Recent publications
Article
Du Plessis, L, Mccrone, JT, Zarebski, AE, Hill, V, Ruis, C, Gutierrez, B, Raghwani, J, Ashworth, J, Colquhoun, R, Connor, TR, Faria, NR, Jackson, B, Loman, NJ, O’toole, Á, Nicholls, SM, Parag, KV, Scher, E, Vasylyeva, TI, Volz, EM, Watts, A, Bogoch, II, Khan, K, COVID-19 Genomics UK (COG-UK) Consortium, Aanensen, DM, Kraemer, MUG, Rambaut, A, Pybus, OG & Beggs, A 2021, 'Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK', Science, vol. 371, no. 6530, pp. 708-712. https://doi.org/10.1126/science.abf2946
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
The COVID-19 Genomics UK (COG-UK) Consortium, Meng, B, Kemp, SA, Papa, G, Datir, R, Ferreira, IATM, Marelli, S, Harvey, WT, Lytras, S, Mohamed, A, Gallo, G, Thakur, N, Collier, DA, Mlcochova, P, Duncan, LM, Carabelli, AM, Kenyon, JC, Lever, AM, De Marco, A, Saliba, C, Culap, K, Cameroni, E, Matheson, NJ, Piccoli, L, Corti, D, James, LC, Robertson, DL, Bailey, D & Gupta, RK 2021, 'Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7', Cell Reports, vol. 35, no. 13, 109292. https://doi.org/10.1016/j.celrep.2021.109292
COVID-19 Genomics UK (COG-UK) Consortium & Beggs, A 2021, 'Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence', Science. https://doi.org/10.1126/science.abj0113
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
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
View all publications in research portal