Professor Nick Loman PhD

Professor Nick Loman

School of Biosciences
Professor of Microbial Genomics and Bioinformatics

Contact details

Address
School of Biosciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Nick works as Professor of Microbial Genomics and Bioinformatics in the Institute for Microbiology and Infection at the University of Birmingham. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. Nick has so far used high-throughput sequencing to investigate outbreaks of important Gram-negative multi-drug resistant pathogens, and recently helped establish real-time genomic surveillance of Ebola in Guinea. His current work focuses on the development of novel sequencing and bioinformatics methods to aid the interpretation of genome and metagenome scale data generated in clinical and public health microbiology.

Postgraduate supervision

Nick Loman works as an Independent Research Fellow in the Institute for Microbiology and Infection at the University of Birmingham, sponsored by a seven-year MRC Fellowship in Microbial Genomics Bioinformatics. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. Dr Loman has so far used high-throughput sequencing to investigate outbreaks of important Gram-negative multi-drug resistant pathogens, and recently helped establish real-time genomic surveillance of Ebola in Guinea. His current work focuses on the development of novel sequencing and bioinformatics methods to aid the interpretation of genome and metagenome scale data generated in clinical and public health microbiology.

Other activities

  • Editorial Board, Microbial Genomics (Microbiology Society) 2015 – present
  • Editorial Board, PeerJ () 2015 – present
  • Affiliate, bioRxiv.org (Cold Spring Harbor Press) 2015 – present
  • Organiser, Applied Bioinformatics and Public Health Microbiology (Wellcome Trust) 2013 –present
  • Organiser, Genome Science () 2015 – present

Publications

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

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