Author

Vivian Ramirez

University of Michigan

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 Microbiology· 1

Signature Assays, Organisms & Methods

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Assay:ChIP-seq· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1 Research Focus:chromatin & epigenetic regulation· 1 Research Focus:gene regulatory network inference· 1 Assay:Hi-C· 1

Frequent Co-Authors

Lydia FreddolinoiD· 2 shared Dagmara JakimowicziD· 1 shared Jeremy W. SchroederiD· 1 shared Lauren Tiller· 1 shared Marcin Jan SzafraniD· 1 shared Marie A. ElliotiD· 1 shared Michael B. WolfeiD· 1 shared Xiafei Zhang· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

8 top collaborators · 18 mutual co-author links

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2 shared papersBioinformatics

Lydia FreddolinoORCID

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2 papers

Recent·Most cited

ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions

Jeremy W. Schroeder, Vivian Ramirez, Michael B. Wolfe, Lydia Freddolino

ShapeME discovers structural DNA motifs that improve prediction of protein-DNA binding beyond traditional PWMs using ChIP-seq data.

Journal of Molecular Biology · Apr 15, 2026Peer-reviewedBioinformatics

LsrL modulates Lsr2-induced chromatin structure to tune biosynthetic gene cluster regulation in Streptomyces venezuelae

Vivian Ramirez, Lauren Tiller, Marcin Jan Szafran, Xiafei Zhang, Dagmara Jakimowicz, Marie A. Elliot, Lydia Freddolino

This study investigates how Lsr2 and LsrL regulate chromatin structure and biosynthetic gene clusters in Streptomyces venezuelae using multi-omics approaches.

bioRxiv · Nov 23, 2025 · PreprintMicrobiology