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Employment (1)

European Bioinformatics Institute: Cambridge, Cambridgeshire, GB

2022-01 to present | Research group leader
Employment
Source: Self-asserted source
John Lees

Professional activities (1)

Society for General Microbiology: London, GB

2021-09-01 to 2024-08-31 | Microbial Genomics editor
Service
Source: Self-asserted source
John Lees

Works (50 of 69)

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Page 1 of 2

Seamless, rapid, and accurate analyses of outbreak genomic data using splitk-mer analysis

Genome Research
2024-10 | Journal article
DOI: 10.1101/gr.279449.124
Contributors: Romain Derelle; Johanna von Wachsmann; Tommi Mäklin; Joel Hellewell; Timothy Russell; Ajit Lalvani; Leonid Chindelevitch; Nicholas J. Croucher; Simon R. Harris; John A. Lees
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Crossref

Reference-free variant calling with local graph construction with ska lo (SKA)

2024-10-03 | Preprint
DOI: 10.1101/2024.10.02.616334
Contributors: Romain Derelle; Kieran Madon; Joel Hellewell; Víctor Rodríguez-Bouza; Nimalan Arinaminpathy; Ajit Lalvani; Nicholas J. Croucher; Simon R. Harris; John A. Lees; Leonid Chindelevitch
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Crossref

CELEBRIMBOR: core and accessory genes from metagenomes

Bioinformatics
2024-09-02 | Journal article
DOI: 10.1093/bioinformatics/btae542
Contributors: Joel Hellewell; Samuel T Horsfield; Johanna von Wachsmann; Tatiana A Gurbich; Robert D Finn; Zamin Iqbal; Leah W Roberts; John A Lees; Can Alkan
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Crossref

Optimising machine learning prediction of minimum inhibitory concentrations in Klebsiella pneumoniae

Microbial Genomics
2024-03-26 | Journal article
DOI: 10.1099/mgen.0.001222
Contributors: Gherard Batisti Biffignandi; Leonid Chindelevitch; Marta Corbella; Edward J. Feil; Davide Sassera; John A. Lees
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Crossref

Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

Nature Communications
2024-03-13 | Journal article
DOI: 10.1038/s41467-024-46530-2
Contributors: Ouli Xie; Jacqueline M. Morris; Andrew J. Hayes; Rebecca J. Towers; Magnus G. Jespersen; John A. Lees; Nouri L. Ben Zakour; Olga Berking; Sarah L. Baines; Glen P. Carter et al.
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Crossref

AllTheBacteria - all bacterial genomes assembled, available and searchable

2024-03-11 | Preprint
DOI: 10.1101/2024.03.08.584059
Contributors: Martin Hunt; Leandro Lima; Daniel Anderson; Jane Hawkey; Wei Shen; John Lees; Zamin Iqbal
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Crossref

Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

2024-02-12 | Preprint
DOI: 10.1101/2024.02.11.579857
Contributors: Samuel T. Horsfield; Basil Fok; Yuhan Fu; Paul Turner; John A. Lees; Nicholas J. Croucher
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Crossref

Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia

Nature Communications
2023-11-13 | Journal article
DOI: 10.1038/s41467-023-43002-x
Contributors: Lloyd A. C. Chapman; Maite Aubry; Noémie Maset; Timothy W. Russell; Edward S. Knock; John A. Lees; Henri-Pierre Mallet; Van-Mai Cao-Lormeau; Adam J. Kucharski
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Crossref

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

Bioinformatics
2023-11-01 | Journal article
DOI: 10.1093/bioinformatics/btad648
Contributors: Romain Derelle; John Lees; Jody Phelan; Ajit Lalvani; Nimalan Arinaminpathy; Leonid Chindelevitch; Can Alkan
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Crossref

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

Genome Research
2023-09 | Journal article
DOI: 10.1101/gr.277733.123
Contributors: Samuel T. Horsfield; Gerry Tonkin-Hill; Nicholas J. Croucher; John A. Lees
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Crossref

Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia

2023-04-05 | Preprint
DOI: 10.21203/rs.3.rs-2753714/v1
Contributors: Lloyd Chapman; Maite Aubry; Noemie Maset; Timothy Russell; Edward Knock; John Lees; Henri-Pierre Mallet; Van-Mai Cao-Lormeau; Adam Kucharski
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Crossref

Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia

2023-03-29 | Preprint
DOI: 10.1101/2023.03.29.23287906
Contributors: Lloyd AC Chapman; Maite Aubry; Noémie Maset; Timothy W Russell; Edward S Knock; John A Lees; Henri-Pierre Mallet; Van-Mai Cao-Lormeau; Adam J Kucharski
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Crossref

Inferring the heritability of bacterial traits in the era of machine learning

Bioinformatics Advances
2023-01-05 | Journal article
DOI: 10.1093/bioadv/vbad027
Contributors: T Tien Mai; John A Lees; Rebecca A Gladstone; Jukka Corander; Nicola Mulder
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Crossref

BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection

2022-08-06 | Preprint
DOI: 10.1101/2022.08.05.500807
Contributors: Surya D. Aggarwal; John A. Lees; Nathan T. Jacobs; Gavyn Chern Wei Bee; Annie R. Abruzzo; Jeffrey N. Weiser
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Crossref

Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae

Microbial Genomics
2022-04-26 | Journal article
DOI: 10.1099/mgen.0.000784
Contributors: Emily J. Stevens; Daniel J. Morse; Dora Bonini; Seána Duggan; Tarcisio Brignoli; Mario Recker; John A. Lees; Nicholas J. Croucher; Stephen Bentley; Daniel J. Wilson et al.
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Crossref

International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease.

Vaccine
2022-01 | Journal article
DOI: 10.1016/j.vaccine.2021.10.046
PMID: 34996643
Contributors: Gladstone RA; Siira L; Brynildsrud OB; Vestrheim DF; Turner P; Clarke SC; Srifuengfung S; Ford R; Lehmann D; Egorova E et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Pneumococcal capsule blocks protection by immunization with conserved surface proteins.

NPJ vaccines
2021-12 | Journal article
DOI: 10.1038/s41541-021-00413-5
PMID: 34930916
PMC: PMC8688510
Contributors: Zangari T; Zafar MA; Lees JA; Abruzzo AR; Bee GCW; Weiser JN
Source: Self-asserted source
John Lees via Europe PubMed Central

Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation

2021-10 | Preprint
DOI: 10.1101/2021.10.28.466232
PPR: PPR412909
Contributors: Lees JA; Tonkin-Hill G; Yang Z; Corander J
Source: Self-asserted source
John Lees via Europe PubMed Central

Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study.

Lancet (London, England)
2021-10 | Journal article
DOI: 10.1016/s0140-6736(21)02276-5
PMID: 34717829
PMC: PMC8550916
Contributors: Sonabend R; Whittles LK; Imai N; Perez-Guzman PN; Knock ES; Rawson T; Gaythorpe KAM; Djaafara BA; Hinsley W; FitzJohn RG et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

The role of interspecies recombination in the evolution of antibiotic-resistant pneumococci.

eLife
2021-07 | Journal article
DOI: 10.7554/elife.67113
PMID: 34259624
PMC: PMC8321556
Contributors: D'Aeth JC; van der Linden MP; McGee L; de Lencastre H; Turner P; Song JH; Lo SW; Gladstone RA; Sá-Leão R; Ko KS et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England

Science Translational Medicine
2021-07-14 | Journal article
DOI: 10.1126/scitranslmed.abg4262
Contributors: Edward S. Knock; Lilith K. Whittles; John A. Lees; Pablo N. Perez-Guzman; Robert Verity; Richard G. FitzJohn; Katy A. M. Gaythorpe; Natsuko Imai; Wes Hinsley; Lucy C. Okell et al.
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Crossref

Modelling intensive care unit capacity under different epidemiological scenarios of the COVID-19 pandemic in three Western European countries

International Journal of Epidemiology
2021-07-09 | Journal article
DOI: 10.1093/ije/dyab034
Contributors: Ruth McCabe; Mara D Kont; Nora Schmit; Charles Whittaker; Alessandra Løchen; Marc Baguelin; Edward Knock; Lilith K Whittles; John Lees; Nicholas F Brazeau et al.
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Crossref

Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate [version 2; peer review: 2 approved]

2021-06-10 | Journal article
DOI: 10.12688/wellcomeopenres.16466.2
Part of ISSN: 2398-502X
Contributors: Richard G. FitzJohn; Edward S. Knock; Lilith K. Whittles; Pablo N. Perez-Guzman; Sangeeta Bhatia; Fernando Guntoro; Oliver J. Watson; Charles Whittaker; Neil M. Ferguson; Anne Cori et al.
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Wellcome Open Research

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

The ISME Journal
2021-05-01 | Journal article
DOI: 10.1038/s41396-020-00867-w
Contributors: Gabrielle L Harrow; John A Lees; William P Hanage; Marc Lipsitch; Jukka Corander; Caroline Colijn; Nicholas J Croucher
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Crossref

Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus, Syria.

Nature communications
2021-04 | Journal article
DOI: 10.1038/s41467-021-22474-9
PMID: 33888698
PMC: PMC8062464
Contributors: Watson OJ; Alhaffar M; Mehchy Z; Whittaker C; Akil Z; Brazeau NF; Cuomo-Dannenburg G; Hamlet A; Thompson HA; Baguelin M et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Within-country age-based prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: A mathematical modelling analysis.

Vaccine
2021-04 | Journal article
DOI: 10.1016/j.vaccine.2021.04.002
PMID: 33933313
PMC: PMC8030738
Contributors: Hogan AB; Winskill P; Watson OJ; Walker PGT; Whittaker C; Baguelin M; Brazeau NF; Charles GD; Gaythorpe KAM; Hamlet A et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.

Nature communications
2021-03 | Journal article
DOI: 10.1038/s41467-021-21749-5
PMID: 33750782
PMC: PMC7943827
Contributors: Pöntinen AK; Top J; Arredondo-Alonso S; Tonkin-Hill G; Freitas AR; Novais C; Gladstone RA; Pesonen M; Meneses R; Pesonen H et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Pneumococcal genetic variability influences age-dependent bacterial carriage

2021-03 | Preprint
DOI: 10.1101/2021.03.03.433546
PPR: PPR292063
Contributors: Kremer P; Ferwerda B; Bootsma H; Rots N; Wijmega-Monsuur A; Sanders E; Trzciński K; Wyllie A; Turner P; van der Ende A et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Reduction in mobility and COVID-19 transmission.

Nature communications
2021-02 | Journal article
DOI: 10.1038/s41467-021-21358-2
PMID: 33597546
PMC: PMC7889876
Contributors: Nouvellet P; Bhatia S; Cori A; Ainslie KEC; Baguelin M; Bhatt S; Boonyasiri A; Brazeau NF; Cattarino L; Cooper LV et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

SARS-CoV-2 infection prevalence on repatriation flights from Wuhan City, China.

Journal of travel medicine
2020-12 | Journal article
DOI: 10.1093/jtm/taaa135
PMID: 32830853
PMC: PMC7499665
Contributors: Thompson HA; Imai N; Dighe A; Ainslie KEC; Baguelin M; Bhatia S; Bhatt S; Boonyasiri A; Boyd O; Brazeau NF et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

State-level tracking of COVID-19 in the United States.

Nature communications
2020-12 | Journal article
DOI: 10.1038/s41467-020-19652-6
PMID: 33273462
PMC: PMC7712910
Contributors: Unwin HJT; Mishra S; Bradley VC; Gandy A; Mellan TA; Coupland H; Ish-Horowicz J; Vollmer MAC; Whittaker C; Filippi SL et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Genetic Variation in <i>Neisseria meningitidis</i> Does Not Influence Disease Severity in Meningococcal Meningitis.

Frontiers in medicine
2020-11 | Journal article
DOI: 10.3389/fmed.2020.594769
PMID: 33262994
PMC: PMC7686797
Contributors: Kremer PHC; Lees JA; Ferwerda B; van de Ende A; Brouwer MC; Bentley SD; van de Beek D
Source: Self-asserted source
John Lees via Europe PubMed Central

Database of epidemic trends and control measures during the first wave of COVID-19 in mainland China.

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
2020-10 | Journal article
DOI: 10.1016/j.ijid.2020.10.075
PMID: 33130212
PMC: PMC7603985
Contributors: Fu H; Wang H; Xi X; Boonyasiri A; Wang Y; Hinsley W; Fraser KJ; McCabe R; Olivera Mesa D; Skarp J et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Diversification in immunogenicity genes caused by selective pressures in invasive meningococci

Microbial Genomics
2020-09-01 | Journal article
DOI: 10.1099/mgen.0.000422
Contributors: Philip H.C. Kremer; John A. Lees; Bart Ferwerda; Merijn W. Bijlsma; Neil MacAlasdair; Arie van der Ende; Matthijs C. Brouwer; Stephen D. Bentley; Diederik van de Beek
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Crossref

The potential public health consequences of COVID-19 on malaria in Africa.

Nature medicine
2020-08 | Journal article
DOI: 10.1038/s41591-020-1025-y
PMID: 32770167
Contributors: Sherrard-Smith E; Hogan AB; Hamlet A; Watson OJ; Whittaker C; Winskill P; Ali F; Mohammad AB; Uhomoibhi P; Maikore I et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

mBio
2020-08-25 | Journal article
DOI: 10.1128/mBio.01344-20
Contributors: John A. Lees; T. Tien Mai; Marco Galardini; Nicole E. Wheeler; Samuel T. Horsfield; Julian Parkhill; Jukka Corander; Jacques Ravel
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Crossref

Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study.

The Lancet. Global health
2020-07 | Journal article
DOI: 10.1016/s2214-109x(20)30288-6
PMID: 32673577
PMC: PMC7357988
Contributors: Hogan AB; Jewell BL; Sherrard-Smith E; Vesga JF; Watson OJ; Whittaker C; Hamlet A; Smith JA; Winskill P; Verity R et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Producing polished prokaryotic pangenomes with the Panaroo pipeline.

Genome biology
2020-07 | Journal article
DOI: 10.1186/s13059-020-02090-4
PMID: 32698896
PMC: PMC7376924
Contributors: Tonkin-Hill G; MacAlasdair N; Ruis C; Weimann A; Horesh G; Lees JA; Gladstone RA; Lo S; Beaudoin C; Floto RA et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

2020-06-06 | Other
DOI: 10.1101/2020.06.05.118836
Contributors: Gabrielle L. Harrow; John A. Lees; William P. Hanage; Marc Lipsitch; Jukka Corander; Caroline Colijn; Nicholas J. Croucher
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Crossref

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

Science Advances
2020-05-22 | Journal article
DOI: 10.1126/sciadv.aaz6137
Contributors: Sonja Lehtinen; Claire Chewapreecha; John Lees; William P. Hanage; Marc Lipsitch; Nicholas J. Croucher; Stephen D. Bentley; Paul Turner; Christophe Fraser; Rafał J. Mostowy
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Crossref

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates

Microbial Genomics
2020-05-01 | Journal article
DOI: 10.1099/mgen.0.000357
Contributors: Rebecca A. Gladstone; Stephanie W. Lo; Richard Goater; Corin Yeats; Ben Taylor; James Hadfield; John A. Lees; Nicholas J. Croucher; Andries J. van Tonder; Leon J. Bentley et al.
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Crossref

Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

2020-01-28 | Preprint
DOI: 10.1101/2020.01.28.922989
Contributors: Gerry Tonkin-Hill; Neil MacAlasdair; Christopher Ruis; Aaron Weimann; Gal Horesh; John A. Lees; Rebecca A Gladstone; Stephanie Lo; Christopher Beaudoin; R Andrés Floto et al.
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Crossref

Immune exclusion by naturally acquired secretory IgA against pneumococcal pilus-1

Journal of Clinical Investigation
2020-01-13 | Journal article
DOI: 10.1172/JCI132005
Contributors: Ulrike Binsker; John A. Lees; Alexandria J. Hammond; Jeffrey N. Weiser
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Crossref

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

Nucleic acids research
2019-10 | Journal article
DOI: 10.1093/nar/gkz656
PMID: 31361894
PMC: PMC6765119
Contributors: Pensar J; Puranen S; Arnold B; MacAlasdair N; Kuronen J; Tonkin-Hill G; Pesonen M; Xu Y; Sipola A; Sánchez-Busó L et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Contrasting approaches to genome-wide association studies impact the detection of resistance mechanisms in Staphylococcus aureus

2019-09 | Preprint
DOI: 10.1101/758144
PPR: PPR91227
Contributors: Wheeler NE; Reuter S; Chewapreecha C; Lees JA; Blane B; Horner C; Enoch D; Brown NM; Estée Török M; Aanensen DM et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study.

The Lancet. Infectious diseases
2019-06 | Journal article
DOI: 10.1016/s1473-3099(19)30297-x
PMID: 31196809
PMC: PMC7641901
Contributors: Lo SW; Gladstone RA; van Tonder AJ; Lees JA; du Plessis M; Benisty R; Givon-Lavi N; Hawkins PA; Cornick JE; Kwambana-Adams B et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Fast hierarchical Bayesian analysis of population structure

Nucleic Acids Research
2019-06-20 | Journal article
DOI: 10.1093/nar/gkz361
Contributors: Gerry Tonkin-Hill; John A Lees; Stephen D Bentley; Simon D W Frost; Jukka Corander
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Crossref

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics.

Nature genetics
2019-05 | Journal article
DOI: 10.1038/s41588-019-0417-8
PMID: 31133745
PMC: PMC6650292
Contributors: Davies MR; McIntyre L; Mutreja A; Lacey JA; Lees JA; Towers RJ; Duchêne S; Smeesters PR; Frost HR; Price DJ et al.
Source: Self-asserted source
John Lees via Europe PubMed Central

Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

Nature Communications
2019-05-15 | Journal article
DOI: 10.1038/s41467-019-09976-3
Contributors: John A. Lees; Bart Ferwerda; Philip H. C. Kremer; Nicole E. Wheeler; Mercedes Valls Serón; Nicholas J. Croucher; Rebecca A. Gladstone; Hester J. Bootsma; Nynke Y. Rots; Alienke J. Wijmega-Monsuur et al.
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Crossref

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.

EBioMedicine
2019-04 | Journal article
DOI: 10.1016/j.ebiom.2019.04.021
PMID: 31003929
PMC: PMC6557916
Contributors: Gladstone RA; Lo SW; Lees JA; Croucher NJ; van Tonder AJ; Corander J; Page AJ; Marttinen P; Bentley LJ; Ochoa TJ et al.
Source: Self-asserted source
John Lees via Europe PubMed Central
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