See https://www.bacpop.org/publications/ for an annotated list, or here for google scholar.

For a background to our work, the following may be of interest:

Hunt, M., Lima, L., Anderson, D., Bouras, G., Hall, M. B., Hawkey, J., Schwengers, O., Shen, W., Lees, J., & Iqbal, Z. (2024). AllTheBacteria – all bacterial genomes assembled, available and searchable. In bioRxiv (p. 2024.03.08.584059).

https://doi.org/10.1101/2024.03.08.584059
https://www.allthebacteria.org

John A Lees, Timothy W Russell, Liam P Shaw, Joel Hellewell (2024). Recent approaches in computational modelling for controlling pathogen threats Life Science Alliance 7(9) e202402666

https://doi.org/10.26508/lsa.202402666

Romain Derelle, Johanna von Wachsmann, Tommi Mäklin, Joel Hellewell, Timothy Russell, Ajit Lalvani, Leonid Chindelevitch, Nicholas J. Croucher, Simon R. Harris, John A. Lees (2024). Seamless, rapid and accurate analyses of outbreak genomic data using Split K-mer Analysis (SKA) bioRxiv

https://www.biorxiv.org/content/10.1101/2024.03.25.586631.abstract