See full list on Google Scholar and ORCID.


John Lees, Simon Harris, Gerry Tonkin-Hill, Rebecca Gladstone, Stephanie Lo, Jeffrey Weiser, Jukka Corander, Stephen Bentley, and Nicholas Croucher. Fast and Flexible Bacterial Genomic Epidemiology with PopPUNK. Genome Research 29:304-316. doi:10.1101/gr.241455.118 (2019).

John Lees, Marco Galardini, Stephen Bentley, Jeffrey Weiser, Jukka Corander. pyseer: a comprehensive tool for microbial pangenome-wide association studies. Bioinformatics 34:4310-4312. doi:10.1093/bioinformatics/bty539 (2018).

John Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen Bentley, Simon Harris. Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study. Wellcome Open Research 3:33. doi:10.12688/wellcomeopenres.14265.2 (2018).

John Lees, Nicholas Croucher, David Goldblatt, François Nosten, Julian Parkhill, Claudia Turner, Paul Turner, Stephen Bentley. Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLife 6:e26255. doi:10.7554/eLife.26255 (2017).

John Lees, Philip Kremer, Ana Manso, Nicholas Croucher, Bart Ferwerda, Mercedes Valls Serón, Marco Oggioni, Julian Parkhill, Matthijs Brouwer, Arie van der Ende, Diederik van de Beek, Stephen Bentley. Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis. Microbial Genomics 3:e000103. doi:10.1099/mgen.0.000103 (2017).

John Lees, Matthijs Brouwer, Arie van der Ende, Julian Parkhill, Diederik van de Beek, Stephen Bentley. Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis. Infect Immun 85:e01061–16. doi:10.1128/IAI.01061-16 (2017).

John Lees, Minna Vehkala, Niko Välimäki, Simon Harris, Claire Chewapreecha, Nicholas Croucher, Pekka Marttinen, Mark Davies, Andrew Steer, Steven Tong, Antti Honkela, Julian Parkhill, Stephen Bentley, Jukka Corander. Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nat Commun 7:12797. doi:10.1038/ncomms12797 (2016).

Richard Copin, William Sause, Yi Fulmer, Divya Balasubramanian, Sophie Dyzenhaus, Jamil Ahmed, Krishan Kumar, John Lees, Anna Stachel, Jason Fisher, Karl Drlica, Michael Phillips, Jeffrey Weiser, Paul Planet, Anne-Catrin Uhlemann, Harm van Bakel, Jennifer Lighter, Victor Torres, Bo Shopsin. Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus. PNAS 116:1745-1754. doi:10.1073/pnas.1814265116 (2019).

Pamela Shen, John Lees, Gavyn Bee, Sam Brown, Jeffrey Weiser, Pneumococcal quorum sensing drives an asymmetric owner–intruder competitive strategy during carriage via the competence regulon. Nature Microbiology 4:198–208. doi:10.1038/s41564-018-0314-4 (2019).

Gerry Tonkin-Hill, John Lees, Stephen Bentley, Simon Frost, and Jukka Corander. 2018. RhierBAPS: An R Implementation of the Population Clustering Algorithm hierBAPS. Wellcome Open Research 3:93. doi:10.12688/wellcomeopenres.14694.1 (2018).

Santeri Puranen, Maiju Pesonen, Johan Pensar, Ying Ying Xu, John Lees, Stephen Bentley, Nicholas  Croucher, and Jukka Corander. SuperDCA for Genome-Wide Epistasis Analysis. Microbial Genomics 4:e000184 doi:10.1099/mgen.0.000184 (2018).

Philip Kremer, John Lees, Merel Koopmans, Bart Ferwerda, Agaath Arends, Monique Feller, Kim Schipper, Mercedes Valls Seron, Arie van der Ende, Matthijs Brouwer, Diederik van de Beek, Stephen Bentley. Benzalkonium tolerance genes and outcome in Listeria monocytogenes meningitis. Clinical Microbiology and Infection. doi:10.1016/j.cmi.2016.12.008 (2016).

Ula Khatib, Diederik van de Beek, John Lees, Matthijs Brouwer. Adults with suspected central nervous system infection: A prospective study of diagnostic accuracy. J. Infect. 74:1-9. doi:10.1016/j.jinf.2016.09.007 (2016).

Sophia David, Christophe Rusniok, Massimo Mentasti, Laura Gomez-Valero, Simon Harris, Pierre Lechat, John Lees, Christophe Ginevra, Philippe Glaser, Laurence Ma, Christiane Bouchier, Anthony Underwood, Sophie Jarraud, Timothy Harrison, Julian Parkhill, Carmen Buchrieser. Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently. Genome Research. 26:1555–1564. doi:10.1101/gr.209536.116 (2016).


John Lees, Gerry Tonkin-Hill and Stephen Bentley. Stronger Together. Nat Rev Micro 15:9. doi: 10.1038/nrmicro.2017.95 (2017).

John Lees, and Stephen Bentley. Bacterial GWAS: not just gilding the lily. Nat Rev Micro 14:406. doi: 10.1038/nrmicro.2016.82 (2016).

John Lees, and Rebecca Gladstone. R–M systems go on the offensive. Nat Rev Micro 13:3. doi: 10.1038/nrmicro3435 (2015).

Amy Cain and John Lees. Using genomics to combat infectious diseases on a global scale. Genome Biology. 16:250. doi: 10.1186/s13059-015-0822-y (2015).


John Lees, Bart Ferwerda, Philip Kremer, Nicole Wheeler, Mercedes Valls Serón, Nicholas Croucher, …  Jeffrey Barrett, Stephen Bentley, Diederik van de Beek. Joint Sequencing of Human and Pathogen Genomes Reveals the Genetics of Pneumococcal Meningitis. bioRxiv. doi:10.1101/386078 (2018)