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Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species.

mSphere - 28 Jan 2025

Chauhan Siddharth M, Ardalani Omid, Hyun Jason C, Monk Jonathan M, Phaneuf Patrick V, Palsson Bernhard O

Abstract excerpt

Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of Escherichia coli for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define...

Topics

Escherichia coli
Genome, Bacterial
Phylogeny
Shigella
Machine Learning
Multilocus Sequence Typing
Genetic Variation

Source

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Identifiers

PMID: 39745367
DOI: 10.1128/msphere.00532-24
PMCID: PMC11774025

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PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 31 Aug 2026.

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