Simon R Harris

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
    Simon R Harris
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:413-9, S1. 2012
  2. ncbi Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
    Mark W Silby
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Centre for Adaptation Genetics and Drug Resistance, Boston, MA 02111, USA
    Genome Biol 10:R51. 2009
  3. ncbi Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
    Helena M B Seth-Smith
    Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, SO16 6YD, UK
    BMC Genomics 10:239. 2009
  4. ncbi BamView: visualizing and interpretation of next-generation sequencing read alignments
    Tim Carver
    Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Brief Bioinform 14:203-12. 2013
  5. ncbi Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study
    Simon R Harris
    Wellcome Trust Sanger Institute, Cambridge, UK
    Lancet Infect Dis 13:130-6. 2013
  6. ncbi Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa
    Chinyere K Okoro
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:1215-21. 2012
  7. ncbi Emergence and global spread of epidemic healthcare-associated Clostridium difficile
    Miao He
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Genet 45:109-13. 2013
  8. ncbi A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    Michael A Quail
    Wellcome Trust Sanger Institute, Hinxton, UK
    BMC Genomics 13:341. 2012
  9. ncbi A high-resolution view of genome-wide pneumococcal transformation
    Nicholas J Croucher
    Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 8:e1002745. 2012
  10. ncbi Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae
    Helena M B Seth-Smith
    Pathogen Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    J Bacteriol 194:1494-504. 2012

Collaborators

Detail Information

Publications13

  1. ncbi Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing
    Simon R Harris
    Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:413-9, S1. 2012
    ..We used our phylogenetic framework to show how genetic exchange has manifested itself in ocular, urogenital and LGV C. trachomatis strains, including the epidemic LGV serotype L2b...
  2. ncbi Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
    Mark W Silby
    Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Centre for Adaptation Genetics and Drug Resistance, Boston, MA 02111, USA
    Genome Biol 10:R51. 2009
    ..A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species...
  3. ncbi Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
    Helena M B Seth-Smith
    Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, SO16 6YD, UK
    BMC Genomics 10:239. 2009
    ..This is essential knowledge if the plasmid is to be continued to be relied on as a key diagnostic marker, and for an understanding of the evolution of Chlamydia trachomatis...
  4. ncbi BamView: visualizing and interpretation of next-generation sequencing read alignments
    Tim Carver
    Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Brief Bioinform 14:203-12. 2013
    ..Availability: BamView and Artemis are freely available software. These can be downloaded from their home pages: http://bamview.sourceforge.net/; http://www.sanger.ac.uk/resources/software/artemis/. Requirements: Java 1.6 or higher...
  5. ncbi Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study
    Simon R Harris
    Wellcome Trust Sanger Institute, Cambridge, UK
    Lancet Infect Dis 13:130-6. 2013
    ..We assessed the use of whole-genome sequencing to enhance detection of MRSA transmission between these settings...
  6. ncbi Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa
    Chinyere K Okoro
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Genet 44:1215-21. 2012
    ....
  7. ncbi Emergence and global spread of epidemic healthcare-associated Clostridium difficile
    Miao He
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
    Nat Genet 45:109-13. 2013
    ..Our analysis identifies key genetic changes linked to the rapid transcontinental dissemination of epidemic C. difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system...
  8. ncbi A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    Michael A Quail
    Wellcome Trust Sanger Institute, Hinxton, UK
    BMC Genomics 13:341. 2012
    ..3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy...
  9. ncbi A high-resolution view of genome-wide pneumococcal transformation
    Nicholas J Croucher
    Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 8:e1002745. 2012
    ....
  10. ncbi Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae
    Helena M B Seth-Smith
    Pathogen Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    J Bacteriol 194:1494-504. 2012
    ..We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae...
  11. ncbi Genome sequence of the zoonotic pathogen Chlamydophila psittaci
    Helena M B Seth-Smith
    Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    J Bacteriol 193:1282-3. 2011
    ..A comparison with previously sequenced Chlamydophila genomes shows that, as in other chlamydiae, most of the genome diversity is restricted to the plasticity zone. The C. psittaci plasmid was also sequenced...
  12. ncbi Evidence for several waves of global transmission in the seventh cholera pandemic
    Ankur Mutreja
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nature 477:462-5. 2011
    ..Additionally, we show how the acquisition of the SXT family of antibiotic resistance elements has shaped pandemic spread, and show that this family was first acquired at least ten years before its discovery in V. cholerae...
  13. ncbi Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
    Tim Carver
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 28:464-9. 2012
    ....