Publications

A chronological list of peer-reviewed publications authored and co-authored by members of the Bioinformatics group.

Journal Articles

Latest Articles

• Buckton AJ, Bissett SL, Myers RE, Beddows S, Edwards S, Cane PA, Pillay D. Development and optimization of an internally controlled dried blood spot assay for surveillance of human immunodeficiency virus type-1 drug resistance. Journal of Antimicrobial Chemotherapy 2008 Dec;62(6):1191-8]
  Pubmed [ Abstract ]     Journal [ Homepage ]
• Cui A, Myers R, Xu W, Jin L. Analysis of the genetic variability of the mumps SH gene in viruses circulating in the UK between 1996 and 2005. Infection, Genetics and Evolution 2008 Oct 19. [Epub ahead of print]
  Pubmed [ Abstract ]     Journal [ Homepage ]
• Myers RE, Pillay D. Analysis of Natural Sequence Variation and Covariation in Human Immunodeficiency Virus Type-1 Integrase. Journal of Virology 2008 Sept;82(18);9228-9235
  PubMed [ Abstract ]     Journal [ Homepage ]
• Grant A, Arnold C, Thorne N, Gharbia S, Underwood A. Mathematical modelling of Mycobacterium tuberculosis VNTR loci estimates a very slow mutation rate for the repeats. Journal of Molecular Evolution 2008 Jun;66(6):565-574.
  PubMed [ Abstract ]     Journal [ Homepage ]
• Dallman T, Neal S, Green J,, Efstratiou A. Development of an online database for diphtheria molecular epidemiology under the remit of the DIPNET project. Eurosurveillance 2008;13(19)
  Available online [Full Text ]      Journal [ Homepage ]
• Myers R., Gnaneshan S., Ijaz S., Tedder R., Ramsay M., Green J. HepSEQ--an integrated hepatitis B epidemiology and sequence analysis platform. Euro Surveillance 2008;13(19)
  Available online [Full Text ]      Journal [ Homepage ]
• Takeuchi Y., Myers R., Danos O. Recombination and population mosaic of a multifunctional viral gene, adeno-associated virus capPLoS ONE 2008 Feb 20;3(2) e1634
  PubMed [ Abstract ]     Journal [ Homepage ]

  2007

• Afshar B, Fry NK, Bellamy W, Underwood AP, Harrison TG; Members of the European Working Group for Legionella Infections. External quality assessment of a DNA sequence-based scheme for epidemiological typing of Legionella pneumophila by an international network of laboratories. Journal of Clinical Microbiology 2007; Oct;45(10):3251-3256
  PubMed [ Abstract ]     Journal [ Homepage ]
• Chang CH, Chang YC, Underwood AP, Chiou CS, Kao CY. VNTRDB: A Bacterial Variable Number Tandem Repeat locus database.
  Nucleic Acids Research 2007; 35 (Database Issue) : D416-421
  PubMed [ Abstract ]    Journal [ Homepage ]    Database[ Webpage ]
• Gnaneshan S, Ijaz S, Moran J, Ramsay M, Green J. HepSeq - International Public Health Repository for Hepatitis B. Nucleic Acids Research 2007; 35 (Database Issue): D367-370
  PubMed [ Abstract ]    Journal [ Homepage ]    Database[ Webpage ]
• Fry NK, Afshar B, Bellamy W, Underwood AP, Ratcliff RM, Harrison TG; European Working Group for Legionella Infections. Identification of Legionella spp. by 19 European reference laboratories: results of the European Working Group for Legionella Infections External Quality Assessment Scheme using DNA sequencing of the macrophage infectivity potentiator gene and dedicated online tools. Clinical Microbiology and Infection 2007 Nov;13(11):1119-1124.
  PubMed [ Abstract ]     Journal [ Homepage ]
• Peters TM, Berghold C, Brown D, Coia J, Dionisi AM, Echeita A, Fisher IS, Gatto AJ, Gill N, Green J, Gerner-Smidt P, Heck M, Lederer I, Lukinmaa S, Luzzi I, Maguire C, Prager R, Usera M, Siitonen A, Threlfall EJ, Torpdahl M, Tschäpe H, Wannet W, Zwaluw WK. Relationship of pulsed-field profiles with key phage types of Salmonella enterica serotype Enteritidis in Europe: results of an international multi-centre study. Epidemiology and Infection 2007 Nov;135(8):1274-1281.
  PubMed [ Abstract ]     Journal [ Homepage ]

  2006

• Armah GE, Gallimore CI, Binka FN, Asmah RH, Green J, Ugoji U, Anto F, Brown DW, Gray JJ. Characterisation of norovirus strains in rural Ghanaian children with acute diarrhoea. Journal of Medical Virology 2006; 78(11); 1480-1485
  PubMed [ Abstract ]     Journal [ Homepage ]
• Gatto AJ , Green J, Threlfall J, et al. Distribution of molecular subtypes within Salmonella enterica serotype Entiriditis phage type 4 and S. Typhimurium definitive phage type 104 in nine European countries, 2000-2004: results of an international multi-centre study. Epidemiology and Infection 2006; 134(4); 729-736.
  PubMed [ Abstract ]     Journal [ Homepage ]
• Platt S, Pichon B, George R, Green J. A bioinformatics pipeline for high-throughput multilocus sequence typing (MLST) analyses. Clinical Microbiology and Infection 2006; 12 (11); 1144-1146
  PubMed [ Abstract ]     Journal [ Homepage ]
• Arnold C, Thorne N, Underwood A, Baster K, Gharbia S. Evolution of short sequence repeats in Mycobacterium tuberculosis. FEMS Microbiology Letters 2006 Mar;256(2):340-346
  PubMed [ Abstract ]     Journal [ Homepage ]
• Leoni F, Gallimore CI, Green J, McLauchlin J. Characterisation of small double stranded RNA molecule in Cryptosporidium hominis, Cryptosporidium felis and Cryptosporidium meleagridis/ Parasitology International 2006 Dec;55(4):299-306.
  PubMed [ Abstract ]     Journal [ Homepage ]

  2005

• Underwood AP, Mulder A, Gharbia S, Green J. Virulence Searcher: a tool for searching raw genome sequences from bacterial genomes for putative virulence factors. Clinical Microbiology and Infection 2005; 11(9); 770-772
  PubMed [ Abstract ]     Journal [ Homepage ]
• Arnold C, Westland L, Mowat G, Underwood A, Magee J, Gharbia S. Single-nucleotide polymorphism-based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum. Clinical Microbiology and Infection 2005 Feb;11(2):122-30.
  PubMed [ Abstract ]     Journal [ Homepage ]
• Fry NK, Afshar B, Visca P, Jonas D, Duncan J, Nebuloso E, Underwood A, Harrison TG. Assessment of fluorescent amplified fragment length polymorphism analysis for epidemiological genotyping of Legionella pneumophila serogroup 1. Clinical Microbiology and Infection 2005 Sep;11(9):704-712.
  PubMed [ Abstract ]     Journal [ Homepage ]

  2004

• Underwood AP, Green J. MOP-UP: an online tool for finding strain specific primers or motifs in DNA or protein alignments. Clinical Microbiology and Infection 2004; 10 (10); 948-950
  PubMed [ Abstract ]     Journal [ Homepage ]
• Gallimore CI, Green J, Richards AF, Cotterill H, Curry A, Brown DW, Gray JJ. Methods for the detection and characterisation of noroviruses associated with outbreaks of gastroenteritis: outbreaks occurring in the north-west of England during two norovirus seasons. Journal of Medical Virology 2004 Jun;73(2):280-288.
  PubMed [ Abstract ]     Journal [ Homepage ]
• Gallimore CI, Green J, Lewis D, Richards AF, Lopman BA, Hale AD, Eglin R, Gray JJ, Brown DW. Diversity of noroviruses cocirculating in the north of England from 1998 to 2001. Journal of Clinical Microbiolog 2004 Apr;42(4):1396-1401.
  PubMed [ Abstract ]     Journal [ Homepage ]
• Green J, Gallimore CI, Shore J, Sellwood J, Brown DW. Application of the heteroduplex mobility assay (HMA) for the investigation of the genomic diversity among noroviruses in environmental samples. Journal of Virological Methods 2004 Sep 1;120(1):59-67.
  PubMed [ Abstract ]     Journal [ Homepage ]
• Saunders NA, Underwood A, Kearns AM, Hallas G. A virulence-associated gene microarray: a tool for investigation of the evolution and pathogenic potential of Staphylococcus aureus. Microbiology. 2004 Nov;150(Pt 11):3763-3771.
  PubMed [ Abstract ]     Journal [ Homepage ]

Last reviewed: 18 December 2008