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.

Biography

  • Professor of Microbial Genomics and Bioinformatics, May 2017 – Present
    • Institute of Microbiology and Infection, University of Birmingham
  • Independent Research Fellow, Sep 2012 – May 2017
    • Institute of Microbiology and Infection, University of Birmingham
  • Research Associate, Apr 2007 – May 2012
    • Biosciences, University of Birmingham
  • Senior House Officer (Medical Rotation), Aug 2005 – Mar 2007
    • Mid-Essex Hospital Services NHS Trust
  • Pre-Registration House Officer, Aug 2004 – Jul 2004
    • Colchester Hospital University NHS Trust

Postgraduate supervision

With Tim Mitchell, Nick co-supervises a PhD student, Josh Quick. Josh is investigating the role of microbial communities in wound healing in burns and trauma through the NIHR Centre for Surgical Reconstruction and Microbiology, as well as the spread of nosocomial pathogens in our local patient population.

Research

MicrobesNG

MicrobesNG is a 5-year, 1.2m BBSRC-funded project to produce a world-leading microbial genome sequencing service and strain archiving resource, which launched at the SGM in March 2015. See the website for further details.

CLIMB

The Cloud Infrastructure for Microbial Genomics (CLIMB) is an 8.4m MRC-funded project to invest in bioinformatics and "big data" capacity building for the UK microbial genomics community. At heart it is four-site (Birmingham, Warwick, Cardiff and Swansea) connected virtual computing infrastructure. It is optimised for specific applications such as microbial genome alignment, de novo assembly and metagenomics. See the website for further details.

The E. coli O104:H4 outbreak in Germany

Nick was involved with the crowd-sourced analysis of genomics data from the Shiga-toxin producing E. coli O104:H4 outbreak in Germany. This outbreak caused more than 4,000 cases of disease and 50 deaths. Nick performed an initial assembly of data from the BGI on the 2nd of June 2011 which helped spark a flurry of crowd-sourced analysis, documented on the Github Wiki. Recently, the BBSRC made a video about this project which can be viewed below.

Bioinformatics projects

In his previous role, Nick was responsible for the maintenance and development of the comparative bacterial genomics database, xBASE. Although funding for this project has ceased, he continues to develop the high-throughput sequencing pipeline xBASE-NG to support their local sequencing efforts, as well as the rapid bacterial genome annotation service xBASE Annotation.

In collaboration with Lex Nederbragt, they are developing an open-source repository of sequencing and bioinformatics benchmarking datasets entitled Seqbench.

Nick aims to publish accompanying Github repositories with manuscripts as an aid to extensible and reproducible research, please see Nick's Github page for details.

With James Hadfield, Nick built Omicsmaps.com, a map of high-throughput sequencing instruments.

Professor Nick Loman's talk as part of the Life Sciences in Six event, held at University of Birmingham on 22 November 2016

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

Selected publications

Google Scholar ID: RBacoAEAAAAJ

  1. Faria, N. R., Quick, J., Claro, I. M., Thézé, J., Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., Costa, A. C., Franco, L. C., Silva, S. P., Wu, C.-H., Raghwani, J., Cauchemez, S., Plessis, L., Verotti, M. P., Oliveira, W. K., Carmo, E. H., Coelho, G. E., Santelli, A. C. F. S., Vinhal, L. C., Henriques, C. M., Simpson, J. T., Loose, M., Andersen, K. G., Grubaugh, N. D., Somasekar, S., Chiu, C. Y., Muñoz-Medina, J. E., Gonzalez-Bonilla, C. R., Arias, C. F., Lewis-Ximenez, L. L., Baylis, S. A., Chieppe, A. O., Aguiar, S. F., Fernandes, C. A., Lemos, P. S., Nascimento, B. L. S., Monteiro, H. A. O., Siqueira, I. C., Queiroz, M. G., Souza, T. R., Bezerra, J. F., Lemos, M. R., Pereira, G. F., Loudal, D., Moura, L. C., Dhalia, R., França, R. F., Magalhães, T., Marques, E. T., Jaenisch, T., Wallau, G. L., Lima, M. C., Nascimento, V., Cerqueira, E. M., Lima, M. M., Mascarenhas, D. L., Neto, J. P. M., Levin, A. S., Tozetto-Mendoza, T. R., Fonseca, S. N., Mendes-Correa, M. C., Milagres, F. P., Segurado, A., Holmes, E. C., Rambaut, A., Bedford, T., Nunes, M. R. T., Sabino, E. C., Alcantara, L. C. J., Loman, N. J., Pybus, O. G., “Establishment and cryptic transmission of Zika virus in Brazil and the Americas,” en, Nature, 24 5 2017, issn: 0028-0836, 1476-4687. doi: 10.1038/nature22401.
  2. Quick, J., Grubaugh, N. D., Pullan, S. T., Claro, I. M., Smith, A. D., Gangavarapu, K., Oliveira, G., Robles-Sikisaka, R., Rogers, T. F., Beutler, N. A., Burton, D. R., Lewis-Ximenez, L. L., Jesus, J. G., Giovanetti, M., Hill, S. C., Black, A., Bedford, T., Carroll, M. W., Nunes, M., Alcantara, L. C., Sabino, E. C., Baylis, S. A., Faria, N. R., Loose, M., Simpson, J. T., Pybus, O. G., Andersen, K. G., Loman, N. J., “Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples,” en, Nature protocols, vol. 12, no. 6, pp. 1261–1276, 24 5 2017, issn: 1754-2189, 1750-2799. doi: 10.1038/nprot.2017.066.
  3. Dudas, G., Carvalho, L. M., Bedford, T., Tatem, A. J., Baele, G., Faria, N. R., Park, D. J., Ladner, J. T., Arias, A., Asogun, D., Bielejec, F., Caddy, S. L., Cotten, M., D’Ambrozio, J., Dellicour, S., Di Caro, A., Diclaro, J. W., Duraffour, S., Elmore, M. J., Fakoli, L. S., Faye, O., Gilbert, M. L., Gevao, S. M., Gire, S., Gladden-Young, A., Gnirke, A., Goba, A., Grant, D. S., Haagmans, B. L., Hiscox, J. A., Jah, U., Kugelman, J. R., Liu, D., Lu, J., Malboeuf, C. M., Mate, S., Matthews, D. A., Matranga, C. B., Meredith, L. W., Qu, J., Quick, J., Pas, S. D., Phan, M. V. T., Pollakis, G., Reusken, C. B., Sanchez-Lockhart, M., Schaffner, S. F., Schieffelin, J. S., Sealfon, R. S., Simon-Loriere, E., Smits, S. L., Stoecker, K., Thorne, L., Tobin, E. A., Vandi, M. A., Watson, S. J., West, K., Whitmer, S., Wiley, M. R., Winnicki, S. M., Wohl, S., Wölfel, R., Yozwiak, N. L., Andersen, K. G., Blyden, S. O., Bolay, F., Carroll, M. W., Dahn, B., Diallo, B., Formenty, P., Fraser, C., Gao, G. F., Garry, R. F., Goodfellow, I., Günther, S., Happi, C. T., Holmes, E. C., Kargbo, B., Keïta, S., Kellam, P., Koopmans, M. P. G., Kuhn, J. H., Loman, N. J., Magassouba, N., Naidoo, D., Nichol, S. T., Nyenswah, T., Palacios, G., Pybus, O. G., Sabeti, P. C., Sall, A., Ströher, U., Wurie, I., Suchard, M. A., Lemey, P., Rambaut, A., “Virus genomes reveal factors that spread and sustained the Ebola epidemic,” en, Nature, vol. 544, no. 7650, pp. 309–315, 20 4 2017, issn: 0028-0836, 1476-4687. doi: 10.1038/nature22040.
  4. Diallo, B., Sissoko, D., Loman, N. J., Bah, H. A., Bah, H., Worrell, M. C., Conde, L. S., Sacko, R., Mesfin, S., Loua, A., Kalonda, J. K., Erondu, N. A., Dahl, B. A., Handrick, S., Goodfellow, I., Meredith, L. W., Cotten, M., Jah, U., Guetiya Wadoum, R. E., Rollin, P., Magassouba, N., Malvy, D., Anglaret, X., Carroll, M. W., Aylward, R. B., Djingarey, M. H., Diarra, A., Formenty, P., Keïta, S., Günther, S., Rambaut, A., Duraffour, S., “Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days,” en, Clinical infectious diseases: an official publication of the Infectious Diseases Society of America, vol. 63, no. 10, pp. 1353–1356, 15 11 2016, issn: 1058-4838, 1537-6591. doi: 10.1093/cid/ciw601.
  5. Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L., Bore, J. A., Koundouno, R., Dudas, G., Mikhail, A., Ouédraogo, N., Afrough, B., Bah, A., Baum, J. H. J., Becker-Ziaja, B., Boettcher, J. P., Cabeza-Cabrerizo, M., Camino-Sánchez, Á., Carter, L. L., Doerrbecker, J., Enkirch, T., García-Dorival, I., Hetzelt, N., Hinzmann, J., Holm, T., Kafetzopoulou, L. E., Koropogui, M., Kosgey, A., Kuisma, E., Logue, C. H., Mazzarelli, A., Meisel, S., Mertens, M., Michel, J., Ngabo, D., Nitzsche, K., Pallasch, E., Patrono, L. V., Portmann, J., Repits, J. G., Rickett, N. Y., Sachse, A., Singethan, K., Vitoriano, I., Yemanaberhan, R. L., Zekeng, E. G., Racine, T., Bello, A., Sall, A. A., Faye, O., Faye, O., Magassouba, N., Williams, C. V., Amburgey, V., Winona, L., Davis, E., Gerlach, J., Washington, F., Monteil, V., Jourdain, M., Bererd, M., Camara, A., Somlare, H., Camara, A., Gerard, M., Bado, G., Baillet, B., Delaune, D., Nebie, K. Y., Diarra, A., Savane, Y., Pallawo, R. B., Gutierrez, G. J., Milhano, N., Roger, I., Williams, C. J., Yattara, F., Lewandowski, K., Taylor, J., Rachwal, P., Turner, D. J., Pollakis, G., Hiscox, J. A., Matthews, D. A., O’Shea, M. K., Johnston, A. M., Wilson, D., Hutley, E., Smit, E., Di Caro, A., Wölfel, R., Stoecker, K., Fleischmann, E., Gabriel, M., Weller, S. A., Koivogui, L., Diallo, B., Keïta, S., Rambaut, A., Formenty, P., Günther, S., Carroll, M. W., “Real-time, portable genome sequencing for Ebola surveillance,” en, Nature, vol. 530, no. 7589, pp. 228–232, Nov. 2016, issn: 0028-0836, 1476-4687. doi: 10.1038/nature16996.
  6. Gardy, J., Loman, N. J., Rambaut, A., “Real-time digital pathogen surveillance - the time is now,” en, Genome biology, vol. 16, no. 1, p. 155, 30 7 2015, issn: 1465-6906. doi: 10.1186/s13059- 015-0726-x.
  7. Loman, N. J., Quick, J., Simpson, J. T., “A complete bacterial genome assembled de novo using only nanopore sequencing data,” en, Nature methods, vol. 12, no. 8, pp. 733–735, 15 6 2015, issn: 1548-7091, 1548-7105. doi: 10.1038/nmeth.3444.
  8. Quick, J., Ashton, P., Calus, S., Chatt, C., Gossain, S., Hawker, J., Nair, S., Neal, K., Nye, K., Peters, T., De Pinna, E., Robinson, E., Struthers, K., Webber, M., Catto, A., Dallman, T. J., Hawkey, P., Loman, N. J., “Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella,” Genome biology, vol. 16, no. 1, p. 114, 30 5 2015, issn: 1465-6906, 1465-6914. doi: 10.1186/s13059-015-0677-2.
  9. Loman, N. J., Constantinidou, C., Christner, M., Rohde, H., Chan, J. Z.-M., Quick, J., Weir, J. C., Quince, C., Smith, G. P., Betley, J. R., Aepfelbacher, M., Pallen, M. J., “A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4,” en, JAMA: the journal of the American Medical Association, vol. 309, no. 14, pp. 1502–1510, Oct. 2013, issn: 0098-7484, 1538-3598. doi: 10.1001/jama.2013.3231.
  10. Rohde, H., Qin, J., Cui, Y., Li, D., Loman, N. J., Hentschke, M., Chen, W., Pu, F., Peng, Y., Li, J., Xi, F., Li, S., Li, Y., Zhang, Z., Yang, X., Zhao, M., Wang, P., Guan, Y., Cen, Z., Zhao, X., Christner, M., Kobbe, R., Loos, S., Oh, J., Yang, L., Danchin, A., Gao, G. F., Song, Y., Li, Y., Yang, H., Wang, J., Xu, J., Pallen, M. J., Wang, J., Aepfelbacher, M., Yang, R., E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium, “Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4,” The New England journal of medicine, vol. 365, no. 8, pp. 718–724, 25 8 2011, issn: 0028-4793, 1533-4406. doi: 10.1056/NEJMoa1107643.