How to Cite EnteroBase?

If you use data or metadata from EnteroBase, or perform analyses based on these data, please cite the following:

AMR Genotyping, Bubbleplots, and Novel Databases

  • Dyer NP, Päuker B, Baxter L, Gupta A, Bunk B, Overmann J, Diricks M, Dreyer V, Niemann S, Holt KE, Rahman M, Brown PE, Stark R, Zhou Z, Ott S, Nübel U (2024). EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens, Nucleic Acids Research.

Hierarchical Clustering (HierCC)

  • Zhou Z, Charlesworth J, Achtman M (2021). HierCC: A multi-level clustering scheme for population assignments based on core genome MLST, Bioinformatics, 37(20):3645–3646.

EnteroBase User's Guide

  • Zhou Z, Alikhan NF, Mohamed K, the Agama Study Group, Achtman M (2020). The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity, Genome Research, 30:138-152.

GrapeTree

  • Zhou Z, Alikhan NF, et al. (2018). GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens, Genome Research, 28:1395-1404.

Publications Using EnteroBase

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