Using genomics to combat infectious diseases on a global scale

por Cain, Amy K., Lees, John A.
Publicado en Genome Biol (2015)

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

por Binsker, Ulrike, Lees, John A., Hammond, Alexandria J., Weiser, Jeffrey N.
Publicado en J Clin Invest (2020)

Adults with suspected central nervous system infection: a prospective study of diagnostic accuracy

por Khatib, Ula, van de Beek, Diederik, Lees, John A., Brouwer, Matthijs C.
Publicado en J Infect (2017)

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

por Lees, John A, Galardini, Marco, Bentley, Stephen D, Weiser, Jeffrey N, Corander, Jukka
Publicado en Bioinformatics (2018)

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

por Lees, John A., Kendall, Michelle, Parkhill, Julian, Colijn, Caroline, Bentley, Stephen D., Harris, Simon R.
Publicado en Wellcome Open Res (2018)

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS

por Tonkin-Hill, Gerry, Lees, John A., Bentley, Stephen D., Frost, Simon D.W., Corander, Jukka
Publicado en Wellcome Open Res (2018)

Pneumococcal quorum sensing drives an asymmetric owner-intruder competitive strategy during carriage via the competence regulon

por Shen, Pamela, Lees, John A, Bee, Gavyn Chern Wei, Brown, Sam P, Weiser, Jeffrey N
Publicado en Nat Microbiol (2018)

Fast hierarchical Bayesian analysis of population structure

por Tonkin-Hill, Gerry, Lees, John A, Bentley, Stephen D, Frost, Simon D W, Corander, Jukka
Publicado en Nucleic Acids Res (2019)

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

por Lees, John A., Mai, T. Tien, Galardini, Marco, Wheeler, Nicole E., Horsfield, Samuel T., Parkhill, Julian, Corander, Jukka
Publicado en mBio (2020)

Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis

por Lees, John A., Brouwer, Matthijs, van der Ende, Arie, Parkhill, Julian, van de Beek, Diederik, Bentley, Stephen D.
Publicado en Infect Immun (2017)

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

por Harrow, Gabrielle L., Lees, John A., Hanage, William P., Lipsitch, Marc, Corander, Jukka, Colijn, Caroline, Croucher, Nicholas J.
Publicado en ISME J (2021)

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

por Lees, John A, Croucher, Nicholas J, Goldblatt, David, Nosten, François, Parkhill, Julian, Turner, Claudia, Turner, Paul, Bentley, Stephen D
Publicado en eLife (2017)

SuperDCA for genome-wide epistasis analysis

por Puranen, Santeri, Pesonen, Maiju, Pensar, Johan, Xu, Ying Ying, Lees, John A., Bentley, Stephen D., Croucher, Nicholas J., Corander, Jukka
Publicado en Microb Genom (2018)

Genetic Variation in Neisseria meningitidis Does Not Influence Disease Severity in Meningococcal Meningitis

por Kremer, Philip H. C., Lees, John A., Ferwerda, Bart, van de Ende, Arie, Brouwer, Matthijs C., Bentley, Stephen D., van de Beek, Diederik
Publicado en Front Med (Lausanne) (2020)

Fast and flexible bacterial genomic epidemiology with PopPUNK

por Lees, John A., Harris, Simon R., Tonkin-Hill, Gerry, Gladstone, Rebecca A., Lo, Stephanie W., Weiser, Jeffrey N., Corander, Jukka, Bentley, Stephen D., Croucher, Nicholas J.
Publicado en Genome Res (2019)

Diversification in immunogenicity genes caused by selective pressures in invasive meningococci

por Kremer, Philip H.C., Lees, John A., Ferwerda, Bart, Bijlsma, Merijn W., MacAlasdair, Neil, van der Ende, Arie, Brouwer, Matthijs C., Bentley, Stephen D., van de Beek, Diederik
Publicado en Microb Genom (2020)

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

por Lees, John A., Vehkala, Minna, Välimäki, Niko, Harris, Simon R., Chewapreecha, Claire, Croucher, Nicholas J., Marttinen, Pekka, Davies, Mark R., Steer, Andrew C., Tong, Steven Y. C., Honkela, Antti, Parkhill, Julian, Bentley, Stephen D., Corander, Jukka
Publicado en Nat Commun (2016)

Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

por Lees, John A., Kremer, Philip H. C., Manso, Ana S., Croucher, Nicholas J., Ferwerda, Bart, Serón, Mercedes Valls, Oggioni, Marco R., Parkhill, Julian, Brouwer, Matthijs C., van der Ende, Arie, van de Beek, Diederik, Bentley, Stephen D.
Publicado en Microb Genom (2017)

Producing polished prokaryotic pangenomes with the Panaroo pipeline

por Tonkin-Hill, Gerry, MacAlasdair, Neil, Ruis, Christopher, Weimann, Aaron, Horesh, Gal, Lees, John A., Gladstone, Rebecca A., Lo, Stephanie, Beaudoin, Christopher, Floto, R. Andres, Frost, Simon D.W., Corander, Jukka, Bentley, Stephen D., Parkhill, Julian
Publicado en Genome Biol (2020)

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

por Pensar, Johan, Puranen, Santeri, Arnold, Brian, MacAlasdair, Neil, Kuronen, Juri, Tonkin-Hill, Gerry, Pesonen, Maiju, Xu, Yingying, Sipola, Aleksi, Sánchez-Busó, Leonor, Lees, John A, Chewapreecha, Claire, Bentley, Stephen D, Harris, Simon R, Parkhill, Julian, Croucher, Nicholas J, Corander, Jukka
Publicado en Nucleic Acids Res (2019)