Author

M. Achtman

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 4

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 4 Research Focus:clustering· 3 Approach:statistical model· 3 Organism:bacteria (other)· 2 Research Focus:phylogenetics / evolution· 2 Research Focus:cell type annotation· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:database / resource· 1

Frequent Co-Authors

Z. Zhou· 4 shared N.-F. Alikhan· 2 shared A. Christophersen· 1 shared A. Indra· 1 shared A. K. Fotakis· 1 shared A. Tran-Dien· 1 shared B. Bunk· 1 shared C. Quince· 1 shared

Activity by Year

2017-2022 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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4 shared papersMicrobiology

Z. Zhou

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4 papers

Recent·Most cited

EnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations

M. Achtman, Z. Zhou, J. Charlesworth, L. A. Baxter

EnteroBase uses HierCC to cluster bacterial genomes into species/subspecies and populations, outperforming traditional methods for several genera.

bioRxiv · Jan 11, 2022Microbiology

Global genomic population structure of Clostridioides difficile

M. Frentrup, Z. Zhou, M. Steglich, J. P. Meier-Kolthoff, M. Goker, T. Riedel, B. Bunk, C. Sproer, J. Overmann, M. Blaschitz, A. Indra, L. von Muller, T. A. Kohl, S. Niemann, C. Seyboldt, , U. Nubel

This study introduces EnteroBase, a database for C. difficile genomic data, showing it can identify related genomes with 89% consistency between cgMLST and SNPs.

Microbial Genomics · Aug 1, 2020Peer-reviewedMicrobiology

The user's guide to comparative genomics with EnteroBase, including case studies on transmissions of micro-clades of Salmonella, the phylogeny of ancient and modern Yersinia pestis genomes, and the core genomic diversity of all Escherichia.

Z. Zhou, N.-F. Alikhan, K. Mohamed, Y. Fan, the Agama Study Group, M. Achtman

The paper introduces EnteroBase, a software environment for comparative genomics, and demonstrates its use in analyzing bacterial population structures through three case studies.

bioRxiv · Nov 25, 2019Microbiology

Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica

Z. Zhou, I. Lundstrom, A. Tran-Dien, S. Duchene, N.-F. Alikhan, M. J. Sergeant, G. Langridge, A. K. Fotakis, S. Nair, H. K. Stenoien, S. S. Hamre, S. Casjens, A. Christophersen, C. Quince, N. R. Thomson, , M. Achtman

The study analyzes an 800-year-old Paratyphi C genome to show its origin from swine pathogens and its long history as a human pathogen.

bioRxiv · Feb 14, 2017Microbiology