Parkhill, Julian

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature

Gut microbiota and healthGenomics and Phylogenetic Studies

Cited by 11,624

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., et al. (1998) · Nature

Tuberculosis Research and EpidemiologyGenomics and Phylogenetic Studies

Cited by 7,847

Roary: rapid large-scale prokaryote pan genome analysis

Page, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T. G., Fookes, M., Falush, D., Keane, J. A., & Parkhill, J. (2015) · Bioinformatics

Genomics and Phylogenetic StudiesBacterial Genetics and Biotechnology

Cited by 5,736

Richness of human gut microbiome correlates with metabolic markers

Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature

Gut microbiota and healthAdipokines, Inflammation, and Metabolic Diseases

Cited by 4,662

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology

Genomics and Phylogenetic StudiesGut microbiota and health

Cited by 3,463

Massive gene decay in the leprosy bacillus.

Cole, S. T., Eiglmeier, K., Parkhill, J., James, K. D., Thomson, N. R., Wheeler, P. R., Honoré, N., Garnier, T., Churcher, C., Harris, D., et al. (2001) · Nature

Leprosy Research and TreatmentGenomics and Phylogenetic Studies

Cited by 1,777

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., Bergerat, A., et al. (2011) · The ISME Journal

Gut microbiota and healthProbiotics and Fermented Foods

Cited by 1,632

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., et al. (2007) · PLoS Biology

Gut microbiota and healthSalmonella and Campylobacter epidemiology

Cited by 1,048

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

Parkhill, J., Sebaihia, M., Preston, A., Murphy, L. D., Thomson, N., Harris, D. E., Holden, M. T. G., Churcher, C. M., Bentley, S. D., Mungall, K. L., et al. (2003) · Nature Genetics

Bacterial Infections and VaccinesMicrobial infections and disease research

Cited by 1,037

Human placenta has no microbiome but can contain potential pathogens

de Goffau, M. C., Lager, S., Sovio, U., Gaccioli, F., Cook, E., Peacock, S. J., Parkhill, J., Charnock-Jones, D. S., & Smith, G. C. S. (2019) · Nature

Neonatal and Maternal InfectionsPreterm Birth and Chorioamnionitis

Cited by 691

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

Adler, C. J., Dobney, K., Weyrich, L. S., Kaidonis, J., Walker, A. W., Haak, W., Bradshaw, C. J. A., Townsend, G., Sołtysiak, A., Alt, K. W., et al. (2013) · Nature Genetics

Oral microbiology and periodontitis researchPaleopathology and ancient diseases

Cited by 621

Genome plasticity of BCG and impact on vaccine efficacy

Brosch, R., Gordon, S. V., Garnier, T., Eiglmeier, K., Frigui, W., Valenti, P., Dos Santos, S., Duthoy, S., Lacroix, C., Garcia-Pelayo, C., et al. (2007) · Proceedings of the National Academy of Sciences

Tuberculosis Research and EpidemiologyBacterial Genetics and Biotechnology

Cited by 574

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

Stinear, T. P., Seemann, T., Harrison, P. F., Jenkin, G. A., Davies, J. K., Johnson, P. D. R., Abdellah, Z., Arrowsmith, C., Chillingworth, T., Churcher, C., et al. (2008) · Genome Research

Tuberculosis Research and EpidemiologyMycobacterium research and diagnosis

Cited by 570

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

Sun, Z., Harris, H. M. B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I. B., Cooney, J. C., Kagawa, T. F., et al. (2015) · Nature Communications

Probiotics and Fermented FoodsGenomics and Phylogenetic Studies

Cited by 543

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

Lawley, T. D., Clare, S., Walker, A. W., Stares, M. D., Connor, T. R., Raisen, C., Goulding, D., Rad, R., Schreiber, F., Brandt, C., et al. (2012) · PLoS Pathogens

Clostridium difficile and Clostridium perfringens researchGut microbiota and health

Cited by 540

Modulation of the human gut microbiota by dietary fibres occurs at the species level

Chung, W. S. F., Walker, A. W., Louis, P., Parkhill, J., Vermeiren, J., Bosscher, D., Duncan, S. H., & Flint, H. J. (2016) · BMC Biology

Gut microbiota and healthMicrobial Metabolites in Food Biotechnology

Cited by 409

Genome Project Standards in a New Era of Sequencing

Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., et al. (2009) · Science

Genomics and Phylogenetic StudiesResearch Data Management Practices

Cited by 400

Antibiotic Treatment of Clostridium difficile Carrier Mice Triggers a Supershedder State, Spore-Mediated Transmission, and Severe Disease in Immunocompromised Hosts

Lawley, T. D., Clare, S., Walker, A. W., Goulding, D., Stabler, R. A., Croucher, N., Mastroeni, P., Scott, P., Raisen, C., Mottram, L., et al. (2009) · Infection and Immunity

Clostridium difficile and Clostridium perfringens researchGut microbiota and health

Cited by 349

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

Supply, P., Marceau, M., Mangenot, S., Roche, D., Rouanet, C., Khanna, V., Majlessi, L., Criscuolo, A., Tap, J., Pawlik, A., et al. (2013) · Nature Genetics

Tuberculosis Research and EpidemiologyMycobacterium research and diagnosis

Cited by 305

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

Walker, A. W., Martin, J. C., Scott, P., Parkhill, J., Flint, H. J., & Scott, K. P. (2015) · Microbiome

Gut microbiota and healthInfant Nutrition and Health

Cited by 273

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

Feasey, N. A., Hadfield, J., Keddy, K. H., Dallman, T. J., Jacobs, J., Deng, X., Wigley, P., Barquist, L., Langridge, G. C., Feltwell, T., et al. (2016) · Nature Genetics

Salmonella and Campylobacter epidemiologyEscherichia coli research studies

Cited by 217

Rapid Emergence of Multidrug Resistant, H58-Lineage Salmonella Typhi in Blantyre, Malawi

Feasey, N. A., Gaskell, K., Wong, V., Msefula, C., Selemani, G., Kumwenda, S., Allain, T. J., Mallewa, J., Kennedy, N., Bennett, A., et al. (2015) · PLOS Neglected Tropical Diseases

Salmonella and Campylobacter epidemiologyAntibiotic Resistance in Bacteria

Cited by 167

Staphylococcus aureus Adapts to Oxidative Stress by Producing H 2 O 2 -Resistant Small-Colony Variants via the SOS Response

Painter, K. L., Strange, E., Parkhill, J., Bamford, K. B., Armstrong-James, D., & Edwards, A. M. (2015) · Infection and Immunity

Antimicrobial Resistance in StaphylococcusBacterial Genetics and Biotechnology

Cited by 153

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

Barquist, L., Langridge, G. C., Turner, D. J., Phan, M.-D., Turner, A. K., Bateman, A., Parkhill, J., Wain, J., & Gardner, P. P. (2013) · Nucleic Acids Research

Bacterial Genetics and BiotechnologySalmonella and Campylobacter epidemiology

Cited by 121