Author

Eitan Yaffe

VA Palo Alto Health Care SystemORCID 0000-0002-2896-3349Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Assay:metagenomics· 1 Organism:mouse· 1 Approach:statistical model· 1

Frequent Co-Authors

Benjamin H. GoodiD· 1 shared Chinmay K LalgudiiD· 1 shared David A. RelmaniD· 1 shared Feiqiao Brian YuiD· 1 shared Handuo ShiiD· 1 shared Jamie Alcira LopeziD· 1 shared Justin Laine SonnenburgiD· 1 shared Katharine M. NgiD· 1 shared

Activity by Year

2022-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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1 shared paperMicrobiology

Benjamin H. GoodORCID

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2 papers

Recent·Most cited

Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics

Chinmay K Lalgudi, Masakazu Kotaka, Eitan Yaffe, Jamie Alcira Lopez, Feiqiao Brian Yu, Katharine M. Ng, Justin Laine Sonnenburg, Benjamin H. Good, Kerwyn Casey Huang, Handuo Shi

This study shows that gut microbiome recovery after antibiotics is path-dependent, shaped by ecological and evolutionary dynamics including strain sweeps, genetic changes, and phage activity.

bioRxiv · May 23, 2026 · PreprintMicrobiology

Precise genotyping of circular mobile elements uncovers human associated plasmids with surprisingly recent common ancestors

Nitan Shalon, David A. Relman, Eitan Yaffe

The paper develops an algorithm to accurately reconstruct circular mobile genomes from metagenomic data, revealing plasmids with recently diverged common ancestors.

Genome Research · May 1, 2022Peer-reviewedGenomics