Author

Lily Hoefner

The University of Texas at Austin

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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Bioinformatics· 1 Molecular Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:gene regulatory network inference· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1 Organism:multiple species· 1

Frequent Co-Authors

Alexandra J. Lukasiewicz· 2 shared Lydia M. ContrerasiD· 2 shared Abigail N. Leistra· 1 shared Ani Savk· 1 shared Bryan Zorn· 1 shared Cindy J. Gode· 1 shared Erika Monzon· 1 shared Kayley H. JansseniD· 1 shared

Activity by Year

2024-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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2 shared papersMolecular Biology

Alexandra J. Lukasiewicz

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2 papers

Recent·Most cited

Modeling binding of the conserved Csr/Rsm protein family across species of the γ-proteobacteria reveals niche-specific adaptation of the post-transcriptional regulon

Alexandra J. Lukasiewicz, Lily Hoefner, Ani Savk, Lydia M. Contreras

The paper predicts CsrA/RsmA target regulons across 16 γ-proteobacterial species, showing that regulatory evolution occurs through changes in RNA targets rather than the protein itself.

bioRxiv · Feb 6, 2026 · PreprintMolecular Biology

Thermodynamic modeling of Csr/Rsm- RNA interactions capture novel, direct binding interactions across the Pseudomonas aeruginosa transcriptome

Alexandra J. Lukasiewicz, Abigail N. Leistra, Lily Hoefner, Erika Monzon, Cindy J. Gode, Bryan Zorn, Kayley H. Janssen, Timothy L. Yahr, Matthew C. Wolfgang, Lydia M. Contreras

This study uses thermodynamic modeling to predict RsmA-mRNA binding interactions in Pseudomonas aeruginosa, identifying 1043 interactions including 457 novel targets, validated through experimental assays.

bioRxiv · Aug 1, 2024 · PreprintBioinformatics