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@bham.ac.uk
Twitter
Address
W129, School of Biosciences
黑料吃瓜网
Edgbaston
Birmingham
B15 2TT
UK

Professor Loman is the Director of the Institute of Microbiology and Infection at the 黑料吃瓜网, 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. 

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 黑料吃瓜网. 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. 

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  of data from the BGI on the 2nd of June 2011 which helped spark a flurry of , 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, . Although funding for this project has ceased, he continues to develop the high-throughput sequencing pipeline  to support their local sequencing efforts, as well as the rapid bacterial genome annotation service .

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

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

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, '', Scientific Reports, vol. 15, no. 1, 5795.

Colquhoun, R, O鈥橳oole, 脕, Hill, V, McCrone, JT, Yu, X, Nicholls, SM, Poplawski, R, Whalley, T, Groves, N, Ellaby, N, Loman, N, Connor, T & Rambaut, A 2024, '', Virus evolution, vol. 10, no. 1.

Mirza, JD, de Oliveira Guimar茫es, 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, '', Microbial Genomics, vol. 10, no. 1, 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, '', Wellcome Open Research, vol. 6, 241.

The COVID-19 Genomics U. K. (COG-UK) Consortium, Modat, M, Hammers, A, Spector, TD, Steves, CJ, Sudre, CH, Ourselin, S & Duncan, EL 2022, '', Scientific Reports, vol. 12, no. 1, 10904.

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, '', Virus evolution, vol. 8, no. 2, veac050.

The COVID-19 Genomics UK (COG-UK) Consortium, Smallman-Raynor, MR & Cliff, AD 2022, '', Epidemiology and Infection, vol. 150, e145.

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鈥檛oole, 脕, 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, '', Science, vol. 371, no. 6530, pp. 708-712.

COG-UK Consortium, Volz, E, Hill, V, McCrone, JT, Price, A, Jorgensen, D, O'Toole, 脕, 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, '', Cell, vol. 184, no. 1, pp. 64-75.e11.

The COVID-19 Genomics UK (COG-UK) Consortium, Sanger Covid Team, Jackson, B, Nicholls, SM, Poplawski, R, Loman, NJ & Rambaut, A 2021, '', Cell, vol. 184, no. 20, pp. 5179-5188.e8.

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, '', Cell Reports, vol. 35, no. 13, 109292.

COVID-19 Genomics UK (COG-UK) Consortium & Beggs, A 2021, '', Science, vol. 373, no. 6557, pp. 889-895.

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, '', eLife, vol. 9, e63430, pp. 1-13.

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, '', BMJ open, vol. 9, no. 11, e030659.

Nicholls, SM, Quick, JC, Tang, S & Loman, NJ 2019, '', GigaScience.