Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Croucher, Nicholas J, Page, Andrew J, Connor, Thomas R, Delaney, Aidan J, Keane, Jacqueline A, Bentley, Stephen D, Parkhill, Julian, Harris, Simon R
Published in Nucleic acids research (18.02.2015)
Published in Nucleic acids research (18.02.2015)
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Journal Article
Phandango: an interactive viewer for bacterial population genomics
Hadfield, James, Croucher, Nicholas J, Goater, Richard J, Abudahab, Khalil, Aanensen, David M, Harris, Simon R
Published in Bioinformatics (15.01.2018)
Published in Bioinformatics (15.01.2018)
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Journal Article
Circlator: automated circularization of genome assemblies using long sequencing reads
Hunt, Martin, Silva, Nishadi De, Otto, Thomas D, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R
Published in Genome Biology (29.12.2015)
Published in Genome Biology (29.12.2015)
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Journal Article
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
Quail, Michael A, Smith, Miriam, Coupland, Paul, Otto, Thomas D, Harris, Simon R, Connor, Thomas R, Bertoni, Anna, Swerdlow, Harold P, Gu, Yong
Published in BMC genomics (24.07.2012)
Published in BMC genomics (24.07.2012)
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Journal Article
Bayesian inference of ancestral dates on bacterial phylogenetic trees
Didelot, Xavier, Croucher, Nicholas J, Bentley, Stephen D, Harris, Simon R, Wilson, Daniel J
Published in Nucleic acids research (14.12.2018)
Published in Nucleic acids research (14.12.2018)
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Journal Article
Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
Kallonen, Teemu, Brodrick, Hayley J, Harris, Simon R, Corander, Jukka, Brown, Nicholas M, Martin, Veronique, Peacock, Sharon J, Parkhill, Julian
Published in Genome research (01.08.2017)
Published in Genome research (01.08.2017)
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Journal Article
Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study
Casali, Nicola, Broda, Agnieszka, Harris, Simon R, Parkhill, Julian, Brown, Timothy, Drobniewski, Francis
Published in PLoS medicine (04.10.2016)
Published in PLoS medicine (04.10.2016)
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Journal Article
Evolution and transmission of drug-resistant tuberculosis in a Russian population
Casali, Nicola, Nikolayevskyy, Vladyslav, Balabanova, Yanina, Harris, Simon R, Ignatyeva, Olga, Kontsevaya, Irina, Corander, Jukka, Bryant, Josephine, Parkhill, Julian, Nejentsev, Sergey, Horstmann, Rolf D, Brown, Timothy, Drobniewski, Francis
Published in Nature genetics (01.03.2014)
Published in Nature genetics (01.03.2014)
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Journal Article
Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study
Baker, Kate S, PhD, Dallman, Timothy J, PhD, Ashton, Philip M, PhD, Day, Martin, BSc, Hughes, Gwenda, PhD, Crook, Paul D, MSc, Gilbart, Victoria L, MSc, Zittermann, Sandra, PhD, Allen, Vanessa G, MD, Howden, Benjamin P, Prof, Tomita, Takehiro, PhD, Valcanis, Mary, MPH, Harris, Simon R, PhD, Connor, Thomas R, PhD, Sintchenko, Vitali, PhD, Howard, Peter, BSc, Brown, Jeremy D, MBBS, Petty, Nicola K, PhD, Gouali, Malika, PharmD, Thanh, Duy Pham, MSc, Keddy, Karen H, BSc (Med), Smith, Anthony M, PhD, Talukder, Kaisar A, PhD, Faruque, Shah M, PhD, Parkhill, Julian, Prof, Baker, Stephen, Prof, Weill, François-Xavier, PhD, Jenkins, Claire, PhD, Thomson, Nicholas R, Prof
Published in The Lancet infectious diseases (01.08.2015)
Published in The Lancet infectious diseases (01.08.2015)
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Journal Article
Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data
Hicks, Allison L, Wheeler, Nicole, Sánchez-Busó, Leonor, Rakeman, Jennifer L, Harris, Simon R, Grad, Yonatan H
Published in PLoS computational biology (01.09.2019)
Published in PLoS computational biology (01.09.2019)
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Journal Article
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
Skwark, Marcin J, Croucher, Nicholas J, Puranen, Santeri, Chewapreecha, Claire, Pesonen, Maiju, Xu, Ying Ying, Turner, Paul, Harris, Simon R, Beres, Stephen B, Musser, James M, Parkhill, Julian, Bentley, Stephen D, Aurell, Erik, Corander, Jukka
Published in PLoS genetics (16.02.2017)
Published in PLoS genetics (16.02.2017)
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Journal Article
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study
Bryant, Josephine M, BSc, Grogono, Dorothy M, MRCP, Greaves, Daniel, MRCP, Foweraker, Juliet, FRCPath, Roddick, Iain, BSc, Inns, Thomas, MSc, Reacher, Mark, FFPH, Haworth, Charles S, FRCP, Curran, Martin D, PhD, Harris, Simon R, PhD, Peacock, Sharon J, Prof, Parkhill, Julian, Prof, Floto, R Andres, Dr
Published in The Lancet (British edition) (04.05.2013)
Published in The Lancet (British edition) (04.05.2013)
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Journal Article
The novel 2016 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations: phenotypic, genetic and reference genome characterization
Unemo, Magnus, Golparian, Daniel, Sánchez-Busó, Leonor, Grad, Yonatan, Jacobsson, Susanne, Ohnishi, Makoto, Lahra, Monica M, Limnios, Athena, Sikora, Aleksandra E, Wi, Teodora, Harris, Simon R
Published in Journal of antimicrobial chemotherapy (01.11.2016)
Published in Journal of antimicrobial chemotherapy (01.11.2016)
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Journal Article
Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000–2013
Grad, Yonatan H., Harris, Simon R., Kirkcaldy, Robert D., Green, Anna G., Marks, Debora S., Bentley, Stephen D., Trees, David, Lipsitch, Marc
Published in The Journal of infectious diseases (15.11.2016)
Published in The Journal of infectious diseases (15.11.2016)
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Journal Article
Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes
Chewapreecha, Claire, Marttinen, Pekka, Croucher, Nicholas J, Salter, Susannah J, Harris, Simon R, Mather, Alison E, Hanage, William P, Goldblatt, David, Nosten, Francois H, Turner, Claudia, Turner, Paul, Bentley, Stephen D, Parkhill, Julian
Published in PLoS genetics (01.08.2014)
Published in PLoS genetics (01.08.2014)
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Journal Article
Fast and flexible bacterial genomic epidemiology with PopPUNK
Lees, John A, Harris, Simon R, Tonkin-Hill, Gerry, Gladstone, Rebecca A, Lo, Stephanie W, Weiser, Jeffrey N, Corander, Jukka, Bentley, Stephen D, Croucher, Nicholas J
Published in Genome research (01.02.2019)
Published in Genome research (01.02.2019)
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Journal Article
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Hunt, Martin, Mather, Alison E, Sánchez-Busó, Leonor, Page, Andrew J, Parkhill, Julian, Keane, Jacqueline A, Harris, Simon R
Published in Microbial genomics (01.10.2017)
Published in Microbial genomics (01.10.2017)
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Journal Article
SNP-sites : rapid efficient extraction of SNPs from multi-FASTA alignments
Page, Andrew J, Taylor, Ben, Delaney, Aidan J, Soares, Jorge, Seemann, Torsten, Keane, Jacqueline A, Harris, Simon R
Published in Microbial genomics (01.04.2016)
Published in Microbial genomics (01.04.2016)
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Journal Article
Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila
David, Sophia, Sánchez-Busó, Leonor, Harris, Simon R, Marttinen, Pekka, Rusniok, Christophe, Buchrieser, Carmen, Harrison, Timothy G, Parkhill, Julian
Published in PLoS genetics (26.06.2017)
Published in PLoS genetics (26.06.2017)
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