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• JOURNAL ARTICLE
  Ainsworth D, Sternberg MJE, Raczy C, Butcher SAet al., 2017,

  k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets

  , NUCLEIC ACIDS RESEARCH, Vol: 45, Pages: 1649-1656, ISSN: 0305-1048
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  • Citations: 1
• JOURNAL ARTICLE
  Erasmus JC, Bruche S, Pizarro L, Maimari N, Pogglioli T, Tomlinson C, Lees J, Zalivina I, Wheeler A, Alberts A, Russo A, Braga VMMet al., 2016,

  Defining functional interactions during biogenesis of epithelial junctions

  , Nature Communications, Vol: 7, ISSN: 2041-1723
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  • Citations: 1
• JOURNAL ARTICLE
  Florea M, Hagemann H, Santosa G, Abbott J, Micklem CN, Spencer-Milnes X, Garcia LDA, Paschou D, Lazenbatt C, Kong D, Chughtai H, Jensen K, Freemont PS, Kitney R, Reeve B, Ellis Tet al., 2016,

  Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain

  , PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 113, Pages: E3431-E3440, ISSN: 0027-8424
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  • Citations: 3
• JOURNAL ARTICLE
  Florea M, Reeve B, Abbott J, Freemont PS, Ellis Tet al., 2016,

  Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582.

  , Scientific Reports, Vol: 6, ISSN: 2045-2322

  Bacterial cellulose is a strong, highly pure form of cellulose that is used in a range of applications in industry, consumer goods and medicine. Gluconacetobacter hansenii ATCC 53582 is one of the highest reported bacterial cellulose producing strains and has been used as a model organism in numerous studies of bacterial cellulose production and studies aiming to increased cellulose productivity. Here we present a high-quality draft genome sequence for G. hansenii ATCC 53582 and find that in addition to the previously described cellulose synthase operon, ATCC 53582 contains two additional cellulose synthase operons and several previously undescribed genes associated with cellulose production. In parallel, we also develop optimized protocols and identify plasmid backbones suitable for transformation of ATCC 53582, albeit with low efficiencies. Together, these results provide important information for further studies into cellulose synthesis and for future studies aiming to genetically engineer G. hansenii ATCC 53582 for increased cellulose productivity.

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• JOURNAL ARTICLE
  Giotis ES, Robey RC, Skinner NG, Tomlinson CD, Goodbourn S, Skinner MAet al., 2016,

  Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-alpha)

  , VETERINARY RESEARCH, Vol: 47, ISSN: 0928-4249
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  • Citations: 2
• JOURNAL ARTICLE
  Grundmann H, Glasner C, Albiger B, Aanensen DM, Tomlinson CT, Andrasević AT, Cantón R, Carmeli Y, Friedrich AW, Giske CG, Glupczynski Y, Gniadkowski M, Livermore DM, Nordmann P, Poirel L, Rossolini GM, Seifert H, Vatopoulos A, Walsh T, Woodford N, Monnet DL, European Survey of Carbapenemase-Producing Enterobacteriaceae EuSCAPE Working Groupet al., 2016,

  Occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE): a prospective, multinational study.

  , Lancet Infect Dis, Vol: 17, Pages: 153-163

  BACKGROUND: Gaps in the diagnostic capacity and heterogeneity of national surveillance and reporting standards in Europe make it difficult to contain carbapenemase-producing Enterobacteriaceae. We report the development of a consistent sampling framework and the results of the first structured survey on the occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in European hospitals. METHODS: National expert laboratories recruited hospitals with diagnostic capacities, who collected the first ten carbapenem non-susceptible clinical isolates of K pneumoniae or E coli and ten susceptible same-species comparator isolates and pertinent patient and hospital information. Isolates and data were relayed back to national expert laboratories, which made laboratory-substantiated information available for central analysis. FINDINGS: Between Nov 1, 2013, and April 30, 2014, 455 sentinel hospitals in 36 countries submitted 2703 clinical isolates (2301 [85%] K pneumoniae and 402 (15%) E coli). 850 (37%) of 2301 K pneumoniae samples and 77 (19%) of 402 E coli samples were carbapenemase (KPC, NDM, OXA-48-like, or VIM) producers. The ratio of K pneumoniae to E coli was 11:1. 1·3 patients per 10 000 hospital admissions had positive clinical specimens. Prevalence differed greatly, with the highest rates in Mediterranean and Balkan countries. Carbapenemase-producing K pneumoniae isolates showed high resistance to last-line antibiotics. INTERPRETATION: This initiative shows an encouraging commitment by all participants, and suggests that challenges in the establishment of a continent-wide enhanced sentinel surveillance for carbapenemase-producing Enterobacteriaeceae can be overcome. Strengthening infection control efforts in hospitals is crucial for controlling spread through local and national health care networks. FUNDING: European Centre for Disease Prevention and Control.

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• JOURNAL ARTICLE
  Chambers JC, Loh M, Lehne B, Drong A, Kriebel J, Motta V, Wahl S, Elliott HR, Rota F, Scott WR, Zhang W, Tan S-T, Campanella G, Chadeau-Hyam M, Yengo L, Richmond RC, Adamowicz-Brice M, Afzal U, Bozaoglu K, Mok ZY, Ng HK, Pattou F, Prokisch H, Rozario MA, Tarantini L, Abbott J, Ala-Korpela M, Albetti B, Ammerpohl O, Bertazzi PA, Blancher C, Caiazzo R, Danesh J, Gaunt TR, de Lusignan S, Gieger C, Illig T, Jha S, Jones S, Jowett J, Kangas AJ, Kasturiratne A, Kato N, Kotea N, Kowlessur S, Pitkaeniemi J, Punjabi P, Saleheen D, Schafmayer C, Soininen P, Tai E-S, Thorand B, Tuomilehto J, Wickremasinghe AR, Kyrtopoulos SA, Aitman TJ, Herder C, Hampe J, Cauchi S, Relton CL, Froguel P, Soong R, Vineis P, Jarvelin M-R, Scott J, Grallert H, Bollati V, Elliott P, McCarthy MI, Kooner JSet al., 2015,

  Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study

  , LANCET DIABETES & ENDOCRINOLOGY, Vol: 3, Pages: 526-534, ISSN: 2213-8587
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  • Citations: 54
• JOURNAL ARTICLE
  Kato N, Loh M, Takeuchi F, Verweij N, Wang X, Zhang W, Kelly TN, Saleheen D, Lehne B, Leach IM, Drong AW, Abbott J, Wahl S, Tan S-T, Scott WR, Campanella G, Chadeau-Hyam M, Afzal U, Ahluwalia TS, Bonder MJ, Chen P, Dehghan A, Edwards TL, Esko T, Go MJ, Harris SE, Hartiala J, Kasela S, Kasturiratne A, Khor C-C, Kleber ME, Li H, Mok ZY, Nakatochi M, Sapari NS, Saxena R, Stewart AFR, Stolk L, Tabara Y, Teh AL, Wu Y, Wu J-Y, Zhang Y, Aits I, Alves ADSC, Das S, Dorajoo R, Hopewell JC, Kim YK, Koivula RW, Luan J, Lyytikainen L-P, Nguyen QN, Pereira MA, Postmus I, Raitakari OT, Bryan MS, Scott RA, Sorice R, Tragante V, Traglia M, White J, Yamamoto K, Zhang Y, Adair LS, Ahmed A, Akiyama K, Asif R, Aung T, Barroso I, Bjonnes A, Braun TR, Cai H, Chang L-C, Chen C-H, Cheng C-Y, Chong Y-S, Collins R, Courtney R, Davies G, Delgado G, Do LD, Doevendans PA, Gansevoort RT, Gao Y-T, Grammer TB, Grarup N, Grewal J, Gu D, Wander GS, Hartikainen A-L, Hazen SL, He J, Heng C-K, Hixson JE, Hofman A, Hsu C, Huang W, Husemoen LLN, Hwang J-Y, Ichihara S, Igase M, Isono M, Justesen JM, Katsuy T, Kibriya MG, Kim YJ, Kishimoto M, Koh W-P, Kohara K, Kumari M, Kwek K, Lee NR, Lee J, Liao J, Lieb W, Liewald DCM, Matsubara T, Matsushita Y, Meitinger T, Mihailov E, Milani L, Mills R, Mononen N, Mueller-Nurasyid M, Nabika T, Nakashima E, Ng HK, Nikus K, Nutile T, Ohkubo T, Ohnaka K, Parish S, Paternoster L, Peng H, Peters A, Pham ST, Pinidiyapathirage MJ, Rahman M, Rakugi H, Rolandsson O, Rozario MA, Ruggiero D, Sala CF, Sarju R, Shimokawa K, Snieder H, Sparso T, Spiering W, Starr JM, Stott DJ, Stram DO, Sugiyama T, Szymczak S, Tang WHW, Tong L, Trompet S, Turjanmaa V, Ueshima H, Uitterlinden AG, Umemura S, Vaarasmaki M, van Dam RM, van Gilst WH, van Veldhuisen DJ, Viikari JS, Waldenberger M, Wang Y, Wang A, Wilson R, Wong T-Y, Xiang Y-B, Yamaguchi S, Ye X, Young RD, Young TL, Yuan J-M, Zhou X, Asselbergs FW, Ciullo M, Clarke R, Deloukas P, Franke A, Franks PW, Franks S, Friedlander Y, Gross MD, Guoet al., 2015,

  Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation

  , NATURE GENETICS, Vol: 47, Pages: 1282-+, ISSN: 1061-4036
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  • Citations: 47
• JOURNAL ARTICLE
  Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novere N, Mueller W, Snoep J, Goble Cet al., 2015,

  The evolution of standards and data management practices in systems biology

  , MOLECULAR SYSTEMS BIOLOGY, Vol: 11, ISSN: 1744-4292
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  • Citations: 3
• JOURNAL ARTICLE
  Turner CE, Abbott J, Lamagni T, Holden MTG, David S, Jones MD, Game L, Efstratiou A, Sriskandan Set al., 2015,

  Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom

  , MBIO, Vol: 6, ISSN: 2150-7511
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  • Citations: 10
• JOURNAL ARTICLE
  Chambers JC, Abbott J, Zhang W, Turro E, Scott WR, Tan S-T, Afzal U, Afaq S, Loh M, Lehne B, O'Reilly P, Gaulton KJ, Pearson RD, Li X, Lavery A, Vandrovcova J, Wass MN, Miller K, Sehmi J, Oozageer L, Kooner IK, Al-Hussaini A, Mills R, Grewal J, Panoulas V, Lewin AM, Northwood K, Wander GS, Geoghegan F, Li Y, Wang J, Aitman TJ, McCarthy MI, Scott J, Butcher S, Elliott P, Kooner JSet al., 2014,

  The South Asian Genome

  , PLOS ONE, Vol: 9, ISSN: 1932-6203
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  • Citations: 10
• JOURNAL ARTICLE
  Harries P, Davies M, Gilhooly K, Gilhooly M, Tomlinson Cet al., 2014,

  Educating novice practitioners to detect elder financial abuse: a randomised controlled trial

  , BMC Medical Education, Vol: 14
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• JOURNAL ARTICLE
  Cohen J, Filippis I, Woodbridge M, Bauer D, Hong NC, Jackson M, Butcher S, Colling D, Darlington J, Fuchs B, Harvey Met al., 2013,

  RAPPORT: running scientific high-performance computing applications on the cloud

  , PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, Vol: 371, ISSN: 1364-503X
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  • Citations: 2
• JOURNAL ARTICLE
  Filippis I, Lopez-Cobollo R, Abbott J, Butcher S, Bishop GJet al., 2013,

  Using a periclinal chimera to unravel layer-specific gene expression in plants

  , PLANT JOURNAL, Vol: 75, Pages: 1039-1049, ISSN: 0960-7412
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  • Citations: 4
• JOURNAL ARTICLE
  Jenkins VA, Barton GR, Robertson BD, Williams KJet al., 2013,

  Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis

  , BMC GENOMICS, Vol: 14, ISSN: 1471-2164
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  • Citations: 18
• JOURNAL ARTICLE
  Sheppard C, James E, Barton G, Matthews S, Severinov K, Wigneshweraraj Set al., 2013,

  A non-bacterial transcription factor inhibits bacterial transcription by a multipronged mechanism

  , RNA BIOLOGY, Vol: 10, Pages: 495-501, ISSN: 1547-6286
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  • Citations: 1
• JOURNAL ARTICLE
  Tomlinson CD, Barton GR, Woodbridge M, Butcher SAet al., 2013,

  XperimentR: painless annotation of a biological experiment for the laboratory scientist

  , BMC BIOINFORMATICS, Vol: 14, ISSN: 1471-2105
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  • Citations: 1
• JOURNAL ARTICLE
  Williams KJ, Bennett MH, Barton GR, Jenkins VA, Robertson BDet al., 2013,

  Adenylylation of mycobacterial Glnk (PII) protein is induced by nitrogen limitation

  , TUBERCULOSIS, Vol: 93, Pages: 198-206, ISSN: 1472-9792
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  • Citations: 6
• JOURNAL ARTICLE
  Williams KJ, Bryant WA, Jenkins VA, Barton GR, Witney AA, Pinney JW, Robertson BDet al., 2013,

  Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules

  , BMC GENOMICS, Vol: 14, ISSN: 1471-2164
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  • Citations: 9
• JOURNAL ARTICLE
  Woodbridge M, Fagiolo G, O'Regan DP, 2013,

  MRIdb: Medical Image Management for Biobank Research

  , JOURNAL OF DIGITAL IMAGING, Vol: 26, Pages: 886-890, ISSN: 0897-1889
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  • Citations: 5

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