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Number of items: 99.

Gally, David, Maiden, Martin, Jolley, Keith, McIntyre, K. Marie, Ott, Sascha, Darby, Alistair, Loman, Nick, Kingsley, Robert A., Chalka, Antonia, Holt, Kathryn, McNally, Alan, Baker, Kate, Avison, Matthew, AbuOun, Manal, Graham, David, Jenkins, Claire, Chattaway, Marie, Nair, Satheesh, Connor, Thomas

, Vallejo-Trujillo, Adriana, King, Jason, Haynes, Edward, Ellis, Richard, McElhiney, Jacqui, Dorey-Robinson, Daniel, Gilmour, Matthew, Painset, Anaïs, Egli, Adrian, Reimer, Aleisha, Mather, Alison, Allard, Marc, Stevens, Eric, Yahara, Koji, Lehours, Phillippe, Seemann, Torsten, Jenkins, Claire, Hendriksen, Rene S., Aarestrup, Frank, Aanensen, David, Acton, Richard, Alikhan, Nabil-Fareed, Blanton, Angela, Baker, James, Walker, Jude, Lewis-Woodhouse, Georgina, Connor, Diana, Yeats, Corin, Abudahab, Khalil, Shinde, Pranit and Vegvari, Carolin 2025. PATH-SAFE consortium recommendations for genomic surveillance of food-borne diseases Escherichia coli and Listeria monocytogenes. FSA Research and Evidence 10.46756/001c.143984

Dallman, Tim, Maiden, Martin, Jolley, Keith, McIntyre, Marie, Gally, David, Ott, Sascha, Darby, Alistair, Loman, Nick, Hinton, Jay, Kingsley, Robert A, Holt, Kathryn, Wheeler, Nicole, Graham, David, Chattaway, Marie, Nair, Satheesh, Connor, Tom

, Traka, Maria, Vallejo-Trujillo, Adriana, King, Jason, Haynes, Edward, Daspan, Tigan, Line, Kirsty, Ellis, Richard, Callaghan, Kathryn, James, Marianne, Larkin, Lesley, Petrovska, Liljana, Gilmour, Matthew, Mather, Alison, Allard, Marc, Stevens, Eric, Yahara, Koji, Lehours, Phillippe, Seemann, Torsten, Jenkins, Claire, Hendriksen, Rene S., Aarestrup, Frank, Aanensen, David, Acton, Richard, Blanton, Angela, Baker, James, Walker, Jude, Lewis-Woodhouse, Georgina, Connor, Diana, Yeats, Corin, Abudahab, Khalil, Shinde, Pranit and Vegvari, Carolin 2025. PATH-SAFE consortium recommendations for genomic surveillance of foodborne diseases, using Salmonella as an exemplar. FSA Research and Evidence 10.46756/001c.143833

Pacchiarini, Nicole, Simkin, Felicity, Postans, Mark, Ahern, George, Song, Jiao, Brown, Clare, Smith, Josie, Williams, Catie, Backx, Matthijs, Thomas, Daniel, Connor, Thomas R.

and Williams, Christopher 2025. Genomic epidemiology of Mycobacterium tuberculosis in Wales. Scientific Reports 15 (1) , 31106. 10.1038/s41598-025-15076-8

Morris, Arthur V., Robinson, Guy, Chalmers, Rachel, Cacciò, Simone and Connor, Thomas

2025. Parapipe: a pipeline for parasite next-generation sequencing data analysis applied to Cryptosporidium. Access Microbiology 7 (8) 10.1099/acmi.0.000993.v3

Wei, Kuangyi Charles, Purushothaman, Srinithi, Azzato, Francesca, Baker, Kate S., Birkeland, Kira Waagner, Brunet, Sofia, Campos, Josefina, Connor, Thomas R.

, Giske, Christian G., Greub, Gilbert, Hallbäck, Erika Tång, Harmsen, Dag, Hodcroft, Emma B., Holden, Matthew T.G., Jacob, Jobin, Kahles, Andre, Lagos, Amaya Campillay, Lipworth, Samuel, Loo, Elin, Miotto, Paolo, Neher, Richard A., Neves, Aitana, Ready, Derren, Roloff, Tim, Rooney, Ashley, Rousseau, Emilie, Schrenzel, Jacques, Sundqvist, Martin, Viegas, Sofia, Wegner, Fanny, Aamot, Hege Vangstein, Niemann, Stefan, Williamson, Deborah A., Mölling, Paula and Egli, Adrian 2025. Conference report: The second bacterial genome sequencing Pan-European network conference. Microbes and Infection 10.1016/j.micinf.2025.105557

Pacchiarini, Nicole, McKerr, Caoimhe, Morgan, Mari, Connor, Thomas R.

and Williams, Christopher 2025. The potential of genomic epidemiology: capitalizing on its practical use for impact in the healthcare setting. Frontiers in Public Health 13 , 1504796. 10.3389/fpubh.2025.1504796

Colquhoun, Rachel, O’Toole, Áine, Hill, Verity, McCrone, Jt, Yu, Xiaoyu, Nicholls, Samuel M, Poplawski, Radoslaw, Whalley, Thomas, Groves, Natalie, Ellaby, Nicholas, Loman, Nick, Connor, Tom

and Rambaut, Andrew 2024. A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK. Virus Evolution 10 (1) , veae083. 10.1093/ve/veae083

Postans, Mark, Pacchiarini, Nicole

, Song, Jiao, Cottrell, Simon, Williams, Catie, Beazer, Andrew, Moore, Catherine, Connor, Thomas R.

and Williams, Christopher 2024. Evaluating the risk of SARS-CoV-2 reinfection with the Omicron or Delta variant in Wales, UK. PLoS ONE 19 (9) , e0309645. 10.1371/journal.pone.0309645

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.

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

Mack, Andrew H., Menzies, Georgina

, Southgate, Alex, Jones, D. Dafydd

, Connor, Thomas R.

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

Morris, Arthur V., Price, Anna and Connor, Tom

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

Parfitt, Kasia M., Green, Angharad E., Connor, Thomas R.

, Neill, Daniel R. and Mahenthiralingam, Eshwar

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

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.

, 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

Pacchiarini, Nicole

, Cronin, Michelle, Sawyer, Clare, Williams, Catie, Beazer, Andrew, Cottrell, Simon, Morgan, Mari, Saunders, Vince, Moore, Catherine, Connor, Thomas R.

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

Cotton, S., McHugh, M.P., Dewar, R., Haas, J.G., Templeton, K., Robson, Samuel C., Connor, Thomas R.

, 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

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.

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

O’Toole, Aine, Hill, Verity, Jackson, Ben, Dewar, Rebecca, Sahadeo, Nikita, Colquhoun, Rachel, Rooke, Stefan, McCrone, J. T., Duggan, Kate, McHugh, Martin P., Nicholls, Samuel M., Poplawski, Radoslaw, The COVID-19 Genomics, UK (COG-UK) Consortium, COVID-19 Impact Project, t (Trinidad and Tobago Group, Aanensen, David, Holden, Matt, Connor, Tom

, Loman, Nick, Goodfellow, Ian, Carrington, Christine V. F., Templeton, Kate, Rambaut, Andrew and AAA ORCA, TEAM 2022. Genomics-informed outbreak investigations of SARS-CoV-2 using civet. PLOS Global Public Health 2 (12) , e0000704. 10.1371/journal.pgph.0000704

Cunningham-Oakes, Edward, Pointon, Tom, Murphy, Barry, Connor, Thomas R

and Mahenthiralingam, Eshwar

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

McCrone, John T., Hill, Verity, Bajaj, Sumali, Evans Pena, Rosario, Lambert, Ben C., Inward, Rhys, Bhatt, Samir and Connor, Thomas

2022. Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature 610 , pp. 154-160. 10.1038/s41586-022-05200-3

Attwood, Stephen W., Hill, Sarah C., Aanensen, David M., Connor, Thomas R.

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

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.

, 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. 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Chloe, Chalker, Vicki, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Holden, Matthew T.G., Shaaban, Sharif, Birchley, Alec, Adams, Alexander, Davies, Alisha, Gaskin, Amy, Plimmer, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Moore, Catherine, Williams, Chris, Heyburn, David, De Lacy, Elen, Hilvers, Ember, Downing, Fatima, Shankar, Giri, Jones, Hannah, Asad, Hibo, Coombes, Jason, Watkins, Joanne, Evans, Johnathan M., Fina, Laia, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Perry, Malorie, Morgan, Mari, Cronin, Michelle, Craine, Noel, Jones, Rachel, Howe, Robin, Corden, Sally, Rey, Sara, Kumziene-Summerhayes, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, O’Grady, Justin, Page, Andrew J., Wain, John, Webber, Mark A., Mather, Alison E., Baker, David J., Rudder, Steven, Yasir, Muhammad, Thomson, Nicholas M., Aydin, Alp, Tedim, Ana P., Kay, Gemma L., Trotter, Alexander J., Gilroy, Rachel A.J., Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, 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., 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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

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

, Davies, Jan, Davies, Chris, Thomas, Daniel Rhys, Williams, Christopher, Emmerson, Chris, Cottrell, Simon, Connor, Thomas

, Taylor, Chris

, 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

Mullins, Alex J.

, Jones, Cerith

, Bull, Matthew, Webster, Gordon

, Parkhill, Julian, Connor, Thomas R.

, Murray, James A. H.

, Challis, Gregory L. and Mahenthiralingam, Eshwar

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

Alm, Erik, Broberg, Eeva K., Connor, Thomas

, 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

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

, 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

Southgate, J.A., Bull, M.J., Brown, C.M., Watkins, J., Corden, S., Southgate, B., Moore, C. and Connor, T.R.

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

Cunningham-Oakes, Edward, Pointon, Tom, Murphy, Barry, Connor, Thomas R

and Mahenthiralingam, Eshwar

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

Bush, Stephen J., Connor, Thomas R.

, 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

Webster, Gordon

, Mullins, Alex J

, Bettridge, Aimee, Jones, Cerith

, Cunningham-Oakes, Edward, Connor, Thomas R

, Parkhill, Julian and Mahenthiralingam, Eshwar

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

Mullins, Alex J.

, Murray, James A. H.

, Bull, Matthew J., Jenner, Matthew, Jones, Cerith

, Webster, Gordon

, Green, Angharad E., Neill, Daniel R., Connor, Thomas R.

, Parkhill, Julian, Challis, Gregory L. and Mahenthiralingam, Eshwar

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

Weiser, Rebecca

, Green, Angharad E., Bull, Matthew J., Cunningham-Oakes, Edward, Jolley, Keith A., Maiden, Martin C.J., Hall, Amanda J., Winstanley, Craig, Weightman, Andrew J.

, Donoghue, Denise, Amezquita, Alejandro, Connor, Thomas R.

and Mahenthiralingam, Eshwar

2019. Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes. Microbial Genomics , 000276. 10.1099/mgen.0.000276

Green, Angharad, Amezquita, Alejandro, Le-Marc, Yvan, Bull, Matthew, Connor, Thomas

and Mahenthiralingam, Eshwar

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

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

, Szomolay, Barbara

, Dolton, Garry and Sewell, Andrew K.

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

Knetsch, C. W., Kumar, N., Forster, S. C., Connor, Thomas

, 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

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

, 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

Pollard, Dominic J., Young, Joanna C., Covarelli, Valentina, Herrera-León, Silvia, Connor, Thomas Richard

, Fookes, Maria, Walker, Danielle, Echeita, Aurora, Thomson, Nicholas R., Berger, Cedric N.

, 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

Connor, Thomas R.

, 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

Ryan, Edward T., Karlsson, Stefan L., Thomson, Nicholas, Mutreja, Ankur, Connor, Thomas Richard

, 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

Wong, Vanessa K., Baker, Stephen, Connor, Thomas R.

, 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

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

2016. Molecular surveillance identifies multiple transmissions of typhoid in West Africa. PLOS Neglected Tropical Diseases 10 (9) , e0004781. 10.1371/journal.pntd.0004781

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

, 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

, 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

Laugel, Bruno, Lloyd, Angharad, Meermeier, Erin W., Crowther, Michael D., Connor, Thomas

, Dolton, Garry Michael, Miles, John James, Burrows, Scott R., Gold, Marielle C., Lewinsohn, David M. and Sewell, Andrew K.

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

Petrovska, Liljana, Mather, Alison E., AbuOun, Manal, Branchu, Priscilla, Harris, Simon R., Connor, Thomas Richard

, 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.

, 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

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

, 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.

, 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

, 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

Okoro, Chinyere K., Barquist, Lars, Connor, Thomas Richard

, 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

Vehkala, Minna, Shubin, Mikhail, Connor, Thomas Richard

, 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

Croucher, Nicholas J., Page, Andrew J., Connor, Thomas R.

, 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

Jones, Lim Stephen, Carvalho, Maria, Toleman, Mark Alexander Howard

, White, Peter, Connor, Thomas Richard

, Mushtaq, Ammara, Weeks, Janis Lesley, Kumarasamy, Karthikeyan K., Raven, Katherine E., Török, M. Estée, Peacock, Sharon J., Howe, Robin A. and Walsh, Timothy Rutland

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.

, 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

, 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

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.

von Mentzer, Astrid, Connor, Thomas R.

, 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

, 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.

Lamelas, A., Harris, S. R., Roltgen, K., Dangy, J.-P., Hauser, J., Kingsley, R. A., Connor, Thomas Richard

, 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

Reuter, Sandra, Connor, Thomas R.

, 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

, Méric, Guillaume, de Haan, Caroline P. A., Llarena, Ann-Katrin, Marttinen, Pekka, Vidal, Ana, Ridley, Anne, Clifton-Hadley, Felicity, Connor, Thomas Richard

, 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

Cheng, Lu

, Connor, Thomas Richard

, 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

Shepheard, Marcus A., Fleming, Vicki M., Connor, Thomas Richard

, 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

Dziva, F., Hauser, H., Connor, Thomas Richard

, 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

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

, 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

Kingsley, R. A., Kay, S., Connor, Thomas Richard

, 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

McDonnell, J., Dallman, T., Atkin, S., Turbitt, D. A., Connor, Thomas Richard

, 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

He, Miao, Miyajima, Fabio, Roberts, Paul, Ellison, Louise, Pickard, Derek J., Martin, Melissa J., Connor, Thomas Richard

, 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

, 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

, 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

Quail, Michael, Smith, Miriam E., Coupland, Paul, Otto, Thomas D., Harris, Simon R., Connor, Thomas Richard

, 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

Corander, Jukka, Connor, Thomas Richard

, 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

, 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

, 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

, 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

, 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

, 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

Cheng, Lu

, Connor, Thomas Richard

, 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

Hanage, William Paul, Fraser, Christophe, Tang, Jing, Connor, Thomas Richard

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

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

This list was generated on Thu Oct 30 14:29:53 2025 GMT.