2010 · Nature
A human gut microbial gene catalogue established by metagenomic sequencing
11,939 citationsRead
Most cited
1,164 papers in total1998 · Nature
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
7,937 citationsRead
2015 · Bioinformatics
Roary: rapid large-scale prokaryote pan genome analysis
6,242 citationsRead
2013 · Nature
Richness of human gut microbiome correlates with metabolic markers
4,860 citationsRead
2014 · BMC Biology
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
3,674 citationsRead
2002 · Nature
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
3,298 citationsRead
Newest first
1,164 papers in total2023
- Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studiesNature · 389 citations
2022
- Emergence of methicillin resistance predates the clinical use of antibioticsNature · 293 citations
2021
- Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary historyMicrobial Genomics · 212 citations
- Stepwise pathogenic evolution of Mycobacterium abscessusScience · 162 citations
2020
- Producing polished prokaryotic pangenomes with the Panaroo pipelineGenome biology · 1,449 citations
- A decade of advances in transposon-insertion sequencingNature Reviews Genetics · 443 citations
- Lung function and microbiota diversity in cystic fibrosisMicrobiome · 278 citations
- Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniaeProceedings of the National Academy of Sciences · 189 citations
- Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial EcosystemmSystems · 180 citations
- Definition of a genetic relatedness cutoff to exclude recent transmission of meticillin-resistant Staphylococcus aureus: a genomic epidemiology analysisThe Lancet Microbe · 165 citations
2019
- Human placenta has no microbiome but can contain potential pathogensNature · 725 citations
- Emergence of dominant toxigenic M1T1 Streptococcus pyogenes clone during increased scarlet fever activity in England: a population-based molecular epidemiological studyThe Lancet Infectious Diseases · 260 citations
- One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus LivestockmBio · 230 citations
- Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomicsNature Genetics · 216 citations
- Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian SubcontinentmBio · 153 citations
2018
- Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosisNature Genetics · 433 citations
- Recognizing the reagent microbiomeNature Microbiology · 411 citations
- Gene exchange drives the ecological success of a multi-host bacterial pathogenNature Ecology & Evolution · 256 citations
- The Capsule Regulatory Network of Klebsiella pneumoniae Defined by density-TraDISortmBio · 161 citations
2017
- ARIBA: rapid antimicrobial resistance genotyping directly from sequencing readsMicrobial Genomics · 650 citations
- Genomic history of the seventh pandemic of cholera in AfricaScience · 390 citations
- Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practiceGenome biology · 335 citations
- Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131Genome Research · 307 citations
- Global and regional dissemination and evolution of Burkholderia pseudomalleiNature Microbiology · 193 citations
- Integrated view of Vibrio cholerae in the AmericasScience · 181 citations
2016
- Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacteriumScience · 608 citations
- Modulation of the human gut microbiota by dietary fibres occurs at the species levelBMC Biology · 423 citations
- Microbial genome-wide association studies: lessons from human GWASNature Reviews Genetics · 341 citations
- Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina dataMicrobial Genomics · 275 citations
- The TraDIS toolkit: sequencing and analysis for dense transposon mutant librariesBioinformatics · 269 citations
Research in numbers
From OpenAlex- article181
- preprint14
- review4
- erratum1
- Nature Genetics18
- Nature17
- Proceedings of the National Academy of Sciences14
- Genome Research13
- Science11
- Stephen D. Bentley58
- Michael Andrew Quail54
- Nicholas Robert Thomson49
- Simon R. Harris43
- Matthew T. G. Holden42
Experience and education
Universities
2005 to 2014Queen's University Belfast
2009University of Copenhagen
2005University of British Columbia
1999Dalhousie University
Industry and labs
2016Centers for Disease Control and Prevention
2011Center for Infectious Disease Research
2009Centre for Human Genetics
2008European Bioinformatics Institute
2005Marine Biological Association of the United Kingdom
2004Defence Science and Technology Laboratory