Author

Yiyi Liu

University of Wisconsin–MadisonORCID 0000-0002-2188-6336Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Systems Biology· 2

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Organism:mouse· 2 Research Focus:differential expression· 1 Approach:experimental assay· 1 Approach:machine learning (classical)· 1 Approach:statistical model· 1

Frequent Co-Authors

Jaron C. ThompsoniD· 2 shared Ophelia S. VenturelliiD· 2 shared Daniel Amador‐NogueziD· 1 shared Eugenio I. Vivas· 1 shared Federico E. ReyiD· 1 shared Gabriel I Miranda-ContrerasiD· 1 shared Hanhyeok ImiD· 1 shared Kaixiang Loke· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 30 mutual co-author links

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2 shared papersSystems Biology

Jaron C. ThompsonORCID

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2 papers

Recent·Most cited

Mechanistic and machine learning models design human gut consortia that robustly inhibit Clostridioides difficile

Hanhyeok Im, Yiyi Liu, Jaron C. Thompson, Gabriel I Miranda-Contreras, Kaixiang Loke, Rebecca Bacon, Lauren Lucas, Daniel Amador‐Noguez, Simon M. Gray, Ophelia S. Venturelli

The paper designs synthetic gut microbial communities using mechanistic and machine learning models to robustly inhibit C. difficile growth in vitro and in vivo.

bioRxiv · Aug 5, 2026 · PreprintSystems Biology

Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway

Yiyi Liu, Yu‐Yu Cheng, Jaron C. Thompson, Zhichao Zhou, Eugenio I. Vivas, Matthew F Warren, Federico E. Rey, Karthik Anantharaman, Ophelia S. Venturelli

This study shows that controlling the arginine dihydrolase pathway in E. coli affects gut community assembly and butyrate production in vitro and in mice.

bioRxiv · Jan 10, 2023 · PreprintSystems Biology