Items where Author is "Smith, Darren"

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

Colton, Hayley, Parker, Matthew D., Stirrup, Oliver, Blackstone, James, Loose, Matthew, McClure, C. Patrick, Roy, Sunando, Williams, Charlotte, McLeod, Julie, Smith, Darren, Taha, Yusri, Zhang, Peijun, Hsu, Sharon Nienyun, Kele, Beatrix, Harris, Kathryn, Mapp, Fiona, Williams, Rachel, COG-UK HOCI Investigators, The COVID-19 Genomics UK (COG-UK) Con, , Flowers, Paul, Breuer, Judith, Partridge, David G., de Silva, Thushan I., Bashton, Matthew and Crown, Matthew (2023) Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: Analysis of data from the COG-UK HOCI study. Journal of Hospital Infection, 131. pp. 34-42. ISSN 0195-6701

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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Dawson, Frances, Yew, Wen Chyin, Orme, Bethany, Markwell, Christopher, Aguilar, Rodrigo Ledesma, Perry, Justin, Shortman, Ian, Smith, Darren, Torun, Hamdi, Wells, Gary and Unthank, Matthew (2022) Self-assembled, hierarchical structured surfaces for applications in (super)hydrophobic antiviral coatings. Langmuir, 38 (34). pp. 10632-10641. ISSN 0743-7463

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

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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

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, PITCH Consortium, , The COVID-19 Genomics UK (COG-UK) Consortium, , Haughney, John, Robertson, David L., Palmarini, Massimo, Ray, Surajit, Thomson, Emma C., Smith, Darren, Young, Greg, Bashton, Matthew, McCann, Clare, Henderson, John, Crown, Matthew and Yew, Wen Chyin (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7 (8). pp. 1161-1179. ISSN 2058-5276

Furber, Matthew J. W., Young, Greg, Holt, Giles S., Pyle, Simone, Davison, Glen, Roberts, Michael G., Roberts, Justin D., Howatson, Glyn and Smith, Darren (2022) Gut Microbial Stability is Associated with Greater Endurance Performance in Athletes Undertaking Dietary Periodization. mSystems, 7 (3). pp. 1-15. ISSN 2379-5077

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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

Snell, Luke B, Wang, Wenjuan, Alcolea-Medina, Adela, Charalampous, Themoula, Batra, Rahul, de Jongh, Leonardo, Higgins, Finola, Nebbia, Gaia, Wang, Yanzhong, Edgeworth, Jonathan, Curcin, Vasa, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren and Crown, Matthew (2022) Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London. BMJ Open, 12 (2). e055474. ISSN 2044-6055

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

Taha, Yusri, Wardle, Hayley, Evans, Adam B., Hunter, Ewan R., Marr, Helen, Osborne, Wendy, Bashton, Matthew, Smith, Darren, Burton-Fanning, Shirelle, Schmid, Matthias L. and Duncan, Christopher J. A. (2021) Persistent SARS-CoV-2 infection in patients with secondary antibody deficiency: successful clearance following combination casirivimab and imdevimab (REGN-COV2) monoclonal antibody therapy. Annals of Clinical Microbiology and Antimicrobials, 20 (1). p. 85. ISSN 1476-0711

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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

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

Frost, Freddy, Young, Greg, Wright, Laura, Miah, Nahida, Smith, Darren, Winstanley, Craig, Walshaw, Martin J., Fothergill, Joanne L. and Nazareth, Dilip (2021) The clinical and microbiological utility of inhaled aztreonam lysine for the treatment of acute pulmonary exacerbations of cystic fibrosis: An open-label randomised crossover study (AZTEC-CF). Journal of Cystic Fibrosis, 20 (6). pp. 994-1002. ISSN 1569-1993

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

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

Leary, Shay, Gaudieri, Silvana, Parker, Matthew D., Chopra, Abha, James, Ian, Pakala, Suman, Alves, Eric, John, Mina, Lindsey, Benjamin B., Keeley, Alexander J., Rowland-Jones, Sarah L., Swanson, Maurice S., Ostrov, David A., Bubenik, Jodi L., Das, Suman R., Sidney, John, Sette, Alessandro, The COVID-19 Genomics UK (COG-UK) Consortium, , De Silva, Thushan, Phillips, Elizabeth, Mallal, Simon, Smith, Darren, Bashton, Matthew, Young, Greg, Nelson, Andrew, McCann, Clare and Yew, Wen Chyin (2021) Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Pathogens and Immunity, 6 (2). pp. 27-49. ISSN 2469-2964

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Tonkin-Hill, Gerry, Martincorena, Inigo, Amato, Roberto, Lawson, Andrew RJ, Gerstung, Moritz, Johnston, Ian, Jackson, David K, Park, Naomi, Lensing, Stefanie V, Quail, Michael A, Gonçalves, Sónia, Ariani, Cristina, Spencer Chapman, Michael, Hamilton, William L, Meredith, Luke W, Hall, Grant, Jahun, Aminu S, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L, Georgana, Iliana, Yakovleva, Anna, Caller, Laura G, Caddy, Sarah L, Feltwell, Theresa, Khokhar, Fahad A, Houldcroft, Charlotte J, Curran, Martin D, Parmar, Surendra, Alderton, Alex, Nelson, Rachel, Harrison, Ewan M, Sillitoe, John, Bentley, Stephen D, Barrett, Jeffrey C, Torok, M Estee, Goodfellow, Ian G, Langford, Cordelia, Kwiatkowski, Dominic, The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and McCann, Clare (2021) Patterns of within-host genetic diversity in SARS-CoV-2. eLife, 10. ISSN 2050-084X

Li, Kathy K., Woo, Y. Mun, Stirrup, Oliver, Hughes, Joseph, Ho, Antonia, Filipe, Ana Da Silva, Johnson, Natasha, Smollett, Katherine, Mair, Daniel, Carmichael, Stephen, Tong, Lily, Nichols, Jenna, Aranday-Cortes, Elihu, Brunker, Kirstyn, Parr, Yasmin A., Nomikou, Kyriaki, McDonald, Sarah E., Niebel, Marc, Asamaphan, Patawee, Sreenu, Vattipally B., Robertson, David L., Taggart, Aislynn, Jesudason, Natasha, Shah, Rajiv, Shepherd, James, Singer, Josh, Taylor, Alison H.M., Cousland, Zoe, Price, Jonathan, Lees, Jennifer S., Jones, Timothy P.W., Lopez, Carlos Varon, MacLean, Alasdair, Starinskij, Igor, Gunson, Rory, Morris, Scott T.W., Thomson, Peter C., Geddes, Colin C., Traynor, Jamie P., Breuer, Judith, Thomson, Emma C., Mark, Patrick B., Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg and The COVID-19 Genomics UK (COG-UK) consortium, (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – A high risk community-hospital interface. Journal of Infection, 83 (1). pp. 96-103. ISSN 0163-4453

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

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Puethe, Christoph, Quail, Michael A, Rajatileka, Shavanthi, Scott, Carol, Shirley, Lesley, Sillitoe, John, Spencer Chapman, Michael H, Thurston, Scott AJ, Tonkin-Hill, Gerry, Weldon, Danni, Rajan, Diana, Bronner, Iraad F, Aigrain, Louise, Redshaw, Nicholas M, Lensing, Stefanie V, Davies, Robert, Whitwham, Andrew, Liddle, Jennifier, Lewis, Kevin, Tovar-Corona, Jaime M, Leonard, Steven, Durham, Jillian, Bassett, Andrew R, McCarthy, Shane, Moll, Robin J, James, Keith, Oliver, Karen, Makunin, Alex, Barrett, Jeff and Gunson, Rory N (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. 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Nelson, Andrew, Stewart, Christopher J., Kennedy, Nicholas A., Lodge, John, Tremelling, Mark, Probert, Chris S., Parkes, Miles, Mansfield, John C., Smith, Darren, Hold, Georgina L., Lees, Charlie W., Bridge, Simon, Lamb, Christopher A. and UK IBD Genetics Consortium, (2021) The Impact of NOD2 Genetic Variants on the Gut Mycobiota in Crohn’s Disease Patients in Remission and Individuals Without Gastrointestinal Inflammation. Journal of Crohn's and Colitis, 15 (5). pp. 800-812. ISSN 1873-9946

Lythgoe, Katrina A., Hall, Matthew, Ferretti, Luca, de Cesare, Mariateresa, MacIntyre-Cockett, George, Trebes, Amy, Andersson, Monique, Otecko, Newton, Wise, Emma L., Moore, Nathan, Lynch, Jessica, Kidd, Stephen, Cortes, Nicholas, Mori, Matilde, Williams, Rebecca, Vernet, Gabrielle, Justice, Anita, Green, Angie, Nicholls, Samuel M., Ansari, M. Azim, Abeler-Dörner, Lucie, Moore, Catrin E., Peto, Timothy E. A., Eyre, David W., Shaw, Robert, Simmonds, Peter, Buck, David, Todd, John A., Connor, Thomas R., Ashraf, Shirin, da Silva Filipe, Ana, Shepherd, James, Thomson, Emma C., Bonsall, David, Fraser, Christophe, Golubchik, Tanya, Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg, Oxford Virus Sequencing Analysis Group (OVSG), and The COVID-19 Genomics UK (COG-UK) Consortium, (2021) SARS-CoV-2 within-host diversity and transmission. Science, 372 (6539). eabg0821. ISSN 0036-8075

Emary, Katherine R W, Golubchik, Tanya, Aley, Parvinder K, Ariani, Cristina V, Angus, Brian, Bibi, Sagida, Blane, Beth, Bonsall, David, Cicconi, Paola, Charlton, Sue, Clutterbuck, Elizabeth A, Collins, Andrea M, Cox, Tony, Darton, Thomas C, Dold, Christina, Douglas, Alexander D, Duncan, Christopher J A, Ewer, Katie J, Flaxman, Amy L, Faust, Saul N, Ferreira, Daniela M, Feng, Shuo, Finn, Adam, Folegatti, Pedro M, Fuskova, Michelle, Galiza, Eva, Goodman, Anna L, Green, Catherine M, Green, Christopher A, Greenland, Melanie, Hallis, Bassam, Heath, Paul T, Hay, Jodie, Hill, Helen C, Jenkin, Daniel, Kerridge, Simon, Lazarus, Rajeka, Libri, Vincenzo, Lillie, Patrick J, Ludden, Catherine, Marchevsky, Natalie G, Minassian, Angela M, McGregor, Alastair C, Mujadidi, Yama F, Phillips, Daniel J, Plested, Emma, Pollock, Katrina M, Robinson, Hannah, Smith, Andrew, Song, Rinn, Snape, Matthew D, Sutherland, Rebecca K, Thomson, Emma C, Toshner, Mark, Turner, David P J, Vekemans, Johan, Villafana, Tonya L, Williams, Christopher J, Hill, Adrian V S, Lambe, Teresa, Gilbert, Sarah C, Voysey, Merryn, Ramasamy, Maheshi N, Pollard, Andrew J, Bashton, Matthew, Young, Greg, Nelson, Andrew and Smith, Darren (2021) Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial. The Lancet, 397 (10282). pp. 1351-1362. ISSN 0140-6736

Davies, Nicholas G., Abbott, Sam, Barnard, Rosanna C., Jarvis, Christopher I., Kucharski, Adam J., Munday, James D., Pearson, Carl A. B., Russell, Timothy W., Tully, Damien C., Washburne, Alex D., Wenseleers, Tom, Gimma, Amy, Waites, William, Wong, Kerry L. M., van Zandvoort, Kevin, Silverman, Justin D., Diaz-Ordaz, Karla, Keogh, Ruth, Eggo, Rosalind M., Funk, Sebastian, Jit, Mark, Atkins, Katherine E., Edmunds, W. John, CMMID COVID-19 Working Group, , COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg and Nelson, Andrew (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372 (6538). eabg3055. ISSN 0036-8075

Hosie, Margaret J., Epifano, Ilaria, Herder, Vanessa, Orton, Richard J., Stevenson, Andrew, Johnson, Natasha, MacDonald, Emma, Dunbar, Dawn, McDonald, Michael, Howie, Fiona, Tennant, Bryn, Herrity, Darcy, Da Silva Filipe, Ana, Streicker, Daniel G., Willett, Brian J., Murcia, Pablo R., Jarrett, Ruth F., Robertson, David L., Weir, William, Bashton, Matthew, Nelson, Andrew, Smith, Darren, Young, Greg and The COVID‐19 Genomics UK (COG‐UK) consortium, (2021) Detection of SARS‐CoV‐2 in respiratory samples from cats in the UK associated with human‐to‐cat transmission. Veterinary Record, 188 (8). e247. ISSN 0042-4900

Parker, Matthew D., Lindsey, Benjamin B., Leary, Shay, Gaudieri, Silvana, Chopra, Abha, Wyles, Matthew, Angyal, Adrienn, Green, Luke R., Parsons, Paul, Tucker, Rachel M., Brown, Rebecca, Groves, Danielle, Johnson, Katie, Carrilero, Laura, Heffer, Joe, Partridge, David G., Evans, Cariad, Raza, Mohammad, Keeley, Alexander J., Smith, Nikki, Filipe, Ana Da Silva, Shepherd, James G., Davis, Chris, Bennett, Sahan, Sreenu, Vattipally B., Kohl, Alain, Aranday-Cortes, Elihu, Tong, Lily, Nichols, Jenna, Thomson, Emma C., Wang, Dennis, Mallal, Simon, de Silva, Thushan I., The COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Young, Greg, Allan, John, Loh, Joshua, Nelson, Andrew, Smith, Darren and Yew, Wen Chyin (2021) Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31 (4). pp. 645-658. ISSN 1088-9051

Thomson, Emma C., Rosen, Laura E., Shepherd, James G., Spreafico, Roberto, da Silva Filipe, Ana, Wojcechowskyj, Jason A., Davis, Chris, Piccoli, Luca, Pascall, David J., Dillen, Josh, Lytras, Spyros, Czudnochowski, Nadine, Shah, Rajiv, Meury, Marcel, Jesudason, Natasha, De Marco, Anna, Li, Kathy, Bassi, Jessica, O’Toole, Aine, Pinto, Dora, Colquhoun, Rachel M., Culap, Katja, Jackson, Ben, Zatta, Fabrizia, Rambaut, Andrew, Jaconi, Stefano, Sreenu, Vattipally B., Nix, Jay, Zhang, Ivy, Jarrett, Ruth F., Glass, William G., Beltramello, Martina, Nomikou, Kyriaki, Pizzuto, Matteo, Tong, Lily, Cameroni, Elisabetta, Croll, Tristan I., Johnson, Natasha, Di Iulio, Julia, Wickenhagen, Arthur, Ceschi, Alessandro, Harbison, Aoife M., Mair, Daniel, Ferrari, Paolo, Smollett, Katherine, Sallusto, Federica, Carmichael, Stephen, Garzoni, Christian, Nichols, Jenna, Galli, Massimo, Hughes, Joseph, Riva, Agostino, Ho, Antonia, Schiuma, Marco, Semple, Malcolm G., Openshaw, Peter J.M., Fadda, Elisa, Baillie, J. Kenneth, Chodera, John D., Rihn, Suzannah J., Lycett, Samantha J., Virgin, Herbert W., Telenti, Amalio, Corti, Davide, Robertson, David L., Snell, Gyorgy, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg and the COVID-19 Genomics UK (COG-UK) Consortium, (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184 (5). 1171-1187.e20. ISSN 0092-8674

du Plessis, Louis, McCrone, John T., Zarebski, Alexander E., Hill, Verity, Ruis, Christopher, Gutierrez, Bernardo, Raghwani, Jayna, Ashworth, Jordan, Colquhoun, Rachel, Connor, Thomas R., Faria, Nuno R., Jackson, Ben, Loman, Nicholas J., O’Toole, Áine, Nicholls, Samuel M., Parag, Kris V., Scher, Emily, Vasylyeva, Tetyana I., Volz, Erik M., Watts, Alexander, Bogoch, Isaac I., Khan, Kamran, Aanensen, David M., Kraemer, Moritz U. G., Rambaut, Andrew, Pybus, Oliver G., COVID-19 Genomics UK (COG-UK) Consortium, , Bashton, Matthew, Smith, Darren, Young, Greg and Nelson, Andrew (2021) Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, 371 (6530). pp. 708-712. ISSN 0036-8075

Volz, Erik, Hill, Verity, McCrone, John T., Price, Anna, Jorgensen, David, O’Toole, Áine, Southgate, Joel, Johnson, Robert, Jackson, Ben, Nascimento, Fabricia F., Rey, Sara M., Nicholls, Samuel M., Colquhoun, Rachel M., da Silva Filipe, Ana, Shepherd, James, Pascall, David J., Shah, Rajiv, Jesudason, Natasha, Li, Kathy, Jarrett, Ruth, Pacchiarini, Nicole, Bull, Matthew, Geidelberg, Lily, Siveroni, Igor, Goodfellow, Ian, Loman, Nicholas J., Pybus, Oliver G., Robertson, David L., Thomson, Emma C., Rambaut, Andrew, Connor, Thomas R., Koshy, Cherian, Wise, Emma, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Mori, Matilde, Fairley, Derek J., Curran, Tanya, McKenna, James P., Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Moore, Catrin, Caddy, Sarah L., Khokhar, Fahad A., 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., Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C., Beckett, Angela, Loveson, Katie F., 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, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Holmes, Christopher, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, 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., Feltwell, Theresa, Houldcroft, Charlotte J., Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver, du Plessis, Louis, Zarebski, Alex, Raghwani, Jayna, Kraemer, Moritz, Francois, Sarah, Attwood, Stephen, Vasylyeva, Tetyana, Torok, M. 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Samir, Stanley, Rachael, Prakash, Reenesh, Stuart, Claire, Elumogo, Ngozi, Sethi, Dheeraj K., Meader, Emma J., Coupland, Lindsay J., Potter, Will, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, Yew, Wen C., Resende Silva, Paola C., Andersson, Monique, Shaw, Robert, Peto, Timothy, Justice, Anita, Eyre, David, Crooke, Derrick, Hoosdally, Sarah, Sloan, Tim J., Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J., Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Butcher, Ethan, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Allara, Elias, Pearson, Clare, Muir, Peter, Vipond, Ian B., Hopes, Richard, Pymont, Hannah M., Hutchings, Stephanie, Curran, Martin D., Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Platt, Steven, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Chand, Meera, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Myers, Richard, 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T., Gavriil, Artemis, Mestek-Boukhibar, Lamia, Weeks, Sam, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Harrison, Ewan M., Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Bellis, Katherine L., Girgis, Sophia T., Naydenova, Plamena, Blane, Beth, Sridhar, Sushmita, Ruis, Chris, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Hadjirin, Nazreen F., Aggarwal, Dinesh, Griffith, Luke, Swingler, Tracey, Davidson, Rose K., Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., O'Toole, Áine, Rooke, Stefan, Jackson, Ben, Colquhoun, Rachel, Ashworth, Jordan, Hill, Verity, McCrone, J.T., Scher, Emily, Yu, Xiaoyu, Williamson, Kathleen A., Stanton, Thomas D., Michell, Stephen L., Bewshea, Claire M., Temperton, Ben, Michelsen, Michelle L., Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James W., Sambles, Christine M., Studholme, David J., Jeffries, Aaron R., Darby, Alistair C., Hiscox, Julian A., Paterson, Steve, Iturriza-Gomara, Miren, Jackson, Kathryn A., Lucaci, Anita O., Vamos, Edith E., Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Turtle, Lance, Haldenby, Sam T., Gregory, Richard, Gemmell, Matthew, Kwiatkowski, Dominic, de Silva, Thushan I., Smith, Nikki, Angyal, Adrienn, Lindsey, Benjamin B., Groves, Danielle C., Green, Luke R., Wang, Dennis, Freeman, Timothy M., Parker, Matthew D., Keeley, Alexander J., Parsons, Paul J., Tucker, Rachel M., Brown, Rebecca, Wyles, Matthew, Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey K.J., Bridgewater, Hannah E., Frost, Lucy R., Taylor-Joyce, Grace, Stark, Richard, Baxter, Laura, Alam, Mohammad T., Brown, Paul E., McClure, Patrick C., Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Gramatopoulos, Dimitris, Buck, David, Todd, John A., Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Langford, Cordelia, Alderton, Alex, Amato, Roberto, Goncalves, Sonia, Jackson, David K., Johnston, Ian, Sillitoe, John, Palmer, Steve, Lawniczak, Mara, Berriman, Matt, Danesh, John, Livett, Rich, Shirley, Lesley, Farr, Ben, Quail, Mike, Thurston, Scott, Park, Naomi, Betteridge, Emma, Weldon, Danni, Goodwin, Scott, Nelson, Rachel, Beaver, Charlotte, Letchford, Laura, Jackson, David A., Foulser, Luke, McMinn, Liz, Prestwood, Liam, Kay, Sally, Kane, Leanne, Dorman, Matthew J., Martincorena, Inigo, Puethe, Christoph, Keatley, Jon-Paul, Tonkin-Hill, Gerry, Smith, Christen, Jamrozy, Dorota, Beale, Mathew A., Patel, Minal, Ariani, Cristina, Spencer-Chapman, Michael, Drury, Eleanor, Lo, Stephanie, Rajatileka, Shavanthi, Scott, Carol, James, Keith, Buddenborg, Sarah K., Berger, Duncan J., Patel, Gaurang, Garcia-Casado, Maria V., Dibling, Thomas, McGuigan, Samantha, Rogers, Hazel A., Hunter, Adam D., Souster, Emily and Neaverson, Alexandra S. (2021) Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184 (1). 64-75.e11. 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

The COVID-19 Genomics UK (COG-UK) consortium, , Smith, Darren and Bashton, Matthew (2020) An integrated national scale SARS-CoV-2 genomic surveillance network. The Lancet Microbe, 3 (1). E99-E100. ISSN 2666-5247

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

Young, Gregory, van der Gast, Christopher J., Smith, Darren, Berrington, Janet E., Embleton, Nicholas D. and Lanyon, Clare (2020) Acquisition and Development of the Extremely Preterm Infant Microbiota Across Multiple Anatomical Sites. Journal of Pediatric Gastroenterology and Nutrition, 70 (1). pp. 12-19. ISSN 0277-2116

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

Young, Gregory, Smith, Darren, Embleton, Nicholas D., Berrington, Janet Elizabeth, Schwalbe, Ed, Cummings, Stephen Paul, van der Gast, Christopher J. and Lanyon, Clare (2018) Response: Commentary: Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis. Frontiers in Cellular and Infection Microbiology, 8. p. 374. ISSN 2235-2988

Cullen, Louise, O’Connor, Andrew, McCormack, Sarah, Owens, Rebecca, Holt, Giles, Collins, Cassandra, Callaghan, Máire, Doyle, Sean, Smith, Darren, Schaffer, Kirsten, Fitzpatrick, David and McClean, Siobhán (2018) The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection. Scientific Reports, 8 (1). p. 13386. ISSN 2045-2322

Connerton, Phillippa, Richards, Philip, Lafontaine, Geraldine, O’Kane, Peter, Ghaffar, Nacheervan, Cummings, Nicola, Smith, Darren, Fish, Neville and Connerton, Ian (2018) The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens. Microbiome, 6 (1). p. 88. ISSN 2049-2618

Augustyniak, Daria, Seredyński, Rafał, McClean, Siobhán, Roszkowiak, Justyna, Roszniowski, Bartosz, Smith, Darren, Drulis-Kawa, Zuzanna and Mackiewicz, Paweł (2018) Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution. Scientific Reports, 8 (1). p. 4955. ISSN 2045-2322

Carro, Lorena, Nouioui, Imen, Sangal, Vartul, Meier-Kolthoff, Jan P., Trujillo, Martha E., Montero-Calasanz, Maria del Carmen, Sahin, Nevzat, Smith, Darren, Kim, Kristi E., Peluso, Paul, Deshpande, Shweta, Woyke, Tanja, Shapiro, Nicole, Kyrpides, Nikos, Klenk, Hans-Peter, Göker, Markus and Goodfellow, Michael (2018) Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential. Scientific Reports, 8 (1). ISSN 2045-2322

Grosse-Kock, Steffen, Kolodkina, Valentina, Schwalbe, Ed, Blom, Jochen, Burkovski, Andreas, Hoskisson, Paul, Brisse, Sylvain, Smith, Darren, Sutcliffe, Iain, Titov, Leonid and Sangal, Vartul (2017) Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s. BMC Genomics, 18. p. 873. ISSN 1471-2164

Young, Gregory, Smith, Darren, Embleton, Nicholas, Berrington, Janet, Schwalbe, Ed, Cummings, Stephen, van der Gast, Christopher and Lanyon, Clare (2017) Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis. Frontiers in Cellular and Infection Microbiology, 7. p. 237. ISSN 2235-2988

Holt, Giles, Lodge, John, McCarthy, Alan, Graham, A. K., Young, Gregory, Bridge, Simon, Brown, Alistair, Veses-Garcia, M., Lanyon, Clare, Sails, A., Allison, Heather and Smith, Darren (2017) Shigatoxin encoding Bacteriophage φ24B modulates bacterial metabolism to raise antimicrobial tolerance. Scientific Reports, 7. p. 40424. ISSN 2045-2322

Scalacci, Nicolò, Brown, Alistair, Pavan, Fernando, Ribeiro, Camila, Manetti, Fabrizio, Bhakta, Sanjib, Maitra, Arundhati, Smith, Darren, Petricci, Elena and Castagnolo, Daniele (2017) Synthesis and SAR evaluation of novel thioridazine derivatives active against drug-resistant tuberculosis. European Journal of Medicinal Chemistry, 127. pp. 147-158. ISSN 0223-5234

Roszniowski, Bartosz, Latka, Agnieszka, Maciejewska, Barbara, Vandenheuvel, Dieter, Olszak, Tomasz, Briers, Yves, Holt, Giles, Valvano, Miguel, Lavigne, Rob, Smith, Darren and Drulis-Kawa, Zuzanna (2017) The temperate Burkholderia phage AP3 of the Peduovirinae shows efficient antimicrobial activity against B. cenocepacia of the IIIA lineage. Applied Microbiology and Biotechnology, 101 (3). pp. 1203-1216. ISSN 0175-7598

Giardiello, Marco, Liptrott, Neill, McDonald, Tom, Moss, Darren, Siccardi, Marco, Martin, Phil, Smith, Darren, Gurjar, Rohan, Rannard, Steven and Owen, Andrew (2016) Accelerated oral nanomedicine discovery from miniaturized screening to clinical production exemplified by paediatric HIV nanotherapies. Nature Communications, 7. p. 13184. ISSN 2041-1723

Siccardi, Marco, Martin, Phillip, Smith, Darren, Curley, Paul, McDonald, Tom, Giardiello, Marco, Liptrott, Neill, Rannard, Steven and Owen, Andrew (2016) Towards a rational design of solid drug nanoparticles with optimised pharmacological properties. Journal of Interdisciplinary Nanomedicine, 1 (3). pp. 110-123. ISSN 2058-3273

Leon-Velarde, Carlos, Happonen, Lotta, Pajunen, Maria, Leskinen, Katarzyna, Kropinski, Andrew, Mattinen, Laura, Rajtor, Monika, Zur, Joanna, Smith, Darren, Chen, Shu, Nawaz, Ayesha, Johnson, Roger, Odumeru, Joseph, Griffiths, Mansel and Skurnik, Mikael (2016) Yersinia enterocolitica-Specific Infection by Bacteriophages TG1 and ϕR1-RT Is Dependent on Temperature-Regulated Expression of the Phage Host Receptor OmpF. Applied and Environmental Microbiology, 82 (17). pp. 5340-5353. ISSN 0099-2240

Holt, Giles, McCarthy, A. J., Lodge, John, Brown, A. K., Lanyon, Clare, Allison, H. E. and Smith, Darren (2016) Bacteriophage ɸ24B modulates microbial physiology and antimicrobial tolerance by hijacking the fatty acid synthesis pathway. In: EMBO Conference - Viruses of Microbes 2016, 18th - 22nd July 2016, Liverpool, UK.

Everest, Francesca, Holt, Giles, Robinson, Carl, Waller, Andrew and Smith, Darren (2016) Isolating Streptococcus equi bacteriophages from manure and water samples. In: EMBO Conference - Viruses of Microbes 2016, 18th - 22nd July 2016, Liverpool, UK.

Everest, Francesca, Tariq, Mohammad, Holt, Giles, Lodge, John, Perry, Audrey, Perry, John, Bourke, Stephen, Lanyon, Clare, Cummings, Stephen, de Soyza, Anthony and Smith, Darren (2016) Mapping the progression and evolution of chronic respiratory diseases using mixed temperate phage communities isolated from Pseudomonas aeruginosa. In: 21st Biennial Evergreen International Phage Meeting, 2nd - 7th August 2015, Washington, USA.

Everest, Francesca, Tariq, Mohammad, Holt, Giles, Lodge, John, Perry, Audrey, Perry, John, Bourke, S., Lanyon, Clare, Cummings, Stephen, de Soyza, Anthony and Smith, Darren (2016) Metabolite and metabolism characterisation of Pseudomonas aeruginosa pellicle formation and the impact of converting temperate phages. In: EMBO Conference - Viruses of Microbes 2016, 18th - 22nd July 2016, Liverpool, UK.

Tariq, Mohammad, Everest, Francesca, Cowley, Lauren, Holt, Giles, de Soyza, Anthony, Perry, Audrey, Perry, John and Smith, Darren (2016) A metagenomic approach to characterise temperate bacteriophages induced from Pseudomonas aeruginosa and Burkholderia cepacia complex, originating from the lungs of Cystic Fibrosis and Bronchiectasis patients. In: EMBO Conference - Viruses of Microbes 2016, 18th - 22nd July 2016, Liverpool, UK.

Martin, Philip, Giardiello, Marco, McDonald, Tom, Smith, Darren, Siccardi, Marco, Rannard, Steven and Owen, Andrew (2015) Augmented inhibition of CYP3A4 in human primary hepatocytes by ritonavir solid drug nanoparticles. Molecular Pharmaceutics, 12 (10). pp. 3556-3568. ISSN 1543-8384

Tariq, Mohammad, Holt, Giles, Everest, Francesca, Cowley, Lauren, Lodge, John, Perry, Audrey, Perry, John, Bourke, Stephen, Lanyon, Clare, Cummings, Stephen, Barr, Jeremy, de Soyza, Anthony and Smith, Darren (2015) Temperate bacteriophages adding functionality and complexity to an ever evolving bacterial host. In: 21st Biennial Evergreen International Phage Meeting, 2nd - 7th August 2015, Washington, USA.

Tariq, Mohammad, Everest, Francesca, Cowley, Lauren, de Soyza, Anthony, Holt, Giles, Bridge, Simon, Perry, Audrey, Perry, John, Bourke, Stephen, Cummings, Stephen, Lanyon, Clare, Barr, Jeremy and Smith, Darren (2015) A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients. Frontiers in Microbiology, 6 (97). ISSN 1664-302X

Tariq, Mohammad, Holt, Giles, Everest, Francesca, de Soyza, Anthony, Perry, Audrey, Perry, John, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2014) Characterising temperate bacteriophages induced from Burkholderia Cepacia Complex, originating from the lungs of Cystic Fibrosis patients. In: Viruses of microbes: Structure and function, from molecules to communities, 14 - 18 July, 2014, Zurich, Switzerland.

Smith, Darren (2014) Temperate bacteriophages; adaptive evolution in chronic respiratory disease and the impact of phage subversion. In: Viruses of microbes: Structure and function, from molecules to communities, 14 - 18 July, 2014, Zurich, Switzerland.

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

Tariq, Mohammad, Everest, Francesca, de Soyza, Anthony, Perry, Audrey, Perry, John, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2014) Characterising temperate bacteriophage induced from Burkholderia Cepacia Complex isolates, originating from the lungs of Cystic Fibrosis patients. In: Society for General Microbiology Annual Conference, 14 - 17 April 2014, Liverpool, UK.

Holt, Giles, Allison, Heather, Kinghan, S., McCarthy, Alan, Lodge, John, Brown, Alistair, Lanyon, Clare and Smith, Darren (2014) Stx-phage vB_EcoP 24B sculpting host bacterial function. In: Society for General Microbiology Annual Conference, 14 - 17 April 2014, Liverpool, UK.

Holt, Giles, Allison, Heather, Kinghan, S., McCarthy, Alan, Lodge, John, Brown, Alistair, Lanyon, Clare and Smith, Darren (2014) Stx-phage vB_EcoP 24B sculpting host bacterial function. In: Viruses of microbes: Structure and function, from molecules to communities, 14 - 18 July, 2014, Zurich, Switzerland.

Smith, Darren (2014) The evolution of temperate bacteriohages of Pseudomonas aeruginosa and mapping their additive effect in colonising the chronic lung. In: Viruses of microbes: Structure and function, from molecules to communities, 14 - 18 July, 2014, Zurich, Switzerland.

Everest, Francesca, Tariq, Mohammad, Wilson, Rhys, de Soyza, Anthony, Perry, Audrey, Perry, John, Bourke, Stephen, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2014) The evolution of temperate bacteriophages of Pseudomonas aeruginosa and mapping their additive effect in colonising the chronic lung. In: Viruses of microbes: Structure and function, from molecules to communities, 14 - 18 July, 2014, Zurich, Switzerland.

Everest, Francesca, Tariq, Mohammad, de Soyza, Anthony, Perry, Audrey, Perry, John, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2014) The influence of temperate phage on Pseudomonas aeruginosa and their effect on Chronic Respiratory Disease sufferers. In: Society for General Microbiology Annual Conference, 14 - 17 April 2014, Liverpool, UK.

McDonald, Tom, Giardiello, Marco, Martin, Philip, Siccardi, Marco, Liptrott, Neill, Smith, Darren, Roberts, Phill, Curley, Paul, Schipani, Alessandro, Khoo, Saye, Long, James, Foster, Alison, Rannard, Steven and Owen, Andrew (2014) Antiretroviral Solid Drug Nanoparticles with Enhanced Oral Bioavailability: Production, Characterization, and In Vitro-In Vivo Correlation. Advanced Healthcare Materials, 3 (3). pp. 400-411. ISSN 21922640

Smith, Darren (2014) Temperate phages infecting Pseudomonas aeruginosa in chronic lung infections. In: Euroscicon: Exploiting bacteriophages for bioscience, biotechnology and medicine (the 5th in a biennial series), 23 Jan 2014, London, UK.

Smith, Darren (2013) Temperate phages of pseudomonas aeruginosa. In: Postgraduate Research Day, 11 December 2013, Newcastle University, Newcastle upon Tyne.

Everest, Francesca, Tariq, Mohammad, de Soyza, Anthony, Perry, Audrey, Perry, John, Bourke, Stephen, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2013) Characterising the impact of bacterial viruses of Pseudomonas aeruginosa isolated from Cystic Fibrosis patients. In: Society for General Microbiology Autumn Conference, 2-4 September 2013, Sussex, UK.

Tariq, Mohammad, Everest, Francesca, Kahn, A., de Soyza, Anthony, Bulmer, D., Perry, Audrey, Perry, John, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2013) Comparison of temperate bacteriophages isolated from Pseudomonas aeruginosa isolated from non-Cystic Fibrosis Bronchiectasis patients. In: Society for General Microbiology Autumn Conference, 2-4 September 2013, Sussex, UK.

Kinghan, S., Everest, Francesca, de Soyza, Anthony, Perry, Audrey, Perry, John, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2013) Does phage subversion by temperate bacteriophages alter host bacterial physiology. In: Society for General Microbiology Autumn Conference, 2-4 September 2013, Sussex, UK.

Everest, Francesca, Tariq, Mohammad, de Soyza, Anthony, Perry, Audrey, Perry, John, Bourke, Stephen, Khan, A., Cummings, Stephen, Lanyon, Clare and Smith, Darren (2013) The impact of temperate bacterial viruses on the microbiota of chronic respiratory disease. In: Phages 2013, 10 - 12 September 2013, Oxford, UK.

University of Liverpool, Giardello, Marco Norman, McDonald, Thomas Oliver, Owen, Andrew, Rannard, Steven Paul, Martin, Philip John, Smith Darren (2013) Compositions of efavirenz. WO2013034925.

University of Liverpool, Giardello, Marco Norman, McDonald, Thomas Oliver, Owen, Andrew, Rannard, Steven Paul, Long, James, Martin, Philip John, Smith Darren (2013) Compositions of lopinavir. WO2013034926.

University of Liverpool, Giardello, Marco Norman, McDonald, Thomas Oliver, Owen, Andrew, Rannard, Steven Paul, Martin, Philip John, Smith Darren (2013) Compositions of lopinavir and ritonavir. WO2013034927.

Everest, Francesca, Tariq, Mohammad, de Soyza, Anthony, Perry, Audrey, Perry, John, Bourke, Stephen, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2013) Characterising the temperate bacteriophage of Pseudomonas aeruginosa isolated from a Cystic Fibrosis background. In: Cystic Fibrosis Conference, 2013, Liverpool, UK.

Martin, Philip, Liptrott, Neill, McDonald, Tom, Giardiello, Marco, Roberts, Phill, Curley, Paul, Smith, Darren, Siccardi, Marco, Rannard, Steven and Owen, Andrew (2013) Enhanced pharmacological properties of efavirenz formulated as solid drug nanoparticles. In: 20th Conference on Retroviruses and Opportunistic Infections (CROI 2013), 3 - 6 March 2013, Atlanta, USA.

Roszniowski, Bartosz, Holt, Giles, de Soyza, Anthony, Perry, Audrey, Perry, John, Cummings, Stephen, Lanyon, Clare and Smith, Darren (2013) Spontaneous temperate phage induction as evolutionary selection in host Pseudomonas aeruginosa isolated from cystic fibrosis and non-cystic fibrosis bronchiectasis patients. In: Society for General Microbiology Autumn Conference, 2-4 September 2013, Sussex, UK.

Smith, Darren, Rooks, David, Fogg, Paul, Darby, Alistair, Thomson, Nicholas, McCarthy, Alan and Allison, Heather (2012) Comparative genomics of Shiga toxin encoding bacteriophages. BMC Genomics, 13 (1). p. 311. ISSN 1471-2164

Olszak, Tomasz, Danis, Katarzyna, Roszniowski, Bartosz, Drevinek, Pavel, Smith, Darren, de Soyza, Anthony, Kaca, Wiesław and Drulis-Kawa, Zuzanna (2012) Isolation and antibacterial activity of environmental bacteriophages propagated on Pseudomonas aeruginosa strains isolated from CF patients. In: Viruses of Microbes Conference, 16 - 20 July 2012, Brussels, Belgium.

McDonald, Tom, Martin, Philip, Patterson, Joseph, Smith, Darren, Giardiello, Marco, Marcello, Marco, See, Violaine, O'Reilly, Rachel, Owen, Andrew and Rannard, Steven (2012) Multicomponent organic nanoparticles for fluorescence studies in biological systems. Advanced Functional Materials, 22 (12). pp. 2469-2478. ISSN 1616-301X

Volponi, Giorgio, Rooks, David, Smith, Darren, Picozzi, Claudia, Allison, Heather, Vigentini, Iorenzo, Foschino, Roberto and McCarthy, Alan (2012) Short communication: Characterization of Shiga toxin 2-carrying bacteriophages induced from Shiga-toxigenic Escherichia coli isolated from Italian dairy products. Journal of Dairy Science, 95 (12). pp. 6949-6956. ISSN 0022-0302

Smith, Darren, Saunders, Jon, McCarthy, Alan and Allison, Heather (2011) Inhibition of infection of short tailed Stx-phage through changes at the E. coli cell surface. In: 161st Society for General Microbiology Meeting, 3 - 6 September 2011, Edinburgh, UK.

Moss, Darren, Kwan, Wai San, Liptrott, Neill, Smith, Darren, Siccardi, Marco, Khoo, Saye, Back, David and Owen, Andrew (2011) Raltegravir Is a Substrate for SLC22A6: a Putative Mechanism for the Interaction between Raltegravir and Tenofovir. Antimicrobial Agents and Chemotherapy, 55 (2). pp. 879-887. ISSN 0066-4804

McDonald, Tom, Martin, Philip, Giardiello, Marco, Smith, Darren, Owen, Andrew and Rannard, Steven (2011) Multi-component organic nanoparticles for magnetic and fluorescent studies in biological systems. In: 2nd Nano Today Conference, Waikoloa, Hawaii, USA.

Smith, Darren, Martin, Philip, McDonald, Tom, Giardiello, Marco and Owen, Andrew (2011) Relationship Between Particle And Biological Properties Of Emulsion-Templated, Freeze-Dried Lopinavir Nanoparticle Dispersions. In: 18th Conference on Retroviruses and Opportunistic Infection (CROI), 27 February - 3 March 2011, Boston, Massachusetts, USA.

Rooks, David, Smith, Darren, McDonald, James, Woodward, Martin, McCarthy, Alan and Allison, Heather (2010) 454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology. Genes, 1 (2). pp. 210-226. ISSN 2073-4425

McDonald, James, Smith, Darren, Fogg, Paul, McCarthy, Alan and Allison, Heather (2010) High-Throughput Method for Rapid Induction of Prophages from Lysogens and Its Application in the Study of Shiga Toxin-Encoding Escherichia coli Strains. Applied and Environmental Microbiology, 76 (7). pp. 2360-2365. ISSN 0099-2240

Edwards, Jennifer, Smith, Darren, Connolly, John, McDonald, James, Cox, Michael, Joint, Ian, Edwards, Clive and McCarthy, Alan (2010) Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes. Genes, 1 (3). pp. 371-384. ISSN 2073-4425

Martin, Philip, McDonald, Tom, Smith, Darren, Giardiello, Marco, Rannard, Steven and Owen, Andrew (2010) Influence of particle size and surface charge on the cytotoxicity of nanodispersions. Drug Metabolism Reviews, 42 (S1). p. 49. ISSN 0360-2532

Smith, Darren (2010) Stx phage mosaicism: lessons learned from genome sequencing. In: Viruses of Microbes, 21 - 25 June 2010, Pasteur Institute, Paris, France.

Wareing, Brian, Smith, Darren, Saunders, Jon, McCarthy, Alan and Allison, Heather (2007) Multilocus PCR typing of Shigatoxin - encoding bacteriophages. In: 161st Society for General Microbiology Meeting, 3 - 6 September 2011, Edinburgh, UK.

Smith, Darren, Saunders, Jon, McCarthy, Alan and Allison, Heather (2007) Dissemination of stx-genes by bacteriophages that recognise an essential outer membrane protein in E. Coli. In: 107th General Meeting: American Society for Microbiology, 21 - 25 may 2007, Toronto, Canada.

Fogg, Paul, Gossage, Sharon, Smith, Darren, Saunders, Jon, McCarthy, Alan and Allison, Heather (2007) Identification of multiple integration sites for Stx-phage 24B in the Escherichia coli genome, description of a novel integrase and evidence for a functional anti-repressor. Microbiology, 153 (12). pp. 4098-4110. ISSN 1350-0872

Smith, Darren, Wareing, Brian, Fogg, Paul, Riley, Laura, Spencer, Matthew, Cox, Michael, Saunders, Jon, McCarthy, Alan and Allison, Heather (2007) Multilocus Characterization Scheme for Shiga Toxin-Encoding Bacteriophages. Applied and Environmental Microbiology, 73 (24). pp. 8032-8040. ISSN 0099-2240

Wareing, Brian, Smith, Darren, Saunders, Jon, McCarthy, Alan and Allison, Heather (2007) Multilocus PCR typing of Shigatoxin - encoding bacteriophages. In: 107th General Meeting: American Society for Microbiology, 21 - 25 may 2007, Toronto, Canada.

Smith, Darren, James, Chloe, Sergeant, Martin, Yaxian, Yan, Saunders, Jon, McCarthy, Alan and Allison, Heather (2007) Short-Tailed Stx Phages Exploit the Conserved YaeT Protein To Disseminate Shiga Toxin Genes among Enterobacteria. Journal of Bacteriology, 189 (20). pp. 7223-7233. ISSN 0021-9193

Smith, Darren, Saunders, Jon, Allison, Heather and McCarthy, Alan (2006) Inhibition of infection of short tailed Stx-phage through changes at the E. coli cell surface. In: 158th Society for General Microbiology Meeting, 3 - 6 April 2006, Warwick, UK.

Riley, Laura, Smith, Darren, Fogg, Paul, Wareing, Brian, McCormick, Margaret, Saunders, Jon, Allison, Heather and McCarthy, Alan (2006) Shiga-toxin encoding bacteriophages - Ecology and role in disease. In: 158th Society for General Microbiology Meeting, 3 - 6 April 2006, Warwick, UK.

Johannessen, Gro, James, Chloe, Allison, Heather, Smith, Darren, Saunders, Jon and McCarthy, Alan (2005) Survival of a Shiga toxin-encoding bacteriophage in a compost model. FEMS Microbiology Letters, 245 (2). pp. 369-375. ISSN 03781097

Allison, Heather, Smith, Darren, Loughnane, Paul, Saunders, Jon and McCarthy, Alan (2004) Identification of an outer membrane protein that enables infection of Escherichia coli by Shiga toxin encoding bacteriophage. In: 155th Society for General Microbiology Meeting, September 2004, Dublin, Ireland.

Smith, Darren (2004) Phage Biology. In: ASM Conference on the New Phage Biology, 1 -5 August 2004, Key Biscayne, Florida.

Smith, Darren, Loughnane, Paul, Fogg, Paul, Saunders, Jon, McCarthy, Alan and Allison, Heather (2004) The VT-phage infection process in Escherichia coli. In: 3rd Viral Ecology Group Meeting, 18-19 February 2004, Leamington Spa, UK.

Smith, Darren (2003) Shiga-toxin. In: 5th International Symposium on 'Shiga Toxin (Verocytotoxin)-Producing E coli infections', 8 - 11 June 2003, Edinburgh, UK.

Allison, Heather, Sergeant, Martin, James, Chloe, Saunders, Jon, Smith, Darren, Sharp, Richard, Marks, Trevor and McCarthy, Alan (2003) Immunity Profiles of Wild-Type and Recombinant Shiga-Like Toxin-Encoding Bacteriophages and Characterization of Novel Double Lysogens. Infection and Immunity, 71 (6). pp. 3409-3418. ISSN 0019-9567

McDonald, Tom, Giardiello, Marco, Smith, Darren, Martin, Philip, Owen, Andrew and Rannard, Steven (2001) Drug delivery systems - A focus on nanotechnology and its implications in treatment of HIV. In: Médecins Sans Frontières Campaign for Access to Essential Medicines - ART sequencing workshop, 2011, Geneva.