Imperial College London


Faculty of MedicineSchool of Public Health

Visiting Researcher



+44 (0)20 7594 2939j.lees Website




UG4Sir Alexander Fleming BuildingSouth Kensington Campus





I work on bacterial GWAS and genomic epidemiology, and have published software to perform these types of analysis. More generally, I’m interested in methodology and software to analyse populations of microbial genomes. In the past I have mostly studied genetic variation affecting the pathogenesis of Streptococcus pneumoniae.

Selected Publications

Journal Articles

Lees JA, Ferwerda B, Kremer PHC, et al., 2019, Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis, Nature Communications, Vol:10, ISSN:2041-1723

Lees JA, Harris SR, Tonkin-Hill G, et al., 2019, Fast and flexible bacterial genomic epidemiology with PopPUNK, Genome Research, Vol:29, ISSN:1088-9051, Pages:304-316

Lees JA, Galardini M, Bentley SD, et al., 2018, pyseer: a comprehensive tool for microbial pangenome-wide association studies, Bioinformatics, Vol:34, ISSN:1367-4803, Pages:4310-4312

Lees JA, Croucher NJ, Goldblatt D, et al., 2017, Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration, Elife, Vol:6, ISSN:2050-084X

Lees JA, Vehkala M, Välimäki N, et al., 2016, Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes, Nature Communications, Vol:7, ISSN:2041-1723

More Publications