Gunson, Rory N., Gallagher, Abbie, Wastnedge, Elizabeth, Templeton, Kate E., McHugh, Martin P., Dewar, Rebecca, Cotton, Seb, Coupland, Lindsay, Stanley, Rachael, Dervisevic, Samir, Spurgin, Lewis G., Smith, Louise, Graham, Clive, Padgett, Debra, Barton, Edward, Scott, Garren, Cross, Aidan, Mirfenderesky, Mariyam, Swindells, Emma, Greenaway, Jane, Denton-Smith, Rebecca, Turnbull, Robyn, Idle, Giles, Cole, Kevin, Hollis, Amy, Nelson, Andrew, McCann, Clare M., Henderson, John H., Crown, Matthew R., Yew, Wen C., Stanley, William, Duckworth, Nichola, Clarke, Phillip, Walsh, Sarah, Sloan, Tim J., Bicknell, Kelly, Impey, Robert, Wyllie, Sarah, Elliott, Scott, Glaysher, Sharon, Bradley, Declan T., Killough, Nicholas F., Wyatt, Tim, Bosworth, Andrew, Vipond, Barry B., Pearson, Clare, Allara, Elias, Robinson, Esther, Pymont, Hannah M., Osman, Husam, Muir, Peter, Hopes, Richard, Hutchings, Stephanie, Curran, Martin D., Parmar, Surendra, Thornton, Alicia, Lackenby, Angie, Bishop, Chloe, Bibby, David, Lee, David, Gallagher, Eileen, Dabrera, Gavin, Harrison, Ian, Hubb, Jonathan, Twohig, Katherine A., Chand, Meera, Ellaby, Nicholas, Manesis, Nikos, Myers, Richard, Platt, Steven, Mbisa, Tamyo, Chalker, Vicki, Yebra, Gonzalo, Holden, Matthew T. G., Shaaban, Sharif, Rooke, Stefan, Birchley, Alec, Adams, Alexander, Davies, Alisha, Gaskin, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Moore, Catherine, Williams, Catryn, Williams, Chris, Heyburn, David, De Lacy, Elen, Hilvers, Ember, Downing, Fatima, Pugh, Georgia, Jones, Hannah, Asad, Hibo, Coombes, Jason, Hey, Jessica, Powell, Jessica, Watkins, Joanne, Evans, Johnathan M., Fina, Laia, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Perry, Malorie, Morgan, Mari, Bull, Matthew, Pacchiarini, Nicole, Craine, Noel, Corden, Sally, Kumziene-Summerhayes, Sara, Rey, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, Annett, Tara, Trotter, Alexander J., Mather, Alison E., Aydin, Alp, Page, Andrew J., Baker, David J., Foster-Nyarko, Ebenezer, Kay, Gemma L., O'Grady, Justin, de Oliveira Martins, Leonardo, Meadows, Lizzie, Alikhan, Nabil-Fareed, Prosolek, Sophie J., Rudder, Steven, Le-Viet, Thanh, Casey, Anna, Ratcliffe, Liz, Singh, Aditi, Mariappan, Arun, Baxter, Chris, Radulescu, Clara, Simpson, David A., Lavin, Deborah, Rogan, Fiona, Miskelly, Julia, Fuchs, Marc, Tang, Miao, Carvalho, Sílvia F., Bridgett, Stephen, Skvortsov, Timofey, Molnar, Zoltan, Ramadan, Newara A., Knight, Bridget A., Jones, Christopher R., Auckland, Cressida, Morcrette, Helen, Poyner, Jennifer, Irish-Tavares, Dianne, Witele, Eric, Hart, Jennifer, Mahungu, Tabitha W., Haque, Tanzina, Bourgeois, Yann, Fearn, Christopher, Cook, Kate F., Loveson, Katie F., Goudarzi, Salman, Evans, Cariad, Partridge, David G., Johnson, Kate, Yavus, Mehmet, Raza, Mohammad, Mower, Craig, Baker, Paul, Essex, Sarah, Bonner, Stephen, Murray, Leanne J., Watson, Louisa K., Liggett, Steven, Lawton, Andrew I., Lyons, Ronan A., Payne, Brendan A. 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K., Samaraweera, Buddhini, Wilson-Davies, Eleri, Pelosi, Emanuela, Umpleby, Helen, Wheeler, Helen, Prieto, Jacqui A., Saeed, Kordo, Harvey, Matthew, Jeremiah, Sarah, Silviera, Siona, Aplin, Stephen, Sass, Thea, Macklin, Ben, Crudgington, Dorian, Sheridan, Liz A., Cogger, Benjamin J., Malone, Cassandra S., Munemo, Florence, Huckson, Hannah, Lewis, Jonathan, Easton, Lisa J., Mutingwende, Manasa, Erkiert, Michelle J., Hassan-Ibrahim, Mohammed O., Chaloner, Nicola J., Podplomyk, Olga, Randell, Paul, Nicodemi, Roberto, Lowdon, Sarah, Somassa, Thomas, Richter, Alex, Beggs, Andrew, Hesketh, Andrew R., Smith, Colin P., Bucca, Giselda, Ruis, Chris, Cormie, Claire, Higginson, Ellen E., Young, Jamie, Dias, Joana, Kermack, Leanne M., Maes, Mailis, Gupta, Ravi K., Forrest, Sally, Girgis, Sophia T., Davidson, Rose K., O'Toole, Áine, Rambaut, Andrew, Jackson, Ben, Balcazar, Carlos E., Maloney, Daniel, Scher, Emily, McCrone, J. 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Dolton, Garry, Rius, Cristina, Hasan, Md Samiul, Wall, Aaron, Szomolay, Barbara ORCID: https://orcid.org/0000-0002-5375-5533, Behiry, Enas, Whalley, Thomas, Southgate, Joel, Fuller, Anna, Morin, Théo, Topley, Katie, Tan, Li Rong, Goulder, Philip J.R., Spiller, Owen B. ORCID: https://orcid.org/0000-0002-9117-6911, Rizkallah, Pierre J. ORCID: https://orcid.org/0000-0002-9290-0369, Jones, Lucy C. ORCID: https://orcid.org/0000-0002-3872-4376, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 and Sewell, Andrew K. ORCID: https://orcid.org/0000-0003-3194-3135 2022. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 185 (16) , pp. 2936-2951. 10.1016/j.cell.2022.07.002
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Eales, Oliver, Page, Andrew J., de Oliveira Martins, Leonardo, Wang, Haowei, Bodinier, Barbara, Haw, David, Jonnerby, Jakob, Atchison, Christina, Robson, Samuel C., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Loman, Nicholas J., Golubchik, Tanya, Nunez, Rocio T. Martinez, Bonsall, David, Rambaut, Andrew, Snell, Luke B., Livett, Rich, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Johnston, Ian, Lythgoe, Katrina, Torok, M. Estee, Goodfellow, Ian G., Prieto, Jacqui A., Saeed, Kordo, Jackson, David K., Houlihan, Catherine, Frampton, Dan, Hamilton, William L., Witney, Adam A., Bucca, Giselda, Pope, Cassie F., Moore, Catherine, Thomson, Emma C., Harrison, Ewan M., Smith, Colin P., Rogan, Fiona, Beckwith, Shaun M., Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A., Randell, Paul, Jackson, Leigh M., Ariani, Cristina V., Gonçalves, Sónia, Fairley, Derek J., Loose, Matthew W., Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Amato, Roberto, Smith, Darren L., Aanensen, David M., Barrett, Jeffrey C., Aggarwal, Dinesh, Shepherd, James G., Curran, Martin D., Parmar, Surendra, Parker, Matthew D., Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P., Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F., Byott, Matthew, Carabelli, Alessandro M., Templeton, Kate E., de Silva, Thushan I., Wang, Dennis, Langford, Cordelia F., Sillitoe, John, Gunson, Rory N., Cottrell, Simon, O'Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J., Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J., Mahungu, Tabitha W., Liggett, Steven, Beckett, Angela H., Holden, Matthew T. 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D., Shah, Divya, Alcolea-Medina, Adela, Ohemeng-Kumi, Natasha, Ramble, John, Sehmi, Jasveen, Williams, Rebecca, Chatterton, Wendy, Pusok, Monika, Everson, William, Castigador, Anibolina, Macnaughton, Emily, Bouzidi, Kate El, Lampejo, Temi, Sudhanva, Malur, Breen, Cassie, Sluga, Graciela, Ahmad, Shazaad S. Y., George, Ryan P., Machin, Nicholas W., Binns, Debbie, James, Victoria, Blacow, Rachel, Coupland, Lindsay, Smith, Louise, Barton, Edward, Padgett, Debra, Scott, Garren, Cross, Aidan, Mirfenderesky, Mariyam, Greenaway, Jane, Cole, Kevin, Clarke, Phillip, Duckworth, Nichola, Walsh, Sarah, Bicknell, Kelly, Impey, Robert, Wyllie, Sarah, Hopes, Richard, Bishop, Chloe, Chalker, Vicki, Harrison, Ian, Gifford, Laura, Molnar, Zoltan, Auckland, Cressida, Evans, Cariad, Johnson, Kate, Partridge, David G., Raza, Mohammad, Baker, Paul, Bonner, Stephen, Essex, Sarah, Murray, Leanne J., Lawton, Andrew I., Burton-Fanning, Shirelle, Payne, Brendan A. I., Waugh, Sheila, Gomes, Andrea N., Kimuli, Maimuna, Murray, Darren R., Ashfield, Paula, Dobie, Donald, Ashford, Fiona, Best, Angus, Crawford, Liam, Cumley, Nicola, Mayhew, Megan, Megram, Oliver, Mirza, Jeremy, Moles-Garcia, Emma, Percival, Benita, Driscoll, Megan, Ensell, Leah, Lowe, Helen L., Maftei, Laurentiu, Mondani, Matteo, Chaloner, Nicola J., Cogger, Benjamin J., Easton, Lisa J., Huckson, Hannah, Lewis, Jonathan, Lowdon, Sarah, Malone, Cassandra S., Munemo, Florence, Mutingwende, Manasa, Nicodemi, Roberto, Podplomyk, Olga, Somassa, Thomas, Beggs, Andrew, Richter, Alex, Cormie, Claire, Dias, Joana, Forrest, Sally, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Davidson, Rose K., Jackson, Kathryn A., Turtle, Lance, Keeley, Alexander J., Ball, Jonathan, Byaruhanga, Timothy, Chappell, Joseph G., Dey, Jayasree, Hill, Jack D., Park, Emily J., Fanaie, Arezou, Hilson, Rachel A., Yaze, Geraldine, Lo, Stephanie, Afifi, Safiah, Beer, Robert, Maksimovic, Joshua, McCluggage, Kathryn, Spellman, Karla, Bresner, Catherine, Fuller, William, Marchbank, Angela, Workman, Trudy, Shelest, Ekaterina, Debebe, Johnny, Sang, Fei, Zamudio, Marina Escalera, Francois, Sarah, Gutierrez, Bernardo, Vasylyeva, Tetyana I., Flaviani, Flavia, Ragonnet-Cronin, Manon, Smollett, Katherine L., Broos, Alice, Mair, Daniel, Nichols, Jenna, Nomikou, Kyriaki, Tong, Lily, Tsatsani, Ioulia, O?Brien, Prof Sarah, Rushton, Steven, Sanderson, Roy, Perkins, Jon, Cotton, Seb, Gallagher, Abbie, Allara, Elias, Pearson, Clare, Bibby, David, Dabrera, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Hubb, Jonathan, Lackenby, Angie, Lee, David, Manesis, Nikos, Mbisa, Tamyo, Platt, Steven, Twohig, Katherine A., Morgan, Mari, Aydin, Alp, Baker, David J., Foster-Nyarko, Ebenezer, Prosolek, Sophie J., Rudder, Steven, Baxter, Chris, Carvalho, Sílvia F., Lavin, Deborah, Mariappan, Arun, Radulescu, Clara, Singh, Aditi, Tang, Miao, Morcrette, Helen, Bayzid, Nadua, Cotic, Marius, Balcazar, Carlos E., Gallagher, Michael D., Maloney, Daniel, Stanton, Thomas D., Williamson, Kathleen A., Manley, Robin, Michelsen, Michelle L., Sambles, Christine M., Studholme, David J., Warwick-Dugdale, Joanna, Eccles, Richard, Gemmell, Matthew, Gregory, Richard, Hughes, Margaret, Nelson, Charlotte, Rainbow, Lucille, Vamos, Edith E., Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Angyal, Adrienn, Green, Luke R., Whiteley, Max, Betteridge, Emma, Bronner, Iraad F., Farr, Ben W., Goodwin, Scott, Lensing, Stefanie V., McCarthy, Shane A., Quail, Michael A., Rajan, Diana, Redshaw, Nicholas M., Scott, Carol, Shirley, Lesley, Thurston, Scott A. J., Rowe, Will, Gaskin, Amy, Le-Viet, Thanh, Bonfield, James, Liddle, Jennifier, Whitwham, Andrew, Ashby, Deborah, Barclay, Wendy, Taylor, Graham, Cooke, Graham, Ward, Helen, Darzi, Ara, Riley, Steven, Chadeau-Hyam, Marc, Donnelly, Christl A. and Elliott, Paul 2022. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases 22 (1) , 647. 10.1186/s12879-022-07628-4
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Nickbakhsh, Sema, Hughes, Joseph, Christofidis, Nicolaos, Griffiths, Emily, Shaaban, Sharif, Enright, Jessica, Smollett, Katherine, Nomikou, Kyriaki, Palmalux, Natasha, Tong, Lily, Carmichael, Stephen, Sreenu, Vattipally B., Orton, Richard, Goldstein, Emily J., Tomb, Rachael M., Robson, Samuel C., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Loman, Nicholas J., Golubchik, Tanya, Nunez, Rocio T. Martinez, Bonsall, David, Rambaut, Andrew, Snell, Luke B., Livett, Rich, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Johnston, Ian, Lythgoe, Katrina, Torok, M. 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Ashford, Fiona, Best, Angus, Dunn, Steven J., Ahmed, Zahra, Siddiqui, Henna, Melville, Jordan, Wilkinson, Samuel, Mirza, Jeremy, Cumley, Nicola, Stockton, Joanne, Ferguson, Jack, Wheatley, Lucy, Ratcliffe, Elizabeth, Casey, Anna, Plant, Tim, The COVID-19 Genomics UK (COG-UK) Consortium, Quick, Joshua, Richter, Alex, Loman, Nicholas, McNally, Alan and Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 2022. Sars-cov-2 testing in the community: testing positive samples with the taqman sars-cov-2 mutation panel to find variants in real time. Journal of Clinical Microbiology 60 (4) , e02408-21. 10.1128/jcm.02408-21
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Adamson, James P., Smith, Christopher, Pacchiarini, Nicole, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Wallsgrove, Janet, Coles, Ian, Frost, Clare, Edwards, Angharad, Sinha, Jaisi, Moore, Catherine, Perrett, Steph, Craddock, Christie, Sawyer, Clare, Waldram, Alison, Barrasa, Alicia, Thomas, Daniel Rh., Daniels, Philip and Lewis, Heather 2022. A large outbreak of COVID-19 in a UK prison, October 2020 to April 2021. Epidemiology and Infection 150 , e134. 10.1017/S0950268822000991
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Hillary, Luke S., Farkas, Kata, Maher, Kathryn H., Lucaci, Anita, Thorpe, Jamie, Distaso, Marco A., Gaze, William H., Paterson, Steve, Burke, Terry, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, McDonald, James E., Malham, Shelagh K. and Jones, David L. 2021. Monitoring SARS-CoV-2 in municipal wastewater to evaluate the success of lockdown measures for controlling COVID-19 in the UK. Water Research 200 , 117214. 10.1016/j.watres.2021.117214

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Meadows, Lizzie, Kolyva, Anastasia, Diaz, Maria, Bell, Andrew, Gutierrez, Ana Victoria, Charles, Ian G., Adriaenssens, Evelien M., Kingsley, Robert A., Casey, Anna, Simpson, David A., Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane A.H., Knight, Bridget A., Hattersley, Andrew, Ellard, Sian, Auckland, Cressida, Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Bourgeois, Yann, Scarlett, Garry P., Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Essex, Sarah, Lyons, Ronan A., Caller, Laura G., Castellano, Sergi, Williams, Rachel J., Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A., Dyal, Patricia L., Tutill, Helena J., Panchbhaya, Yasmin N., Forrest, Leysa M., Niola, Paola, Findlay, Jacqueline, Brooks, Tony T., Gavriil, Artemis, Mestek-Boukhibar, Lamia, Weeks, Sam, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Harrison, Ewan M., Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Bellis, Katherine L., Girgis, Sophia T., Naydenova, Plamena, Blane, Beth, Sridhar, Sushmita, Ruis, Chris, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Hadjirin, Nazreen F., Aggarwal, Dinesh, Griffith, Luke, Swingler, Tracey, Davidson, Rose K., Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., Rooke, Stefan, Colquhoun, Rachel, Ashworth, Jordan, McCrone, J.T., Scher, Emily, Yu, Xiaoyu, Williamson, Kathleen A., Stanton, Thomas D., Michell, Stephen L., Bewshea, Claire M., Temperton, Ben, Michelsen, Michelle L., Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James W., Sambles, Christine M., Studholme, David J., Jeffries, Aaron R., Darby, Alistair C., Hiscox, Julian A., Paterson, Steve, Iturriza-Gomara, Miren, Jackson, Kathryn A., Lucaci, Anita O., Vamos, Edith E., Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Turtle, Lance, Haldenby, Sam T., Gregory, Richard, Gemmell, Matthew, Kwiatkowski, Dominic, de Silva, Thushan I., Smith, Nikki, Angyal, Adrienn, Lindsey, Benjamin B., Groves, Danielle C., Green, Luke R., Wang, Dennis, Freeman, Timothy M., Parker, Matthew D., Keeley, Alexander J., Parsons, Paul J., Tucker, Rachel M., Brown, Rebecca, Wyles, Matthew, Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey K.J., Bridgewater, Hannah E., Frost, Lucy R., Taylor-Joyce, Grace, Stark, Richard, Baxter, Laura, Alam, Mohammad T., Brown, Paul E., McClure, Patrick C., Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Gramatopoulos, Dimitris, Buck, David, Todd, John A., Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Langford, Cordelia, Alderton, Alex, Amato, Roberto, Goncalves, Sonia, Jackson, David K., Johnston, Ian, Sillitoe, John, Palmer, Steve, Lawniczak, Mara, Berriman, Matt, Danesh, John, Livett, Rich, Shirley, Lesley, Farr, Ben, Quail, Mike, Thurston, Scott, Park, Naomi, Betteridge, Emma, Weldon, Danni, Goodwin, Scott, Nelson, Rachel, Beaver, Charlotte, Letchford, Laura, Jackson, David A., Foulser, Luke, McMinn, Liz, Prestwood, Liam, Kay, Sally, Kane, Leanne, Dorman, Matthew J., Martincorena, Inigo, Puethe, Christoph, Keatley, Jon-Paul, Tonkin-Hill, Gerry, Smith, Christen, Jamrozy, Dorota, Beale, Mathew A., Patel, Minal, Ariani, Cristina, Spencer-Chapman, Michael, Drury, Eleanor, Lo, Stephanie, Rajatileka, Shavanthi, Scott, Carol, James, Keith, Buddenborg, Sarah K., Berger, Duncan J., Patel, Gaurang, Garcia-Casado, Maria V., Dibling, Thomas, McGuigan, Samantha, Rogers, Hazel A., Hunter, Adam D., Souster, Emily and Neaverson, Alexandra S. 2021. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell 184 (1) , 64-75.e11. 10.1016/j.cell.2020.11.020
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Lyons, Jane, Akbari, Ashley, Torabi, Fatemeh, Davies, Gareth, North, Laura, Griffiths, Rowena, Bailey, Rowena, Hollinghurst, Joe, Fry, Richard, Turner, Samantha, Thompson, Daniel, Rafferty, James, Mizen, Amy., Orton, Chris, Ellwood-Thompson, Simon, Au-Yeung, Lee, Cross, Lynsey, Gravenor, Mike, Brophy, Sinead, Lucini, Biagio, John, Ann, Szakmany, Tamas ORCID: https://orcid.org/0000-0003-3632-8844, Davies, Jan, Davies, Chris, Thomas, Daniel Rhys, Williams, Christopher, Emmerson, Chris, Cottrell, Simon, Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Taylor, Chris ORCID: https://orcid.org/0000-0002-9146-9167, Pugh, Richard, Diggle, Peter J., John, Gareth, Scourfield, Simon, Hunt, Joe, Cunningham, Anne Marie, Helliwell, Kathryn and Lyons, Ronan A. 2020. Understanding and responding to COVID-19 in Wales: protocol for a privacy protecting data platform for enhanced epidemiology and evaluation of interventions. BMJ Open 10 (10) , e043010. 10.1136/bmjopen-2020-043010
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Mullins, Alex J. ORCID: https://orcid.org/0000-0001-5804-9008, Jones, Cerith ORCID: https://orcid.org/0000-0001-6275-0235, Bull, Matthew, Webster, Gordon ORCID: https://orcid.org/0000-0002-9530-7835, Parkhill, Julian, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Murray, James A. H. ORCID: https://orcid.org/0000-0002-2282-3839, Challis, Gregory L. and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2020. Genomic assemblies of members of Burkholderia and related genera as a resource for natural product discovery. Microbiology Resource Announcements 9 , e00485-20. 10.1128/MRA.00485-20
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Alm, Erik, Broberg, Eeva K., Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Hodcroft, Emma B., Komissarov, Andrey B., Maurer-Stroh, Sebastian, Melidou, Angeliki, Neher, Richard A., O'Toole, Áine, Pereyaslov, Dmitriy, Bresner, Catherine and Workman, Trudy 2020. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020. Eurosurveillance 25 (32) , 2001410. 10.2807/1560-7917.ES.2020.25.32.2001410
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Millar, Jane R., Bengu, Nomonde, Fillis, Rowena, Sprenger, Ken, Ntlantsana, Vuyokazi, Vieira, Vinicius A., Khambati, Nisreen, Archary, Moherndran, Muenchhoff, Maximilian, Groll, Andreas, Grayson, Nicholas, Adamson, John, Govender, Katya, Dong, Krista, Kiepiela, Photini, Walker, Bruce D., Bonsall, David, Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Bull, Matthew J., Nxele, Nelisiwe, Roider, Julia, Ismail, Nasreen, Adland, Emily, Puertas, Maria C., Martinez-Picado, Javier, Matthews, Philippa C., Ndung'u, Thumbi and Goulder, Philip 2020. High-frequency failure of combination antiretroviral therapy in paediatric HIV infection is associated with unmet maternal needs causing maternal non-adherence. EClinicalMedicine 22 , 100344. 10.1016/j.eclinm.2020.100344
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Southgate, J.A., Bull, M.J., Brown, C.M., Watkins, J., Corden, S., Southgate, B., Moore, C. and Connor, T.R. ORCID: https://orcid.org/0000-0003-2394-6504 2020. Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications. Bioinformatics 36 (6) , pp. 1681-1688. 10.1093/bioinformatics/btz814
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Cunningham-Oakes, Edward, Pointon, Tom, Murphy, Barry, Connor, Thomas R ORCID: https://orcid.org/0000-0003-2394-6504 and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2020. Genome sequence of pluralibacter gergoviae ECO77, a unique multireplicon isolate of industrial origin. Microbiology Resource Announcements 9 (9) , e01561-19. 10.1128/MRA.01561-19
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Bush, Stephen J., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Peto, Tim E.A., Crook, Derrick W. and Walker, A. Sarah 2020. Evaluation of methods for detecting human reads in microbial sequencing datasets. Microbial Genomics 6 (7) , pp. 5-18. 10.1099/mgen.0.000393
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Webster, Gordon ORCID: https://orcid.org/0000-0002-9530-7835, Mullins, Alex J ORCID: https://orcid.org/0000-0001-5804-9008, Bettridge, Aimee, Jones, Cerith ORCID: https://orcid.org/0000-0001-6275-0235, Cunningham-Oakes, Edward, Connor, Thomas R ORCID: https://orcid.org/0000-0003-2394-6504, Parkhill, Julian and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2019. Genome sequences of three Paraburkholderia spp. strains isolated from Wood-decay fungi reveals them as novel taxa with antimicrobial biosynthetic potential. Microbiology Resource Announcements 8 (34) , e00778-19. 10.1128/MRA.00778-19
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Mullins, Alex J. ORCID: https://orcid.org/0000-0001-5804-9008, Murray, James A. H. ORCID: https://orcid.org/0000-0002-2282-3839, Bull, Matthew J., Jenner, Matthew, Jones, Cerith ORCID: https://orcid.org/0000-0001-6275-0235, Webster, Gordon ORCID: https://orcid.org/0000-0002-9530-7835, Green, Angharad E., Neill, Daniel R., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Parkhill, Julian, Challis, Gregory L. and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2019. Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria. Nature Microbiology 4 , pp. 996-1005. 10.1038/s41564-019-0383-z
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Weiser, Rebecca ORCID: https://orcid.org/0000-0003-3983-3272, Green, Angharad E., Bull, Matthew J., Cunningham-Oakes, Edward, Jolley, Keith A., Maiden, Martin C.J., Hall, Amanda J., Winstanley, Craig, Weightman, Andrew J. ORCID: https://orcid.org/0000-0002-6671-2209, Donoghue, Denise, Amezquita, Alejandro, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504 and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2019. Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. Microbial Genomics , 000276. 10.1099/mgen.0.000276
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Green, Angharad, Amezquita, Alejandro, Le-Marc, Yvan, Bull, Matthew, Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504 and Mahenthiralingam, Eshwar ORCID: https://orcid.org/0000-0001-9014-3790 2018. The consistent differential expression of genetic pathways following exposure of an industrial Pseudomonas aeruginosa strain to preservatives and a laundry detergent formulation. FEMS Microbiology Letters 365 (9) , fny062. 10.1093/femsle/fny062
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Rius, Cristina, Attaf, Meriem, Tungatt, Katie, Bianchi, Valentina, Legut, Mateusz, Bovay, Amandine, Donia, Marco, Straten, Per thor, Peakman, Mark, Svane, Inge Marie, Ott, Sascha, Connor, Tom ORCID: https://orcid.org/0000-0003-2394-6504, Szomolay, Barbara ORCID: https://orcid.org/0000-0002-5375-5533, Dolton, Garry and Sewell, Andrew K. ORCID: https://orcid.org/0000-0003-3194-3135 2018. Peptide-MHC class 1 tetramers can fail to detect relevant functional T cell clonotypes and underestimate antigen-reactive T cell populations. Journal of Immunology 200 (7) , pp. 2263-2279. 10.4049/jimmunol.1700242
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Knetsch, C. W., Kumar, N., Forster, S. C., Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Browne, H. P., Harmanus, C., Sanders, I. M., Harris, S. R., Turner, L., Morris, T., Perry, M., Miyajima, F., Roberts, P., Pirmohamed, M., Songer, J. G., Weese, J. S., Indra, A., Corver, J., Rupnik, M., Wren, B. W., Riley, T. V., Kuijper, E. J. and Lawley, T. D. 2018. Zoonotic transfer of clostridium difficile harboring antimicrobial resistance between farm animals and humans. Journal of Clinical Microbiology 56 (3) , e01384-17. 10.1128/JCM.01384-17
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Baker, K.S., Campos, J., Pichel, M., Della Gaspera, A., Duarte-Martínez, F., Campos-Chacón, E., Bolaños-Acuña, H.M., Guzmán-Verri, C., Mather, A.E., Diaz Velasco, S., Zamudio Rojas, M.L., Forbester, J.L., Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Keddy, K.H., Smith, A.M., López de Delgado, E.A., Angiolillo, G., Cuaical, N., Fernández, J., Aguayo, C., Morales Aguilar, M., Valenzuela, C., Morales Medrano, A.J., Sirok, A., Weiler Gustafson, N., Diaz Guevara, P.L., Montaño, L.A., Perez, E. and Thomson, N.R. 2017. Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses. Clinical Microbiology and Infection 23 (11) , pp. 845-853. 10.1016/j.cmi.2017.03.021
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Pollard, Dominic J., Young, Joanna C., Covarelli, Valentina, Herrera-León, Silvia, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Fookes, Maria, Walker, Danielle, Echeita, Aurora, Thomson, Nicholas R., Berger, Cedric N. ORCID: https://orcid.org/0000-0002-1316-5985, Frankel, Gad and Young, V. B. 2016. The Type III secretion system effector SeoC of salmonella enterica subsp. salamae and S. enterica subsp. arizonae ADP-Ribosylates Src and Inhibits Opsonophagocytosis. Infection and Immunity 84 (12) , pp. 3618-3628. 10.1128/IAI.00704-16
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Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Loman, Nicholas J., Thompson, Simon, Smith, Andy, Southgate, Joel, Poplawski, Radoslaw, Bull, Matthew J., Richardson, Emily, Ismail, Matthew, Elwood-Thompson, Simon, Kitchen, Christine, Guest, Martyn, Bakke, Marius, Sheppard, Samuel K. and Pallen, Mark J. 2016. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microbial Genomics 2 (9) , 000086. 10.1099/mgen.0.000086
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Wong, Vanessa K., Baker, Stephen, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Pickard, Derek, Page, Andrew J., Dave, Jayshree, Murphy, Niamh, Holliman, Richard, Sefton, Armine, Millar, Michael, Dyson, Zoe A., Dougan, Gordon, Holt, Kathryn E., Parkhill, Julian, Feasey, Nicholas A., Kingsley, Robert A., Thomson, Nicholas R., Keane, Jacqueline A., Weill, François- Xavier, Le Hello, Simon, Hawkey, Jane, Edwards, David J., Harris, Simon R., Cain, Amy K., Hadfield, James, Hart, Peter J., Thieu, Nga Tran Vu, Klemm, Elizabeth J., Breiman, Robert F., Watson, Conall H., Edmunds, W. John, Kariuki, Samuel, Gordon, Melita A., Heyderman, Robert S., Okoro, Chinyere, Jacobs, Jan, Lunguya, Octavie, Msefula, Chisomo, Chabalgoity, Jose A., Kama, Mike, Jenkins, Kylie, Dutta, Shanta, Marks, Florian, Campos, Josefina, Thompson, Corinne, Obaro, Stephen, MacLennan, Calman A., Dolecek, Christiane, Keddy, Karen H., Smith, Anthony M., Parry, Christopher M., Karkey, Abhilasha, Dongol, Sabina, Basnyat, Buddha, Arjyal, Amit, Mulholland, E. Kim, Campbell, James I., Dufour, Muriel, Bandaranayake, Don, Toleafoa, Take N., Singh, Shalini Pravin, Hatta, Mochammad, Newton, Paul N., Dance, David, Davong, Viengmon, Onsare, Robert S., Isaia, Lupeoletalalelei, Thwaites, Guy, Wijedoru, Lalith, Crump, John A., De Pinna, Elizabeth, Nair, Satheesh, Nilles, Eric J., Thanh, Duy Pham, Turner, Paul, Soeng, Sona, Valcanis, Mary, Powling, Joan, Dimovski, Karolina, Hogg, Geoff, Farrar, Jeremy, Mather, Alison E. and Amos, Ben 2016. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature Communications 7 , -. 10.1038/ncomms12827
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Ryan, Edward T., Karlsson, Stefan L., Thomson, Nicholas, Mutreja, Ankur, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Sur, Dipika, Ali, Mohammad, Clemens, John, Dougan, Gordon, Holmgren, Jan and Lebens, Michael 2016. Retrospective analysis of serotype switching of Vibrio cholerae O1 in a cholera endemic region Shows it is a non-random process. PLOS Neglected Tropical Diseases 10 (10) , e0005044. 10.1371/journal.pntd.0005044
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International Typhoid Consortium, Wong, Vanessa K., Baker, Stephen, Holt, Kathryn E., Okoro, Chinyere, Pickard, Derek J., Marks, Florian, Page, Andrew J., Olanipekun, Grace, Munir, Huda, Alter, Roxanne, Fey, Paul D., Feasey, Nicholas A., Weill, Francois-Xavier, Le Hello, Simon, Hart, Peter J., Kariuki, Samuel, Breiman, Robert F., Gordon, Melita, Heyderman, Robert S., Jacobs, Jan, Lunguya, Octavie, Onsare, Robert S., Msefula, Chisomo, MacLennan, Calman A., Keddy, Karen H., Smith, Anthony M., De Pinna, Elizabeth, Nair, Satheesh, Amos, Ben, Dougan, Gordon, Obaro, Stephen, Ryan, Edward T. and Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504 2016. Molecular surveillance identifies multiple transmissions of typhoid in West Africa. PLOS Neglected Tropical Diseases 10 (9) , e0004781. 10.1371/journal.pntd.0004781
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Baker, Kate S., Dallman, Timothy J., Behar, Adi, Weill, François-Xavier, Gouali, Malika, Sobel, Jeremy, Fookes, Maria, Valinsky, Lea, Gal-Mor, Ohad, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Nissan, Israel, Bertrand, Sophie, Parkhill, Julian, Jenkins, Claire, Cohen, Dani and Thomson, Nicholas R. 2016. Travel- and community-based transmission of multidrug-resistant Shigella sonnei lineage among international Orthodox Jewish communities. Emerging Infectious Diseases 22 (9) , p. 1545. 10.3201/eid2209.151953

Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Owen, Sian V., Langridge, Gemma, Connell, Steve, Nair, Sasheeth, Reuter, Sandra, Dallman, Timothy J., Corander, Jukka, Tabing, Kristine C., Le Hello, Simon, Fookes, Maria, Doublet, Benoit, Zhou, Zhemin, Feltwell, Theresa, Ellington, Matthew J., Herrera, Silvia, Gilmour, Matthew, Cloeckaer, Axel, Achtman, Mark, Parkhill, Julian, Wain, John, De Pinna, Elizabeth, Weill, François-Xavier, Peters, Tansy and Thomson, Nick 2016. What's in a name? Species wide whole genome sequencing resolves invasive and non-invasive Salmonella Paratyphi B. mBio 7 (4) , e00527-16. 10.1128/mBio.00527-16
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Laugel, Bruno, Lloyd, Angharad, Meermeier, Erin W., Crowther, Michael D., Connor, Thomas ORCID: https://orcid.org/0000-0003-2394-6504, Dolton, Garry Michael, Miles, John James, Burrows, Scott R., Gold, Marielle C., Lewinsohn, David M. and Sewell, Andrew K. ORCID: https://orcid.org/0000-0003-3194-3135 2016. Engineering of isogenic cells deficient for MR1 with a CRISPR/Cas9 lentiviral system: tools to study microbial antigen processing and presentation to human MR1-restricted T cells. Journal of Immunology 197 (3) , pp. 971-982. 10.4049/jimmunol.1501402
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Petrovska, Liljana, Mather, Alison E., AbuOun, Manal, Branchu, Priscilla, Harris, Simon R., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Hopkins, K.L., Underwood, A., Lettini, Antonia A., Page, Andrew, Bagnall, Mary, Wain, John, Parkhill, Julian, Dougan, Gordon, Davies, Robert and Kingsley, Robert A. 2016. Microevolution of Monophasic Salmonella Typhimurium during epidemic, United Kingdom, 2005-2010. Emerging infectious diseases 22 (4) , 617. 10.3201/eid2204.150531

Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Barker, Clare R., Baker, Kate S., Weill, François-Xavier, Talukder, Kaisar Ali, Smith, Anthony M., Baker, Stephen, Gouali, Malika, Pham Thanh, Duy, Azmi, Ishrat Jahan, Dias da Silveira, Wanderley, Semmler, Torsten, Wieler, Lothar H., Jenkins, Claire, Cravioto, Alejandro, Faruque, Shah M., Parkhill, Julian, Kim, Dong Wook, Keddy, Karen H. and Thomson, Nicholas R. 2015. Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri. eLife 4 , e07335. 10.7554/eLife.07335
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Baker, Kate S, Dallman, Timothy J., Ashton, Philip M, Day, Martin, Hughes, Gwenda, Crook, Paul D, Gilbart, Victoria L., Zittermann, Sandra, Allen, Vanessa G., Howden, Benjamin P., Tomita, Takehiro, Valcanis, Mary, Harris, Simon R., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Sintchenko, Vitali, Howard, Peter, Brown, Jeremy D., Petty, Nicola K., Gouali, Malika, Thanh, Duy Pham, Keddy, Karen H., Smith, Anthony M, Talukder, Kaisar A, Faruque, Shah M., Parkhill, Julian, Baker, Stephen, Weill, François-Xavier, Jenkins, Claire and Thomson, Nicholas R 2015. Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. The Lancet Infectious Diseases 15 (8) , pp. 913-921. 10.1016/S1473-3099(15)00002-X

Holt, Kathryn E., Wertheim, Heiman, Zadoks, Ruth N., Baker, Stephen, Whitehouse, Chris A., Dance, David, Jenney, Adam, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Hsu, Li Yang, Severin, Juliëtte, Brisse, Sylvain, Cao, Hanwei, Wilksch, Jonathan, Gorrie, Claire, Schultz, Mark B., Edwards, David J., Nguyen, Kinh Van, Nguyen, Trung Vu, Dao, Trinh Tuyet, Mensink, Martijn, Minh, Vien Le, Nhu, Nguyen Thi Khanh, Schultsz, Constance, Kuntaman, Kuntaman, Newton, Paul N., Moore, Catrin E., Strugnell, Richard A. and Thomson, Nicholas R. 2015. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health. Proceedings of the National Academy of Sciences of the United States of America 112 (27) , E3574-E3581. 10.1073/pnas.1501049112

Okoro, Chinyere K., Barquist, Lars, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Harris, Simon R., Clare, Simon, Stevens, Mark P., Arends, Mark J., Hale, Christine, Kane, Leanne, Pickard, Derek J., Hill, Jennifer, Harcourt, Katherine, Parkhill, Julian, Dougan, Gordon and Kingsley, Robert A. 2015. Correction: Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from Sub-Saharan Africa. PLOS Neglected Tropical Diseases 9 (6) , e0003848. 10.1371/journal.pntd.0003848
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Okoro, Chinyere K., Barquist, Lars, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Harris, Simon R., Clare, Simon, Stevens, Mark P., Arends, Mark J., Hale, Christine, Kane, Leanne, Pickard, Derek J., Hill, Jennifer, Harcourt, Katherine, Parkhill, Julian, Dougan, Gordon and Kingsley, Robert A. 2015. Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from Sub-Saharan Africa. PLOS Neglected Tropical Diseases 9 (3) , e0003611. 10.1371/journal.pntd.0003611
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Vehkala, Minna, Shubin, Mikhail, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Thomson, Nicholas R. and Corander, Jukka 2015. Novel R pipeline for analyzing biolog phenotypic microarray data. PLoS ONE 10 (3) , e0118392. 10.1371/journal.pone.0118392
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Croucher, Nicholas J., Page, Andrew J., Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Delaney, Aidan J., Keane, Jacqueline A., Bentley, Stephen D., Parkhill, Julian and Harris, Simon R. 2015. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Research 43 (3) , e15. 10.1093/nar/gku1196
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Jones, Lim Stephen, Carvalho, Maria, Toleman, Mark Alexander Howard ORCID: https://orcid.org/0000-0002-9497-0512, White, Peter, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Mushtaq, Ammara, Weeks, Janis Lesley, Kumarasamy, Karthikeyan K., Raven, Katherine E., Török, M. Estée, Peacock, Sharon J., Howe, Robin A. and Walsh, Timothy Rutland ORCID: https://orcid.org/0000-0003-4315-4096 2015. Characterization of plasmids in extensively drug-resistant acinetobacter strains isolated in India and Pakistan. Antimicrobial Agents and Chemotherapy 59 (2) , pp. 923-929. 10.1128/AAC.03242-14

Langridge, Gemma C., Fookes, Maria, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Feltwell, Theresa, Feasey, Nicholas, Parsons, Bryony N., Seth-Smith, Helena M. B., Barquist, Lars, Stedman, Anna, Humphrey, Tom, Wigley, Paul, Peters, Sarah E., Maskell, Duncan J., Corander, Jukka, Chabalgoity, Jose A., Barrow, Paul, Parkhill, Julian, Dougan, Gordon and Thomson, Nicholas R. 2015. Patterns of genome evolution that have accompanied host adaptation in Salmonella. Proceedings of the National Academy of Sciences 112 (3) , pp. 863-868. 10.1073/pnas.1416707112

Hall, Miquette, Chattaway, Marie A., Reuter, Sandra, Savin, Cyril, Strauch, Eckhard, Carniel, Elisabeth, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Van Damme, Inge, Rajakaruna, Lakshani, Rajendram, Dunstan, Jenkins, Claire, Thomson, Nicholas R., McNally, Alan and Ledeboer, N. A. 2015. Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels. Journal of Clinical Microbiology 53 (1) , pp. 35-42. 10.1128/JCM.02395-14

Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504 and Southgate, Joel 2015. Automated cloud brokerage based upon continuous real-time benchmarking. Presented at: 2015 IEEE/ACM 8th International Conference on Utility and Cloud Computing, Limassol, Cyprus, 7 - 0 December 2015.
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von Mentzer, Astrid, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Wieler, Lothar H., Semmler, Torsten, Iguchi, Atsushi, Thomson, Nicholas R., Rasko, David A., Joffre, Enrique, Corander, Jukka, Pickard, Derek, Wiklund, Gudrun, Svennerholm, Ann-Mari, Sjöling, Åsa and Dougan, Gordon 2014. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nature Genetics 46 (12) , pp. 1321-1326. 10.1038/ng.3145

Knetsch, C. W., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Mutreja, A., van Dorp, S. M., Sanders, I. M., Browne, H. P., Harris, D., Lipman, L., Keessen, E. C. and Corver, J. 2014. Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011. Eurosurveillance 19 (45) , 20954.
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Lamelas, A., Harris, S. R., Roltgen, K., Dangy, J.-P., Hauser, J., Kingsley, R. A., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Sie, A., Hodgson, A., Dougan, G., Parkhill, J., Bentley, S. D. and Pluschke, G. 2014. Emergence of a new epidemic Neisseria meningitidis serogroup A clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion. mBio 5 (5) , e01974-14. 10.1128/mBio.01974-14
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Reuter, Sandra, Connor, Thomas R. ORCID: https://orcid.org/0000-0003-2394-6504, Barquist, Lars, Walker, Danielle, Feltwell, Theresa, Dufour, Muriel, Harris, Simon R., Fookes, Maria, Hall, Miquette E., Petty, Nicola K., Fuchs, Thilo M., Corander, Jukka, Ringwood, Tamara, Savin, Cyril, Bouchier, Christiane, Martin, Liliane, Miettinen, Minna, Shubin, Mikhail, Riehm, Julia M., Laukkanen-Ninios, Riikka, Sihvonen, Leila M., Siitonen, Anja, Skurnik, Mikael, Falcao, Juliana Pfrimer, Fukushima, Hiroshi, Scholz, Holger C., Prentice, Michael B., Wren, Brendan W., Parkhill, Julian, Carniel, Elisabeth, Achtman, Mark, McNally, Alan and Thomson, Nicholas R. 2014. Parallel independent evolution of pathogenicity within the genus Yersinia. Proceedings of the National Academy of Sciences 111 (18) , pp. 6768-6773. 10.1073/pnas.1317161111

Sheppard, Samuel K., Cheng, Lu ORCID: https://orcid.org/0000-0002-6391-2360, Méric, Guillaume, de Haan, Caroline P. A., Llarena, Ann-Katrin, Marttinen, Pekka, Vidal, Ana, Ridley, Anne, Clifton-Hadley, Felicity, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Strachan, Norval J. C., Forbes, Ken, Colles, Frances M., Jolley, Keith A., Bentley, Stephen D., Maiden, Martin C. J., Hänninen, Marja-Liisa, Parkhill, Julian, Hanage, William P. and Corander, Jukka 2014. Cryptic ecology among host generalist Campylobacter jejuniin domestic animals. Molecular Ecology 23 (10) , pp. 2442-2451. 10.1111/mec.12742
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Shepheard, Marcus A., Fleming, Vicki M., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Corander, Jukka, Feil, Edward J., Fraser, Christophe and Hanage, William P. 2013. Historical zoonoses and other changes in host tropism of staphylococcus aureus, identified by phylogenetic analysis of a population dataset. PLoS ONE 8 (5) , e62369. 10.1371/journal.pone.0062369
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Cheng, Lu ORCID: https://orcid.org/0000-0002-6391-2360, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Siren, J., Aanensen, D. M. and Corander, J. 2013. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Molecular Biology and Evolution 30 (5) , pp. 1224-1228. 10.1093/molbev/mst028

Dziva, F., Hauser, H., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, van Diemen, P. M., Prescott, G., Langridge, G. C., Eckert, S., Chaudhuri, R. R., Ewers, C., Mellata, M., Mukhopadhyay, S., Curtiss, R., Dougan, G., Wieler, L. H., Thomson, N. R., Pickard, D. J. and Stevens, M. P. 2013. Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms. Infection and Immunity 81 (3) , pp. 838-849. 10.1128/IAI.00585-12
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McDonnell, J., Dallman, T., Atkin, S., Turbitt, D. A., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Grant, K. A., Thomson, N. R. and Jenkins, C. 2013. Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK. Epidemiology and Infection 141 (12) , pp. 2568-2575. 10.1017/S0950268813000137

Kingsley, R. A., Kay, S., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Barquist, L., Sait, L., Holt, K. E., Sivaraman, K., Wileman, T., Goulding, D., Clare, S., Hale, C., Seshasayee, A., Harris, S., Thomson, N. R., Gardner, P., Rabsch, W., Wigley, P., Humphrey, T., Parkhill, J. and Dougan, G. 2013. Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. mBio 4 (5) , e00565-13. 10.1128/mBio.00565-13

Mather, A. E., Reid, S. W. J., Maskell, D. J., Parkhill, J., Fookes, M. C., Harris, S. R., Brown, D. J., Coia, J. E., Mulvey, M. R., Gilmour, M. W., Petrovska, L., de Pinna, E., Kuroda, M., Akiba, M., Izumiya, H., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Suchard, M. A., Lemey, P., Mellor, D. J., Haydon, D. T. and Thomson, N. R. 2013. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science 341 (6153) , pp. 1514-1517. 10.1126/science.1240578

He, Miao, Miyajima, Fabio, Roberts, Paul, Ellison, Louise, Pickard, Derek J., Martin, Melissa J., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Harris, Simon R., Fairley, Derek, Bamford, Kathleen B., D'Arc, Stephanie, Brazier, J. S., Brown, Derek, Coia, John E., Douce, Gill, Gerding, Dale, Kim, Hee Jung, Koh, Tse Hsien, Kato, Haru, Senoh, Mitsutoshi, Louie, Tom, Michell, Stephen, Butt, Emma, Peacock, Sharon J., Brown, Nick M., Riley, Tom, Songer, Glen, Wilcox, Mark, Pirmohamed, Munir, Kuijper, Ed, Hawkey, Peter, Wren, Brendan W., Dougan, Gordon, Parkhill, Julian and Lawley, Trevor D. 2012. Emergence and global spread of epidemic healthcare-associated Clostridium difficile [Letter]. Nature Genetics 45 (1) , pp. 109-113. 10.1038/ng.2478

Okoro, Chinyere K., Kingsley, Robert A., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Harris, Simon R., Parry, Christopher M., Al-Mashhadani, Manar N., Kariuki, Samuel, Msefula, Chisomo L., Gordon, Melita A., de Pinna, Elizabeth, Wain, John, Heyderman, Robert S., Obaro, Stephen, Alonso, Pedro L., Mandomando, Inacio, MacLennan, Calman A., Tapia, Milagritos D., Levine, Myron M., Tennant, Sharon M., Parkhill, Julian and Dougan, Gordon 2012. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nature Genetics 44 (11) , pp. 1215-1221. 10.1038/ng.2423

Lawley, Trevor D., Clare, Simon, Walker, Alan W., Stares, Mark D., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Raisen, Claire, Goulding, David, Rad, Roland, Schreiber, Fernanda, Brandt, Cordelia, Deakin, Laura J., Pickard, Derek J., Duncan, Sylvia H., Flint, Harry J., Clark, Taane G., Parkhill, Julian and Dougan, Gordon 2012. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing clostridium difficile disease in mice. PLoS Pathogens 8 (10) , e1002995. 10.1371/journal.ppat.1002995
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Quail, Michael, Smith, Miriam E., Coupland, Paul, Otto, Thomas D., Harris, Simon R., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Bertoni, Anna, Swerdlow, Harold P. and Gu, Yong 2012. A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics 13 (1) , 341. 10.1186/1471-2164-13-341
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Corander, Jukka, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, O'Dwyer, Cliona A., Kroll, J. Simon and Hanage, William Paul 2012. Population structure in the Neisseria, and the biological significance of fuzzy species. Journal of The Royal Society Interface 9 (71) , pp. 1208-1215. 10.1098/rsif.2011.0601

Murchison, Elizabeth P., Schulz-Trieglaff, Ole B., Ning, Zemin, Alexandrov, Ludmil B., Bauer, Markus J., Fu, Beiyuan, Hims, Matthew, Ding, Zhihao, Ivakhno, Sergii, Stewart, Caitlin, Ng, Bee Ling, Wong, Wendy, Aken, Bronwen, White, Simon, Alsop, Amber, Becq, Jennifer, Bignell, Graham R., Cheetham, R. Keira, Cheng, William, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Cox, Anthony J., Feng, Zhi-Ping, Gu, Yong, Grocock, Russell J., Harris, Simon R., Khrebtukova, Irina, Kingsbury, Zoya, Kowarsky, Mark, Kreiss, Alexandre, Luo, Shujun, Marshall, John, McBride, David J., Murray, Lisa, Pearse, Anne-Maree, Raine, Keiran, Rasolonjatovo, Isabelle, Shaw, Richard, Tedder, Philip, Tregidgo, Carolyn, Vilella, Albert J., Wedge, David C., Woods, Gregory M., Gormley, Niall, Humphray, Sean, Schroth, Gary, Smith, Geoffrey, Hall, Kevin, Searle, Stephen M.J., Carter, Nigel P., Papenfuss, Anthony T., Futreal, P. Andrew, Campbell, Peter J., Yang, Fengtang, Bentley, David R., Evers, Dirk J. and Stratton, Michael R. 2012. Genome sequencing and analysis of the Tasmanian Devil and its transmissible cancer. Cell 148 (4) , pp. 780-791. 10.1016/j.cell.2011.11.065

Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Corander, Jukka and Hanage, William Paul 2012. Population subdivision and the detection of recombination in non-typable Haemophilus influenzae. Microbiology 158 (12) , pp. 2958-2964. 10.1099/mic.0.063073-0

Marttinen, Pekka, Hanage, William Paul, Croucher, Nicholas J., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Harris, Simon R., Bentley, Stephen D. and Corander, Jukka 2011. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Research 40 (1) , e6. 10.1093/nar/gkr928

Mutreja, Ankur, Kim, Dong Wook, Thomson, Nicholas R., Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Lee, Je Hee, Kariuki, Samuel, Croucher, Nicholas J., Choi, Seon Young, Harris, Simon R., Lebens, Michael, Niyogi, Swapan Kumar, Kim, Eun Jin, Ramamurthy, T., Chun, Jongsik, Wood, James L. N., Clemens, John D., Czerkinsky, Cecil, Nair, G. Balakrish, Holmgren, Jan, Parkhill, Julian and Dougan, Gordon 2011. Evidence for several waves of global transmission in the seventh cholera pandemic [Letter]. Nature 477 (7365) , pp. 462-465. 10.1038/nature10392

Fookes, Maria, Schroeder, Gunnar N., Langridge, Gemma C., Blondel, Carlos J., Mammina, Caterina, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Seth-Smith, Helena, Vernikos, Georgios S., Robinson, Keith S., Sanders, Mandy, Petty, Nicola K., Kingsley, Robert A., Bäumler, Andreas J., Nuccio, Sean-Paul, Contreras, Inés, Santiviago, Carlos A., Maskell, Duncan, Barrow, Paul, Humphrey, Tom, Nastasi, Antonino, Roberts, Mark, Frankel, Gad, Parkhill, Julian, Dougan, Gordon and Thomson, Nicholas R. 2011. Salmonella bongori provides insights into the evolution of the Salmonellae. PLoS Pathogens 7 (8) , e1002191. 10.1371/journal.ppat.1002191
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Cheng, Lu ORCID: https://orcid.org/0000-0002-6391-2360, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504, Aanensen, David M., Spratt, Brian G. and Corander, Jukka 2011. Bayesian semi-supervised classification of bacterial samples using MLST databases. BioMed Central Bioinformatics 12 (1) , 302. 10.1186/1471-2105-12-302
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Hanage, William Paul, Fraser, Christophe, Tang, Jing, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504 and Corander, Jukka 2009. Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science 324 (5933) , pp. 1454-1457. 10.1126/science.1171908

Turner, Katherine M. E., Hanage, William P., Fraser, Christophe, Connor, Thomas Richard ORCID: https://orcid.org/0000-0003-2394-6504 and Spratt, Brian G. 2007. Assessing the reliability of eBURST using simulated populations with known ancestry. BMC Microbiology 7 (1) , pp. 30-43. 10.1186/1471-2180-7-30
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This list was generated on Fri Jun 21 06:39:23 2024 BST.