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

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Outgoing claims: the papers this work cites, builds on, or argues with.

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inferredcites →https://doi.org/10.1016/j.febslet.2007.03.049openalex-snapshot

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inferredcites →https://doi.org/10.1016/j.jas.2013.07.004openalex-snapshot

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inferredcites →https://doi.org/10.1098/rspb.1994.0006openalex-snapshot

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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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