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

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

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

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

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, Loose, M & Loman, N 2018, 'Nanopore sequencing and assembly of a human genome with ultra-long reads', Nature Biotechnology. https://doi.org/10.1038/nbt.4060

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

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

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

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

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

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

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

Mcmurray, CL, Hardy, KJ, Calus, ST, Loman, NJ & Hawkey, PM 2016, 'Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing', Microbiome, vol. 4, 63. https://doi.org/10.1186/s40168-016-0210-1

Keita, M, Duraffour, S, Loman, NJ, Rambaut, A, Diallo, B, Magassouba, N, Carroll, MW, Quick, J, Sall, AA, Glynn, JR, Formenty, P, Subissi, L & Faye, O 2016, 'Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015', Emerging infectious diseases, vol. 22, no. 12, pp. 2149-2152. https://doi.org/10.3201/eid2212.160847

Diallo, B, Sissoko, D, Loman, NJ, Bah, HA, Bah, H, Worrell, MC, Conde, LS, Sacko, R, Mesfin, S, Loua, A, Kalonda, JK, Erondu, NA, Dahl, BA, Handrick, S, Goodfellow, I, Meredith, LW, Cotten, M, Jah, U, Guetiya Wadoum, RE, Rollin, P, Magassouba, NF, Malvy, D, Anglaret, X, Carroll, MW, Aylward, RB, Djingarey, MH, Diarra, A, Formenty, P, Keïta, S, Günther, S, Rambaut, A & Duraffour, S 2016, 'Resurgence of Ebola virus disease in guinea linked to a survivor with virus persistence in seminal fluid for more than 500 days', Clinical Infectious Diseases, vol. 63, no. 10, pp. 1353-1356. https://doi.org/10.1093/cid/ciw601

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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