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COG-UK Consortium, Volz, E, Hill, V, McCrone, JT, Price, A, Jorgensen, D, O'Toole, Á, Southgate, J, Johnson, R, Jackson, B, Nascimento, FF, Rey, SM, Nicholls, SM, Colquhoun, RM, da Silva Filipe, A, Shepherd, J, Pascall, DJ, Shah, R, Jesudason, N, Li, K, Jarrett, R, Pacchiarini, N, Bull, M, Geidelberg, L, Siveroni, I, Goodfellow, I, Loman, NJ, Pybus, OG, Robertson, DL, Thomson, EC, Rambaut, A & Connor, TR 2021, 'Evaluating the effects of SARS-CoV-2 spike mutation D614G on transmissibility and pathogenicity', Cell, vol. 184, no. 1, pp. 64-75.e11. https://doi.org/10.1016/j.cell.2020.11.020
Gregorova, M, Morse, D, Brignoli, T, Steventon, J, Hamilton, F, Albur, M, Arnold, D, Thomas, M, Halliday, A, Baum, H, Rice, C, Avison, MB, Davidson, AD, Santopaolo, M, Oliver, E, Goenka, A, Finn, A, Wooldridge, L, Amulic, B, Boyton, RJ, Altmann, DM, Butler, DK, McMurray, C, Stockton, J, Nicholls, S, Cooper, C, Loman, N, Cox, MJ, Rivino, L & Massey, RC 2020, 'Post-acute COVID-19 associated with evidence of bystander t-cell activation and a recurring antibiotic-resistant bacterial pneumonia', eLife, vol. 9, e63430, pp. 1-13. https://doi.org/10.7554/eLife.63430
Quraishi, MN, Yalchin, M, Blackwell, C, Segal, JP, Sharma, N, Hawkey, P, McCune, V, Hart, A, Gaya, DR, Ives, N, Magill, L, Loi, S, Hewitt, C, Gerasimidis, K, Loman, N, Hansen, R, McMullan, C, Mathers, J, Quince, C, Crees, N & Iqbal, T 2019, 'STOP-Colitis pilot trial protocol: a prospective, open-label, randomised pilot study to assess two possible routes of faecal microbiota transplant delivery in patients with ulcerative colitis', BMJ open, vol. 9, no. 11, e030659. https://doi.org/10.1136/bmjopen-2019-030659
Nicholls, SM, Quick, JC, Tang, S & Loman, NJ 2019, 'Ultra-deep, long-read nanopore sequencing of mock microbial community standards', GigaScience. https://doi.org/10.1093/gigascience/giz043
Azevedo Antunes, C, Richardson, EJ, Quick, J, Fuentes-utrilla, P, Isom, GL, Goodall, EC, Möller, J, Hoskisson, PA, Mattos-guaraldi, AL, Cunningham, AF, Loman, NJ, Sangal, V, Burkovski, A & Henderson, IR 2018, 'Complete Closed Genome Sequence of Nontoxigenic Invasive Corynebacterium diphtheriae bv. mitis Strain ISS 3319', Genome Announcements, vol. 6, no. 5, 01566-17, pp. e01566-17. https://doi.org/10.1128/genomeA.01566-17
Pini, A, Zomahoun, D, Duraffour, S, Derrough, T, Charles, M, Quick, J, Loman, N, Cowley, L, Leno, M, Ouedraogo, N, Thiam, O, Hernández-Romieu, A, Iko, A, Keita, H, Konate, D, Soumah, AA, Bouchouar, E, Ileka-Priouzeau, S, Keita, S, Diallo, B, Cisse, F, Jansa, J, Carroll, M, Günther, S, Severi, E & Formenty, P 2018, 'Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015', Euro surveillance : bulletin européen sur les maladies transmissibles = European communicable disease bulletin, vol. 23, no. 12, 17-00140. https://doi.org/10.2807/1560-7917.ES.2018.23.12.17-00140
Jain, M, Koren, S, Miga, KH, Quick, J, Rand, AC, Sasani, TA, Tyson, JR, Beggs, AD, Dilthey, AT, Fiddes, IT, Malla, S, Marriott, H, Nieto, T, O'Grady, J, Olsen, HE, Pedersen, BS, Rhie, A, Richardson, H, Quinlan, AR, Snutch, TP, Tee, L, Paten, B, Phillippy, AM, Simpson, JT, Loman, N & Loose, M 2018, 'Nanopore sequencing and assembly of a human genome with ultra-long reads', Nature Biotechnology, vol. 36, no. 4, pp. 338–345. https://doi.org/10.1038/nbt.4060
Faria, NR, Quick, J, Claro, IM, Thézé, J, de Jesus, JG, Giovanetti, M, Kraemer, MUG, Hill, SC, Black, A, da Costa, AC, Franco, LC, Silva, SP, Wu, C-H, Raghwani, J, Cauchemez, S, du Plessis, L, Verotti, MP, de Oliveira, WK, Carmo, EH, Coelho, GE, Santelli, ACFS, Vinhal, LC, Henriques, CM, Simpson, JT, Loose, M, Andersen, KG, Grubaugh, ND, Somasekar, S, Chiu, CY, Muñoz-Medina, JE, Gonzalez-Bonilla, CR, Arias, CF, Lewis-Ximenez, LL, Baylis, SA, Chieppe, AO, Aguiar, SF, Fernandes, CA, Lemos, PS, Nascimento, BLS, Monteiro, HAO, Siqueira, IC, de Queiroz, MG, de Souza, TR, Bezerra, JF, Lemos, MR, Pereira, GF, Loudal, D, Moura, LC, Dhalia, R, França, RF, Magalhães, T, Marques, ET, Jaenisch, T, Wallau, GL, de Lima, MC, Nascimento, V, de Cerqueira, EM, de Lima, MM, Mascarenhas, DL, Neto, JPM, Levin, AS, Tozetto-Mendoza, TR, Fonseca, SN, Mendes-Correa, MC, Milagres, FP, Segurado, A, Holmes, EC, Rambaut, A, Bedford, T, Nunes, MRT, Sabino, EC, Alcantara, LCJ, Loman, NJ & Pybus, OG 2017, 'Establishment and cryptic transmission of Zika virus in Brazil and the Americas', Nature, vol. 546, no. 7658, pp. 406-410. https://doi.org/10.1038/nature22401
Márquez, S, Carrera, J, Pullan, ST, Lewandowski, K, Paz, V, Loman, N, Quick, J, Bonsall, D, Powell, R, Thézé, J, Pybus, OG, Klenerman, P, Eisenberg, J, Coloma, J, Carroll, MW, Trueba, G & Logue, CH 2017, 'First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador', Genome Announcements, vol. 5, no. 8, e01673-16. https://doi.org/10.1128/genomeA.01673-16
Grubaugh, ND, Ladner, JT, Kraemer, MUG, Dudas, G, Tan, AL, Gangavarapu, K, Wiley, MR, White, S, Thézé, J, Magnani, DM, Prieto, K, Reyes, D, Bingham, AM, Paul, LM, Robles-Sikisaka, R, Oliveira, G, Pronty, D, Barcellona, CM, Metsky, HC, Baniecki, ML, Barnes, KG, Chak, B, Freije, CA, Gladden-Young, A, Gnirke, A, Luo, C, MacInnis, B, Matranga, CB, Park, DJ, Qu, J, Schaffner, SF, Tomkins-Tinch, C, West, KL, Winnicki, SM, Wohl, S, Yozwiak, NL, Quick, J, Fauver, JR, Khan, K, Brent, SE, Reiner, RC, Lichtenberger, PN, Ricciardi, MJ, Bailey, VK, Watkins, DI, Cone, MR, Kopp, EW, Hogan, KN, Cannons, AC, Jean, R, Monaghan, AJ, Garry, RF, Loman, NJ, Faria, NR, Porcelli, MC, Vasquez, C, Nagle, ER, Cummings, DAT, Stanek, D, Rambaut, A, Sanchez-Lockhart, M, Sabeti, PC, Gillis, LD, Michael, SF, Bedford, T, Pybus, OG, Isern, S, Palacios, G & Andersen, KG 2017, 'Genomic epidemiology reveals multiple introductions of Zika virus into the United States', Nature, vol. 546, no. 7658, pp. 401-405. https://doi.org/10.1038/nature22400
Quick, J, Grubaugh, ND, Pullan, ST, Claro, IM, Smith, AD, Gangavarapu, K, Oliveira, G, Robles-Sikisaka, R, Rogers, TF, Beutler, NA, Burton, DR, Lewis-Ximenez, LL, de Jesus, JG, Giovanetti, M, Hill, SC, Black, A, Bedford, T, Carroll, MW, Nunes, M, Alcantara, LC, Sabino, EC, Baylis, SA, Faria, NR, Loose, M, Simpson, JT, Pybus, OG, Andersen, KG & Loman, NJ 2017, 'Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples', Nature protocols, vol. 12, no. 6, pp. 1261-1276. https://doi.org/10.1038/nprot.2017.066
Dunne, K, Chaudhuri, R, Rossiter, A, Beriotto, I, Cunningham, A, Browning, DF, Squire, D, Cunningham, A, Cole, J, Loman, N & Henderson, I 2017, 'Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain', Microbial Genomics, vol. 3, no. 3, pp. mgen000106. https://doi.org/10.1099/mgen.0.000106
Dudas, G, Carvalho, LM, Bedford, T, Tatem, AJ, Baele, G, Faria, NR, Park, DJ, Ladner, JT, Arias, A, Asogun, D, Bielejec, F, Caddy, SL, Cotten, M, D'Ambrozio, J, Dellicour, S, Di Caro, A, Diclaro, JW, Duraffour, S, Elmore, MJ, Fakoli, LS, Faye, O, Gilbert, ML, Gevao, SM, Gire, S, Gladden-Young, A, Gnirke, A, Goba, A, Grant, DS, Haagmans, BL, Hiscox, JA, Jah, U, Kugelman, JR, Liu, D, Lu, J, Malboeuf, CM, Mate, S, Matthews, DA, Matranga, CB, Meredith, LW, Qu, J, Quick, J, Pas, SD, Phan, MVT, Pollakis, G, Reusken, CB, Sanchez-Lockhart, M, Schaffner, SF, Schieffelin, JS, Sealfon, RS, Simon-Loriere, E, Smits, SL, Stoecker, K, Thorne, L, Tobin, EA, Vandi, MA, Watson, SJ, West, K, Whitmer, S, Wiley, MR, Winnicki, SM, Wohl, S, Wölfel, R, Yozwiak, NL, Andersen, KG, Blyden, SO, Bolay, F, Carroll, MW, Dahn, B, Diallo, B, Formenty, P, Fraser, C, Gao, GF, Garry, RF, Goodfellow, I, Günther, S, Happi, CT, Holmes, EC, Kargbo, B, Keïta, S, Kellam, P, Koopmans, MPG, Kuhn, JH, Loman, NJ, Magassouba, NF, Naidoo, D, Nichol, ST, Nyenswah, T, Palacios, G, Pybus, OG, Sabeti, PC, Sall, A, Ströher, U, Wurie, I, Suchard, MA, Lemey, P & Rambaut, A 2017, 'Virus genomes reveal factors that spread and sustained the Ebola epidemic', Nature, vol. 544, no. 7650, pp. 309-315. https://doi.org/10.1038/nature22040
Sissoko, D, Keïta, M, Diallo, B, Aliabadi, N, Fitter, DL, Dahl, BA, Akoi Bore, J, Raymond Koundouno, F, Singethan, K, Meisel, S, Enkirch, T, Mazzarelli, A, Amburgey, V, Faye, O, Alpha Sall, A, Magassouba, NF, Carroll, MW, Anglaret, X, Malvy, D, Formenty, P, Bruce Aylward, R, Keïta, S, Harouna Djingarey, M, Loman, NJ, Günther, S & Duraffour, S 2016, 'Ebola virus persistence in breast milk after no reported illness: A likely source of virus transmission from mother to child', Clinical Infectious Diseases. https://doi.org/10.1093/cid/ciw793
Review article
Gardy, JL & Loman, N 2018, 'Towards a genomics-informed, real-time, global pathogen surveillance system', Nature Reviews Genetics, vol. 19, no. 1, pp. 9-20. https://doi.org/10.1038/nrg.2017.88
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