ORCID: 0000-0002-9843-8988

My Google Scholar profile.


Abrahams, K.A. et al., 2016. Identification of KasA as the cellular target of an anti-tubercular scaffold. Nature communications, 7, p.12581. Available at:

Connor, T.R. et al., 2016. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microbial Genomics, 2(9). Available at: [Accessed November 8, 2016].

Diallo, B. et al., 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: an official publication of the Infectious Diseases Society of America, 63(10), pp.1353–1356. Available at:

Dudas, G. et al., 2016. Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic. bioRxiv, p.071779. Available at: [Accessed November 7, 2016].

Faria, N.R. et al., 2016. Mobile real-time surveillance of Zika virus in Brazil. Genome medicine, 8(1), p.97. Available at:

Gerasimidis, K. et al., 2016. The effect of DNA extraction methodology on gut microbiota research applications. BMC research notes, 9, p.365. Available at:

Keita, M. et al., 2016. Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015. Emerging infectious diseases, 22(12), pp.2149–2152. Available at:

McMurray, C.L. et al., 2016. Staphylococcal species heterogeneity in the nasal microbiome following antibiotic prophylaxis revealed by tuf gene deep sequencing. Microbiome, 4(1), p.63. Available at:

Quick, J. et al., 2016. Real-time, portable genome sequencing for Ebola surveillance. Nature, 530(7589), pp.228–232. Available at:

Sissoko, D. et al., 2016. Ebola virus persistence in breast milk after no reported illness: a likely source of virus transmission from mother to child. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America. Available at:

Stoiber, M.H. et al., 2016. De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. bioRxiv, p.094672. Available at: [Accessed December 31, 2016].


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 LJ Parallel 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 MJ Eighteenth-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 GS Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation. PLoS One 2015;10(3):e0121492 (10.1371/journal.pone.0121492)


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 Microbiol 2014 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 Dis 2014 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)


Davis IJ, Wallis C, Deusch O, Colyer A, Milella L, Loman N, and Harris S A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis. PLoS One 2013;8(12):e83158 (10.1371/journal.pone.0083158)

Loman N and Watson M So you want to be a computational biologist? Nat Biotechnol 2013 Nov;31(11):996-8 (10.1038/nbt.2740)

Snyder LA, Loman NJ, Faraj LA, Levi K, Weinstock G, Boswell TC, Pallen MJ, and Ala'Aldeen DA Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing. Euro Surveill 2013 Oct 17;18(42) ()

Rihn SJ, Wilson SJ, Loman NJ, Alim M, Bakker SE, Bhella D, Gifford RJ, Rixon FJ, and Bieniasz PD Extreme genetic fragility of the HIV-1 capsid. PLoS Pathog 2013;9(6):e1003461 (10.1371/journal.ppat.1003461)

Loman NJ, Gladstone RA, Constantinidou C, Tocheva AS, Jefferies JM, Faust SN, O'Connor L, Chan J, Pallen MJ, and Clarke SC Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine. PLoS One 2013;8(5):e64731 (10.1371/journal.pone.0064731)

Remuiñán MJ, Pérez-Herrán E, Rullás J, Alemparte C, Martínez-Hoyos M, Dow DJ, Afari J, Mehta N, Esquivias J, Jiménez E, Ortega-Muro F, Fraile-Gabaldón MT, Spivey VL, Loman NJ, Pallen MJ, Constantinidou C, Minick DJ, Cacho M, Rebollo-López MJ, González C, Sousa V, Angulo-Barturen I, Mendoza-Losana A, Barros D, Besra GS, Ballell L, and Cammack N Tetrahydropyrazolo[1,5-a]pyrimidine-3-carboxamide and N-benzyl-6',7'-dihydrospiro[piperidine-4,4'-thieno[3,2-c]pyran] analogues with bactericidal efficacy against Mycobacterium tuberculosis targeting MmpL3. PLoS One 2013;8(4):e60933 (10.1371/journal.pone.0060933)

Loman NJ, Constantinidou C, Christner M, Rohde H, Chan JZ, Quick J, Weir JC, Quince C, Smith GP, Betley JR, Aepfelbacher M, and Pallen MJ A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4. JAMA 2013 Apr 10;309(14):1502-10 (10.1001/jama.2013.3231)

Martin K, Baddal B, Mustafa N, Perry C, Underwood A, Constantidou C, Loman N, Kenna DT, and Turton JF Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK. J Med Microbiol 2013 Jul;62(Pt 7):988-1000 (10.1099/jmm.0.054841-0)


Chan JZ, Halachev MR, Loman NJ, Constantinidou C, and Pallen MJ Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 2012 Dec 23;12:302 (10.1186/1471-2180-12-302)

Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, and Pallen MJ High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 2012 Sep;10(9):599-606 (10.1038/nrmicro2850)

Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, and Pallen MJ Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012 May;30(5):434-9 (10.1038/nbt.2198)

Ricci V, Loman N, Pallen M, Ivens A, Fookes M, Langridge GC, Wain J, and Piddock LJ The TCA cycle is not required for selection or survival of multidrug-resistant Salmonella. J Antimicrob Chemother 2012 Mar;67(3):589-99 (10.1093/jac/dkr515)

Abrahams KA, Cox JA, Spivey VL, Loman NJ, Pallen MJ, Constantinidou C, Fernández R, Alemparte C, Remuiñán MJ, Barros D, Ballell L, and Besra GS Identification of novel imidazo[1,2-a]pyridine inhibitors targeting M. tuberculosis QcrB. PLoS One 2012;7(12):e52951 (10.1371/journal.pone.0052951)

Williams TM, Loman NJ, Ebruke C, Musher DM, Adegbola RA, Pallen MJ, Weinstock GM, and Antonio M Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. PLoS One 2012;7(10):e26742 (10.1371/journal.pone.0026742)


Clarke DJ, Chaudhuri RR, Martin HM, Campbell BJ, Rhodes JM, Constantinidou C, Pallen MJ, Loman NJ, Cunningham AF, Browning DF, and Henderson IR Complete genome sequence of the Crohn's disease-associated adherent-invasive Escherichia coli strain HM605. J Bacteriol 2011 Sep;193(17):4540 (10.1128/JB.05374-11)

Rohde H, Qin J, Cui Y, Li D, Loman NJ, 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 GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R, and E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 2011 Aug 25;365(8):718-24 (10.1056/NEJMoa1107643)

Pallen MJ and Loman NJ Are diagnostic and public health bacteriology ready to become branches of genomic medicine? Genome Med 2011 Aug 23;3(8):53 (10.1186/gm269)

Hornsey M, Loman N, Wareham DW, Ellington MJ, Pallen MJ, Turton JF, Underwood A, Gaulton T, Thomas CP, Doumith M, Livermore DM, and Woodford N Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. J Antimicrob Chemother 2011 Jul;66(7):1499-503 (10.1093/jac/dkr168)

Zarrilli R, Giannouli M, Rocco F, Loman NJ, Haines AS, Constantinidou C, Pallen MJ, Triassi M, and Di Nocera PP Genome sequences of three Acinetobacter baumannii strains assigned to the multilocus sequence typing genotypes ST2, ST25, and ST78. J Bacteriol 2011 May;193(9):2359-60 (10.1128/JB.00245-11)

Halachev MR, Loman NJ, and Pallen MJ Calculating orthologs in bacteria and Archaea: a divide and conquer approach. PLoS One 2011;6(12):e28388 (10.1371/journal.pone.0028388)


Pallen MJ, Loman NJ, and Penn CW High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Curr Opin Microbiol 2010 Oct;13(5):625-31 (10.1016/j.mib.2010.08.003)

Loman NJ and Pallen MJ EntrezAJAX: direct web browser access to the Entrez Programming Utilities. Source Code Biol Med 2010 Jun 21;5:6 (10.1186/1751-0473-5-6)

Lewis T, Loman NJ, Bingle L, Jumaa P, Weinstock GM, Mortiboy D, and Pallen MJ High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak. J Hosp Infect 2010 May;75(1):37-41 (10.1016/j.jhin.2010.01.012)

Snyder LA, Loman NJ, Linton JD, Langdon RR, Weinstock GM, Wren BW, and Pallen MJ Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching. BMC Genomics 2010 Jan 27;11:67 (10.1186/1471-2164-11-67)


Loman NJ, Snyder LA, Linton JD, Langdon R, Lawson AJ, Weinstock GM, Wren BW, and Pallen MJ Genome sequence of the emerging pathogen Helicobacter canadensis. J Bacteriol 2009 Sep;191(17):5566-7 (10.1128/JB.00729-09)

Spear AM, Loman NJ, Atkins HS, and Pallen MJ Microbial TIR domains: not necessarily agents of subversion? Trends Microbiol 2009 Sep;17(9):393-8 (10.1016/j.tim.2009.06.005)

Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, Lok S, and Yuen KY The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet 2009 Mar;5(3):e1000416 (10.1371/journal.pgen.1000416)

Snyder LA, Loman N, Pallen MJ, and Penn CW Next-generation sequencing--the promise and perils of charting the great microbial unknown. Microb Ecol 2009 Jan;57(1):1-3 (10.1007/s00248-008-9465-9)

Snyder LA, Loman NJ, Fütterer K, and Pallen MJ Bacterial flagellar diversity and evolution: seek simplicity and distrust it? Trends Microbiol 2009 Jan;17(1):1-5 (10.1016/j.tim.2008.10.002)


Loman NJ and Pallen MJ XDR-TB genome sequencing: a glimpse of the microbiology of the future. Future Microbiol 2008 Apr;3(2):111-3 (10.2217/17460913.3.2.111)

Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, and Pallen MJ xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res 2008 Jan;36(Database issue):D543-6 (10.1093/nar/gkm928)


Pallen MJ, Lam AC, and Loman N Tricorn-like proteases in bacteria. Trends Microbiol 2001 Nov;9(11):518-21 ()

Pallen MJ, Lam AC, Loman NJ, and McBride A An abundance of bacterial ADP-ribosyltransferases--implications for the origin of exotoxins and their human homologues. Trends Microbiol 2001 Jul;9(7):302-7; discussion 308 ()


Karlsson J, Prior RG, Williams K, Lindler L, Brown KA, Chatwell N, Hjalmarsson K, Loman N, Mack KA, Pallen M, Popek M, Sandström G, Sjöstedt A, Svensson T, Tamas I, Andersson SG, Wren BW, Oyston PC, and Titball RW Sequencing of the Francisella tularensis strain Schu 4 genome reveals the shikimate and purine metabolic pathways, targets for the construction of a rationally attenuated auxotrophic vaccine. Microb Comp Genomics 2000;5(1):25-39 (10.1089/10906590050145249)


Pallen M and Loman N Videos, photographs, and patient consent. Medical educationalists can free themselves from constraints of "real world" images. BMJ 1998 Nov 28;317(7171):1522 ()