Imperial College London

DrMichaelCox

Faculty of MedicineNational Heart & Lung Institute

Research Associate
 
 
 
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Contact

 

+44 (0)20 7594 7974michael.cox1 Website

 
 
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Location

 

413Guy Scadding BuildingRoyal Brompton Campus

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Summary

 

Publications

Publication Type
Year
to

57 results found

Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AWet al., 2014, Reagent and laboratory contamination can critically impact sequence-based microbiome analyses, BMC BIOLOGY, Vol: 12, ISSN: 1741-7007

JOURNAL ARTICLE

Sim K, Shaw AG, Randell P, Cox MJ, McClure ZE, Li M-S, Haddad M, Langford PR, Cookson WOCM, Moffatt MF, Kroll JSet al., 2014, Dysbiosis Anticipating Necrotizing Enterocolitis in Very Premature Infants, Clinical Infectious Diseases, Vol: 60, Pages: 389-397, ISSN: 1537-6591

JOURNAL ARTICLE

Molyneaux PL, Cox MJ, Willis-Owen SAG, Mallia P, Russell KE, Russel A-M, Murphy E, Johnston SL, Schwarte DA, Wells AU, Cookson WOC, Maher TM, Moffatt MFet al., 2014, The Role of Bacteria in the Pathogenesis and Progression of Idiopathic Pulmonary Fibrosis, AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, Vol: 190, Pages: 906-913, ISSN: 1073-449X

JOURNAL ARTICLE

Salter S, Cox M, Turek E, Calus S, Cookson W, Moffatt M, Turner P, Parkhill J, Loman N, Walker Aet al., 2014, Reagent contamination can critically impact sequence-based microbiome analyses

The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Concurrent sequencing of negative control samples is strongly advised.

JOURNAL ARTICLE

Molyneaux PL, Cox MJ, Mallia P, Johnston SL, Moffatt MF, Cookson WOC, Maher TMet al., 2013, THE ROLE OF THE RESPIRATORY MICROBIOME IN IDIOPATHIC PULMONARY FIBROSIS, Winter Meeting of the British-Thoracic-Society, Publisher: BMJ PUBLISHING GROUP, Pages: A22-A22, ISSN: 0040-6376

CONFERENCE PAPER

Molyneaux PL, Mallia P, Cox MJ, Footitt J, Willis-Owen SAG, Homola D, Trujillo-Torralbo M-B, Elkin S, Kon OM, Cookson WOC, Moffatt MF, Johnston SLet al., 2013, Outgrowth of the Bacterial Airway Microbiome after Rhinovirus Exacerbation of Chronic Obstructive Pulmonary Disease, AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, Vol: 188, Pages: 1224-1231, ISSN: 1073-449X

JOURNAL ARTICLE

Cox MJ, Cookson WOCM, Moffatt MF, 2013, Sequencing the human microbiome in health and disease, HUMAN MOLECULAR GENETICS, Vol: 22, Pages: R88-R94, ISSN: 0964-6906

JOURNAL ARTICLE

Duff RM, Simmonds NJ, Davies JC, Wilson R, Alton EW, Pantelidis P, Cox MJ, Cookson WOCM, Bilton D, Moffatt MFet al., 2013, A molecular comparison of microbial communities in bronchiectasis and cystic fibrosis, EUROPEAN RESPIRATORY JOURNAL, Vol: 41, Pages: 991-993, ISSN: 0903-1936

JOURNAL ARTICLE

Cardenas PA, Cooper PJ, Cox MJ, Chico M, Arias C, Moffatt MF, Cookson WOet al., 2012, Upper Airways Microbiota in Antibiotic-Naive Wheezing and Healthy Infants from the Tropics of Rural Ecuador, PLOS ONE, Vol: 7, ISSN: 1932-6203

JOURNAL ARTICLE

Cox MJ, Schaefer H, Nightingale PD, McDonald IR, Murrell JCet al., 2012, Diversity of methyl halide-degrading microorganisms in oceanic and coastal waters, FEMS MICROBIOLOGY LETTERS, Vol: 334, Pages: 111-118, ISSN: 0378-1097

JOURNAL ARTICLE

Sim K, Cox MJ, Wopereis H, Martin R, Knol J, Li M-S, Cookson WOCM, Moffatt MF, Kroll JSet al., 2012, Improved Detection of Bifidobacteria with Optimised 16S rRNA-Gene Based Pyrosequencing, PLOS ONE, Vol: 7, ISSN: 1932-6203

JOURNAL ARTICLE

Cox MJ, Jones AL, Loebinger MR, Duff RM, Simmonds NJ, Davies JC, Wilson R, Alton EW, Cookson WOCM, Bilton D, Moffatt MFet al., 2011, MUCOIDY AND THE MICROBIOME: COMMUNITY COMPOSITION IN RELATION TO THE PRESENCE OF CULTURABLE, MUCOID PSEUDOMONAS AERUGINOSA, Winter Meeting of the British-Thoracic-Society, Publisher: B M J PUBLISHING GROUP, Pages: A24-A24, ISSN: 0040-6376

CONFERENCE PAPER

Cox MJ, Duff RM, Simmonds NJ, Davies J, Wilson R, Alton E, Pantolidis P, Cookson WO, Bilton D, Moffatt MFet al., 2011, Comparison Of The Microbiomes Of Two Chronic Airway Diseases Using High-Throughput Sequencing, Publisher: AMER THORACIC SOC, ISSN: 1073-449X

CONFERENCE PAPER

Edwards JL, Smith DL, Connolly J, McDonald JE, Cox MJ, Joint I, Edwards C, McCarthy AJet al., 2010, Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes, GENES, Vol: 1, Pages: 371-384, ISSN: 2073-4425

JOURNAL ARTICLE

Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL, Zoratti EM, Woodcroft KJ, Bobbitt KR, Wegienka G, Boushey HA, Lynch SVet al., 2010, Man's best friend? The effect of pet ownership on house dust microbial communities, JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, Vol: 126, ISSN: 0091-6749

JOURNAL ARTICLE

Roediger FC, Slusher NA, Allgaier S, Cox MJ, Pletcher SD, Goldberg AN, Lynch SVet al., 2010, Nucleic acid extraction efficiency and bacterial recovery from maxillary sinus mucosal samples obtained by brushing or biopsy, AMERICAN JOURNAL OF RHINOLOGY & ALLERGY, Vol: 24, Pages: 263-265, ISSN: 1945-8924

JOURNAL ARTICLE

Cox MJ, Allgaier M, Taylor B, Baek MS, Huang YJ, Daly RA, Karaoz U, Andersen GL, Brown R, Fujimura KE, Wu B, Tran D, Koff J, Kleinhenz ME, Nielson D, Brodie EL, Lynch SVet al., 2010, Airway Microbiota and Pathogen Abundance in Age-Stratified Cystic Fibrosis Patients, PLOS ONE, Vol: 5, ISSN: 1932-6203

JOURNAL ARTICLE

Huang YJ, Kim E, Cox MJ, Brodie EL, Brown R, Wiener-Kronish JP, Lynch SVet al., 2010, A Persistent and Diverse Airway Microbiota Present during Chronic Obstructive Pulmonary Disease Exacerbations, OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, Vol: 14, Pages: 9-59, ISSN: 1536-2310

JOURNAL ARTICLE

Cox MJ, Huang YJ, Fujimura KE, Liu JT, McKean M, Boushey HA, Segal MR, Brodie EL, Cabana MD, Lynch SVet al., 2010, Lactobacillus casei Abundance Is Associated with Profound Shifts in the Infant Gut Microbiome, PLOS ONE, Vol: 5, ISSN: 1932-6203

JOURNAL ARTICLE

de Menezes AB, Lockhart RJ, Cox MJ, Allison HE, McCarthy AJet al., 2008, Cellulose Degradation by Micromonosporas Recovered from Freshwater Lakes and Classification of These Actinomycetes by DNA Gyrase B Gene Sequencing, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 74, Pages: 7080-7084, ISSN: 0099-2240

JOURNAL ARTICLE

McDonald JE, Lockhart RJ, Cox MJ, Allison HE, McCarthy AJet al., 2008, Detection of novel Fibrobacter populations in landfill sites and determination of their relative abundance via quantitative PCR, ENVIRONMENTAL MICROBIOLOGY, Vol: 10, Pages: 1310-1319, ISSN: 1462-2912

JOURNAL ARTICLE

Smith DL, Wareing BM, Fogg PCM, Riley LM, Spencer M, Cox MJ, Saunders JR, McCarthy AJ, Allison HEet al., 2007, Multilocus characterization scheme for Shiga toxin-encoding bacteriophages, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol: 73, Pages: 8032-8040, ISSN: 0099-2240

JOURNAL ARTICLE

Neufeld JD, Schafer H, Cox MJ, Boden R, McDonald IR, Murrell JCet al., 2007, Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism, ISME JOURNAL, Vol: 1, Pages: 480-491, ISSN: 1751-7362

JOURNAL ARTICLE

Cox M, 2006, Fate of marine bacteria, NEW SCIENTIST, Vol: 191, Pages: 22-22, ISSN: 0262-4079

JOURNAL ARTICLE

McDonald IR, Kampfer P, Topp E, Warner KL, Cox MJ, Hancock TLC, Miller LG, Larkin MJ, Ducrocq V, Coulter C, Harper DB, Murrell JC, Oremland RSet al., 2005, Aminobacter ciceronei sp nov and Aminobacter lissarensis sp nov., isolated from various terrestrial environments, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol: 55, Pages: 1827-1832, ISSN: 1466-5026

JOURNAL ARTICLE

Borodina E, Cox MJ, McDonald IR, Murrell JCet al., 2005, Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil, ENVIRONMENTAL MICROBIOLOGY, Vol: 7, Pages: 1318-1328, ISSN: 1462-2912

JOURNAL ARTICLE

Wilson WH, Tarran GA, Schroeder D, Cox M, Oke J, Malin Get al., 2002, Isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel, JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM, Vol: 82, Pages: 369-377, ISSN: 0025-3154

JOURNAL ARTICLE

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