Professor Nick Loman PhD

Professor Nick Loman

School of Biosciences
Independent Research Fellow

Contact details

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

Nick 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. 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

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 of Microbial Genomics

Publications

2015

Loman NJ, Quick J, and Simpson JT A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 2015 Jun 15; (10.1038/nmeth.3444)

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 TJ, Hawkey P, and Loman NJ Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 2015 May 30;16(1):114 (10.1186/s13059-015-0677-2)

Webber MA, Whitehead RN, Mount M, Loman NJ, Pallen MJ, and Piddock LJParallel evolutionary pathways to antibiotic resistance selected by biocide exposure. J Antimicrob Chemother 2015 May 7; (10.1093/jac/dkv109)

Kay GL, Sergeant MJ, Zhou Z, Chan JZ, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, and Pallen MJEighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat Commun 2015 Apr 7;6:6717 (10.1038/ncomms7717)

Loman NJ and Watson M Successful test launch for nanopore sequencing.Nat Methods 2015 Apr;12(4):303-4 (10.1038/nmeth.3327)

Mugumbate G, Abrahams KA, Cox JA, Papadatos G, van Westen G, Lelièvre J, Calus ST, Loman NJ, Ballell L, Barros D, Overington JP, and Besra GSMycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation. PLoS One2015;10(3):e0121492 (10.1371/journal.pone.0121492)

2014

Gurcha SS, Usha V, Cox JA, Fütterer K, Abrahams KA, Bhatt A, Alderwick LJ, Reynolds RC, Loman NJ, Nataraj V, Alemparte C, Barros D, Lloyd AJ, Ballell L, Hobrath JV, and Besra GS Biochemical and structural characterization of mycobacterial aspartyl-tRNA synthetase AspS, a promising TB drug target.PLoS One 2014;9(11):e113568 (10.1371/journal.pone.0113568)

Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, and Walker AW Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014 Nov 12;12:87 (10.1186/s12915-014-0087-z)

Quick J, Quinlan AR, and Loman NJ A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.Gigascience 2014;3:22 (10.1186/2047-217X-3-22)

Quick J, Cumley N, Wearn CM, Niebel M, Constantinidou C, Thomas CM, Pallen MJ, Moiemen NS, Bamford A, Oppenheim B, and Loman NJ Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing. BMJ Open 2014 Nov 4;4(11):e006278 (10.1136/bmjopen-2014-006278)

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, and Quince C Binning metagenomic contigs by coverage and composition. Nat Methods 2014 Nov;11(11):1144-6 (10.1038/nmeth.3103)

Fothergill JL, Neill DR, Loman N, Winstanley C, and Kadioglu A Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs. Nat Commun 2014 Sep 2;5:4780 (10.1038/ncomms5780)

Loman NJ and Quinlan AR Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 2014 Dec 1;30(23):3399-401 (10.1093/bioinformatics/btu555)

Johnson MD, Bell J, Clarke K, Chandler R, Pathak P, Xia Y, Marshall RL, Weinstock GM, Loman NJ, Winn PJ, and Lund PA Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli. Mol Microbiol2014 Sep;93(5):911-27 (10.1111/mmi.12704)

Gerasimidis K, Russell R, Hansen R, Quince C, Loman N, Bertz M, Hanske L, Blaut M, McGrogan P, and Edwards CA Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter? Inflamm Bowel Dis2014 Jul;20(7):E18-9 (10.1097/MIB.0000000000000079)

Quick J, Constantinidou C, Pallen MJ, Oppenheim B, and Loman NJ Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound. Genome Announc 2014 May 8;2(3) (10.1128/genomeA.00355-14)