Development of robust analytical pipelines for the analysis of microbial community data from clinical samples

Research output

Research output per year 2012 2013 2014 2015 2016

• 28 Article

Research output per year

Research output per year

Search results

• 2016

  Real-time, portable genome sequencing for Ebola surveillance

  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., & 82 othersEnkirch, 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, NF., 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., 11 Feb 2016, In: Nature. 530, 7589, p. 228-232 5 p.

  Research output: Contribution to journal › Article › peer-review

  • Epidemics 100%
  • Genome 98%
  • Ebolavirus 78%
  • Disease Outbreaks 77%
  • Nanopore Sequencing 49%
  614 Citations (Scopus)
• 2015

  A complete bacterial genome assembled de novo using only nanopore sequencing data

  Loman, N. J., Quick, J. & Simpson, J. T., Aug 2015, In: Nature Methods. 12, 8, p. 733-5 3 p.

  Research output: Contribution to journal › Article › peer-review

  • Nanopore Sequencing 100%
  • Nanopores 91%
  • Bacterial Genomes 79%
  • Chromosomes, Human, Pair 12 78%
  • Gene Order 76%
  476 Citations (Scopus)

• Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe

  Kay, G. L., Sergeant, M. J., Zhou, Z., Chan, J. Z-M., Millard, A., Quick, J., Szikossy, I., Pap, I., Spigelman, M., Loman, N. J., Achtman, M., Donoghue, H. D. & Pallen, M. J., 7 Apr 2015, In: Nature Communications. 6, 9 p., 6717.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • tuberculosis 100%
  • genome 78%
  • infectious diseases 75%
  • Coinfection 58%
  • Tuberculosis 49%
  92 Citations (Scopus)

  141 Downloads (Pure)

• Mycobacterial dihydrofolate reductase inhibitors identified using chemogenomic methods and in vitro validation

  Mugumbate, G., Abrahams, K. A., Cox, J. A. G., Papadatos, G., van Westen, G., Lelièvre, J., Calus, S. T., Loman, N. J., Ballell, L., Barros, D., Overington, J. P. & Besra, G. S., 23 Mar 2015, In: PLoS ONE. 10, 3, e0121492.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Dihydrofolate Reductase Inhibitor 100%
  • Folic Acid Antagonists 85%
  • dihydrofolate reductase 82%
  • Antitubercular 78%
  • Dihydrofolates 78%
  30 Citations (Scopus)

  342 Downloads (Pure)

• Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure

  Webber, M. A., Whitehead, R. N., Mount, M., Loman, N., Pallen, M. J. & Piddock, L. J. V., Aug 2015, In: Journal of Antimicrobial Chemotherapy. 70, 8, p. 2241-2248

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Disinfectants 100%
  • Microbial Drug Resistance 81%
  • Anti-Bacterial Agents 30%
  • Triclosan 16%
  • Salmonella enterica 14%
  51 Citations (Scopus)

  157 Downloads (Pure)

• Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella

  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., 30 May 2015, In: Genome Biology. 16, 1, p. 114

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Nanopore Sequencing 100%
  • nanopores 89%
  • salmonella 66%
  • Salmonella 61%
  • hospital 56%
  157 Citations (Scopus)

  98 Downloads (Pure)

• Successful test launch for nanopore sequencing

  Loman, N. J. & Watson, M., Apr 2015, In: Nature Methods. 12, 4, p. 303-304 2 p.

  Research output: Contribution to journal › Article
  72 Citations (Scopus)

• Twenty years of bacterial genome sequencing

  Loman, N. J. & Pallen, M. J., Dec 2015, In: Nature Reviews Microbiology. 13, p. 787-794 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Bacterial Genomes 100%
  • Bacteriology 97%
  • TimeLine 48%
  • Whole Genome Sequencing 43%
  • Haemophilus influenzae 42%
  134 Citations (Scopus)
• 2014

  A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer

  Quick, J., Quinlan, A. R. & Loman, N. J., 20 Oct 2014, In: GigaScience. 3, 22.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Nanopores 100%
  • Bacterial Genomes 86%
  • Genomics 67%
  • Molecules 62%
  • Datasets 51%
  143 Citations (Scopus)

  231 Downloads (Pure)

• Binning metagenomic contigs by coverage and composition

  Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F. & Quince, C., Nov 2014, In: Nature Methods. 11, 11, p. 1144-6 3 p.

  Research output: Contribution to journal › Article › peer-review

  • Metagenomics 100%
  • Genome 54%
  • Molecular Cluster 52%
  • Metagenome 28%
  • Firearms 22%
  540 Citations (Scopus)

• Biochemical and structural characterization of Mycobacterial aspartyl-tRNA synthetase aspS, a promising TB drug target

  Gurcha, S. S., Veeraraghavan, U., Cox, J. A. G., Fütterer, K., Abrahams, K. A., Bhatt, A., Alderwick, L. J., Reynolds, R. C., Loman, N. J., Nataraj, V-S., Alemparte, C., Barros, D., Lloyd, A. J., Ballell, L., Hobrath, J. V. & Besra, G. S., 19 Nov 2014, In: PLoS ONE. 9, 11, e113568.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Aspartate-tRNA Ligase 100%
  • aspartate-tRNA ligase 98%
  • RNA, Transfer, Asp 96%
  • Viperidae 73%
  • Mycobacterium tuberculosis 64%
  22 Citations (Scopus)

  217 Downloads (Pure)

• Characterization of mutations in the PAS domain of the EvgS sensor kinase selected by laboratory evolution for acid resistance in Escherichia coli

  Johnson, M. D., Bell, J., Clarke, K., Chandler, R., Pathak, P., Xia, Y., Marshall, R. L., Weinstock, G. M., Loman, N. J., Winn, P. J. & Lund, P. A., 29 Aug 2014, In: Molecular Microbiology. 93, 5, p. 911–927

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Phosphotransferases 100%
  • Acids 97%
  • Escherichia coli 90%
  • Mutation 72%
  • Sigma Factor 21%
  24 Citations (Scopus)

  209 Downloads (Pure)

• Draft Genome Sequence of Elizabethkingia meningoseptica Isolated from a Traumatic Wound

  Quick, J., Constantinidou, C., Pallen, M. J., Oppenheim, B. & Loman, N. J., 8 May 2014, In: Genome Announcements. 2, 3, e00355-14.

  Research output: Contribution to journal › Article › peer-review

  • Genome 100%
  • Wounds and Injuries 71%
  • Explosive Agents 46%
  • Leg 30%
  • Equipment and Supplies 22%
  7 Citations (Scopus)

• Poretools: a toolkit for analyzing nanopore sequence data

  Loman, N. J. & Quinlan, A. R., 1 Dec 2014, In: Bioinformatics. 30, 23, p. 3399-401 3 p.

  Research output: Contribution to journal › Article › peer-review

  • Nanopores 100%
  • Nanopore Sequencing 43%
  • Boidae 37%
  • Disruptive Technology 23%
  • Datasets 20%
  224 Citations (Scopus)

• Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs

  Fothergill, J. L., Neill, D. R., Loman, N., Winstanley, C., Kadioglu, A. & Loman, N., 2014, In: Nature Communications. 5, p. 4780

  Research output: Contribution to journal › Article › peer-review

  • pseudomonas 100%
  • infectious diseases 87%
  • lungs 75%
  • Pseudomonas aeruginosa 64%
  • bacteria 49%
  41 Citations (Scopus)

• Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

  Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J. & Walker, A. W., 12 Nov 2014, In: BMC Biology. 12, 87.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Metagenomics 100%
  • Biomass 99%
  • rRNA Genes 84%
  • 16S Ribosomal RNA 83%
  • Microbiota 80%
  1370 Citations (Scopus)

• Role of Faecalibacterium prausnitzii in Crohn's Disease: friend, foe, or does not really matter?

  Gerasimidis, K., Russell, R., Hansen, R., Quince, C., Loman, N., Bertz, M., Hanske, L., Blaut, M., McGrogan, P., Edwards, C. A. & Loman, N., Jul 2014, In: Inflammatory Bowel Diseases. 20, 7, p. E18-9

  Research output: Contribution to journal › Article › peer-review
  6 Citations (Scopus)

• Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing

  Quick, J., Cumley, N., Wearn, C. M., Niebel, M., Constantinidou, C., Thomas, C. M., Pallen, M. J., Moiemen, N. S., Bamford, A., Oppenheim, B. & Loman, N. J., 4 Nov 2014, In: BMJ open. 4, 11, e006278.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pseudomonas Infections 100%
  • Whole Genome Sequencing 93%
  • Pseudomonas aeruginosa 74%
  • Observational Studies 62%
  • Water 29%
  65 Citations (Scopus)
• 2013

  A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis

  Davis, I. J., Wallis, C., Deusch, O., Colyer, A., Milella, L., Loman, N., Harris, S. & Loman, N., 2013, In: PLoS ONE. 8, 12, p. e83158

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • gingivitis 100%
  • gingiva 90%
  • periodontitis 88%
  • Gingivitis 80%
  • cross-sectional studies 73%
  40 Citations (Scopus)

• A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4

  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., 10 Apr 2013, In: JAMA The Journal of the American Medical Association. 309, 14, p. 1502-10 9 p.

  Research output: Contribution to journal › Article › peer-review

  • Escherichia coli O104 100%
  • Shiga-Toxigenic Escherichia coli 77%
  • Metagenomics 70%
  • Disease Outbreaks 50%
  • Disease Management 28%
  194 Citations (Scopus)

• Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine

  Loman, N. J., Gladstone, R. A., Constantinidou, C., Tocheva, A. S., Jefferies, J. M. C., Faust, S. N., O'Connor, L., Chan, J., Pallen, M. J., Clarke, S. C. & Loman, N., 2013, In: PLoS ONE. 8, 5, p. e64731

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Lantibiotic 100%
  • Plastic Property 75%
  • Serogroup 59%
  • vaccines 56%
  • serotypes 56%
  17 Citations (Scopus)

• Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK

  Martin, K., Baddal, B., Mustafa, N., Perry, C., Underwood, A., Constantidou, C., Loman, N., Kenna, D. T., Turton, J. F. & Loman, N., Jul 2013, In: Journal of Medical Microbiology. 62, Pt 7, p. 988-1000 13 p.

  Research output: Contribution to journal › Article › peer-review

  • Pseudomonas aeruginosa 100%
  • Minisatellite Repeats 91%
  • High-Throughput Nucleotide Sequencing 68%
  • Patient Advocacy 46%
  • Hospital Laboratories 45%
  34 Citations (Scopus)

• Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing

  Snyder, L. A., Loman, N. J., Faraj, L. A., Levi, K., Weinstock, G., Boswell, T. C., Pallen, M. J. & Ala'Aldeen, D. A., 2013, In: Euro surveillance : bulletin européen sur les maladies transmissibles = European communicable disease bulletin. 18, 42

  Research output: Contribution to journal › Article › peer-review

  • Whole Genome Sequencing 100%
  • Pseudomonas aeruginosa 79%
  • Disease Outbreaks 76%
  • Prophages 47%
  • Single Nucleotide Polymorphism 43%
  37 Citations (Scopus)

• Extreme genetic fragility of the HIV-1 capsid

  Rihn, S. J., Wilson, S. J., Loman, N. J., Alim, M., Bakker, S. E., Bhella, D., Gifford, R. J., Rixon, F. J., Bieniasz, P. D. & Loman, N., 2013, In: PLoS pathogens. 9, 6, p. e1003461

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Human immunodeficiency virus 1 100%
  • capsid 95%
  • Capsid 94%
  • HIV-1 70%
  • mutation 20%
  112 Citations (Scopus)

• So you want to be a computational biologist?

  Loman, N., Watson, M. & Loman, N., Nov 2013, In: Nature Biotechnology. 31, 11, p. 996-8 3 p.

  Research output: Contribution to journal › Article
  18 Citations (Scopus)

• 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

  Remuiñán, M. J., Pérez-Herrán, E., Rullás, J., Alemparte, C., Martínez-Hoyos, M., Dow, D. J., Afari, J., Mehta, N., Esquivias, J., Jiménez, E., Ortega-Muro, F., Fraile-Gabaldón, M. T., Spivey, V. L., Loman, N. J., Pallen, M. J., Constantinidou, C., Minick, D. J., Cacho, M., Rebollo-López, M. J., González, C., & 7 othersSousa, V., Angulo-Barturen, I., Mendoza-Losana, A., Barros, D., Besra, G. S., Ballell, L. & Cammack, N., 2013, In: PLoS ONE. 8, 4, p. e60933

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Pyrans 100%
  • flopropione 94%
  • piperidine 87%
  • piperidines 85%
  • pyrans 84%
  102 Citations (Scopus)
• 2012

  Defining bacterial species in the genomic era : insights from the genus Acinetobacter

  Chan, J. Z., Halachev, M. R., Loman, N. J., Constantinidou, C. & Pallen, M. J., 23 Dec 2012, In: BMC Microbiology. 12, 1, 302.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Acinetobacter 100%
  • Genome 54%
  • Nucleotides 27%
  • Horizontal Gene Transfer 15%
  • Culture Techniques 15%
  127 Citations (Scopus)

  227 Downloads (Pure)

• High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

  Loman, N. J., Constantinidou, C., Chan, J. Z. M., Halachev, M., Sergeant, M., Penn, C. W., Robinson, E. R. & Pallen, M. J., 2012, In: Nature Reviews Microbiology. 10, 9, p. 599-606 8 p.

  Research output: Contribution to journal › Article › peer-review

  • Embarrassment 100%
  • Bacterial Genomes 99%
  • Microbiology 78%
  290 Citations (Scopus)