Items where Author is "Nelson, Andrew"

Ogbanga, Nengi, Nelson, Andrew, Ghignone, Stefano, Voyron, Samuele, Lovisolo, Flavia, Sguazzi, Giulia, Renò, Filippo, Migliario, Mario, Gino, Sarah and Procopio, Noemi (2023) The Oral Microbiome for Geographic Origin: An Italian Study. Forensic Science International: Genetics, 64. p. 102841. ISSN 1872-4973

Farsi, Dominic, Lara Gallegos, Jose, Koutsidis, Georgios, Nelson, Andrew, Finnigan, Tim J. A., Cheung, William, Munoz, Jose and Commane, Daniel (2023) Substituting meat for mycoprotein reduces genotoxicity and increases the abundance of beneficial microbes in the gut: Mycomeat, a randomised crossover control trial. European Journal of Nutrition, 62 (3). pp. 1479-1492. ISSN 1436-6207

Powell, Jason, Powell, Steven, Mather, Michael W., Beck, Lauren, Nelson, Andrew, Palmowski, Pawel, Porter, Andrew, Coxhead, Jonathan, Hedley, Ann, Scott, Jonathan, Rostron, Anthony J., Hellyer, Thomas P., Zaidi, Fatima, Davey, Tracey, Garnett, James P., Agbeko, Rachel, Ward, Chris, Stewart, Christopher J., Taggart, Clifford C., Brodlie, Malcolm and Simpson, A. John (2023) Tracheostomy in children is associated with neutrophilic airway inflammation. Thorax. thorax-2022-219557. ISSN 0040-6376 (In Press)

Cook, Kate F,, Beckett, Angela H., Glaysher, Sharon, Goudarzi, Salman, Fearn, Christopher, Loveson, Katie F., Elliott, Scott, Wyllie, Sarah, Lloyd, Allyson, Bicknell, Kelly, Lumley, Sally, Chauhan, Anoop J., Robson, Samuel C., The COVID-19 Genomics UK (COG-UK) Consortium, , Smith, Darren, Bashton, Matthew, Young, Greg, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William and Yew, Wen Chyin (2023) Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK. Frontiers in Cellular and Infection Microbiology, 12. p. 1066390. ISSN 2235-2988

O’Toole, Áine, Hill, Verity, Jackson, Ben, Dewar, Rebecca, Sahadeo, Nikita, Colquhoun, Rachel, Rooke, Stefan, McCrone, J. T., Duggan, Kate, McHugh, Martin P., SamuNicholls, Samuel M, Poplawski, Radoslaw, The COVID-19 Genomics UK (COG-UK) Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, COVID-19 Impact Project (Trinidad & Tobago Group), COVID-19 Impact Project (Trinidad & Tobago Group), Aanensen, David, Holden, Matt, Connor, Tom, Loman, Nick Loman, Goodfellow, Ian, Carrington, Christine V. F., Templeton, Kate, Rambaut, Andrew, Smith, Darren, Bashton, Matthew, Young, Greg, McCann, Clare, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, Wiliam and Yew, Wen Chyin (2022) Genomics-informed outbreak investigations of SARS-CoV-2 using civet. PLOS Global Public Health, 2 (12). e0000704. ISSN 2767-3375

Kläser, Kerstin, Molteni, Erika, Graham, Mark, Canas, Liane S., Österdahl, Marc F., Antonelli, Michela, Chen, Liyuan, Deng, Jie, Murray, Benjamin, Kerfoot, Eric, Wolf, Jonathan, May, Anna, Fox, Ben, Capdevila, Joan, Aanensen, David M., Abudahab, Khalil, Adams, Helen, Adams, Alexander, Afifi, Safiah, Aggarwal, Dinesh, Ahmad, Shazaad S. Y., Aigrain, Louise, Alcolea-Medina, Adela, Alikhan, Nabil-Fareed, Allara, Elias, Amato, Roberto, Angyal, Adrienn, Annett, Tara, Aplin, Stephen, Ariani, Cristina V., Asad, Hibo, Ash, Amy, Ashfield, Paula, Ashford, Fiona, Atkinson, Laura, Attwood, Stephen W., Auckland, Cressida, Aydin, Alp, Baker, David J., Baker, Paul, Balcazar, Carlos E., Ball, Jonathan, Barrett, Jeffrey C., Barrow, Magdalena, Barton, Edward, Bashton, Matthew, Bassett, Andrew R., Batra, Rahul, Baxter, Chris, Bayzid, Nadua, Beaver, Charlotte, Beckett, Angela H., Beckwith, Shaun M., Bedford, Luke, Beer, Robert, Beggs, Andrew, Bellis, Katherine L., Berry, Louise, Bertolusso, Beatrice, Best, Angus, Betteridge, Emma, Bibby, David, Bicknell, Kelly, Binns, Debbie, Birchley, Alec, Bird, Paul W., Bishop, Chloe, Blacow, Rachel, Blakey, Victoria, Blane, Beth, Bolt, Frances, Bonfield, James, Bonner, Stephen, Bonsall, David, Boswell, Tim, Bosworth, Andrew, Bourgeois, Yann, Boyd, Olivia, Bradley, Declan T., Breen, Cassie, Bresner, Catherine, Breuer, Judith, Bridgett, Stephen, Bronner, Iraad F., Brooks, Ellena, Broos, Alice, Brown, Julianne R., Bucca, Giselda, Buchan, Sarah L., Buck, David, Bull, Matthew, Burns, Phillipa J., Burton-Fanning, Shirelle, Byaruhanga, Timothy, Byott, Matthew, Campbell, Sharon, Carabelli, Alessandro M., Cargill, James S., Carlile, Matthew, Carvalho, Sílvia F., Casey, Anna, Castigador, Anibolina, Catalan, Jana, Chalker, Vicki, Chaloner, Nicola J., Chand, Meera, Chappell, Joseph G., Charalampous, Themoula, Chatterton, Wendy, Chaudhry, Yasmin, Churcher, Carol M., Clark, Gemma, Clarke, Phillip, Cogger, Benjamin J., Cole, Kevin, Collins, Jennifer, Colquhoun, Rachel, Connor, Thomas R., Cook, Kate F., Coombes, Jason, Corden, Sally, Cormie, Claire, Cortes, Nicholas, Cotic, Marius, Cotton, Seb, Cottrell, Simon, Coupland, Lindsay, Cox, MacGregor, Cox, Alison, Craine, Noel, Crawford, Liam, Cross, Aidan, Crown, Matthew, Crudgington, Dorian, Cumley, Nicola, Curran, Tanya, Curran, Martin D., da Silva Filipe, Ana, Dabrera, Gavin, Darby, Alistair C., Davidson, Rose K., Davies, Alisha, Davies, Robert M., Davis, Thomas, de Angelis, Daniela, De Lacy, Elen, de Oliveira Martins, Leonardo, de Silva, Thushan I., Debebe, Johnny, Denton-Smith, Rebecca, Dervisevic, Samir, Dewar, Rebecca, Dey, Jayasree, Dias, Joana, Dobie, Donald, Dorman, Matthew J., Downing, Fatima, Driscoll, Megan, du Plessis, Louis, Duckworth, Nichola, Durham, Jillian, Eastick, Kirstine, Easton, Lisa J., Eccles, Richard, Edgeworth, Jonathan, Edwards, Sue, Bouzidi, Kate El, Eldirdiri, Sahar, Ellaby, Nicholas, Elliott, Scott, Eltringham, Gary, Ensell, Leah, Erkiert, Michelle J., Zamudio, Marina Escalera, Essex, Sarah, Evans, Johnathan M., Evans, Cariad, Everson, William, Fairley, Derek J., Fallon, Karlie, Fanaie, Arezou, Farr, Ben W., Fearn, Christopher, Feltwell, Theresa, Ferguson, Lynne, Fina, Laia, Flaviani, Flavia, Fleming, Vicki M., Forrest, Sally, Foster-Nyarko, Ebenezer, Foulkes, Benjamin H., Foulser, Luke, Fragakis, Mireille, Frampton, Dan, Francois, Sarah, Fraser, Christophe, Freeman, Timothy M., Fryer, Helen, Fuchs, Marc, Fuller, William, Gajee, Kavitha, Galai, Katerina, Gallagher, Abbie, Gallagher, Eileen, Gallagher, Michael D., Gallis, Marta, Gaskin, Amy, Gatica-Wilcox, Bree, Geidelberg, Lily, Gemmell, Matthew, Georgana, Iliana, George, Ryan P., Gifford, Laura, Gilbert, Lauren, Girgis, Sophia T., Glaysher, Sharon, Goldstein, Emily J., Golubchik, Tanya, Gomes, Andrea N., Gonçalves, Sónia, Goodfellow, Ian G., Goodwin, Scott, Goudarzi, Salman, Gourtovaia, Marina, Graham, Clive, Graham, Lee, Grant, Paul R., Green, Luke R., Green, Angie, Greenaway, Jane, Gregory, Richard, Guest, Martyn, Gunson, Rory N., Gupta, Ravi K., Gutierrez, Bernardo, Haldenby, Sam T., Hamilton, William L., Hansford, Samantha E., Haque, Tanzina, Harris, Kathryn A., Harrison, Ian, Harrison, Ewan M., Hart, Jennifer, Hartley, John A., Harvey, William T., Harvey, Matthew, Hassan-Ibrahim, Mohammed O., Heaney, Judith, Helmer, Thomas, Henderson, John, Hesketh, Andrew R., Hey, Jessica, Heyburn, David, Higginson, Ellen E., Hill, Verity, Hill, Jack D., Hilson, Rachel A., Hilvers, Ember, Holden, Matthew T. G., Hollis, Amy, Holmes, Christopher W., Holmes, Nadine, Holmes, Alison H., Hopes, Richard, Hornsby, Hailey R., Hosmillo, Myra, Houlihan, Catherine, Howson-Wells, Hannah C., Hsu, Sharon N., Hubb, Jonathan, Huckson, Hannah, Hughes, Warwick, Hughes, Joseph, Hughes, Margaret, Hutchings, Stephanie, Idle, Giles, Illingworth, Chris J., Impey, Robert, Irish-Tavares, Dianne, Iturriza-Gomara, Miren, Izuagbe, Rhys, Jackson, Chris, Jackson, Ben, Jackson, Leigh M., Jackson, Kathryn A., Jackson, David K., Jahun, Aminu S., James, Victoria, James, Keith, Jeanes, Christopher, Jeffries, Aaron R., Jeremiah, Sarah, Jermy, Andrew, John, Michaela, Johnson, Rob, Johnson, Kate, Johnston, Ian, Jones, Owen, Jones, Sophie, Jones, Hannah, Jones, Christopher R., Jones, Neil, Joseph, Amelia, Judges, Sarah, Kay, Gemma L., Kay, Sally, Keatley, Jon-Paul, Keeley, Alexander J., Kenyon, Anita, Kermack, Leanne M., Khakh, Manjinder, Kidd, Stephen P., Kimuli, Maimuna, Kirk, Stuart, Kitchen, Christine, Kitchman, Katie, Knight, Bridget A., Koshy, Cherian, Kraemer, Moritz U. G., Kumziene-Summerhayes, Sara, Kwiatkowski, Dominic, Lackenby, Angie, Laing, Kenneth G., Lampejo, Temi, Langford, Cordelia F., Lavin, Deborah, Lawton, Andrew I., Lee, Jack C. D., Lee, David, Lensing, Stefanie V., Leonard, Steven, Levett, Lisa J., Le-Viet, Thanh, Lewis, Jonathan, Lewis, Kevin, Liddle, Jennifier, Liggett, Steven, Lillie, Patrick J., Lindsey, Benjamin B., Lister, Michelle M., Livett, Rich, Lo, Stephanie, Loman, Nicholas J., Loose, Matthew W., Louka, Stavroula F., Loveson, Katie F., Lowdon, Sarah, Lowe, Hannah, Lowe, Helen L., Lucaci, Anita O., Ludden, Catherine, Lynch, Jessica, Lyons, Ronan A., Lythgoe, Katrina, Machin, Nicholas W., MacIntyre-Cockett, George, Mack, Andrew, Macklin, Ben, Maclean, Alasdair, Macnaughton, Emily, Madona, Pinglawathee, Maes, Mailis, Maftei, Laurentiu, Mahanama, Adhyana I. K., Mahungu, Tabitha W., Mair, Daniel, Maksimovic, Joshua, Malone, Cassandra S., Maloney, Daniel, Manesis, Nikos, Manley, Robin, Mantzouratou, Anna, Marchbank, Angela, Mariappan, Arun, Martincorena, Inigo, Nunez, Rocio T. Martinez, Mather, Alison E., Maxwell, Patrick, Mayhew, Megan, Mbisa, Tamyo, McCann, Clare, McCarthy, Shane A., McCluggage, Kathryn, McClure, Patrick C., McCrone, J. T., McHugh, Martin P., McKenna, James P., McKerr, Caoimhe, McManus, Georgina M., McMurray, Claire L., McMurray, Claire, McNally, Alan, Meadows, Lizzie, Medd, Nathan, Megram, Oliver, Menegazzo, Mirko, Merrick, Ian, Michell, Stephen L., Michelsen, Michelle L., Mirfenderesky, Mariyam, Mirza, Jeremy, Miskelly, Julia, Moles-Garcia, Emma, Moll, Robin J., Molnar, Zoltan, Monahan, Irene M., Mondani, Matteo, Mookerjee, Siddharth, Moore, Christopher, Moore, Jonathan, Moore, Nathan, Moore, Catherine, Morcrette, Helen, Morgan, Sian, Morgan, Mari, Mori, Matilde, Morriss, Arthur, Moses, Samuel, Mower, Craig, Muir, Peter, Mukaddas, Afrida, Munemo, Florence, Munn, Robert, Murray, Abigail, Murray, Leanne J., Murray, Darren R., Mutingwende, Manasa, Myers, Richard, Nastouli, Eleni, Nebbia, Gaia, Nelson, Andrew, Nelson, Charlotte, Nicholls, Sam, Nichols, Jenna, Nicodemi, Roberto, Nomikou, Kyriaki, O’Grady, Justin, O’Brien, Sarah, Odedra, Mina, Ohemeng-Kumi, Natasha, Oliver, Karen, Orton, Richard J., Osman, Husam, O’Toole, Áine, Pacchiarini, Nicole, Padgett, Debra, Page, Andrew J., Park, Emily J., Park, Naomi R., Parker, Matthew D., Parmar, Surendra, Partridge, David G., Pascall, David, Patel, Amita, Patel, Bindi, Paterson, Steve, Payne, Brendan A. I., Peacock, Sharon J., Pearson, Clare, Pelosi, Emanuela, Percival, Benita, Perkins, Jon, Perry, Malorie, Pinckert, Malte L., Platt, Steven, Podplomyk, Olga, Pohare, Manoj, Pond, Marcus, Pope, Cassie F., Poplawski, Radoslaw, Powell, Jessica, Poyner, Jennifer, Prestwood, Liam, Price, Anna, Price, James R., Prieto, Jacqui A., Pritchard, David T., Prosolek, Sophie J., Pugh, Georgia, Pusok, Monika, Pybus, Oliver G., Pymont, Hannah M., Quail, Michael A., Quick, Joshua, Radulescu, Clara, Raghwani, Jayna, Ragonnet-Cronin, Manon, Rainbow, Lucille, Rajan, Diana, Rajatileka, Shavanthi, Ramadan, Newara A., Rambaut, Andrew, Ramble, John, Randell, Paul A., Randell, Paul, Ratcliffe, Liz, Raviprakash, Veena, Raza, Mohammad, Redshaw, Nicholas M., Rey, Sara, Reynolds, Nicola, Richter, Alex, Robertson, David L., Robinson, Esther, Robson, Samuel C., Rogan, Fiona, Rooke, Stefan, Rowe, Will, Roy, Sunando, Rudder, Steven, Ruis, Chris, Rushton, Steven, Ryan, Felicity, Saeed, Kordo, Samaraweera, Buddhini, Sambles, Christine M., Sanderson, Roy, Sanderson, Theo, Sang, Fei, Sass, Thea, Scher, Emily, Scott, Garren, Scott, Carol, Sehmi, Jasveen, Shaaban, Sharif, Shah, Divya, Shaw, Jessica, Shelest, Ekaterina, Shepherd, James G., Sheridan, Liz A., Sheriff, Nicola, Shirley, Lesley, Sillitoe, John, Silviera, Siona, Simpson, David A., Singh, Aditi, Singleton, Dawn, Skvortsov, Timofey, Sloan, Tim J., Sluga, Graciela, Smith, Ken, Smith, Kim S., Smith, Perminder, Smith, Darren, Smith, Louise, Smith, Colin P., Smith, Nikki, Smollett, Katherine L., Snell, Luke B., Somassa, Thomas, Southgate, Joel, Spellman, Karla, Chapman, Michael H. Spencer, Spurgin, Lewis G., Spyer, Moira J., Stanley, Rachael, Stanley, William, Stanton, Thomas D., Starinskij, Igor, Stockton, Joanne, Stonehouse, Susanne, Storey, Nathaniel, Studholme, David J., Sudhanva, Malur, Swindells, Emma, Taha, Yusri, Tan, Ngee Keong, Tang, Julian W., Tang, Miao, Taylor, Ben E. W., Taylor, Joshua F., Taylor, Sarah, Temperton, Ben, Templeton, Kate E., Thomas, Claire, Thomson, Laura, Thomson, Emma C., Thornton, Alicia, Thurston, Scott A. J., Todd, John A., Tomb, Rachael, Tong, Lily, Tonkin-Hill, Gerry, Torok, M. Estee, Tovar-Corona, Jaime M., Trebes, Amy, Trotter, Alexander J., Tsatsani, Ioulia, Turnbull, Robyn, Turtle, Lance, Twohig, Katherine A., Umpleby, Helen, Underwood, Anthony P., Vamos, Edith E., Vasylyeva, Tetyana I., Vattipally, Sreenu, Vernet, Gabrielle, Vipond, Barry B., Volz, Erik M., Walsh, Sarah, Wang, Dennis, Warne, Ben, Warwick-Dugdale, Joanna, Wastnedge, Elizabeth, Watkins, Joanne, Watson, Louisa K., Waugh, Sheila, Webster, Hermione J., Weldon, Danni, Westwick, Elaine, Whalley, Thomas, Wheeler, Helen, Whitehead, Mark, Whiteley, Max, Whitwham, Andrew, Wierzbicki, Claudia, Willford, Nicholas J., Williams, Lesley-Anne, Williams, Rebecca, Williams, Cheryl, Williams, Chris, Williams, Charlotte A., Williams, Rachel J., Williams, Thomas, Williams, Catryn, Williamson, Kathleen A., Wilson-Davies, Eleri, Witele, Eric, Withell, Karen T., Witney, Adam A., Wolverson, Paige, Wong, Nick, Workman, Trudy, Wright, Victoria, Wright, Derek W., Wyatt, Tim, Wyllie, Sarah, Xu-McCrae, Li, Yavus, Mehmet, Yaze, Geraldine, Yeats, Corin A., Yebra, Gonzalo, Yew, Wen Chyin, Young, Greg, Young, Jamie, Zarebski, Alex E., Zhang, Peijun, Modat, Marc, Hammers, Alexander, Spector, Tim D., Steves, Claire J., Sudre, Carole H., Ourselin, Sebastien and Duncan, Emma L. (2022) COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. Scientific Reports, 12 (1). p. 10904. ISSN 2045-2322

Haskell-Ramsay, Crystal, Dodd, Fiona, Smith, Darren, Cuthbertson, Lewis, Nelson, Andrew, Lodge, John and Jackson, Philippa (2022) Mixed Tree Nuts, Cognition and Gut Microbiota: a 4-week, Placebo-Controlled, Randomized Crossover Trial in Healthy Non-Elderly Adults. Journal of Nutrition, 152 (12). pp. 2778-2788. ISSN 0022-3166

Aggarwal, Dinesh, Page, Andrew J., Schaefer, Ulf, Savva, George M., Myers, Richard, Volz, Erik, Ellaby, Nicholas, Platt, Steven, Groves, Natalie, Gallagher, Eileen, Tumelty, Niamh M., Le Viet, Thanh, Hughes, Gareth J., Chen, Cong, Turner, Charlie, Logan, Sophie, Harrison, Abbie, The COVID-19 Genomics UK (COG, , Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek J., Curran, Tanya, McKenna, James P., Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-Ibrahim, Mohammed O., Malone, Cassandra S., Cogger, Benjamin J., Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Price, Anna, Kitchen, Christine, Gulliver, Huw, Merrick, Ian, Southgate, Joel, Guest, Martyn, Munn, Robert, Workman, Trudy, Connor, Thomas R., Fuller, William, Bresner, Catherine, Snell, Luke B., Patel, Amita, Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C., Beckett, Angela H., Aanensen, David M., Underwood, Anthony P., Yeats, Corin A., Abudahab, Khalil, Taylor, Ben E. W., Menegazzo, Mirko, Clark, Gemma, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M., Lister, Michelle M., Howson-Wells, Hannah C., Berry, Louise, Boswell, Tim, Joseph, Amelia, Willingham, Iona, Jones, Carl, Holmes, Christopher, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Blakey, Victoria, Williams, Lesley-Anne, Loose, Matthew W., Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Wright, Victoria, Sang, Fei, Debebe, Johnny, Coll, Francesc, Signell, Adrian W., Betancor, Gilberto, Wilson, Harry D., Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver G., du Plessis, Louis, Zarebski, Alex E., Raghwani, Jayna, Kraemer, Moritz U. G., Francois, Sarah, Attwood, Stephen W., Vasylyeva, Tetyana I., Zamudio, Marina Escalera, Gutierrez, Bernardo, Torok, M. Estee, Hamilton, William L., Goodfellow, Ian G., Hall, Grant, Jahun, Aminu S., Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L., Georgana, Iliana, Moses, Samuel, Lowe, Hannah, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Fisher, Chloe L., Awan, Ali R., BoYes, John, Breuer, Judith, Harris, Kathryn A., Brown, Julianne R., Shah, Divya, Atkinson, Laura, Lee, Jack C. D., Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Williams, Rebecca, Vernet, Gabrielle, Chapman, Michael R., Levett, Lisa J., Heaney, Judith, Chatterton, Wendy, Pusok, Monika, Xu-McCrae, Li, Smith, Darren, Bashton, Matthew, Young, Greg, Holmes, Alison, Randell, Paul A., Cox, Alison, Madona, Pinglawathee, Bolt, Frances, Price, James, Mookerjee, Siddharth, Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M., Rowan, Aileen, Taylor, Graham P., Smollett, Katherine L., Loman, Nicholas J., Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, McNally, Alan, Nunez, Rocio T. Martinez, Mason, Jenifer, Robinson, Trevor I., O’Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Sluga, Graciela, Machin, Nicholas W., Ahmad, Shazaad S. Y., George, Ryan P., Halstead, Fenella, Sivaprakasam, Venkat, Hogsden, Wendy, Illingworth, Chris J., Jackson, Chris, Thomson, Emma C., Shepherd, James G., Asamaphan, Patawee, Niebel, Marc O., Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., Tong, Lily, Broos, Alice, Mair, Daniel, Nichols, Jenna, Carmichael, Stephen N., Nomikou, Kyriaki, Aranday-Cortes, Elihu, Johnson, Natasha, Starinskij, Igor, da Silva Filipe, Ana, Robertson, David L., Orton, Richard J., Hughes, Joseph, Vattipally, Sreenu, Singer, Joshua B., Nickbakhsh, Seema, Hale, Antony D., Macfarlane-Smith, Louissa R., Harper, Katherine L., Carden, Holli, Taha, Yusri, Payne, Brendan A. I., Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Rushton, Steven, O’Brien, Sarah, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Blacow, Rachel, Templeton, Kate E., McHugh, Martin P., Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Meader, Emma J., Coupland, Lindsay, Smith, Louise, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, McCann, Clare, Yew, Wen Chyin, Andersson, Monique, Peto, Timothy, Justice, Anita, Eyre, David, Crook, Derrick, Sloan, Tim J., Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J., Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Wyatt, Tim, Allara, Elias, Pearson, Clare, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Muir, Peter, Vipond, Ian B., Hopes, Richard, Pymont, Hannah M., Hutchings, Stephanie, Curran, Martin D., Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Gallagher, Eileen, Lee, David, Williams, David, Harrison, Ian, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Bishop, Chloe, Chalker, Vicki, Ledesma, Juan, Twohig, Katherine A., 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, Bull, Matthew, Cronin, Michelle, Pacchiarini, Nicole, Craine, Noel, Jones, Rachel, Howe, Robin, Corden, Sally, Rey, Sara, Kumziene-SummerhaYes, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, O’Grady, Justin, Mather, Alison E., Baker, David J., Rudder, Steven, Aydin, Alp, Kay, Gemma L., Trotter, Alexander J., Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Casey, Anna, Ratcliffe, Liz, Simpson, David A., Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane A. H., Knight, Bridget A., Ellard, Sian, Auckland, Cressida, Jones, Christopher R., Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa L., Dadrah, Ashok, Symmonds, Amanda, Saluja, Tranprit, Bourgeois, Yann, Scarlett, Garry P., Loveson, Katie F., Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Bonner, Stephen, Essex, Sarah, Lyons, Ronan A., Saeed, Kordo, Mahanama, Adhyana I. K., Samaraweera, Buddhini, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Williams, Rachel J., Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A., Cotic, Marius, Bayzid, Nadua, Westhorpe, Adam P., Hartley, John A., Jannoo, Riaz, Lowe, Helen L., Karamani, Angeliki, Ensell, Leah, Prieto, Jacqui A., Jeremiah, Sarah, Grammatopoulos, Dimitris, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Best, Angus, Percival, Benita, Mirza, Jeremy, Megram, Oliver, Mayhew, Megan, Crawford, Liam, Ashcroft, Fiona, Moles-Garcia, Emma, Cumley, Nicola, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Blane, Beth, Girgis, Sophia T., Leek, Danielle, Sridhar, Sushmita, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Gupta, Ravi K., Ludden, Catherine, Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Hadjirin, Nazreen F., Carabelli, Alessandro M., Brooks, Ellena, Smith, Kim S., Galai, Katerina, McManus, Georgina M., Ruis, Chris, Davidson, Rose K., Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., O’Toole, Áine, Rooke, Stefan, Hill, Verity, 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, Wierzbicki, Claudia, Webster, Hermione J., 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, Whiteley, Max, Zhang, Peijun, Gallis, Marta, Louka, Stavroula F., Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey K. 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Stirrup, Oliver, Blackstone, James, Mapp, Fiona, MacNeil, Alyson, Panca, Monica, Holmes, Alison, Machin, Nicholas, Shin, Gee Yen, Mahungu, Tabitha, Saeed, Kordo, Saluja, Tranprit, Taha, Yusri, Mahida, Nikunj, Pope, Cassie, Chawla, Anu, Cutino-Moguel, Maria-Teresa, Tamuri, Asif, Williams, Rachel, Darby, Alistair, Robertson, David L., Flaviani, Flavia, Nastouli, Eleni, Robson, Samuel, Smith, Darren, Laing, Kenneth, Monahan, Irene, Kele, Beatrix, Haldenby, Sam, George, Ryan, Bashton, Matthew, Witney, Adam A., Byott, Matthew, Coll, Francesc, Chapman, Michael, Peacock, Sharon J., Hughes, Joseph, Nebbia, Gaia, Partridge, David G., Parker, Matthew, Price, James Richard, Peters, Christine, Roy, Sunando, Snell, Luke B., de Silva, Thushan I., Thomson, Emma, Flowers, Paul, Copas, Andrew, Breuer, Judith, McCann, Clare, Young, Greg, Nelson, Andrew and The COVID-19 Genomics UK consortium, (2022) Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study. eLife, 11. e78427. ISSN 2050-084X

Hill, Verity, Du Plessis, Louis, Peacock, Thomas P, Aggarwal, Dinesh, Colquhoun, Rachel, Carabelli, Alesandro M, Ellaby, Nicholas, Gallagher, Eileen, Groves, Natalie, Jackson, Ben, McCrone, J T, O’Toole, Áine, Price, Anna, Sanderson, Theo, Scher, Emily, Southgate, Joel, Volz, Erik, Barclay, Wendy S, Barrett, Jeffrey C, Chand, Meera, Connor, Thomas, Goodfellow, Ian, Gupta, Ravindra K, Harrison, Ewan M, Loman, Nicholas, Myers, Richard, Robertson, David L, Pybus, Oliver G, Rambaut, Andrew, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8 (2). veac080. ISSN 2057-1577

Dolton, Garry, Rius, Cristina, Hasan, Md Samiul, Wall, Aaron, Szomolay, Barbara, Behiry, Enas, Whalley, Thomas, Southgate, Joel, Fuller, Anna, Morin, Théo, Topley, Katie, Tan, Li Rong, Goulder, Philip J.R., Spiller, Owen B., Rizkallah, Pierre J., Jones, Lucy C., Connor, Thomas R., Sewell, Andrew K., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The COVID-19 Genomics UK (COG-UK) Consortium, (2022) Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell, 185 (16). 2936-2951.e19. ISSN 0092-8674

Smallman-Raynor, M. R., Cliff, A. D., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and The (COG-UK) Consortium, (2022) Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection, 150. e145. ISSN 0950-2688

Al-Momani, Hafez, Perry, Audrey, Nelson, Andrew, Stewart, Christopher J., Jones, Rhys, Krishnan, Amaran, Robertson, Andrew, Bourke, Stephen, Doe, Simon, Cummings, Stephen, Anderson, Alan, Forrest, Tara, Forrest, Ian, Griffin, Michael, Wilcox, Matthew, Brodlie, Malcolm, Pearson, Jeffrey and Ward, Christopher (2022) Exposure to bile and gastric juice can impact the aerodigestive microbiome in people with cystic fibrosis. Scientific Reports, 12 (1). p. 11114. ISSN 2045-2322

Dabrera, Gavin, Allen, Hester, Zaidi, Asad, Flannagan, Joe, Twohig, Katherine, Thelwall, Simon, Marchant, Elizabeth, Aziz, Nurin Abdul, Lamagni, Theresa, Myers, Richard, Charlett, André, Capelastegui, Fernando, Chudasama, Dimple, Clare, Tom, Coukan, Flavien, Sinnathamby, Mary, Ferguson, Neil, Hopkins, Susan, Chand, Meera, Hope, Russell, Kall, Meaghan, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare and COG-UK Consortium, (2022) Assessment of mortality and hospital admissions associated with confirmed infection with SARS-CoV-2 Alpha variant: a matched cohort and time-to-event analysis, England, October to December 2020. Eurosurveillance, 27 (20). ISSN 1560-7917

Krutikov, Maria, Stirrup, Oliver, Nacer-Laidi, Hadjer, Azmi, Borscha, Fuller, Chris, Tut, Gokhan, Palmer, Tom, Shrotri, Madhumita, Irwin-Singer, Aidan, Baynton, Verity, Hayward, Andrew, Moss, Paul, Copas, Andrew, Shallcross, Laura, The COVID-19 Genomics UK (COG-UK) Consortium, , Smith, Darren, Bashton, Matthew, McCann, Clare, Young, Greg, Nelson, Andrew, Crown, Matthew, Henderson, John, Hollis, Amy, Stanley, William and Yew, Wen Chyin (2022) Outcomes of SARS-CoV-2 omicron infection in residents of long-term care facilities in England (VIVALDI): a prospective, cohort study. The Lancet Healthy Longevity, 3 (5). e347-e355. ISSN 2666-7568

Young, Greg, Yew, Wen Chyin, Nelson, Andrew, Bridge, Simon, Berrington, Janet E., Embleton, Nicholas D. and Smith, Darren (2022) Optimisation and application of a novel method to identify bacteriophage in maternal milk and infant stool identifies host-phage communities within preterm infant gut. Frontiers in Pediatrics, 10. p. 856520. ISSN 2296-2360

Blackstone, James, Stirrup, Oliver, Mapp, Fiona, Panca, Monica, Copas, Andrew, Flowers, Paul, Hockey, Leanne, Price, James, Partridge, David, Peters, Christine, de Silva, Thushan, Nebbia, Gaia, Snell, Luke B, McComish, Rachel, Breuer, Judith, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, McCann, Clare, Nelson, Andrew, Smith, Darren and Young, Greg (2022) Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals. BMJ Open, 12 (4). e052514. ISSN 2044-6055

Nyberg, Tommy, Ferguson, Neil M., Nash, Sophie G., Webster, Harriet H., Flaxman, Seth, Andrews, Nick, Hinsley, Wes, Bernal, Jamie Lopez, Kall, Meaghan, Bhatt, Samir, Blomquist, Paula, Zaidi, Asad, Volz, Erik, Aziz, Nurin Abdul, Harman, Katie, Funk, Sebastian, Abbott, Sam, Hope, Russell, Charlett, Andre, Chand, Meera, Ghani, Azra C., Seaman, Shaun R., Dabrera, Gavin, De Angelis, Daniela, Presanis, Anne M., Thelwall, Simon, Nyberg, Tommy, Ferguson, Neil M., Nash, Sophie G., Webster, Harriet H., Flaxman, Seth, Andrews, Nick, Hinsley, Wes, Lopez Bernal, Jamie, Kall, Meaghan, Bhatt, Samir, Blomquist, Paula, Zaidi, Asad, Volz, Erik, Abdul Aziz, Nurin, Harman, Katie, Funk, Sebastian, Abbott, Sam, Hope, Russell, Charlett, Andre, Chand, Meera, Ghani, Azra C., Seaman, Shaun R., Dabrera, Gavin, De Angelis, Daniela, Presanis, Anne M., Thelwall, Simon, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, McCann, Clare, Smith, Darren, Young, Greg and Nelson, Andrew (2022) Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study. The Lancet, 399 (10332). pp. 1303-1312. ISSN 0140-6736

Chadeau-Hyam, Marc, Wang, Haowei, Eales, Oliver, Haw, David, Bodinier, Barbara, Whitaker, Matthew, Walters, Caroline E, Ainslie, Kylie E C, Atchison, Christina, Fronterre, Claudio, Diggle, Peter J, Page, Andrew J, Trotter, Alexander J, Ashby, Deborah, Barclay, Wendy, Taylor, Graham, Cooke, Graham, Ward, Helen, Darzi, Ara, Riley, Steven, Donnelly, Christl A, Elliott, Paul, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, Nelson, Andrew and McCann, Clare (2022) SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys. The Lancet Respiratory Medicine, 10 (4). pp. 355-366. ISSN 2213-2600

Wright, Derek W., Harvey, William T., Hughes, Joseph, Cox, MacGregor, Peacock, Thomas P., Colquhoun, Rachel, Jackson, Ben, Orton, Richard, Nielsen, Morten, Hsu, Nienyun Sharon, Harrison, Ewan M., de Silva, Thushan I., Rambaut, Andrew, Peacock, Sharon J., Robertson, David L., Carabelli, Alessandro M., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, Nelson, Andrew and McCann, Clare (2022) Tracking SARS-CoV-2 Mutations & Variants Through the COG-UK-Mutation Explorer. Virus Evolution, 8 (1). veac023. ISSN 2057-1577

Terry, Jefferson, Hockney, Rochelle, Orr, Caroline H., Waring, Gareth J., Christiaens, Inge, Taylor, Gillian, Cummings, Stephen, Robson, Stephen C. and Nelson, Andrew (2022) Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research. PLoS ONE, 17 (3). e0265441. ISSN 1932-6203

Aggarwal, Dinesh, Myers, Richard, Hamilton, William L, Bharucha, Tehmina, Tumelty, Niamh M, Brown, Colin S, Meader, Emma J, Connor, Tom, Smith, Darren L, Bradley, Declan T, Robson, Samuel, Bashton, Matthew, Shallcross, Laura, Zambon, Maria, Goodfellow, Ian, Chand, Meera, O'Grady, Justin, Török, M Estée, Peacock, Sharon J, Page, Andrew J, The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Loh, Joshua, Nelson, Andrew, Yew, Wen C. and Young, Gregory R. (2022) The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet Microbe, 3 (2). e151-e158. ISSN 2666-5247

Boshier, Florencia A. T., Pang, Juanita, Penner, Justin, Parker, Matthew, Alders, Nele, Bamford, Alasdair, Grandjean, Louis, Grunewald, Stephanie, Hatcher, James, Best, Timothy, Dalton, Caroline, Bynoe, Patricia Dyal, Frauenfelder, Claire, Köeglmeier, Jutta, Myerson, Phoebe, Roy, Sunando, Williams, Rachel, Silva, Thushan I., Goldstein, Richard A., Breuer, Judith, The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Bashton, Matthew, Loh, Joshua, Nelson, Andrew, Smith, Darren L., Yew, Wen Chyin and Young, Gregory R. (2022) Evolution of viral variants in remdesivir‐treated and untreated SARS‐CoV‐2‐infected pediatrics patients. Journal of Medical Virology, 94 (1). pp. 161-172. ISSN 0146-6615

Twohig, Katherine A, Nyberg, Tommy, Zaidi, Asad, Thelwall, Simon, Sinnathamby, Mary A, Aliabadi, Shirin, Seaman, Shaun R, Harris, Ross J, Hope, Russell, Lopez-bernal, Jamie, Gallagher, Eileen, Charlett, Andre, De Angelis, Daniela, Presanis, Anne M, Dabrera, Gavin, The COVID-19 Genomics UK (COG-UK) Consortium, , Koshy, Cherian, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek, Curran, Tanya, Mckenna, James, Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-ibrahim, Mohammed, Malone, Cassandra, Cogger, Benjamin, Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Smith, Darren, Bashton, Matthew, Young, Greg, Nelson, Andrew, McCann, Clare and Yew, Wen Chyin (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. The Lancet Infectious Diseases, 22 (1). pp. 35-42. ISSN 1473-3099

Allen, Hester, Vusirikala, Amoolya, Flannagan, Joe, Twohig, Katherine A., Zaidi, Asad, Chudasama, Dimple, Lamagni, Theresa, Groves, Natalie, Turner, Charlie, Rawlinson, Christopher, Lopez-Bernal, Jamie, Harris, Ross, Charlett, Andre, Dabrera, Gavin, Kall, Meaghan, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg and McCann, Clare (2022) Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study. The Lancet Regional Health - Europe, 12. p. 100252. ISSN 2666-7762

Francis, Rodric V., Billam, Harriet, Clarke, Mitch, Yates, Carl, Tsoleridis, Theocharis, Berry, Louise, Mahida, Nikunj, Irving, William L., Moore, Christopher, Holmes, Nadine, Ball, Jonathan K., Loose, Matthew, McClure, C. Patrick, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, McCann, Clare and Nelson, Andrew (2022) The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. The Journal of Infectious Diseases, 225 (1). pp. 10-18. ISSN 0022-1899

Elliott, Paul, Haw, David, Wang, Haowei, Eales, Oliver, Walters, Caroline E., Ainslie, Kylie E. C., Atchison, Christina, Fronterre, Claudio, Diggle, Peter J., Page, Andrew J., Trotter, Alexander J., Prosolek, Sophie J., Ashby, Deborah, Donnelly, Christl A., Barclay, Wendy, Taylor, Graham, Cooke, Graham, Ward, Helen, Darzi, Ara, Riley, Steven, Robson, Samuel C., Loman, Nicholas J., Connor, Thomas R., Golubchik, Tanya, Martinez Nunez, Rocio T., Ludden, Catherine, Corden, Sally, Johnston, Ian, Bonsall, David, Smith, Colin P., Awan, Ali R., Bucca, Giselda, Torok, M. Estee, Saeed, Kordo, Prieto, Jacqui A., Jackson, David K., Hamilton, William L., Snell, Luke B., Moore, Catherine, Harrison, Ewan M., Goncalves, Sonia, Jackson, Leigh M., Goodfellow, Ian G., Fairley, Derek J., Loose, Matthew W., Watkins, Joanne, Livett, Rich, Moses, Samuel, Amato, Roberto, Nicholls, Sam, Bull, Matthew, Smith, Darren, Barrett, Jeff, Aanensen, David M., Curran, Martin D., Parmar, Surendra, Aggarwal, Dinesh, Shepherd, James G., Parker, Matthew D., Glaysher, Sharon, Bashton, Matthew, Underwood, Anthony P., Pacchiarini, Nicole, Loveson, Katie F., Carabelli, Alessandro M., Templeton, Kate E., Langford, Cordelia F., Sillitoe, John, de Silva, Thushan I., Wang, Dennis, Kwiatkowski, Dominic, Rambaut, Andrew, O’Grady, Justin, Cottrell, Simon, Holden, Matthew T.G., Thomson, Emma C., Osman, Husam, Andersson, Monique, Chauhan, Anoop J., Hassan-Ibrahim, Mohammed O., Lawniczak, Mara, Gupta, Ravi Kumar, Alderton, Alex, Chand, Meera, Constantinidou, Chrystala, Unnikrishnan, Meera, Darby, Alistair C., Hiscox, Julian A., Paterson, Steve, Martincorena, Inigo, Robertson, David L., Volz, Erik M., Page, Andrew J., Pybus, Oliver G., Bassett, Andrew R., Ariani, Cristina V., Spencer Chapman, Michael H., Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., Taha, Yusri, McHugh, Martin P., Dewar, Rebecca, Jahun, Aminu S., McMurray, Claire, Pandey, Sarojini, McKenna, James P., Nelson, Andrew, Young, Greg, McCann, Clare, Elliott, Scott, Lowe, Hannah, Temperton, Ben, Roy, Sunando, Price, Anna, Rey, Sara, Wyles, Matthew, Rooke, Stefan, Shaaban, Sharif, de Cesare, Mariateresa, Letchford, Laura, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Hosmillo, Myra, O'Toole, Áine, Hesketh, Andrew R., Stark, Richard, du Plessis, Louis, Ruis, Chris, Adams, Helen, Bourgeois, Yann, Michell, Stephen L., Grammatopoulos, Dimitris, Edgeworth, Jonathan, Breuer, Judith, Todd, John A., Fraser, Christophe, Buck, David, John, Michaela, Kay, Gemma L., Palmer, Steve, Peacock, Sharon J., Heyburn, David, Weldon, Danni, Robinson, Esther, McNally, Alan, Muir, Peter, Vipond, Ian B., Boyes, John, Sivaprakasam, Venkat, Saluja, Tranprit, Dervisevic, Samir, Meader, Emma J., Park, Naomi R., Oliver, Karen, Jeffries, Aaron R., Ott, Sascha, da Silva Filipe, Ana, Simpson, David A., Williams, Chris, Masoli, Jane A.H., Knight, Bridget A., Jones, Christopher R., Koshy, Cherian, Ash, Amy, Casey, Anna, Bosworth, Andrew, Ratcliffe, Liz, Xu-McCrae, Li, Pymont, Hannah M., Hutchings, Stephanie, Berry, Lisa, Jones, Katie, Halstead, Fenella, Davis, Thomas, Holmes, Christopher, Iturriza-Gomara, Miren, Lucaci, Anita O., Randell, Paul Anthony, Cox, Alison, Madona, Pinglawathee, Harris, Kathryn Ann, Brown, Julianne Rose, Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa Louise, Liggett, Steven, Graham, Clive, Swindells, Emma, Collins, Jennifer, Eltringham, Gary, Campbell, Sharon, McClure, Patrick C., Clark, Gemma, Sloan, Tim J., Jones, Carl, Lynch, Jessica, Warne, Ben, Leonard, Steven, Durham, Jillian, Williams, Thomas, Haldenby, Sam T., Storey, Nathaniel, Alikhan, Nabil-Fareed, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Perry, Malorie, Craine, Noel, Lyons, Ronan A., Beckett, Angela H., Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Davies, Robert, Blane, Beth, Girgis, Sophia T., Beale, Mathew A., Bellis, Katherine L., Dorman, Matthew J., Drury, Eleanor, Kane, Leanne, Kay, Sally, McGuigan, Samantha, Nelson, Rachel, Prestwood, Liam, Rajatileka, Shavanthi, Batra, Rahul, Williams, Rachel J., Kristiansen, Mark, Green, Angie, Justice, Anita, Mahanama, Adhyana I.K., Samaraweera, Buddhini, Hadjirin, Nazreen F., Quick, Joshua and Poplawski, Radoslaw (2021) Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant. Science, 374 (6574). abl9551. ISSN 0036-8075

Vöhringer, Harald S., Sanderson, Theo, Sinnott, Matthew, De Maio, Nicola, Nguyen, Thuy, Goater, Richard, Schwach, Frank, Harrison, Ian, Hellewell, Joel, Ariani, Cristina V., Gonçalves, Sonia, Jackson, David K., Johnston, Ian, Jung, Alexander W., Saint, Callum, Sillitoe, John, Suciu, Maria, Goldman, Nick, Panovska-Griffiths, Jasmina, Birney, Ewan, Volz, Erik, Funk, Sebastian, Kwiatkowski, Dominic, Chand, Meera, Martincorena, Inigo, Barrett, Jeffrey C., Gerstung, Moritz, The Wellcome Sanger Institute Covid-19 Surveillance Team, , The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, McCann, Clare, Nelson, Andrew, Smith, Darren and Young, Greg (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600 (7889). pp. 506-511. ISSN 0028-0836

Lee, Benhur, Davis, Chris, Logan, Nicola, Tyson, Grace, Orton, Richard, Harvey, William T., Perkins, Jonathan S., Mollett, Guy, Blacow, Rachel M., Peacock, Thomas P., Barclay, Wendy S., Cherepanov, Peter, Palmarini, Massimo, Murcia, Pablo R., Patel, Arvind H., Robertson, David L., Haughney, John, Thomson, Emma C., Willett, Brian J., Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare, Yew, Wen Chyin and The COVID-19 Genomics UK (COG-UK) Consortium, on behalf of the COVID-19 DeplOyed VaccinE (DOVE) Cohort Study (2021) Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLOS Pathogens, 17 (12). e1010022. ISSN 1553-7374

Boshier, Florencia A.T., Venturini, Cristina, Stirrup, Oliver, Guerra-Assunção, José Afonso, Alcolea-Medina, Adela, Becket, Angela H., Byott, Matthew, Charalampous, Themoula, Filipe, Ana da Silva, Frampton, Dan, Glaysher, Sharon, Khan, Tabassum, Kulasegara-Shylini, Raghavendran, Kele, Beatrix, Monahan, Irene M., Mollett, Guy, Parker, Matthew, Pelosi, Emanuela, Randell, Paul, Roy, Sunando, Taylor, Joshua F., Weller, Sophie J., Wilson-Davies, Eleri, Wade, Phillip, Williams, Rachel, Copas, Andrew J., Cutino-Moguel, Teresa, Freemantle, Nick, Hayward, Andrew C., Holmes, Alison, Hughes, Joseph, Mahungu, Tabitha W., Nebbia, Gaia, Nastouli, Eleni, Partridge, David G., Pope, Cassie F., Price, James R., Robson, Samuel C., Saeed, Kordo, Shin, Gee Yen, de Silva, Thushan I., Snell, Luke B., Thomson, Emma C., Witney, Adam A., Breuer, Judith, COG-UK HOCI Variant Substudy consortium, , The COVID-19 Genomics UK (COG-UK) consortium, , Bashton, Matthew, Nelson, Andrew, McCann, Clare, Smith, Darren and Young, Greg (2021) The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. Journal of Infection, 83 (6). pp. 693-700. ISSN 0163-4453

Mashe, Tapfumanei, Takawira, Faustinos Tatenda, de Oliveira Martins, Leonardo, Gudza-Mugabe, Muchaneta, Chirenda, Joconiah, Munyanyi, Manes, Chaibva, Blessmore V., Tarupiwa, Andrew, Gumbo, Hlanai, Juru, Agnes, Nyagupe, Charles, Ruhanya, Vurayai, Phiri, Isaac, Manangazira, Portia, Goredema, Alexander, Danda, Sydney, Chabata, Israel, Jonga, Janet, Munharira, Rutendo, Masunda, Kudzai, Mukeredzi, Innocent, Mangwanya, Douglas, Trotter, Alex, Le Viet, Thanh, Rudder, Steven, Kay, Gemma, Baker, David, Thilliez, Gaetan, Gutierrez, Ana Victoria, O'Grady, Justin, Hove, Maxwell, Mutapuri-Zinyowera, Sekesai, Page, Andrew J., Kingsley, Robert A., Mhlanga, Gibson, The COVID-19 Genomics UK (COG-UK) Consortium, , SARS-CoV-2 Research Group, , Bashton, Matthew, Nelson, Andrew, McCann, Clare, Smith, Darren and Young, Greg (2021) Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data. The Lancet Global Health, 9 (12). e1658-e1666. ISSN 2214-109X

Nicholls, Samuel M., Poplawski, Radoslaw, Bull, Matthew J., Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M., Rowe, Will P. M., Jackson, Ben, Hill, Verity, O’Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M., Peacock, Sharon J., Aanensen, David M., Rambaut, Andrew, Connor, Thomas R., Loman, Nicholas J., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology, 22 (1). p. 196. ISSN 1474-760X

Orr, C. H., Williams, R., Halldórsdóttir, H. H., Birley, A., Greene, E., Nelson, Andrew, Ralebitso-Senior, T. K. and Taylor, G. (2021) Unique chemical parameters and microbial activity lead to increased archaeological preservation at the Roman frontier site of Vindolanda, UK. Scientific Reports, 11 (1). p. 15837. ISSN 2045-2322

Entwistle, Jane, Thompson, Jonathan R., Argyraki, Ariadne, Bashton, Matthew, Bramwell, Lindsay, Crown, Matthew, Hursthouse, Andrew, Jabeen, Khadija, Marinho-Reis, Amélia P., Namdeo, Anil, Nelson, Andrew, Pearce, David, Potgieter-Vermaak, Sanja, Rasmussen, Pat E. and Wragg, Joanna (2021) Bacterial diversity in house dust: characterization of a core indoor microbiome. Frontiers in Environmental Science, 9. p. 754657. ISSN 2296-665X

de Silva, Thushan, Liu, Guihai, Lindsey, Benjamin B., Dong, Danning, Moore, Shona C., Hsu, Nienyun Sharon, Shah, Dhruv, Wellington, Dannielle, Mentzer, Alexander J., Angyal, Adrienn, Brown, Rebecca, Parker, Matthew D., Ying, Zixi, Yao, Xuan, Turtle, Lance, Dunachie, Susanna, Bashton, Matthew, McCann, Clare, Nelson, Andrew, Smith, Darren, Yew, Wen Chyin, Young, Greg, The COVID-19 Genomics UK (COG-UK) Consortium, and ISARIC4C Investigators, (2021) The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. iScience, 24 (11). p. 103353. ISSN 2589-0042

Picton, David M., Luyten, Yvette A., Morgan, Richard D., Nelson, Andrew, Smith, Darren L., Dryden, David T. F., Hinton, Jay C. D. and Blower, Tim R. (2021) The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses. Nucleic Acids Research, 49 (19). pp. 11257-11273. ISSN 0305-1048

Jackson, Ben, Boni, Maciej F., Bull, Matthew J., Colleran, Amy, Colquhoun, Rachel M., Darby, Alistair C., Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T., Nicholls, Samuel M., O’Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Loman, Nicholas J., Connor, Thomas R., Robertson, David L., Pybus, Oliver G., Rambaut, Andrew, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic. Cell, 184 (20). 5179-5188.e8. ISSN 0092-8674

Stirrup, Oliver, Boshier, Florencia, Venturini, Cristina, Guerra-Assunção, José Afonso, Alcolea-Medina, Adela, Beckett, Angela, Charalampous, Themoula, da Silva Filipe, Ana, Glaysher, Sharon, Khan, Tabassum, Kulasegaran Shylini, Raghavendran, Kele, Beatrix, Monahan, Irene, Mollett, Guy, Parker, Matthew, Pelosi, Emanuela, Randell, Paul, Roy, Sunando, Taylor, Joshua, Weller, Sophie, Wilson-Davies, Eleri, Wade, Phillip, Williams, Rachel, Copas, Andrew, Cutino-Moguel, Maria-Teresa, Freemantle, Nick, Hayward, Andrew C, Holmes, Alison, Hughes, Joseph, Mahungu, Tabitha, Nebbia, Gaia, Partridge, David, Pope, Cassie, Price, James, Robson, Samuel, Saeed, Kordo, de Silva, Thushan, Snell, Luke, Thomson, Emma, Witney, Adam A, Breuer, Judith, Bashton, Matthew, Nelson, Andrew, McCann, Clare, Young, Greg, Smith, Darren and The COVID-19 Genomics UK (COG-UK) Consortium, (2021) SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respiratory Research, 8 (1). e001029. ISSN 2052-4439

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Mishra, Swapnil, Mindermann, Sören, Sharma, Mrinank, Whittaker, Charles, Mellan, Thomas A, Wilton, Thomas, Klapsa, Dimitra, Mate, Ryan, Fritzsche, Martin, Zambon, Maria, Ahuja, Janvi, Howes, Adam, Miscouridou, Xenia, Nason, Guy P, Ratmann, Oliver, Semenova, Elizaveta, Leech, Gavin, Sandkühler, Julia Fabienne, Rogers-Smith, Charlie, Vollmer, Michaela, Unwin, H Juliette T, Gal, Yarin, Chand, Meera, Gandy, Axel, Martin, Javier, Volz, Erik, Ferguson, Neil M, Bhatt, Samir, Brauner, Jan M, Flaxman, Seth, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England. EClinicalMedicine, 39. p. 101064. ISSN 2589-5370

Wenlock, R.D., Tausan, M., Mann, R., Garr, W., Preston, R., Arnold, A., Hoban, J., Webb, L., Quick, C., Beckett, A., Loveson, K., Glaysher, S., Elliott, S., Malone, C., Cogger, B., Easton, L., The COVID-19 Genomics UK (COG-UK) Consortium, , Allan, John, Bashton, Matthew, Loh, Joshua, Nelson, Andrew, Smith, Darren L., Yew, Wen Chyin, Young, Gregory R., Robson, S.C., Hassan-Ibrahim, M.O. and Sargent, C. (2021) Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward. Infection Prevention in Practice, 3 (3). p. 100165. ISSN 2590-0889

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Stephenson, Dominic, Perry, Audrey, Nelson, Andrew, Robb, Ali E., Thomas, Matthew F., Bourke, Stephen J., Perry, John D. and Jones, Amanda (2021) Decontamination Strategies Used for AFB Culture Significantly Reduce the Viability of Mycobacterium abscessus Complex in Sputum Samples from Patients with Cystic Fibrosis. Microorganisms, 9 (8). p. 1597. ISSN 2076-2607

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Harvey, William T., Carabelli, Alessandro M., Jackson, Ben, Gupta, Ravindra K., Thomson, Emma C., Harrison, Ewan M., Ludden, Catherine, Reeve, Richard, Rambaut, Andrew, Peacock, Sharon J., Robertson, David L., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology, 19 (7). pp. 409-424. ISSN 1740-1526

Page, Andrew J., Mather, Alison E., Le-Viet, Thanh, Meader, Emma J., Alikhan, Nabil-Fareed, Kay, Gemma L., de Oliveira Martins, Leonardo, Aydin, Alp, Baker, David J., Trotter, Alexander J., Rudder, Steven, Tedim, Ana P., Kolyva, Anastasia, Stanley, Rachael, Yasir, Muhammad, Diaz, Maria, Potter, Will, Stuart, Claire, Meadows, Lizzie, Bell, Andrew, Gutierrez, Ana Victoria, Thomson, Nicholas M., Adriaenssens, Evelien M., Swingler, Tracey, Gilroy, Rachel A. J., Griffith, Luke, Sethi, Dheeraj K., Aggarwal, Dinesh, Brown, Colin S., Davidson, Rose K., Kingsley, Robert A., Bedford, Luke, Coupland, Lindsay J., Charles, Ian G., Elumogo, Ngozi, Wain, John, Prakash, Reenesh, Webber, Mark A., Smith, S. J. Louise, Chand, Meera, Dervisevic, Samir, O’Grady, Justin, The COVID-19 Genomics UK (COG-UK) consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Microbial Genomics, 7 (6). 000589. ISSN 2057-5858

Stirrup, Oliver, Hughes, Joseph, Parker, Matthew, Partridge, David G, Shepherd, James G, Blackstone, James, Coll, Francesc, Keeley, Alexander, Lindsey, Benjamin B, Marek, Aleksandra, Peters, Christine, Singer, Joshua B, Tamuri, Asif, de Silva, Thushan I, Thomson, Emma C, Breuer, Judith, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10. ISSN 2050-084X

Meng, Bo, Kemp, Steven A, Papa, Guido, Datir, Rawlings, Ferreira, Isabella A.T.M., Marelli, Sara, Harvey, William T., Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A., Mlcochova, Petra, The COVID-19 Genomics UK (COG-UK) Consortium, , Bailey, Dalan, Gupta, Ravindra K., Smith, Darren, Bashton, Matthew, Nelson, Andrew, Young, Greg, McCann, Clare and Yew, Wen Chyin (2021) Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Reports, 35 (13). p. 109292. ISSN 2211-1247

Chappell, Joseph G., Tsoleridis, Theocharis, Clark, Gemma, Berry, Louise, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Sang, Fei, Debebe, Bisrat J., Wright, Victoria, Irving, William L., Thomson, Brian J., Boswell, Timothy C. J., Willingham, Iona, Joseph, Amelia, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M., Lister, Michelle M., Howson-Wells, Hannah C., Holmes, Edward C., Loose, Matthew W., Ball, Jonathan K., McClure, C. Patrick, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. Journal of General Virology, 102 (6). 001595. ISSN 0022-1317

Aggarwal, Dinesh, Warne, Ben, Jahun, Aminu, Hamilton, William, Fieldman, Thomas, Plessis, Louis, Hill, Verity, Blane, Beth, Watkins, Emmeline, Wright, Elizabeth, Hall, Grant, Ludden, Catherine, Myers, Richard, Hosmillo, Myra, Goodfellow, Yasmin, Pinckert, Malte, Georgana, Iliana, Izuagbe, Rhys, Leek, Danielle, Nsonwu, Olisaeloka, Hughes, Gareth, Packer, Simon, Page, Andrew, Metaxaki, Marina, Fuller, Stewart, Weale, Gillian, Holgate, Jon, Howes, Rob, McFarlane, Duncan, Dougan, Gordon, Pybus, Oliver, Angelis, Daniela De, Maxwell, Patrick, Peacock, Sharon, Weekes, Michael, Illingworth, Chris, Harrison, Ewan, Matheson, Nicholas, Goodfellow, Ian, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg, Nelson, Andrew and McCann, Clare (2021) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Research Square Platform. pp. 1-25. (Submitted)

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Collier, Dami A., De Marco, Anna, Ferreira, Isabella A.T.M., Meng, Bo, Datir, Rawlings, Walls, Alexandra C., Kemp S, Steven A., Bassi, Jessica, Pinto, Dora, Fregni, Chiara Silacci, Bianchi, Siro, Tortorici, M. Alejandra, Bowen, John, Culap, Katja, Jaconi, Stefano, Cameroni, Elisabetta, Snell, Gyorgy, Pizzuto, Matteo S., Pellanda, Alessandra Franzetti, Garzoni, Christian, Riva, Agostino, Elmer, Anne, Kingston, Nathalie, Graves, Barbara, McCoy, Laura E., Smith, Kenneth G. C., Bradley, John R., Temperton, Nigel, Lourdes Ceron-Gutierrez, L., Barcenas-Morales, Gabriela, Harvey, William, Virgin, Herbert W., Lanzavecchia, Antonio, Piccoli, Luca, Doffinger, Rainer, Wills, Mark, Veesler, David, Corti, Davide, Gupta, Ravindra K., The CITIID-NIHR BioResource COVID-19 Collaboration, , The COVID-19 Genomics UK (COG-UK) consortium, , Bashton, Matthew, Young, Greg, McCann, Clare, Nelson, Andrew and Smith, Darren (2021) Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature, 593 (7857). pp. 136-141. ISSN 0028-0836

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Neaverson, Alexandra S. (2021) Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184 (1). 64-75.e11. ISSN 0092-8674

da Silva Filipe, Ana, Shepherd, James G., Williams, Thomas, Hughes, Joseph, Aranday-Cortes, Elihu, Asamaphan, Patawee, Ashraf, Shirin, Balcazar, Carlos, Brunker, Kirstyn, Campbell, Alasdair, Carmichael, Stephen, Davis, Chris, Dewar, Rebecca, Gallagher, Michael D., Gunson, Rory, Hill, Verity, Ho, Antonia, Jackson, Ben, James, Edward, Jesudason, Natasha, Johnson, Natasha, McWilliam Leitch, E. Carol, Li, Kathy, MacLean, Alasdair, Mair, Daniel, McAllister, David A., McCrone, John T., McDonald, Sarah E., McHugh, Martin P., Morris, A. Keith, Nichols, Jenna, Niebel, Marc, Nomikou, Kyriaki, Orton, Richard J., O’Toole, Áine, Palmarini, Massimo, Parcell, Benjamin J., Parr, Yasmin A., Rambaut, Andrew, Rooke, Stefan, Shaaban, Sharif, Shah, Rajiv, Singer, Joshua B., Smollett, Katherine, Starinskij, Igor, Tong, Lily, Sreenu, Vattipally B., Wastnedge, Elizabeth, Holden, Matthew T. G., Robertson, David L., Templeton, Kate, Thomson, Emma C., Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg and The COVID-19 Genomics UK (COG-UK) consortium, (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6 (1). pp. 112-122. ISSN 2058-5276

Leskinen, Katarzyna, Pajunen, Maria I., Vilanova, Miguel Vincente Gomez-Raya, Kiljunen, Saija, Nelson, Andrew, Smith, Darren and Skurnik, Mikael (2020) YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing. Viruses, 12 (6). p. 620. ISSN 1999-4915

Hockney, Rochelle, Waring, Gareth J., Taylor, Gillian, Cummings, Stephen P., Robson, Stephen C., Orr, Caroline H. and Nelson, Andrew (2020) Fetal membrane bacterial load is increased in histologically confirmed inflammatory chorioamnionitis: A retrospective cohort study. Placenta, 91. pp. 43-51. ISSN 0143-4004

Roberts, S. A., Brabin, L., Diallo, S., Gies, S., Nelson, Andrew, Stewart, C. J., Swinkels, D. W., Geurts-Moespo, A. J., Kazienga, A., Ouedraogo, S., D’Alessandro, U., Tinto, H. and Brabin, B. J. (2019) Mucosal lactoferrin response to genital tract infections is associated with iron and nutritional biomarkers in young Burkinabé women. European Journal of Clinical Nutrition, 73 (11). pp. 1464-1472. ISSN 1476-5640

Tariq, Mohamma, Everest, Francesca, Cowley, Lauren A., Wright, Rosanna, Holt, Giles, Ingram, Hazel, Duignan, Liberty, Nelson, Andrew, Lanyon, Clare, Perry, Audrey, Perry, John D., Bourke, Stephen, Brockhurst, Michael A., Bridge, Simon, de Soyza, Anthony and Smith, Darren (2019) Temperate bacteriophages from chronic Pseudomonas aeruginosa lung infections show disease-specific changes in host range and modulate antimicrobial susceptibility. mSystems, 4 (4). e00191-18. ISSN 2379-5077

Aldred, Nick and Nelson, Andrew (2019) Microbiome acquisition during larval settlement of the barnacle Semibalanus balanoides. Biology Letters, 15 (6). ISSN 1744-9561

Stephenson, Dominic, Perry, Audrey, Appleby, Martin, Lee, David, Davison, John, Johnston, Annette, Jones, Amanda, Nelson, Andrew, Bourke, Stephen, Thomas, Matthew, de Soyza, Anthony, Lordan, James, Lumb, Joanna, Robb, Ali, Samuel, Julie and Walton, Kathy (2019) An evaluation of methods for the isolation of nontuberculous mycobacteria from patients with cystic fibrosis, bronchiectasis and patients assessed for lung transplantation. BMC Pulmonary Medicine, 19 (1). p. 19. ISSN 1471-2466

Houghton, David, Stewart, Christopher, Stamp, Craig, Nelson, Andrew, Ajami, Nadim J., Petrosino, Joseph, Wipat, Anil, Trenell, Michael, Turnbull, Douglass and Greaves, Laura C. (2018) Impact of age-related mitochondrial dysfunction and exercise on intestinal microbiota composition. Journals of Gerontology: Series A, 73 (5). pp. 571-578. ISSN 1758-535X

Powell, Jason, Garnett, James, Mather, Michael W., Cooles, Faye A. H., Nelson, Andrew, Verdon, Bernard, Scott, Jon, Jiwa, Kasim, Ruchaud-Sparagano, Marie-Hélène, Cummings, Stephen, Perry, John, Wright, Stephen, Wilson, Janet, Pearson, Jeffrey, Ward, Chris and Simpson, A. John (2018) Excess Mucin Impairs Subglottic Epithelial Host Defense in Mechanically Ventilated Patients. American Journal of Respiratory and Critical Care Medicine. ISSN 1073-449X

Brabin, Loretta, Roberts, Stephen A., Gies, Sabine, Nelson, Andrew, Diallo, Salou, Stewart, Christopher, Kazienga, Adama, Birtles, Julia, Ouedraogo, Sayouba, Claeys, Yves, Tinto, Halidou, d'Alessandro, Umberto, Faragher, E. Brian and Brabin, Bernard (2017) Effects of long-term weekly iron and folic acid supplementation on lower genital tract infection - a double blind, randomised controlled trial in Burkina Faso. BMC Medicine, 15 (1). p. 206. ISSN 1741-7015

Stewart, Christopher, Embleton, Nicholas, Marrs, Emma, Smith, Daniel, Fofanova, Tatiana, Nelson, Andrew, Skeath, Tom, Perry, John, Petrosino, Joseph, Berrington, Janet and Cummings, Stephen (2017) Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls. Microbiome, 5 (1). p. 75. ISSN 2049-2618

Stewart, Christopher, Embleton, Nicholas, Clements, Elizabeth, Luna, Pamela, Smith, Daniel, Fofanova, Tatiana, Nelson, Andrew, Taylor, Gillian, Orr, Caroline, Petrosino, Joseph, Berrington, Janet and Cummings, Stephen (2017) Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. Frontiers in Microbiology, 8. p. 1008. ISSN 1664-302X

Olakanye, Ayodeji, Nelson, Andrew and Ralebitso-Senior, T. Komang (2017) A comparative in situ decomposition study using still born piglets and leaf litter from a deciduous forest. Forensic Science International, 276. pp. 85-92. ISSN 0379-0738

Stewart, Christopher, Nelson, Andrew, Campbell, Matthew, Walker, Mark, Stevenson, Emma, Shaw, James, Cummings, Stephen and West, Dan (2017) Gut microbiota of Type 1 diabetes patients with good glycaemic control and high physical fitness is similar to people without diabetes: an observational study. Diabetic Medicine, 34 (1). pp. 127-134. ISSN 0742-3071

Stewart, Christopher, Embleton, Nicholas, Marrs, Emma, Smith, Daniel, Nelson, Andrew, Abdulkadir, Bashir, Skeath, Tom, Petrosino, Joseph, Perry, John, Berrington, Janet and Cummings, Stephen (2016) Temporal bacterial and metabolic development of the preterm gut reveals specific signatures in health and disease. Microbiome, 4 (1). p. 67. ISSN 2049-2618

Abdulkadir, Bashir, Nelson, Andrew, Skeath, Tom, Marrs, Emma, Perry, John, Cummings, Stephen, Embleton, Nicholas, Berrington, Janet and Stewart, Christopher (2016) Routine use of probiotics in preterm infants: longitudinal impact on the microbiome and metabolome. Neonatology, 109 (4). pp. 239-247. ISSN 1661-7800

Abdulkadir, Bashir, Nelson, Andrew, Skeath, Tom, Marrs, Emma, Perry, John, Cummings, Stephen, Embleton, Nicholas, Berrington, Janet and Stewart, Christopher (2016) Stool bacterial load in preterm infants with necrotising enterocolitis. Early Human Development, 95. pp. 1-2. ISSN 0378-3782

Emami, Kaveh, Nelson, Andrew, Hack, Ethan, Zhang, Jinwei, Green, David, Caldwell, Gary and Mesbahi, Ehsan (2016) MALDI-TOF Mass Spectrometry Discriminates Known Species and Marine Environmental Isolates of Pseudoalteromonas. Frontiers in Microbiology, 7. p. 104. ISSN 1664-302X

Stewart, Christopher, Skeath, Tom, Nelson, Andrew, Fernstad, Sara Johansson, Marrs, Emma, Perry, John, Cummings, Stephen, Berrington, Janet and Embleton, Nicholas (2015) Preterm gut microbiota and metabolome following discharge from intensive care. Scientific Reports, 5. p. 17141. ISSN 2045-2322

Stewart, Christopher, Nelson, Andrew, Treumann, Achim, Skeath, Tom, Cummings, Stephen, Embleton, Nicholas and Berrington, Janet (2015) Metabolomic and proteomic analysis of serum from preterm infants with necrotising entercolitis and late-onset sepsis. Pediatric Research, 79 (3). pp. 425-431. ISSN 0031-3998

Emami, Kaveh, Hack, Ethan, Nelson, Andrew, Brain, Chelsea, Lyne, Fern, Mesbahi, Ehsan, Day, John and Caldwell, Gary (2015) Proteomic-based biotyping reveals hidden diversity within a microalgae culture collection: An example using Dunaliella. Scientific Reports, 5. p. 10036. ISSN 2045-2322

Purcell, Paul, Jary, Hannah, Perry, Audrey, Perry, John, Stewart, Christopher, Nelson, Andrew, Lanyon, Clare, Smith, Darren, Cummings, Stephen and de Soyza, Anthony (2014) Polymicrobial airway bacterial communities in adult bronchiectasis patients. BMC Microbiology, 14. ISSN 1471-2180

Stewart, Christopher, Marrs, Emma, Nelson, Andrew, Lanyon, Clare, Perry, John, Embleton, Nicholas, Cummings, Stephen and Berrington, Janet (2013) Development of the preterm gut microbiome in twins at risk of necrotising enterocolitis and sepsis. PLoS ONE, 8 (8). e73465. ISSN 1932-6203

Nelson, Andrew, Perry, Audrey, Perry, John, Bourke, Stephen, Cummings, Stephen and de Soyza, Anthony (2013) Determining the influence of environmental and patient specific factors on the polymicrobial communities of the cystic fibrosis airway. Antonie van Leeuwenhoek Journal of Microbiology, 103 (4). pp. 755-762. ISSN 1572-9699

Stewart, Christopher, Nelson, Andrew, Scribbins, David, Marrs, Emma, Lanyon, Clare, Perry, John, Embleton, Nicholas, Cummings, Stephen and Berrington, Janet (2013) Bacterial and fungal viability in the preterm gut: NEC and sepsis. Archives of Disease in Childhood - Fetal and Neonatal Edition, 98 (4). F298-F303. ISSN 1359-2998

Stewart, Christopher, Marrs, Emma, Magorrian, Sinead, Nelson, Andrew, Lanyon, Clare, Perry, John, Embleton, Nicholas, Cummings, Stephen and Berrington, Janet (2012) The preterm gut microbiota: changes associated with necrotizing enterocolitis and infection. Acta Paediatrica, 101 (11). pp. 1121-1127. ISSN 1651-2227

Nelson, Andrew, de Soyza, Anthony, Perry, John, Sutcliffe, Iain and Cummings, Stephen (2012) Polymicrobial challenges to Koch's postulates: ecological lessons from the bacterial vaginosis and cystic fibrosis microbiomes. Innate Immunity, 18 (5). pp. 774-783. ISSN 1753-4267

Nelson, Andrew (2011) An investigtion of the polymicrobial nature of lower respiratory tract infections in cystic fibrosis patients. Doctoral thesis, Northumbria University.

Nelson, Andrew, Bourke, Stephen, Perry, John, de Soyza, Anthony and Cummings, Stephen (2011) P166 Temporal dynamics of polymicrobial communities in the lower respiratory tract of patients with cystic fibrosis. Thorax, 66 (4). A135-A135. ISSN 0040-6376

Purcell, Paul, Nelson, Andrew, Fisher, Andrew, Perry, John, de Soyza, Anthony and Cummings, Stephen (2011) S19 Molecular fingerprinting and metagenomic analysis reveals a polymicrobial element in patients with chronic obstructive pulmonary disease. Thorax, 66 (Suppl). A11-A12. ISSN 0040-6376

Nelson, Andrew, de Soyza, Anthony, Bourke, Stephen, Perry, John and Cummings, Stephen (2010) Assessment of sample handling practices on microbial activity in sputum samples from patients with cystic fibrosis. Letters in Applied Microbiology, 51 (3). pp. 272-277. ISSN 0266-8254

Coulthard, Malcolm, Kalra, Monika, Lambert, Heather, Nelson, Andrew, Smith, Terry and Perry, John (2010) Redefining Urinary Tract Infections by Bacterial Colony Counts. PEDIATRICS, 125 (2). pp. 335-341. ISSN 0031-4005

Cummings, Stephen, Nelson, Andrew, Purcell, Paul, de Soyza, Anthony, Bourke, Stephen and Perry, John (2010) S23 A comparative study of polymicrobial diversity in CF and non-CF bronchiectasis. Thorax, 65 (Suppl). A13-A14. ISSN 0040-6376

Cummings, Stephen, Gyaneshwar, Prasad, Vinuesa, Pablo, Farruggia, Frank, Andrews, Mitchell, Humphry, David, Elliott, Geoffrey, Nelson, Andrew, Orr, Caroline, Pettitt, Deborah, Shah, Gopit, Santos, Scott, Krishnan, Hari, Odee, David, Moreira, Fatima, Sprent, Janet, Young, J. Peter and James, Euan (2009) Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. Environmental Microbiology, 11 (10). pp. 2510-2525. ISSN 1462-2912