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ResearcherID: K-1318-2013

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Employment (3)

Bill & Melinda Gates Foundation: London, GB

2022-02-21 to present | Senior Program Officer
Employment
Source: Self-asserted source
Simon Harris

Microbiotica Limited: Cambridge, GB

2018-11-01 to 2022-02-15 | Director of Bioinformatics
Employment
Source: Self-asserted source
Simon Harris

Wellcome Sanger Institute: Cambridge, Cambridgeshire, GB

2008-08 to 2018-10-31 | Senior Staff Scientist (Pathogen Genomics)
Employment
Source: Self-asserted source
Simon Harris

Works (50 of 72)

Items per page:
Page 1 of 2

A Shared Population of Epidemic Methicillin-Resistant Staphylococcus aureus 15 Circulates in Humans and Companion Animals

mBio
2014 | Journal article
Source: Self-asserted source
Simon Harris

Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes

PLOS Genetics
2014 | Journal article
Source: Self-asserted source
Simon Harris

Dense genomic sampling identifies highways of pneumococcal recombination

Nature genetics
2014 | Journal article
Source: Self-asserted source
Simon Harris

Emergence of a New Epidemic Neisseria meningitidis Serogroup A Clone in the African Meningitis Belt: High-Resolution Picture of Genomic Changes That Mediate Immune Evasion

mBio
2014 | Journal article
Source: Self-asserted source
Simon Harris

Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape

Genome biology and evolution
2014 | Journal article
Source: Self-asserted source
Simon Harris

Evolution and transmission of drug-resistant tuberculosis in a Russian population

Nature Genetics
2014 | Journal article
Source: Self-asserted source
Simon Harris

Genomic epidemiology of< i> Neisseria gonorrhoeae</i> with reduced susceptibility to cefixime in the USA: a retrospective observational study

The Lancet infectious diseases
2014 | Journal article
Source: Self-asserted source
Simon Harris

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi

Journal of Antimicrobial Chemotherapy
2014 | Journal article
Source: Self-asserted source
Simon Harris

Genomic investigations unmask Mycoplasma amphoriforme, a new respiratory pathogen

Clinical Infectious Diseases
2014 | Journal article
Source: Self-asserted source
Simon Harris

Global Population Structure and Evolution of Bordetella pertussis and Their Relationship with Vaccination

mBio
2014 | Journal article
Source: Self-asserted source
Simon Harris

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

PLoS Genetics
2014 | Journal article
Source: Self-asserted source
Simon Harris

Parallel independent evolution of pathogenicity within the genus Yersinia

Proceedings of the National Academy of Sciences
2014 | Journal article
Source: Self-asserted source
Simon Harris

Variable recombination dynamics during the emergence, transmission and'disarming'of a multidrug-resistant pneumococcal clone

BMC biology
2014 | Journal article
Source: Self-asserted source
Simon Harris

Whole genome sequencing of a methicillin-resistant Staphylococcus aureus pseudo-outbreak in a professional football team

Open Forum Infectious Diseases
2014 | Journal article
Source: Self-asserted source
Simon Harris

Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic?

Journal of Antimicrobial Chemotherapy
2014 | Journal article
Source: Self-asserted source
Simon Harris

A genomic portrait of the emergence, evolution and global spread of a methicillin resistant Staphylococcus aureus pandemic

Genome Research
2013 | Journal article
DOI:

10.1101/gr.147710.112
Contributors: Holden, Matthew T. G.; Hsu, Li Yang; Kurt, Kevin; Weinert, Lucy A.; Mather, Alison E.; Harris, Simon R.; Strommenger, Birgit; Layer, Franziska; Witte, Wolfgang; de Lencastre, Hermínia et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Arginine Catabolic Mobile Element in Methicillin-Resistant Staphylococcus aureus (MRSA) Clonal Group ST239-MRSA-III Isolates in Singapore: Implications for PCR-Based Screening Tests

Antimicrobial Agents and Chemotherapy
2013 | Journal article
Source: Self-asserted source
Simon Harris

Bacterial genomes in epidemiology--present and future

Philosophical transactions of the Royal Society of London. Series B, Biological sciences
2013 | Journal article
DOI:

10.1098/rstb.2012.0202
Contributors: Croucher, Nicholas J.; Harris, Simon R.; Grad, Yonatan H.; Hanage, William P.
Source: Self-asserted source
Simon Harris via ResearcherID

Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes

Microbiology (Reading, England)
2013 | Journal article
DOI:

10.1099/mic.0.065391-0
Contributors: O'Neill, C. E.; Seth-Smith, H. M. B.; Van Der Pol, B.; Harris, S. R.; Thomson, N. R.; Cutcliffe, L. T.; Clarke, I. N.
Source: Self-asserted source
Simon Harris via ResearcherID

Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts

Science
2013 | Journal article
DOI:

papers2://publication/doi/10.1126/science.1240578
Contributors: Mather, A. E.; Reid, S. W. J.; Maskell, D. J.; Parkhill, J.; Fookes, M. C.; Harris, S. R.; Brown, D. J.; Coia, J. E.; Mulvey, M. R.; Gilmour, M. W. et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

PLoS genetics
2013 | Journal article
DOI:

papers2://publication/doi/10.1371/journal.pgen.1003868
Contributors: Croucher, Nicholas J.; Mitchell, Andrea M.; Gould, Katherine A.; Inverarity, Donald; Barquist, Lars; Feltwell, Theresa; Fookes, Maria C.; Harris, Simon R.; Dordel, Janina; Salter, Susannah J. et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA

Nature protocols
2013 | Journal article
DOI:

papers2://publication/doi/10.1038/nprot.2013.147
Contributors: Seth-Smith, Helena M. B.; Harris, Simon R.; Scott, Paul; Parmar, Surendra; Marsh, Peter; Unemo, Magnus; Clarke, Ian N.; Parkhill, Julian; Thomson, Nicholas R.
Source: Self-asserted source
Simon Harris via ResearcherID

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA

Nature Protocols
2013 | Journal article
Source: Self-asserted source
Simon Harris

Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar

mBio
2013 | Journal article
DOI:

papers2://publication/doi/10.1128/mBio.00565-13
Contributors: Kingsley, Robert A.; Kay, Sally; Connor, Thomas; Barquist, Lars; Sait, Leanne; Holt, Kathryn E.; Sivaraman, Karthi; Wileman, Thomas; Goulding, David; Clare, Simon et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Genome-level analyses of Mycobacterium bovis lineages reveal the role of SNPs and antisense transcription in differential gene expression

BMC genomics
2013 | Journal article
DOI:

10.1186/1471-2164-14-710
Contributors: Golby, Paul; Nunez, Javier; Witney, Adam; Hinds, Jason; Quail, Michael A.; Bentley, Stephen; Harris, Simon R.; Smith, Noel; Hewinson, R. Glyn; Gordon, Stephen V.
Source: Self-asserted source
Simon Harris via ResearcherID

Genomic Characterisation of Invasive Non-Typhoidal Salmonella enterica Subspecies enterica Serovar Bovismorbificans Isolates from Malawi

PLOS Neglected Tropical Diseases
2013 | Journal article
Source: Self-asserted source
Simon Harris

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi

The Journal of antimicrobial chemotherapy
2013 | Journal article
DOI:

papers2://publication/doi/10.1093/jac/dkt384
Contributors: Cornick, Jennifer E.; Harris, Simon R.; Parry, Christopher M.; Moore, Michael J.; Jassi, Chikondi; Kamng'ona, Arox; Kulohoma, Benard; Heyderman, Robert S.; Bentley, Stephen D.; Everett, Dean B.
Source: Self-asserted source
Simon Harris via ResearcherID

Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

BMC infectious diseases
2013 | Journal article
DOI:

10.1186/1471-2334-13-110
Contributors: Bryant, Josephine M.; Schürch, Anita C.; van Deutekom, Henk; Harris, Simon R.; de Beer, Jessica L.; de Jager, Victor; Kremer, Kristin; van Hijum, Sacha A.; Siezen, Roland J.; Borgdorff, Martien et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

Nature genetics
2013 | Journal article
DOI:

papers2://publication/doi/10.1038/ng.2744
Contributors: Comas, Iñaki; Coscolla, Mireia; Luo, Tao; Borrell, Sonia; Holt, Kathryn E.; Kato-Maeda, Midori; Parkhill, Julian; Malla, Bijaya; Berg, Stefan; Thwaites, Guy et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Playing fast and loose with mutation

Nature reviews Microbiology
2013 | Journal article
DOI:

papers2://publication/doi/10.1038/nrmicro3164
Contributors: Mather, Alison E.; Harris, Simon R.
Source: Self-asserted source
Simon Harris via ResearcherID

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health MicrobiologyFast Whole-Genome Sequencing to Identify OutbreaksFast Whole-Genome Sequencing to Identify Outbreaks

JAMA Internal Medicine
2013 | Journal article
DOI:

papers2://publication/doi/10.1001/jamainternmed.2013.7734
Contributors: Reuter, Sandra; Ellington, Matthew J.; Cartwright, Edward J. P.; Köser, Claudio U.; Török, M. Estée; Gouliouris, Theodore; Harris, Simon R.; Brown, Nicholas M.; Holden, Matthew T. G.; Quail, Mike et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks

Nature biotechnology
2013 | Journal article
DOI:

10.1038/nbt.2616
Contributors: Harris, Simon R.; Török, M. E.; Cartwright, Edward J. P.; Quail, Michael A.; Peacock, Sharon J.; Parkhill, Julian
Source: Self-asserted source
Simon Harris via ResearcherID

The evolutionary path to extra intestinal pathogenic, drug resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome

Genome biology and evolution
2013 | Journal article
DOI:

10.1093/gbe/evt038
Contributors: McNally, Alan; Cheng, Lu; Harris, Simon R.; Corander, Jukka
Source: Self-asserted source
Simon Harris via ResearcherID

Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC

EMBO molecular medicine
2013 | Journal article
DOI:

10.1002/emmm.201202413
Contributors: Harrison, Ewan M.; Paterson, Gavin K.; Holden, Matthew T. G.; Larsen, Jesper; Stegger, Marc; Larsen, Anders Rhod; Petersen, Andreas; Skov, Robert L.; Christensen, Judit Marta; Bak Zeuthen, Anne et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

Genome Research
2013 | Journal article
DOI:

10.1101/gr.150037.112
Contributors: Seth-Smith, Helena M. B.; Harris, Simon R.; Skilton, Rachel J.; Radebe, Frans M.; Golparian, Daniel; Shipitsyna, Elena; Duy, Pham Thanh; Scott, Paul; Cutcliffe, Lesley T.; O'Neill, Colette et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

The Lancet Infectious Diseases
2013 | Journal article
DOI:

10.1016/S1473-3099(12)70268-2
Contributors: Harris, Simon R.; Cartwright, Edward J. P.; Török, M. Estée; Holden, Matthew T. G.; Brown, Nicholas M.; Ogilvy-Stuart, Amanda L.; Ellington, Matthew J.; Quail, Michael A.; Bentley, Stephen D.; Parkhill, Julian et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Whole-genome sequencing to establish relapse or re-infection with< i> Mycobacterium tuberculosis</i>: a retrospective observational study

The Lancet Respiratory Medicine
2013 | Journal article
Source: Self-asserted source
Simon Harris

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

Lancet
2013 | Journal article
DOI:

10.1016/S0140-6736(13)60632-7
Contributors: Bryant, Josephine M.; Grogono, Dorothy M.; Greaves, Daniel; Foweraker, Juliet; Roddick, Iain; Inns, Thomas; Reacher, Mark; Haworth, Charles S.; Curran, Martin D.; Harris, Simon R. et al.
Source: Self-asserted source
Simon Harris via ResearcherID

A high-resolution view of genome-wide pneumococcal transformation

PLoS pathogens
2012 | Journal article
DOI:

10.1371/journal.ppat.1002745
Contributors: Croucher, Nicholas J.; Harris, Simon R.; Barquist, Lars; Parkhill, Julian; Bentley, Stephen D.
Source: Self-asserted source
Simon Harris via ResearcherID

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

BMC genomics
2012 | Journal article
DOI:

10.1186/1471-2164-13-341
Contributors: Quail, Michael; Smith, Miriam E.; Coupland, Paul; Otto, Thomas D.; Harris, Simon R.; Connor, Thomas R.; Bertoni, Anna; Swerdlow, Harold P.; Gu, Yong
Source: Self-asserted source
Simon Harris via ResearcherID

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

Bioinformatics
2012 | Journal article
DOI:

10.1093/bioinformatics/btr703
Contributors: Carver, Tim; Harris, Simon R.; Berriman, Matthew; Parkhill, Julian; McQuillan, Jacqueline A.
Source: Self-asserted source
Simon Harris via ResearcherID

BamView: visualizing and interpretation of next-generation sequencing read alignments

Briefings in bioinformatics
2012 | Journal article
DOI:

10.1093/bib/bbr073
Contributors: Carver, Tim; Harris, Simon R.; Otto, Thomas D.; Berriman, Matthew; Parkhill, Julian; McQuillan, Jacqueline A.
Source: Self-asserted source
Simon Harris via ResearcherID

Detection of recombination events in bacterial genomes from large population samples

Nucleic acids research
2012 | Journal article
DOI:

10.1093/nar/gkr928
Contributors: Marttinen, Pekka; Hanage, William P.; Croucher, Nicholas J.; Connor, Thomas R.; Harris, Simon R.; Bentley, Stephen D.; Corander, Jukka
Source: Self-asserted source
Simon Harris via ResearcherID

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

Nature genetics
2012 | Journal article
DOI:

10.1038/ng.2478
Contributors: He, Miao; Miyajima, Fabio; Roberts, Paul; Ellison, Louise; Pickard, Derek J.; Martin, Melissa J.; Connor, Thomas R.; Harris, Simon R.; Fairley, Derek; Bamford, Kathleen B. et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach

PLoS ONE
2012 | Journal article
DOI:

10.1371/journal.pone.0044250
Contributors: Everett, Dean B.; Cornick, Jennifer; Denis, Brigitte; Chewapreecha, Claire; Croucher, Nicholas; Harris, Simon R.; Parkhill, Julian; Gordon, Stephen; Carrol, Enitan D.; French, Neil et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Genome sequencing and analysis of the tasmanian devil and its transmissible cancer

Cell
2012 | Journal article
DOI:

10.1016/j.cell.2011.11.065
Contributors: Murchison, Elizabeth P.; Schulz-Trieglaff, Ole B.; Ning, Zemin; Alexandrov, Ludmil B.; Bauer, Markus J.; Fu, Beiyuan; Hims, Matthew; Ding, Zhihao; Ivakhno, Sergii; Stewart, Caitlin et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

Nature genetics
2012 | Journal article
DOI:

10.1038/ng.2423
Contributors: Okoro, Chinyere K.; Kingsley, Robert A.; Connor, Thomas R.; Harris, Simon R.; Parry, Christopher M.; Al-Mashhadani, Manar N.; Kariuki, Samuel; Msefula, Chisomo L.; Gordon, Melita A.; de Pinna, Elizabeth et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Microevolution of extensively drug-resistant tuberculosis in Russia

Genome Research
2012 | Journal article
DOI:

10.1101/gr.128678.111
Contributors: Casali, Nicola; Nikolayevskyy, Vladyslav; Balabanova, Yanina; Ignatyeva, Olga; Kontsevaya, Irina; Harris, Simon R.; Bentley, Stephen D.; Parkhill, Julian; Nejentsev, Sergey; Hoffner, Sven E. et al.
Source: Self-asserted source
Simon Harris via ResearcherID

Optimal enzymes for amplifying sequencing libraries

Nature methods
2012 | Journal article
DOI:

10.1038/nmeth.1814
Contributors: Quail, Michael A.; Otto, Thomas D.; Gu, Yong; Harris, Simon R.; Skelly, Thomas F.; McQuillan, Jacqueline A.; Swerdlow, Harold P.; Oyola, Samuel O.
Source: Self-asserted source
Simon Harris via ResearcherID

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak

The New England journal of medicine
2012 | Journal article
DOI:

papers2://publication/doi/10.1056/NEJMoa1109910
Contributors: Köser, Claudio U.; Holden, Matthew T. G.; Ellington, Matthew J.; Cartwright, Edward J. P.; Brown, Nicholas M.; Ogilvy-Stuart, Amanda L.; Hsu, Li Yang; Chewapreecha, Claire; Croucher, Nicholas J.; Harris, Simon R. et al.
Source: Self-asserted source
Simon Harris via ResearcherID
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