Stephen D Bentley

Stephen D Bentley

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Stephen D Bentley

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The impact of antimicrobials on gonococcal evolution.

Nat Microbiol 2019 Nov 29;4(11):1941-1950. Epub 2019 Jul 29.

Pathogen Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1038/s41564-019-0501-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6817357PMC
November 2019

Genome-wide epistasis and co-selection study using mutual information.

Nucleic Acids Res 2019 10;47(18):e112

Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland.

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http://dx.doi.org/10.1093/nar/gkz656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765119PMC
October 2019

Synergistic Activity of Mobile Genetic Element Defences in .

Genes (Basel) 2019 09 13;10(9). Epub 2019 Sep 13.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London W2 1PG, UK.

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http://dx.doi.org/10.3390/genes10090707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771155PMC
September 2019

Fast hierarchical Bayesian analysis of population structure.

Nucleic Acids Res 2019 06;47(11):5539-5549

Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gkz361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582336PMC
June 2019

PANINI: Pangenome Neighbour Identification for Bacterial Populations.

Microb Genom 2019 04 22;5(4). Epub 2018 Nov 22.

1​Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1099/mgen.0.000220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521588PMC
April 2019

Fast and flexible bacterial genomic epidemiology with PopPUNK.

Genome Res 2019 02 24;29(2):304-316. Epub 2019 Jan 24.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, United Kingdom.

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http://dx.doi.org/10.1101/gr.241455.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360808PMC
February 2019

Bayesian inference of ancestral dates on bacterial phylogenetic trees.

Nucleic Acids Res 2018 12;46(22):e134

Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1093/nar/gky783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294524PMC
December 2018

pyseer: a comprehensive tool for microbial pangenome-wide association studies.

Bioinformatics 2018 12;34(24):4310-4312

Department of Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289128PMC
December 2018

Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition.

Nucleic Acids Res 2018 11;46(21):11438-11453

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London W2 1PG, UK.

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http://dx.doi.org/10.1093/nar/gky906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265443PMC
November 2018

A genomic infection control study for in two Ghanaian hospitals.

Infect Drug Resist 2018 11;11:1757-1765. Epub 2018 Oct 11.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK,

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https://www.dovepress.com/a-genomic-infection-control-study-
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http://dx.doi.org/10.2147/IDR.S167639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6188180PMC
October 2018

Pneumococcal Vaccines: Host Interactions, Population Dynamics, and Design Principles.

Annu Rev Microbiol 2018 09;72:521-549

Infection Genomics Programme, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom; email:

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http://dx.doi.org/10.1146/annurev-micro-090817-062338DOI Listing
September 2018

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

Wellcome Open Res 2018 30;3:93. Epub 2018 Jul 30.

Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.

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https://wellcomeopenresearch.org/articles/3-93/v1
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http://dx.doi.org/10.12688/wellcomeopenres.14694.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6178908PMC
July 2018

SuperDCA for genome-wide epistasis analysis.

Microb Genom 2018 06 29;4(6). Epub 2018 May 29.

5​Department of Biostatistics, University of Oslo, 0317 Oslo, Norway.

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http://dx.doi.org/10.1099/mgen.0.000184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096938PMC
June 2018

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

PLoS Pathog 2018 04 4;14(4):e1006966. Epub 2018 Apr 4.

Center for Communicable Disease Dynamics, Department of Epidemiology, T.H. Chan School of Public Health, Harvard University; Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902063PMC
April 2018

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

Wellcome Open Res 2018 23;3:33. Epub 2018 Mar 23.

Infection Genomics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.

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http://dx.doi.org/10.12688/wellcomeopenres.14265.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930550PMC
March 2018

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Nat Ecol Evol 2017 Dec 16;1(12):1950-1960. Epub 2017 Oct 16.

MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, Imperial College London, London, W2 1PG, UK.

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http://dx.doi.org/10.1038/s41559-017-0337-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708525PMC
December 2017

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children.

PLoS Negl Trop Dis 2017 Oct 2;11(10):e0005975. Epub 2017 Oct 2.

Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.

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http://dx.doi.org/10.1371/journal.pntd.0005975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5638608PMC
October 2017

Stronger together.

Nat Rev Microbiol 2017 09 7;15(9):516. Epub 2017 Aug 7.

Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nrmicro.2017.95DOI Listing
September 2017

Adaptation... that's what you need?

Nat Rev Microbiol 2017 08 10;15(8):452. Epub 2017 Jul 10.

Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nrmicro.2017.78DOI Listing
August 2017

Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi.

Vaccine 2017 08 12;35(35 Pt B):4594-4602. Epub 2017 Jul 12.

Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0264410X173090
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http://dx.doi.org/10.1016/j.vaccine.2017.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5571440PMC
August 2017

Phase-variable methylation and epigenetic regulation by type I restriction-modification systems.

FEMS Microbiol Rev 2017 08;41(Supp_1):S3-S15

Department of Genetics, University of Leicester, Leicester LE1 7RH, UK.

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http://dx.doi.org/10.1093/femsre/fux025DOI Listing
August 2017

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore.

J Antimicrob Chemother 2017 04;72(4):1031-1039

School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.

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http://dx.doi.org/10.1093/jac/dkw542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400096PMC
April 2017

The rise and fall of pneumococcal serotypes carried in the PCV era.

Vaccine 2017 03 1;35(9):1293-1298. Epub 2017 Feb 1.

Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton SO16 6YD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.vaccine.2017.01.035DOI Listing
March 2017

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data.

Sci Rep 2017 02 16;7:42808. Epub 2017 Feb 16.

Laboratory of Pediatric Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6525 GA, The Netherlands.

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http://dx.doi.org/10.1038/srep42808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311915PMC
February 2017

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening.

Proc Natl Acad Sci U S A 2017 01 4;114(3):E357-E366. Epub 2017 Jan 4.

Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA 02115.

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http://dx.doi.org/10.1073/pnas.1613937114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5255586PMC
January 2017

Meningococcal Two-Partner Secretion Systems and Their Association with Outcome in Patients with Meningitis.

Infect Immun 2016 09 19;84(9):2534-40. Epub 2016 Aug 19.

Department of Medical Microbiology, Academic Medical Center (AMC), Amsterdam, the Netherlands The Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center (AMC), Amsterdam, the Netherlands

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http://dx.doi.org/10.1128/IAI.00160-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995907PMC
September 2016

Bacterial GWAS: not just gilding the lily.

Nat Rev Microbiol 2016 07 31;14(7):406. Epub 2016 May 31.

Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/nrmicro.2016.82DOI Listing
July 2016

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.

Sci Data 2015 27;2:150058. Epub 2015 Oct 27.

Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health , 677 Huntington Avenue, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/sdata.2015.58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4622223PMC
June 2016

Phylogenetic Analysis of Invasive Serotype 1 Pneumococcus in South Africa, 1989 to 2013.

J Clin Microbiol 2016 05 9;54(5):1326-34. Epub 2016 Mar 9.

Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

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http://dx.doi.org/10.1128/JCM.00055-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844715PMC
May 2016

Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage-Specific Divergence and Niche Adaptation.

Genome Biol Evol 2016 Apr 21;8(4):1243-51. Epub 2016 Apr 21.

Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom Institute for Life Sciences, University of Southampton, Southampton, United Kingdom Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, United Kingdom NIHR Southampton Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom.

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https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/
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http://dx.doi.org/10.1093/gbe/evw066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860696PMC
April 2016

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict.

PLoS Biol 2016 Mar 2;14(3):e1002394. Epub 2016 Mar 2.

Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom.

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http://dx.doi.org/10.1371/journal.pbio.1002394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4774983PMC
March 2016

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.

Genome Res 2016 Feb 15;26(2):263-70. Epub 2015 Dec 15.

Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom; Pathogen Genomics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom; Public Health England, Microbiology Services Division, Addenbrooke's Hospital, Cambridge CB2 0QW, United Kingdom; Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, United Kingdom; London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.

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http://dx.doi.org/10.1101/gr.196709.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728378PMC
February 2016

Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus.

Genome Med 2016 Feb 13;8(1):18. Epub 2016 Feb 13.

Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1186/s13073-016-0274-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752745PMC
February 2016

Genomic perspectives on the evolution and spread of bacterial pathogens.

Proc Biol Sci 2015 Dec;282(1821):20150488

The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

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http://dx.doi.org/10.1098/rspb.2015.0488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4707741PMC
December 2015

The post-vaccine microevolution of invasive Streptococcus pneumoniae.

Sci Rep 2015 Oct 23;5:14952. Epub 2015 Oct 23.

Radboud university medical center, Laboratory of Pediatric Infectious Diseases, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/srep14952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615977PMC
October 2015

Climate induces seasonality in pneumococcal transmission.

Sci Rep 2015 Jun 12;5:11344. Epub 2015 Jun 12.

Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1038/srep11344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4464306PMC
June 2015

Five winters of pneumococcal serotype replacement in UK carriage following PCV introduction.

Vaccine 2015 Apr 14;33(17):2015-21. Epub 2015 Mar 14.

Faculty of Medicine and Institute for Life Sciences, University of Southampton, UK; Southampton NIHR Respiratory Biomedical Research Unit, University Hospital Southampton Foundation NHS Trust, Southampton, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0264410X150030
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http://dx.doi.org/10.1016/j.vaccine.2015.03.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4392391PMC
April 2015

Selective and genetic constraints on pneumococcal serotype switching.

PLoS Genet 2015 Mar 31;11(3):e1005095. Epub 2015 Mar 31.

Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380333PMC
March 2015

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

Nucleic Acids Res 2015 Feb 20;43(3):e15. Epub 2014 Nov 20.

Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

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http://dx.doi.org/10.1093/nar/gku1196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330336PMC
February 2015

Two-phase importance sampling for inference about transmission trees.

Proc Biol Sci 2014 11;281(1794):20141324

Department of Mathematics and Statistics, University of Helsinki, PO Box 68, 00014 Helsinki, Finland.

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http://dx.doi.org/10.1098/rspb.2014.1324DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211445PMC
November 2014

Diversification of bacterial genome content through distinct mechanisms over different timescales.

Nat Commun 2014 Nov 19;5:5471. Epub 2014 Nov 19.

Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1038/ncomms6471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263131PMC
November 2014