Publications by authors named "Derrick W Crook"

100Publications

Risk Factors Associated with Carbapenemase-Producing (CPE) Positivity in the Hospital Wastewater Environment.

Appl Environ Microbiol 2020 Nov 24;86(24). Epub 2020 Nov 24.

Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA

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http://dx.doi.org/10.1128/AEM.01715-20DOI Listing
November 2020

Differential occupational risks to healthcare workers from SARS-CoV-2 observed during a prospective observational study.

Authors:
David W Eyre Sheila F Lumley Denise O'Donnell Mark Campbell Elizabeth Sims Elaine Lawson Fiona Warren Tim James Stuart Cox Alison Howarth George Doherty Stephanie B Hatch James Kavanagh Kevin K Chau Philip W Fowler Jeremy Swann Denis Volk Fan Yang-Turner Nicole Stoesser Philippa C Matthews Maria Dudareva Timothy Davies Robert H Shaw Leon Peto Louise O Downs Alexander Vogt Ali Amini Bernadette C Young Philip George Drennan Alexander J Mentzer Donal T Skelly Fredrik Karpe Matt J Neville Monique Andersson Andrew J Brent Nicola Jones Lucas Martins Ferreira Thomas Christott Brian D Marsden Sarah Hoosdally Richard Cornall Derrick W Crook David I Stuart Gavin Screaton Adam Jr Watson Adan Taylor Alan Chetwynd Alexander Grassam-Rowe Alexandra S Mighiu Angus Livingstone Annabel Killen Caitlin Rigler Callum Harries Cameron East Charlotte Lee Chris Jb Mason Christian Holland Connor Thompson Conor Hennesey Constantinos Savva David S Kim Edward Wa Harris Euan J McGivern Evelyn Qian Evie Rothwell Francesca Back Gabriella Kelly Gareth Watson Gregory Howgego Hannah Chase Hannah Danbury Hannah Laurenson-Schafer Harry L Ward Holly Hendron Imogen C Vorley Isabel Tol James Gunnell Jocelyn Lf Ward Jonathan Drake Joseph D Wilson Joshua Morton Julie Dequaire Katherine O'Byrne Kenzo Motohashi Kirsty Harper Krupa Ravi Lancelot J Millar Liam J Peck Madeleine Oliver Marcus Rex English Mary Kumarendran Matthew Wedlich Olivia Ambler Oscar T Deal Owen Sweeney Philip Cowie Rebecca Te Water Naudé Rebecca Young Rosie Freer Samuel Scott Samuel Sussmes Sarah Peters Saxon Pattenden Seren Waite Síle Ann Johnson Stefan Kourdov Stephanie Santos-Paulo Stoyan Dimitrov Sven Kerneis Tariq Ahmed-Firani Thomas B King Thomas G Ritter Thomas H Foord Zoe De Toledo Thomas Christie Bernadett Gergely David Axten Emma-Jane Simons Heather Nevard Jane Philips Justyna Szczurkowska Kaisha Patel Kyla Smit Laura Warren Lisa Morgan Lucianne Smith Maria Robles Mary McKnight Michael Luciw Michelle Gates Nellia Sande Rachel Turford Roshni Ray Sonam Rughani Tracey Mitchell Trisha Bellinger Vicki Wharton Anita Justice Gerald Jesuthasan Susan Wareing Nurul Huda Mohamad Fadzillah Kathryn Cann Richard Kirton Claire Sutton Claudia Salvagno Gabriella DAmato Gemma Pill Lisa Butcher Lydia Rylance-Knight Merline Tabirao Ruth Moroney Sarah Wright Timothy Ea Peto Bruno Holthof Anne-Marie O'Donnell Daniel Ebner Christopher P Conlon Katie Jeffery Timothy M Walker

Elife 2020 08 21;9. Epub 2020 Aug 21.

Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom.

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http://dx.doi.org/10.7554/eLife.60675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486122PMC
August 2020

Evaluation of methods for detecting human reads in microbial sequencing datasets.

Microb Genom 2020 07;6(7)

National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK.

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http://dx.doi.org/10.1099/mgen.0.000393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478626PMC
July 2020

Multi-Label Random Forest Model for Tuberculosis Drug Resistance Classification and Mutation Ranking.

Front Microbiol 2020 22;11:667. Epub 2020 Apr 22.

Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.3389/fmicb.2020.00667DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7188832PMC
April 2020

Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae.

PLoS One 2019 8;14(11):e0222831. Epub 2019 Nov 8.

National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, John Radcliffe Hospital, Oxford, England, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222831PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839868PMC
March 2020

Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile.

J Clin Microbiol 2019 12 23;58(1). Epub 2019 Dec 23.

Healthcare Associated Infections Research Group, University of Leeds, Leeds, United Kingdom.

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http://dx.doi.org/10.1128/JCM.01037-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6935933PMC
December 2019

Corrigendum: Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of .

Microbiology (Reading) 2019 05;165(5):585

NIHR Health Protection Research Unit in Healthcare Associated Infection, Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.

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http://dx.doi.org/10.1099/mic.0.000795DOI Listing
May 2019

Using hospital network-based surveillance for antimicrobial resistance as a more robust alternative to self-reporting.

PLoS One 2019 25;14(7):e0219994. Epub 2019 Jul 25.

The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0219994PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6657867PMC
March 2020

DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis.

Bioinformatics 2019 09;35(18):3240-3249

Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748723PMC
September 2019

TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data.

Microb Genom 2018 12 22;4(12). Epub 2018 Nov 22.

4​Division of Infectious Disease and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.

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http://dx.doi.org/10.1099/mgen.0.000232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6412039PMC
December 2018

A Candida auris Outbreak and Its Control in an Intensive Care Setting.

N Engl J Med 2018 10;379(14):1322-1331

From Oxford University Hospitals NHS Foundation Trust (D.W.E., H.M., I.M., R.M., L.B., M.M., R.N., M.S., T.C., T.E.A.P., D.W.C., K.J.M.J.) and Nuffield Department of Medicine (D.W.E., A.E.S., T.P.Q., D.G., S.G., D.F., A.S.W., T.E.A.P., D.W.C.), Big Data Institute (D.W.E.), and the National Institute for Health Research Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance (D.W.E., A.E.S., T.P.Q., A.S.W., T.E.A.P., D.W.C.), University of Oxford, Oxford, Public Health England, National Infection Service, Colindale, London (P.H., C.S.B., D.W.C.), the National Mycology Reference Laboratory, Public Health England, Bristol (A.M.B., E.M.J.), and Public Health England, Porton Down, Salisbury (G.M.) - all in the United Kingdom.

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http://dx.doi.org/10.1056/NEJMoa1714373DOI Listing
October 2018

Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing.

N Engl J Med 2018 10 26;379(15):1403-1415. Epub 2018 Sep 26.

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http://dx.doi.org/10.1056/NEJMoa1800474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121966PMC
October 2018

Trends over time in Escherichia coli bloodstream infections, urinary tract infections, and antibiotic susceptibilities in Oxfordshire, UK, 1998-2016: a study of electronic health records.

Lancet Infect Dis 2018 10 17;18(10):1138-1149. Epub 2018 Aug 17.

Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance, Oxford, UK.

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http://dx.doi.org/10.1016/S1473-3099(18)30353-0DOI Listing
October 2018

Robust Prediction of Resistance to Trimethoprim in Staphylococcus aureus.

Cell Chem Biol 2018 03 4;25(3):339-349.e4. Epub 2018 Jan 4.

Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK.

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http://dx.doi.org/10.1016/j.chembiol.2017.12.009DOI Listing
March 2018

Aiming for zero tuberculosis transmission in low-burden countries.

Lancet Respir Med 2017 11 13;5(11):846-848. Epub 2017 Oct 13.

National Institutes of Health Research Oxford Biomedical Research Centre, University of Oxford and the Department of Microbiology and Infectious Disease, Oxford University Hospitals National Health Service (NHS) Trust, Oxford, UK; National Infection Service, Public Health England, London, UK.

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http://dx.doi.org/10.1016/S2213-2600(17)30382-XDOI Listing
November 2017

Staphylococcus aureus in critical care - Authors' reply.

Lancet Infect Dis 2017 06;17(6):580-581

Department of Microbiology and Infection, Royal Sussex County Hospital, Brighton, UK; Public Health England, Royal Sussex County Hospital, Brighton, UK.

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http://dx.doi.org/10.1016/S1473-3099(17)30269-4DOI Listing
June 2017

Mortality risks associated with emergency admissions during weekends and public holidays: an analysis of electronic health records.

Lancet 2017 07 9;390(10089):62-72. Epub 2017 May 9.

Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK; Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.

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http://dx.doi.org/10.1016/S0140-6736(17)30782-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5494289PMC
July 2017

Clostridium difficile in England: can we stop washing our hands? - Authors' reply.

Lancet Infect Dis 2017 05;17(5):478-479

Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; NIHR Health Protection Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford (in partnership with Public Health England), Oxford, UK.

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http://dx.doi.org/10.1016/S1473-3099(17)30185-8DOI Listing
May 2017

The relative importance of large problems far away versus small problems closer to home: insights into limiting the spread of antimicrobial resistance in England.

BMC Med 2017 04 27;15(1):86. Epub 2017 Apr 27.

The National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1186/s12916-017-0844-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5406888PMC
April 2017

Enhanced Klebsiella pneumoniae Carbapenemase Expression from a Novel Tn Deletion.

Antimicrob Agents Chemother 2017 06 24;61(6). Epub 2017 May 24.

Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA

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http://dx.doi.org/10.1128/AAC.00025-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444142PMC
June 2017

Tuberculosis is changing.

Lancet Infect Dis 2017 04 13;17(4):359-361. Epub 2017 Mar 13.

Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK; National Infection Service, Public Health England, London, UK.

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http://dx.doi.org/10.1016/S1473-3099(17)30123-8DOI Listing
April 2017

The Hospital Water Environment as a Reservoir for Carbapenem-Resistant Organisms Causing Hospital-Acquired Infections-A Systematic Review of the Literature.

Clin Infect Dis 2017 May;64(10):1435-1444

Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, and.

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http://dx.doi.org/10.1093/cid/cix132DOI Listing
May 2017

Effects of control interventions on Clostridium difficile infection in England: an observational study.

Lancet Infect Dis 2017 Apr 25;17(4):411-421. Epub 2017 Jan 25.

Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.

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http://dx.doi.org/10.1016/S1473-3099(16)30514-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5368411PMC
April 2017

Re-emergence of methicillin susceptibility in a resistant lineage of Staphylococcus aureus.

J Antimicrob Chemother 2017 05;72(5):1285-1288

Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London W2 1PG, UK.

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http://dx.doi.org/10.1093/jac/dkw570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890754PMC
May 2017

Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene, , in Klebsiella Species Is Elusive but Not Rare.

Antimicrob Agents Chemother 2017 03 23;61(3). Epub 2017 Feb 23.

Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1128/AAC.01823-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5328509PMC
March 2017

Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.

Antimicrob Agents Chemother 2016 11 21;60(11):6948-6951. Epub 2016 Oct 21.

Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.

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http://dx.doi.org/10.1128/AAC.01130-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075115PMC
November 2016

First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131.

Antimicrob Agents Chemother 2016 08 22;60(8):5068-71. Epub 2016 Jul 22.

Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada Snyder Institute for Chronic Diseases, University of Calgary, Calgary, Alberta, Canada Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.

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http://dx.doi.org/10.1128/AAC.00840-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4958194PMC
August 2016

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC.

Antimicrob Agents Chemother 2016 06 23;60(6):3767-78. Epub 2016 May 23.

Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA Clinical Microbiology, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA

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http://dx.doi.org/10.1128/AAC.00464-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879409PMC
June 2016

Capsular Typing Method for Streptococcus agalactiae Using Whole-Genome Sequence Data.

J Clin Microbiol 2016 05 9;54(5):1388-90. Epub 2016 Mar 9.

Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya

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http://dx.doi.org/10.1128/JCM.03142-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844738PMC
May 2016

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

Appl Environ Microbiol 2016 Apr 4;82(8):2516-26. Epub 2016 Apr 4.

Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.

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http://dx.doi.org/10.1128/AEM.03821-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959494PMC
April 2016

Complete Genome Sequence of KPC-Producing Klebsiella pneumoniae Strain CAV1193.

Genome Announc 2016 Jan 28;4(1). Epub 2016 Jan 28.

Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA Clinical Microbiology, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA

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http://dx.doi.org/10.1128/genomeA.01649-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732343PMC
January 2016

Within-host evolution of bacterial pathogens.

Nat Rev Microbiol 2016 Mar 19;14(3):150-62. Epub 2016 Jan 19.

Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053366PMC
http://dx.doi.org/10.1038/nrmicro.2015.13DOI Listing
March 2016

Colistin resistance gene mcr-1 and pHNSHP45 plasmid in human isolates of Escherichia coli and Klebsiella pneumoniae.

Lancet Infect Dis 2016 Mar 8;16(3):285-6. Epub 2016 Jan 8.

Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford OX3 9DU, UK.

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http://www.thelancet.com/pdfs/journals/laninf/PIIS1473-3099(
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http://dx.doi.org/10.1016/S1473-3099(16)00010-4DOI Listing
March 2016

Effects of proton pump inhibitors and histamine-2 receptor antagonists on response to fidaxomicin or vancomycin in patients with Clostridium difficile-associated diarrhoea.

BMJ Open Gastroenterol 2015 2;2(1):e000028. Epub 2015 Mar 2.

Department of Public Health and Family Medicine , Tufts University School of Medicine , Boston, Massachusetts , USA.

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http://dx.doi.org/10.1136/bmjgast-2014-000028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4599152PMC
October 2015

Absence of Atypical Pathogens in Pleural Infection.

Chest 2015 Sep;148(3):e102-e103

NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, England; Department of Microbiology and Infectious Diseases, John Radcliffe Hospital, Oxford, England.

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http://dx.doi.org/10.1378/chest.15-1130DOI Listing
September 2015

Rare variants in MYD88, IRAK4 and IKBKG and susceptibility to invasive pneumococcal disease: a population-based case-control study.

PLoS One 2015 17;10(4):e0123532. Epub 2015 Apr 17.

Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom; Oxford Centre for Respiratory Medicine, Churchill Hospital Site, Oxford University Hospitals, Oxford, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123532PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401548PMC
January 2016